diff --git a/.gitignore b/.gitignore index 1a5bc22..18bf917 100755 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ user_data/* user_uploads/* !user_uploads/index.html +.Rproj.user diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..833da9d --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,12 @@ +Package: genomescope +Title: Reference-free profiling of genomes +Version: 2.0 +Authors@R: person("Timothy", "Ranallo-Benavidez", email = "tbenavi1@jhu.edu", + role = c("aut", "cre")) +Description: GenomeScope analyzes the k-mer histogram to output estimates for genome size, heterozygosity, and repetitiveness, without requiring a reference genome. GenomeScope employs a polyploid-aware mixture model that, within seconds, accurately infers genome properties from unassembled sequencing data. GenomeScope produces a report and several informative plots describing the genome properties. +Depends: R (>= 3.1.0) +Imports: argparse, minpack.lm +License: file LICENSE +LazyData: true +RoxygenNote: 6.1.1 +Encoding: UTF-8 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..78fbe6c --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,71 @@ +# Generated by roxygen2: do not edit by hand + +export(estimate_Genome_peakp) +export(eval_model) +export(nls_peak) +export(predict1_0) +export(predict1_0_unique) +export(predict1_1) +export(predict1_1_unique) +export(predict2_0) +export(predict2_0_unique) +export(predict2_1) +export(predict2_1_unique) +export(predict3_0) +export(predict3_0_unique) +export(predict3_1) +export(predict3_1_unique) +export(predict4_0) +export(predict4_0_unique) +export(predict4_1) +export(predict4_1_unique) +export(predict4_2) +export(predict4_2_unique) +export(predict5_0) +export(predict5_0_unique) +export(predict5_1) +export(predict5_1_unique) +export(predict5_2) +export(predict5_2_unique) +export(predict5_3) +export(predict5_3_unique) +export(predict5_4) +export(predict5_4_unique) +export(predict5_5) +export(predict5_5_unique) +export(predict6_0) +export(predict6_0_unique) +export(predict6_1) +export(predict6_10) +export(predict6_10_unique) +export(predict6_11) +export(predict6_11_unique) +export(predict6_12) +export(predict6_12_unique) +export(predict6_13) +export(predict6_13_unique) +export(predict6_14) +export(predict6_14_unique) +export(predict6_15) +export(predict6_15_unique) +export(predict6_16) +export(predict6_16_unique) +export(predict6_1_unique) +export(predict6_2) +export(predict6_2_unique) +export(predict6_3) +export(predict6_3_unique) +export(predict6_4) +export(predict6_4_unique) +export(predict6_5) +export(predict6_5_unique) +export(predict6_6) +export(predict6_6_unique) +export(predict6_7) +export(predict6_7_unique) +export(predict6_8) +export(predict6_8_unique) +export(predict6_9) +export(predict6_9_unique) +export(report_results) +export(score_model) diff --git a/R/estimate_genome_peak.R b/R/estimate_genome_peak.R new file mode 100644 index 0000000..6bfbe42 --- /dev/null +++ b/R/estimate_genome_peak.R @@ -0,0 +1,68 @@ +#' Function to fit 2p peak model, with p forms +#' +#' @param kmer_hist_orig A data frame of the original histogram data (starting at 1 and with last position removed). +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @param y A numeric vector of the y-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @param k An integer corresponding to the kmer length. +#' @param p An integer corresponding to the ploidy. +#' @param topology An integer corresponding to the topology to use. +#' @param estKmercov An integer corresponding to the estimated kmer coverage of the polyploid genome. +#' Set to -1 if not specified by user. +#' @param round An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process. +#' @param foldername A character vector corresponding to the name of the output directory. +#' @param arguments A data frame of the user-specified inputs. +#' @return A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +#' and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms). +#' @export +estimate_Genome_peakp<-function(kmer_hist_orig, x, y, k, p, topology, estKmercov, round, foldername, arguments) { + if (topology==-1) { + p_to_num_topologies = c(1, 1, 1, 2, 5, 16) + num_topologies = p_to_num_topologies[p] + topologies = 1:num_topologies + } + else { + num_topologies = 1 + topologies = c(topology) + } + numofKmers = sum(as.numeric(x)*as.numeric(y)) + if (estKmercov==-1) { + #In situations with low heterozygosity, the peak with highest amplitude typically corresponds to the homozygous peak (i.e. the p-th peak). + #However, with increasing heterozygosity, the highest amplitude peak may be an earlier peak. + #Thus, when setting the estimated kmer coverage, we will need to iterate through these possibilities. + #num_peak_indices indicates how many possibilities we need to iterate through. + num_peak_indices = p + y_transform = as.numeric(x)**transform_exp*as.numeric(y) + estKmercov1 = x[which(y_transform==max(y_transform))][1] + } + else { + # When the user sets the estimated kmer coverage, we only need to iterate through one possibility + num_peak_indices = 1 + ## We set the estimated kmer coverage to be the user specified value + estKmercov1 = estKmercov + } + estLength1 = numofKmers/estKmercov1 + + nls00 = NULL + peak_indices = 1:num_peak_indices + for (i in peak_indices) { + nls0 = NULL + top_count = 0 + ## We see what happens when we set the estimated kmer coverage to be 1/i times the x-coordinate where the max peak occurs (1 <= i <= p if the user doesn't set the estimated kmer coverage, and i=1 if they do) + estKmercov2 = estKmercov1 / i + estLength2 = numofKmers/estKmercov2 + + if (VERBOSE) {cat(paste("trying with kmercov: ", estKmercov2, "\n"))} + + for (top in topologies) { + if (VERBOSE) {cat(paste("trying with topology: ", top, "\n"))} + top_count = top_count + 1 + nls1 = nls_peak(x, y, k, p, top, estKmercov2, estLength2, MAX_ITERATIONS) + nls0 = eval_model(kmer_hist_orig, nls0, nls1, p, round, foldername, arguments)[[1]] + } + if (i < num_peak_indices) { #if this is not the last evaluation + nls00 = eval_model(kmer_hist_orig, nls00, nls0, p, round, foldername, arguments)[[1]] + } + } + + return(eval_model(kmer_hist_orig, nls00, nls0, p, round, foldername, arguments)) +} diff --git a/R/eval_model.R b/R/eval_model.R new file mode 100644 index 0000000..63484a6 --- /dev/null +++ b/R/eval_model.R @@ -0,0 +1,86 @@ +#' Evaluate distinct model forms, in order to resolve ambiguity of which peak is the homozygous peak +#' +#' @param kmer_hist_orig A data frame of the original histogram data (starting at 1 and with last position removed). +#' @param nls0,nls1 The nlsLM model objects to evaluate and compare. +#' @param p An integer corresponding to the ploidy. +#' @param round An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process. +#' @param foldername A character vector corresponding to the name of the output directory. +#' @param arguments A data frame of the user-specified inputs. +#' @return A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +#' and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms). +#' @export +eval_model<-function(kmer_hist_orig, nls0, nls1, p, round, foldername, arguments) { + nls0score = -1 + nls1score = -1 + + ## Evaluate the score the nls0 + if (!is.null(nls0)) { + nls0score = score_model(kmer_hist_orig, nls0, round+0.1, foldername) + + #if(VERBOSE) {cat(paste("nls0score$all:\t", nls0score$all[[1]], "\n"))} + + if (VERBOSE) { + mdir = paste(foldername, "/round", round, ".1", sep="") + dir.create(mdir, showWarnings=FALSE) + report_results(kmer_prof_orig,kmer_prof_orig, k, p, (list(nls0, nls0score)) , mdir, arguments, TRUE) + } + } + else { + if (VERBOSE) {cat("nls0score failed to converge\n")} + } + + ## Evaluate the score of nls1 + if (!is.null(nls1)) { + nls1score = score_model(kmer_hist_orig, nls1, round+0.2, foldername) + + if(VERBOSE) {cat(paste("nls1score$all:\t", nls1score$all[[1]], "\n"))} + + if (VERBOSE) { + mdir = paste(foldername, "/round", round, ".2", sep="") + dir.create(mdir, showWarnings=FALSE) + report_results(kmer_prof_orig, kmer_prof_orig, k, p, (list(nls1, nls1score)) , mdir, arguments, FALSE) + } + } + else { + if (VERBOSE) {cat("nls1score failed to converge\n")} + } + + ## Return the better of the scores + if (!is.null(nls0)) { + if (!is.null(nls1)) { + pdiff = abs(nls0score$all[[1]] - nls1score$all[[1]]) / max(nls0score$all[[1]], nls1score$all[[1]]) + + if (pdiff < SCORE_CLOSE) { + het0 = nls0$ahet + het1 = nls1$ahet + + #if (het1 * SCORE_HET_FOLD_DIFFERENCE < het0) { + if (het1 + 0.01 < het0) { + if (VERBOSE) {cat("returning nls0, similar score, higher het\n")} + return (list(nls1, nls1score)) + } + #else if (het0 * SCORE_HET_FOLD_DIFFERENCE < het1) { + else if (het0 + 0.01 < het1) { + if (VERBOSE) {cat("returning nls1, similar score, higher het\n")} + return (list(nls0, nls0score)) + } + } + + if (nls0score$all[[1]] < nls1score$all[[1]]) { + if (VERBOSE) {cat("returning nls0, better score\n")} + return (list(nls0, nls0score)) + } + else { + if (VERBOSE) {cat("returning nls1, better score\n")} + return (list(nls1, nls1score)) + } + } + else { + if (VERBOSE) {cat("returning nls0, nls1 fail\n")} + return (list(nls0, nls0score)) + } + } + + if (VERBOSE) {cat("returning nls1 by default\n")} + return (list(nls1, nls1score)) +} diff --git a/R/model_functions.R b/R/model_functions.R new file mode 100644 index 0000000..1c633f9 --- /dev/null +++ b/R/model_functions.R @@ -0,0 +1,2503 @@ +#' Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict1_0 = function(k, d, kmercov, bias, x) +{ + predict1_1(k, d, kmercov, bias, x) +} + +#' Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict1_0_unique = function(k, d, kmercov, bias, x) +{ + predict1_1_unique(k, d, kmercov, bias, x) +} + +#' Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict1_1 = function(k, d, kmercov, bias, x) +{ + r0 = 1 + if (d > 1) {return(0)} + t0 = r0**k + s0 = t0 + alpha_1 = (1-d)*(s0) + alpha_2 = d*(s0) + alpha_1 * dnbinom(x, size=kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size=kmercov*2 / bias, mu = kmercov*2) +} + +#' Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict1_1_unique = function(k, d, kmercov, bias, x) +{ + r0 = 1 + if (d > 1) {return(0)} + t0 = r0**k + s0 = t0 + alpha_1_unique = (1-d)*(s0) + alpha_1_unique * dnbinom(x, size=kmercov*1 / bias, mu = kmercov*1) +} + +#AB -> AA +#' Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1 A numeric corresponding to the nucleotide heterozygosity ab. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict2_0 = function(r1, k, d, kmercov, bias, x) +{ + predict2_1(r1, k, d, kmercov, bias, x) +} + +#AB -> AA +#' Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1 A numeric corresponding to the nucleotide heterozygosity ab. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict2_0_unique = function(r1, k, d, kmercov, bias, x) +{ + predict2_1_unique(r1, k, d, kmercov, bias, x) +} + +#AB -> AA +#' Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1 A numeric corresponding to the nucleotide heterozygosity ab. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict2_1 = function(r1, k, d, kmercov, bias, x) +{ + r0 = 1-r1 #aa + if (r0 < 0 || d > 1) {return(0)} + t0 = r0**k #AA + s0 = t0 #AA + s1 = 1-t0 #AB + alpha_1 = (1-d)*(2*s1) + d*(2*s0*s1 + 2*s1**2) + alpha_2 = (1-d)*(s0) + d*(s1**2) + alpha_3 = d*(2*s0*s1) + alpha_4 = d*(s0**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4) +} + +#AB -> AA +#' Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1 A numeric corresponding to the nucleotide heterozygosity ab. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict2_1_unique = function(r1, k, d, kmercov, bias, x) +{ + r0 = 1-r1 + if (r0 < 0 || d > 1) {return(0)} + t0 = r0**k + s0 = t0 + s1 = 1-t0 + alpha_1_unique = (1-d)*(2*s1) + alpha_2_unique = (1-d)*(s0) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2) +} + +#ABC -> AAB -> AAA +#' Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1,r2 Numerics corresponding to the nucleotide heterozygosities aab and abc respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict3_0 = function(r1, r2, k, d, kmercov, bias, x) +{ + predict3_1(r1, r2, k, d, kmercov, bias, x) +} + +#ABC -> AAB -> AAA +#' Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1,r2 Numerics corresponding to the nucleotide heterozygosities aab and abc respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict3_0_unique = function(r1, r2, k, d, kmercov, bias, x) +{ + predict3_1_unique(r1, r2, k, d, kmercov, bias, x) +} + +#ABC -> AAB -> AAA +#' Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1,r2 Numerics corresponding to the nucleotide heterozygosities aab and abc respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict3_1 = function(r1, r2, k, d, kmercov, bias, x) +{ + r0 = 1-r1-r2 #aaa + if (r0 < 0 || d > 1) {return(0)} + t0 = r0**k #AAA + t1 = (r0+r1)**k #AAA + AAB + s0 = t0 #AAA + s1 = t1-t0 #AAB + s2 = 1-t1 #ABC + alpha_1 = (1-d)*(s1+3*s2) + d*(2*s0*s1 + 4*s0*s2 + 2*s1**2 + 6*s1*s2 + 4*s2**2) + alpha_2 = (1-d)*(s1) + d*(s2**2) + alpha_3 = (1-d)*(s0) + d*(2*s1*s2) + alpha_4 = d*(2*s0*s2 + s1**2) + alpha_5 = d*(2*s0*s1) + alpha_6 = d*(s0**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#ABC -> AAB -> AAA +#' Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param r1,r2 Numerics corresponding to the nucleotide heterozygosities aab and abc respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict3_1_unique = function(r1, r2, k, d, kmercov, bias, x) +{ + r0 = 1-r1-r2 + if (r0 < 0 || d > 1) {return(0)} + t0 = r0**k + t1 = (r0+r1)**k + s0 = t0 + s1 = t1-t0 + s2 = 1-t1 + alpha_1_unique = (1-d)*(s1+3*s2) + alpha_2_unique = (1-d)*(s1) + alpha_3_unique = (1-d)*(s0) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3) +} + +#AAAA -> (AAAB, AABB) -> AABC -> ABCD +#' Produce model estimated (p=4, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaab,raabb,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aaab, aabb, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_0 = function(raaab, raabb, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raaab-raabb-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAAAB = (raaaa+raaab)**k + tAABB = (raaaa+raabb)**k + tAABC = (raaaa+raaab+raabb+raabc)**k + sAAAA = tAAAA + sAAAB = tAAAB-tAAAA + sAABB = tAABB-tAAAA + sAABC = tAABC-tAAAB-tAABB+tAAAA + sABCD = 1-tAABC + alpha_1 = (1-d)*(sAAAB + 2*sAABC + 4*sABCD) + d*(2*sAAAA*sAAAB + 2*sAAAB**2 + 2*sAAAB*sAABB + 4*sAAAA*sAABC + 6*sAAAB*sAABC + 4*sAABB*sAABC + 4*sAABC**2 + 6*sAAAA*sABCD + 8*sAAAB*sABCD + 6*sAABB*sABCD + 10*sAABC*sABCD + 6*sABCD**2) + alpha_2 = (1-d)*(2*sAABB + sAABC) + d*(2*sAAAA*sAABB + 2*sAAAB*sAABB + 2*sAABB**2 + 2*sAABB*sAABC + 2*sAABB*sABCD + sABCD**2) + alpha_3 = (1-d)*(sAAAB) + d*(2*sAABB*sABCD + 2*sAABC*sABCD) + alpha_4 = (1-d)*(sAAAA) + d*(sAABB**2 + 2*sAABB*sAABC + sAABC**2 + 2*sAAAB*sABCD) + alpha_5 = d*(2*sAAAB*sAABB + 2*sAAAB*sAABC + 2*sAAAA*sABCD) + alpha_6 = d*(sAAAB**2 + 2*sAAAA*sAABB + 2*sAAAA*sAABC) + alpha_7 = d*(2*sAAAA*sAAAB) + alpha_8 = d*(sAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8) +} + +#AAAA -> (AAAB, AABB) -> AABC -> ABCD +#' Produce model estimated (p=4, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaab,raabb,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aaab, aabb, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_0_unique = function(raaab, raabb, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raaab-raabb-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAAAB = (raaaa+raaab)**k + tAABB = (raaaa+raabb)**k + tAABC = (raaaa+raaab+raabb+raabc)**k + sAAAA = tAAAA + sAAAB = tAAAB-tAAAA + sAABB = tAABB-tAAAA + sAABC = tAABC-tAAAB-tAABB+tAAAA + sABCD = 1-tAABC + alpha_1_unique = (1-d)*(sAAAB + 2*sAABC + 4*sABCD) + alpha_2_unique = (1-d)*(2*sAABB + sAABC) + alpha_3_unique = (1-d)*(sAAAB) + alpha_4_unique = (1-d)*(sAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4) +} + +#AAAA -> AAAB -> AABC -> ABCD +#' Produce model estimated (p=4, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaab,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aaab, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_1 = function(raaab, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raaab-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAAAB = (raaaa+raaab)**k + tAABC = (raaaa+raaab+raabc)**k + sAAAA = tAAAA + sAAAB = tAAAB-tAAAA + sAABC = tAABC-tAAAB + sABCD = 1-tAABC + alpha_1 = (1-d)*(sAAAB + 2*sAABC + 4*sABCD) + d*(2*sAAAA*sAAAB + 2*sAAAB**2 + 4*sAAAA*sAABC + 6*sAAAB*sAABC + 4*sAABC**2 + 6*sAAAA*sABCD + 8*sAAAB*sABCD + 10*sAABC*sABCD + 6*sABCD**2) + alpha_2 = (1-d)*(sAABC) + d*(sABCD**2) + alpha_3 = (1-d)*(sAAAB) + d*(2*sAABC*sABCD) + alpha_4 = (1-d)*(sAAAA) + d*(sAABC**2 + 2*sAAAB*sABCD) + alpha_5 = d*(2*sAAAB*sAABC + 2*sAAAA*sABCD) + alpha_6 = d*(sAAAB**2 + 2*sAAAA*sAABC) + alpha_7 = d*(2*sAAAA*sAAAB) + alpha_8 = d*(sAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8) +} + +#AAAA -> AAAB -> AABC -> ABCD +#' Produce model estimated (p=4, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaab,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aaab, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_1_unique = function(raaab, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raaab-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAAAB = (raaaa+raaab)**k + tAABC = (raaaa+raaab+raabc)**k + sAAAA = tAAAA + sAAAB = tAAAB-tAAAA + sAABC = tAABC-tAAAB + sABCD = 1-tAABC + alpha_1_unique = (1-d)*(sAAAB + 2*sAABC + 4*sABCD) + alpha_2_unique = (1-d)*(sAABC) + alpha_3_unique = (1-d)*(sAAAB) + alpha_4_unique = (1-d)*(sAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4) +} + +#AAAA -> AABB -> AABC -> ABCD +#' Produce model estimated (p=4, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raabb,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aabb, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_2 = function(raabb, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raabb-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAABB = (raaaa+raabb)**k + tAABC = (raaaa+raabb+raabc)**k + sAAAA = tAAAA + sAABB = tAABB-tAAAA + sAABC = tAABC-tAABB + sABCD = 1-tAABC + alpha_1 = (1-d)*(2*sAABC + 4*sABCD) + d*(4*sAAAA*sAABC + 4*sAABB*sAABC + 4*sAABC**2 + 6*sAAAA*sABCD + 6*sAABB*sABCD + 10*sAABC*sABCD + 6*sABCD**2) + alpha_2 = (1-d)*(2*sAABB + sAABC) + d*(2*sAAAA*sAABB + 2*sAABB**2 + 2*sAABB*sAABC + 2*sAABB*sABCD + sABCD**2) + alpha_3 = (1-d)*(0) + d*(2*sAABB*sABCD + 2*sAABC*sABCD) + alpha_4 = (1-d)*(sAAAA) + d*(sAABB**2 + 2*sAABB*sAABC + sAABC**2) + alpha_5 = d*(2*sAAAA*sABCD) + alpha_6 = d*(2*sAAAA*sAABB + 2*sAAAA*sAABC) + alpha_7 = d*(0) + alpha_8 = d*(sAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8) +} + +#AAAA -> AABB -> AABC -> ABCD +#' Produce model estimated (p=4, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raabb,raabc,rabcd Numerics corresponding to the nucleotide heterozygosities aabb, aabc, and abcd respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict4_2_unique = function(raabb, raabc, rabcd, k, d, kmercov, bias, x) +{ + raaaa = 1-raabb-raabc-rabcd + if (raaaa < 0 || d > 1) {return(0)} + tAAAA = raaaa**k + tAABB = (raaaa+raabb)**k + tAABC = (raaaa+raabb+raabc)**k + sAAAA = tAAAA + sAABB = tAABB-tAAAA + sAABC = tAABC-tAABB + sABCD = 1-tAABC + alpha_1_unique = (1-d)*(2*sAABC + 4*sABCD) + alpha_2_unique = (1-d)*(2*sAABB + sAABC) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4) +} + +#' Produce model estimated (p=5, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raaabb,raaabc,raabbc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_0 = function(raaaab, raaabb, raaabc, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raaabb-raaabc-raabbc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = (raaaaa)**k + tAAAAB = (raaaaa+raaaab)**k + tAAABB = (raaaaa+raaabb)**k + tAAABC = (raaaaa+raaaab+raaabb+raaabc)**k + tAABBC = (raaaaa+raaaab+raabbc)**k + tAABCD = (raaaaa+raaaab+raaabb+raaabc+raabbc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAAABB = tAAABB-tAAAAA + sAAABC = tAAABC-tAAAAB-tAAABB+tAAAAA + sAABBC = tAABBC-tAAAAB + sAABCD = tAABCD-tAAABC-tAABBC+tAAAAB + sABCDE = 1-tAABCD + alpha_1 = (1-d)*(sAAAAB + 2*sAAABC + sAABBC + 3*sAABCD + 5*sABCDE) + d*(2*sAAAAA*sAAAAB + 2*sAAAAB**2 + 2*sAAAAB*sAAABB + 4*sAAAAA*sAAABC + 6*sAAAAB*sAAABC + 4*sAAABB*sAAABC + 4*sAAABC**2 + 2*sAAAAA*sAABBC + 4*sAAAAB*sAABBC + 2*sAAABB*sAABBC + 6*sAAABC*sAABBC + 2*sAABBC**2 + 6*sAAAAA*sAABCD + 8*sAAAAB*sAABCD + 6*sAAABB*sAABCD + 10*sAAABC*sAABCD + 8*sAABBC*sAABCD + 6*sAABCD**2 + 8*sAAAAA*sABCDE + 10*sAAAAB*sABCDE + 8*sAAABB*sABCDE + 12*sAAABC*sABCDE + 10*sAABBC*sABCDE + 14*sAABCD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(sAAABB + 2*sAABBC + sAABCD) + d*(2*sAAAAA*sAAABB + 2*sAAAAB*sAAABB + 2*sAAABB**2 + 2*sAAABB*sAAABC + 2*sAAAAA*sAABBC + 2*sAAAAB*sAABBC + 4*sAAABB*sAABBC + 2*sAAABC*sAABBC + 2*sAABBC**2 + 2*sAAABB*sAABCD + 2*sAABBC*sAABCD + 2*sAAABB*sABCDE + 2*sAABBC*sABCDE + sABCDE**2) + alpha_3 = (1-d)*(sAAABB + sAAABC) + d*(2*sAABBC*sABCDE + 2*sAABCD*sABCDE) + alpha_4 = (1-d)*(sAAAAB) + d*(sAABBC**2 + 2*sAABBC*sAABCD + sAABCD**2 + 2*sAAABB*sABCDE + 2*sAAABC*sABCDE) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAABB*sAABBC + 2*sAAABC*sAABBC + 2*sAAABB*sAABCD + 2*sAAABC*sAABCD + 2*sAAAAB*sABCDE) + alpha_6 = d*(sAAABB**2 + 2*sAAABB*sAAABC + sAAABC**2 + 2*sAAAAB*sAABBC + 2*sAAAAB*sAABCD + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAB*sAAABB + 2*sAAAAB*sAAABC + 2*sAAAAA*sAABBC + 2*sAAAAA*sAABCD) + alpha_8 = d*(sAAAAB**2 + 2*sAAAAA*sAAABB + 2*sAAAAA*sAAABC) + alpha_9 = d*(2*sAAAAA*sAAAAB) + alpha_10 = d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raaabb,raaabc,raabbc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_0_unique = function(raaaab, raaabb, raaabc, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raaabb-raaabc-raabbc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = (raaaaa)**k + tAAAAB = (raaaaa+raaaab)**k + tAAABB = (raaaaa+raaabb)**k + tAAABC = (raaaaa+raaaab+raaabb+raaabc)**k + tAABBC = (raaaaa+raaaab+raabbc)**k + tAABCD = (raaaaa+raaaab+raaabb+raaabc+raabbc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAAABB = tAAABB-tAAAAA + sAAABC = tAAABC-tAAAAB-tAAABB+tAAAAA + sAABBC = tAABBC-tAAAAB + sAABCD = tAABCD-tAAABC-tAABBC+tAAAAB + sABCDE = 1-tAABCD + alpha_1_unique = (1-d)*(sAAAAB + 2*sAAABC + sAABBC + 3*sAABCD + 5*sABCDE) + alpha_2_unique = (1-d)*(sAAABB + 2*sAABBC + sAABCD) + alpha_3_unique = (1-d)*(sAAABB + sAAABC) + alpha_4_unique = (1-d)*(sAAAAB) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=5, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raaabc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaaab, aaabc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_1 = function(raaaab, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raaabc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAAAB = (raaaaa+raaaab)**k + tAAABC = (raaaaa+raaaab+raaabc)**k + tAABCD = (raaaaa+raaaab+raaabc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAAABC = tAAABC-tAAAAB + sAABCD = tAABCD-tAAABC + sABCDE = 1-tAABCD + alpha_1 = (1-d)*(sAAAAB + 2*sAAABC + 3*sAABCD + 5*sABCDE) + d*(2*sAAAAA*sAAAAB + 2*sAAAAB**2 + 4*sAAAAA*sAAABC + 6*sAAAAB*sAAABC + 4*sAAABC**2 + 6*sAAAAA*sAABCD + 8*sAAAAB*sAABCD + 10*sAAABC*sAABCD + 6*sAABCD**2 + 8*sAAAAA*sABCDE + 10*sAAAAB*sABCDE + 12*sAAABC*sABCDE + 14*sAABCD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(sAABCD) + d*(sABCDE**2) + alpha_3 = (1-d)*(sAAABC) + d*(2*sAABCD*sABCDE) + alpha_4 = (1-d)*(sAAAAB) + d*(sAABCD**2 + 2*sAAABC*sABCDE) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAABC*sAABCD + 2*sAAAAB*sABCDE) + alpha_6 = d*(sAAABC**2 + 2*sAAAAB*sAABCD + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAB*sAAABC + 2*sAAAAA*sAABCD) + alpha_8 = d*(sAAAAB**2 + 2*sAAAAA*sAAABC) + alpha_9 = d*(2*sAAAAA*sAAAAB) + alpha_10= d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10* dnbinom(x, size = kmercov*10/ bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raaabc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaaab, aaabc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_1_unique = function(raaaab, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raaabc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAAAB = (raaaaa+raaaab)**k + tAAABC = (raaaaa+raaaab+raaabc)**k + tAABCD = (raaaaa+raaaab+raaabc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAAABC = tAAABC-tAAAAB + sAABCD = tAABCD-tAAABC + sABCDE = 1-tAABCD + alpha_1_unique = (1-d)*(sAAAAB + 2*sAAABC + 3*sAABCD + 5*sABCDE) + alpha_2_unique = (1-d)*(sAABCD) + alpha_3_unique = (1-d)*(sAAABC) + alpha_4_unique = (1-d)*(sAAAAB) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=5, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raabbc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaaab, aabbc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_2 = function(raaaab, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raabbc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAAAB = (raaaaa+raaaab)**k + tAABBC = (raaaaa+raaaab+raabbc)**k + tAABCD = (raaaaa+raaaab+raabbc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAABBC = tAABBC-tAAAAB + sAABCD = tAABCD-tAABBC + sABCDE = 1-tAABCD + alpha_1 = (1-d)*(sAAAAB + sAABBC + 3*sAABCD + 5*sABCDE) + d*(2*sAAAAA*sAAAAB + 2*sAAAAB**2 + 2*sAAAAA*sAABBC + 4*sAAAAB*sAABBC + 2*sAABBC**2 + 6*sAAAAA*sAABCD + 8*sAAAAB*sAABCD + 8*sAABBC*sAABCD + 6*sAABCD**2 + 8*sAAAAA*sABCDE + 10*sAAAAB*sABCDE + 10*sAABBC*sABCDE + 14*sAABCD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(2*sAABBC + sAABCD) + d*(2*sAAAAA*sAABBC + 2*sAAAAB*sAABBC + 2*sAABBC**2 + 2*sAABBC*sAABCD + 2*sAABBC*sABCDE + sABCDE**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBC*sABCDE + 2*sAABCD*sABCDE) + alpha_4 = (1-d)*(sAAAAB) + d*(sAABBC**2 + 2*sAABBC*sAABCD + sAABCD**2) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAAAB*sABCDE) + alpha_6 = d*(2*sAAAAB*sAABBC + 2*sAAAAB*sAABCD + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAA*sAABBC + 2*sAAAAA*sAABCD) + alpha_8 = d*(sAAAAB**2) + alpha_9 = d*(2*sAAAAA*sAAAAB) + alpha_10= d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10* dnbinom(x, size = kmercov*10/ bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaab,raabbc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaaab, aabbc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_2_unique = function(raaaab, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaaab-raabbc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAAAB = (raaaaa+raaaab)**k + tAABBC = (raaaaa+raaaab+raabbc)**k + tAABCD = (raaaaa+raaaab+raabbc+raabcd)**k + sAAAAA = tAAAAA + sAAAAB = tAAAAB-tAAAAA + sAABBC = tAABBC-tAAAAB + sAABCD = tAABCD-tAABBC + sABCDE = 1-tAABCD + alpha_1_unique = (1-d)*(sAAAAB + sAABBC + 3*sAABCD + 5*sABCDE) + alpha_2_unique = (1-d)*(2*sAABBC + sAABCD) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAAB) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=5, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raaabc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aaabc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_3 = function(raaabb, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raaabc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAAABC = (raaaaa+raaabb+raaabc)**k + tAABCD = (raaaaa+raaabb+raaabc+raabcd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAAABC = tAAABC-tAAABB + sAABCD = tAABCD-tAAABC + sABCDE = 1-tAABCD + alpha_1 = (1-d)*(2*sAAABC + 3*sAABCD + 5*sABCDE) + d*(4*sAAAAA*sAAABC + 4*sAAABB*sAAABC + 4*sAAABC**2 + 6*sAAAAA*sAABCD + 6*sAAABB*sAABCD + 10*sAAABC*sAABCD + 6*sAABCD**2 + 8*sAAAAA*sABCDE + 8*sAAABB*sABCDE + 12*sAAABC*sABCDE + 14*sAABCD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(sAAABB + sAABCD) + d*(2*sAAAAA*sAAABB + 2*sAAABB**2 + 2*sAAABB*sAAABC + 2*sAAABB*sAABCD + 2*sAAABB*sABCDE + sABCDE**2) + alpha_3 = (1-d)*(sAAABB + sAAABC) + d*(2*sAABCD*sABCDE) + alpha_4 = (1-d)*(0) + d*(sAABCD**2 + 2*sAAABB*sABCDE + 2*sAAABC*sABCDE) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAABB*sAABCD + 2*sAAABC*sAABCD) + alpha_6 = d*(sAAABB**2 + 2*sAAABB*sAAABC + sAAABC**2 + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAA*sAABCD) + alpha_8 = d*(2*sAAAAA*sAAABB + 2*sAAAAA*sAAABC) + alpha_9 = d*(0) + alpha_10= d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10* dnbinom(x, size = kmercov*10/ bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raaabc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aaabc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_3_unique = function(raaabb, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raaabc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAAABC = (raaaaa+raaabb+raaabc)**k + tAABCD = (raaaaa+raaabb+raaabc+raabcd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAAABC = tAAABC-tAAABB + sAABCD = tAABCD-tAAABC + sABCDE = 1-tAABCD + alpha_1_unique = (1-d)*(2*sAAABC + 3*sAABCD + 5*sABCDE) + alpha_2_unique = (1-d)*(sAAABB + sAABCD) + alpha_3_unique = (1-d)*(sAAABB + sAAABC) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=5, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raabcc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_4 = function(raaabb, raabcc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raabcc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAABCC = (raaaaa+raaabb+raabcc)**k + tAABCD = (raaaaa+raaabb+raabcc+raabcd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAABCC = tAABCC-tAAABB + sAABCD = tAABCD-tAABCC + sABCDE = 1-tAABCD + alpha_1 = (1-d)*(sAABCC + 3*sAABCD + 5*sABCDE) + d*(2*sAAAAA*sAABCC + 2*sAAABB*sAABCC + 2*sAABCC**2 + 6*sAAAAA*sAABCD + 6*sAAABB*sAABCD + 8*sAABCC*sAABCD + 6*sAABCD**2 + 8*sAAAAA*sABCDE + 8*sAAABB*sABCDE + 10*sAABCC*sABCDE + 14*sAABCD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(sAAABB + 2*sAABCC + sAABCD) + d*(2*sAAAAA*sAAABB + 2*sAAABB**2 + 2*sAAAAA*sAABCC + 4*sAAABB*sAABCC + 2*sAABCC**2 + 2*sAAABB*sAABCD + 2*sAABCC*sAABCD + 2*sAAABB*sABCDE + 2*sAABCC*sABCDE + sABCDE**2) + alpha_3 = (1-d)*(sAAABB) + d*(2*sAABCC*sABCDE + 2*sAABCD*sABCDE) + alpha_4 = (1-d)*(0) + d*(sAABCC**2 + 2*sAABCC*sAABCD + sAABCD**2 + 2*sAAABB*sABCDE) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAABB*sAABCC + 2*sAAABB*sAABCD) + alpha_6 = d*(sAAABB**2 + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAA*sAABCC + 2*sAAAAA*sAABCD) + alpha_8 = d*(2*sAAAAA*sAAABB) + alpha_9 = d*(0) + alpha_10= d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10* dnbinom(x, size = kmercov*10/ bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raabcc,raabcd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, aabcd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_4_unique = function(raaabb, raabcc, raabcd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raabcc-raabcd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAABCC = (raaaaa+raaabb+raabcc)**k + tAABCD = (raaaaa+raaabb+raabcc+raabcd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAABCC = tAABCC-tAAABB + sAABCD = tAABCD-tAABCC + sABCDE = 1-tAABCD + alpha_1_unique = (1-d)*(sAABCC + 3*sAABCD + 5*sABCDE) + alpha_2_unique = (1-d)*(sAAABB + 2*sAABCC + sAABCD) + alpha_3_unique = (1-d)*(sAAABB) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=5, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raabcc,rabcdd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, abcdd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_5 = function(raaabb, raabcc, rabcdd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raabcc-rabcdd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAABCC = (raaaaa+raaabb+raabcc)**k + tABCDD = (raaaaa+raaabb+raabcc+rabcdd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAABCC = tAABCC-tAAABB + sABCDD = tABCDD-tAABCC + sABCDE = 1-tABCDD + alpha_1 = (1-d)*(sAABCC + 3*sABCDD + 5*sABCDE) + d*(2*sAAAAA*sAABCC + 2*sAAABB*sAABCC + 2*sAABCC**2 + 4*sAAAAA*sABCDD + 4*sAAABB*sABCDD + 6*sAABCC*sABCDD + 4*sABCDD**2 + 8*sAAAAA*sABCDE + 8*sAAABB*sABCDE + 10*sAABCC*sABCDE + 12*sABCDD*sABCDE + 8*sABCDE**2) + alpha_2 = (1-d)*(sAAABB + 2*sAABCC + sABCDD) + d*(2*sAAAAA*sAAABB + 2*sAAABB**2 + 2*sAAAAA*sAABCC + 4*sAAABB*sAABCC + 2*sAABCC**2 + 2*sAAAAA*sABCDD + 4*sAAABB*sABCDD + 4*sAABCC*sABCDD + 3*sABCDD**2 + 2*sAAABB*sABCDE + 2*sAABCC*sABCDE + 4*sABCDD*sABCDE + sABCDE**2) + alpha_3 = (1-d)*(sAAABB) + d*(2*sAABCC*sABCDD + 2*sAABCC*sABCDE) + alpha_4 = (1-d)*(0) + d*(sAABCC**2 + 2*sAAABB*sABCDD + 2*sAAABB*sABCDE) + alpha_5 = (1-d)*(sAAAAA) + d*(2*sAAABB*sAABCC) + alpha_6 = d*(sAAABB**2 + 2*sAAAAA*sABCDD + 2*sAAAAA*sABCDE) + alpha_7 = d*(2*sAAAAA*sAABCC) + alpha_8 = d*(2*sAAAAA*sAAABB) + alpha_9 = d*(0) + alpha_10= d*(sAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10* dnbinom(x, size = kmercov*10/ bias, mu = kmercov*10) +} + +#' Produce model estimated (p=5, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabb,raabcc,rabcdd,rabcde Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, abcdd, and abcde respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict5_5_unique = function(raaabb, raabcc, rabcdd, rabcde, k, d, kmercov, bias, x) +{ + raaaaa = 1-raaabb-raabcc-rabcdd-rabcde + if (raaaaa < 0 || d > 1) {return(0)} + tAAAAA = raaaaa**k + tAAABB = (raaaaa+raaabb)**k + tAABCC = (raaaaa+raaabb+raabcc)**k + tABCDD = (raaaaa+raaabb+raabcc+rabcdd)**k + sAAAAA = tAAAAA + sAAABB = tAAABB-tAAAAA + sAABCC = tAABCC-tAAABB + sABCDD = tABCDD-tAABCC + sABCDE = 1-tABCDD + alpha_1_unique = (1-d)*(sAABCC + 3*sABCDD + 5*sABCDE) + alpha_2_unique = (1-d)*(sAAABB + 2*sAABCC + sABCDD) + alpha_3_unique = (1-d)*(sAAABB) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5) +} + +#' Produce model estimated (p=6, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabb,raaabbb,raaaabc,raaabbc,raabbcc,raaabcd,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_0 = function(raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, raaabcd, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabb-raaabbb-raaaabc-raaabbc-raabbcc-raaabcd-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + tAAAAAA = (raaaaaa)**k + tAAAAAB = (raaaaaa+raaaaab)**k + tAAAABB = (raaaaaa+raaaabb)**k + tAAABBB = (raaaaaa+raaabbb)**k + tAAAABC = (raaaaaa+raaaaab+raaaabb+raaaabc)**k + tAAABBC = (raaaaaa+raaaaab+raaabbb+raaabbc)**k + tAABBCC = (raaaaaa+raaaabb+raabbcc)**k + tAAABCD = (raaaaaa+raaaaab+raaaabb+raaabbb+raaaabc+raaabbc+raaabcd)**k + tAABBCD = (raaaaaa+raaaaab+raaaabb+raaaabc+raabbcc+raabbcd)**k + tAABCDE = (raaaaaa+raaaaab+raaaabb+raaabbb+raaaabc+raaabbc+raabbcc+raaabcd+raabbcd+raabcde)**k + sAAAAAA = tAAAAAA + sAAAAAB = tAAAAAB-tAAAAAA + sAAAABB = tAAAABB-tAAAAAA + sAAABBB = tAAABBB-tAAAAAA + sAAAABC = tAAAABC-tAAAABB-tAAAAAB+tAAAAAA + sAAABBC = tAAABBC-tAAABBB-tAAAAAB+tAAAAAA + sAABBCC = tAABBCC-tAAAABB + sAAABCD = tAAABCD-tAAABBC-tAAAABC+tAAAAAB + sAABBCD = tAABBCD-tAABBCC-tAAAABC+tAAAABB + sAABCDE = tAABCDE-tAABBCD-tAAABCD+tAAAABC + sABCDEF = 1-tAABCDE + alpha_1 = (1-d)*(sAAAAAB + 2*sAAAABC + sAAABBC + 3*sAAABCD + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 2*sAAAAAB*sAAAABB + 4*sAAAAAA*sAAAABC + 6*sAAAAAB*sAAAABC + 4*sAAAABB*sAAAABC + 4*sAAAABC**2 + 2*sAAAAAB*sAAABBB + 4*sAAAABC*sAAABBB + 2*sAAAAAA*sAAABBC + 4*sAAAAAB*sAAABBC + 2*sAAAABB*sAAABBC + 6*sAAAABC*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 6*sAAAAAA*sAAABCD + 8*sAAAAAB*sAAABCD + 6*sAAAABB*sAAABCD + 10*sAAAABC*sAAABCD + 6*sAAABBB*sAAABCD + 8*sAAABBC*sAAABCD + 6*sAAABCD**2 + 2*sAAAAAB*sAABBCC + 4*sAAAABC*sAABBCC + 2*sAAABBC*sAABBCC + 6*sAAABCD*sAABBCC + 4*sAAAAAA*sAABBCD + 6*sAAAAAB*sAABBCD + 4*sAAAABB*sAABBCD + 8*sAAAABC*sAABBCD + 4*sAAABBB*sAABBCD + 6*sAAABBC*sAABBCD + 10*sAAABCD*sAABBCD + 4*sAABBCC*sAABBCD + 4*sAABBCD**2 + 8*sAAAAAA*sAABCDE + 10*sAAAAAB*sAABCDE + 8*sAAAABB*sAABCDE + 12*sAAAABC*sAABCDE + 8*sAAABBB*sAABCDE + 10*sAAABBC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABBCC*sAABCDE + 12*sAABBCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 10*sAAAABB*sABCDEF + 14*sAAAABC*sABCDEF + 10*sAAABBB*sABCDEF + 12*sAAABBC*sABCDEF + 16*sAAABCD*sABCDEF + 10*sAABBCC*sABCDEF + 14*sAABBCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + sAAABBC + 3*sAABBCC + 2*sAABBCD + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAAAB*sAAAABB + 2*sAAAABB**2 + 2*sAAAABB*sAAAABC + 2*sAAAABB*sAAABBB + 2*sAAAAAA*sAAABBC + 2*sAAAAAB*sAAABBC + 4*sAAAABB*sAAABBC + 2*sAAAABC*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 2*sAAAABB*sAAABCD + 2*sAAABBC*sAAABCD + 4*sAAAAAA*sAABBCC + 4*sAAAAAB*sAABBCC + 6*sAAAABB*sAABBCC + 4*sAAAABC*sAABBCC + 4*sAAABBB*sAABBCC + 6*sAAABBC*sAABBCC + 4*sAAABCD*sAABBCC + 4*sAABBCC**2 + 2*sAAAAAA*sAABBCD + 2*sAAAAAB*sAABBCD + 4*sAAAABB*sAABBCD + 2*sAAAABC*sAABBCD + 2*sAAABBB*sAABBCD + 4*sAAABBC*sAABBCD + 2*sAAABCD*sAABBCD + 6*sAABBCC*sAABBCD + 2*sAABBCD**2 + 2*sAAAABB*sAABCDE + 2*sAAABBC*sAABCDE + 4*sAABBCC*sAABCDE + 2*sAABBCD*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAAABBC*sABCDEF + 4*sAABBCC*sABCDEF + 2*sAABBCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(2*sAAABBB + sAAABBC + sAAABCD) + d*(2*sAAAAAA*sAAABBB + 2*sAAAAAB*sAAABBB + 2*sAAAABB*sAAABBB + 2*sAAAABC*sAAABBB + 2*sAAABBB**2 + 2*sAAABBB*sAAABBC + 2*sAAABBB*sAAABCD + 2*sAAABBB*sAABBCC + 2*sAAABBB*sAABBCD + 2*sAAABBB*sAABCDE + 2*sAAABBB*sABCDEF + 2*sAABBCC*sABCDEF + 2*sAABBCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB + sAAAABC) + d*(sAABBCC**2 + 2*sAABBCC*sAABBCD + sAABBCD**2 + 2*sAABBCC*sAABCDE + 2*sAABBCD*sAABCDE + sAABCDE**2 + 2*sAAABBB*sABCDEF + 2*sAAABBC*sABCDEF + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAABBB*sAABBCC + 2*sAAABBC*sAABBCC + 2*sAAABCD*sAABBCC + 2*sAAABBB*sAABBCD + 2*sAAABBC*sAABBCD + 2*sAAABCD*sAABBCD + 2*sAAABBB*sAABCDE + 2*sAAABBC*sAABCDE + 2*sAAABCD*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAAAABC*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBB**2 + 2*sAAABBB*sAAABBC + sAAABBC**2 + 2*sAAABBB*sAAABCD + 2*sAAABBC*sAAABCD + sAAABCD**2 + 2*sAAAABB*sAABBCC + 2*sAAAABC*sAABBCC + 2*sAAAABB*sAABBCD + 2*sAAAABC*sAABBCD + 2*sAAAABB*sAABCDE + 2*sAAAABC*sAABCDE + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAABB*sAAABBB + 2*sAAAABC*sAAABBB + 2*sAAAABB*sAAABBC + 2*sAAAABC*sAAABBC + 2*sAAAABB*sAAABCD + 2*sAAAABC*sAAABCD + 2*sAAAAAB*sAABBCC + 2*sAAAAAB*sAABBCD + 2*sAAAAAB*sAABCDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAABB*sAAAABC + sAAAABC**2 + 2*sAAAAAB*sAAABBB + 2*sAAAAAB*sAAABBC + 2*sAAAAAB*sAAABCD + 2*sAAAAAA*sAABBCC + 2*sAAAAAA*sAABBCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAB*sAAAABB + 2*sAAAAAB*sAAAABC + 2*sAAAAAA*sAAABBB + 2*sAAAAAA*sAAABBC + 2*sAAAAAA*sAAABCD) + alpha_10 = d*(sAAAAAB**2 + 2*sAAAAAA*sAAAABB + 2*sAAAAAA*sAAAABC) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabb,raaabbb,raaaabc,raaabbc,raabbcc,raaabcd,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_0_unique = function(raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, raaabcd, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabb-raaabbb-raaaabc-raaabbc-raabbcc-raaabcd-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + tAAAAAA = (raaaaaa)**k + tAAAAAB = (raaaaaa+raaaaab)**k + tAAAABB = (raaaaaa+raaaabb)**k + tAAABBB = (raaaaaa+raaabbb)**k + tAAAABC = (raaaaaa+raaaaab+raaaabb+raaaabc)**k + tAAABBC = (raaaaaa+raaaaab+raaabbb+raaabbc)**k + tAABBCC = (raaaaaa+raaaabb+raabbcc)**k + tAAABCD = (raaaaaa+raaaaab+raaaabb+raaabbb+raaaabc+raaabbc+raaabcd)**k + tAABBCD = (raaaaaa+raaaaab+raaaabb+raaaabc+raabbcc+raabbcd)**k + tAABCDE = (raaaaaa+raaaaab+raaaabb+raaabbb+raaaabc+raaabbc+raabbcc+raaabcd+raabbcd+raabcde)**k + sAAAAAA = tAAAAAA + sAAAAAB = tAAAAAB-tAAAAAA + sAAAABB = tAAAABB-tAAAAAA + sAAABBB = tAAABBB-tAAAAAA + sAAAABC = tAAAABC-tAAAABB-tAAAAAB+tAAAAAA + sAAABBC = tAAABBC-tAAABBB-tAAAAAB+tAAAAAA + sAABBCC = tAABBCC-tAAAABB + sAAABCD = tAAABCD-tAAABBC-tAAAABC+tAAAAAB + sAABBCD = tAABBCD-tAABBCC-tAAAABC+tAAAABB + sAABCDE = tAABCDE-tAABBCD-tAAABCD+tAAAABC + sABCDEF = 1-tAABCDE + alpha_1 = (1-d)*(sAAAAAB + 2*sAAAABC + sAAABBC + 3*sAAABCD + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + alpha_2 = (1-d)*(sAAAABB + sAAABBC + 3*sAABBCC + 2*sAABBCD + sAABCDE) + alpha_3 = (1-d)*(2*sAAABBB + sAAABBC + sAAABCD) + alpha_4 = (1-d)*(sAAAABB + sAAAABC) + alpha_5 = (1-d)*(sAAAAAB) + alpha_6 = (1-d)*(sAAAAAA) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_1 = function(raaaaab, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaaabc = (raaaaaa+raaaaab+raaaabc)**k + taaabcd = (raaaaaa+raaaaab+raaaabc+raaabcd)**k + taabcde = (raaaaaa+raaaaab+raaaabc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAAABC = taaaabc-taaaaab + sAAABCD = taaabcd-taaaabc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAAAAB + 2*sAAAABC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 4*sAAAAAA*sAAAABC + 6*sAAAAAB*sAAAABC + 4*sAAAABC**2 + 6*sAAAAAA*sAAABCD + 8*sAAAAAB*sAAABCD + 10*sAAAABC*sAAABCD + 6*sAAABCD**2 + 8*sAAAAAA*sAABCDE + 10*sAAAAAB*sAABCDE + 12*sAAAABC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 14*sAAAABC*sABCDEF + 16*sAAABCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAABCDE) + d*(sABCDEF**2) + alpha_3 = (1-d)*(sAAABCD) + d*(2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABC) + d*(sAABCDE**2 + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAABCD*sAABCDE + 2*sAAAABC*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABCD**2 + 2*sAAAABC*sAABCDE + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAABC*sAAABCD + 2*sAAAAAB*sAABCDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABC**2 + 2*sAAAAAB*sAAABCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAB*sAAAABC + 2*sAAAAAA*sAAABCD) + alpha_10 = d*(sAAAAAB**2 + 2*sAAAAAA*sAAAABC) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_1_unique = function(raaaaab, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaaabc = (raaaaaa+raaaaab+raaaabc)**k + taaabcd = (raaaaaa+raaaaab+raaaabc+raaabcd)**k + taabcde = (raaaaaa+raaaaab+raaaabc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAAABC = taaaabc-taaaaab + sAAABCD = taaabcd-taaaabc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAAAAB + 2*sAAAABC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAABCDE) + alpha_3_unique = (1-d)*(sAAABCD) + alpha_4_unique = (1-d)*(sAAAABC) + alpha_5_unique = (1-d)*(sAAAAAB) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_2 = function(raaaaab, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaaabc = (raaaaaa+raaaaab+raaaabc)**k + taabbcd = (raaaaaa+raaaaab+raaaabc+raabbcd)**k + taabcde = (raaaaaa+raaaaab+raaaabc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAAABC = taaaabc-taaaaab + sAABBCD = taabbcd-taaaabc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAAAAB + 2*sAAAABC + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 4*sAAAAAA*sAAAABC + 6*sAAAAAB*sAAAABC + 4*sAAAABC**2 + 4*sAAAAAA*sAABBCD + 6*sAAAAAB*sAABBCD + 8*sAAAABC*sAABBCD + 4*sAABBCD**2 + 8*sAAAAAA*sAABCDE + 10*sAAAAAB*sAABCDE + 12*sAAAABC*sAABCDE + 12*sAABBCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 14*sAAAABC*sABCDEF + 14*sAABBCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(2*sAABBCD + sAABCDE) + d*(2*sAAAAAA*sAABBCD + 2*sAAAAAB*sAABBCD + 2*sAAAABC*sAABBCD + 2*sAABBCD**2 + 2*sAABBCD*sAABCDE + 2*sAABBCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABC) + d*(sAABBCD**2 + 2*sAABBCD*sAABCDE + sAABCDE**2) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAAABC*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(2*sAAAABC*sAABBCD + 2*sAAAABC*sAABCDE + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAAAB*sAABBCD + 2*sAAAAAB*sAABCDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABC**2 + 2*sAAAAAA*sAABBCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAB*sAAAABC) + alpha_10 = d*(sAAAAAB**2 + 2*sAAAAAA*sAAAABC) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaaabc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_2_unique = function(raaaaab, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaaabc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaaabc = (raaaaaa+raaaaab+raaaabc)**k + taabbcd = (raaaaaa+raaaaab+raaaabc+raabbcd)**k + taabcde = (raaaaaa+raaaaab+raaaabc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAAABC = taaaabc-taaaaab + sAABBCD = taabbcd-taaaabc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAAAAB + 2*sAAAABC + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(2*sAABBCD + sAABCDE) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAABC) + alpha_5_unique = (1-d)*(sAAAAAB) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_3 = function(raaaaab, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taaabcd = (raaaaaa+raaaaab+raaabbc+raaabcd)**k + taabcde = (raaaaaa+raaaaab+raaabbc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAAABCD = taaabcd-taaabbc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAAAAB + sAAABBC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 2*sAAAAAA*sAAABBC + 4*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 6*sAAAAAA*sAAABCD + 8*sAAAAAB*sAAABCD + 8*sAAABBC*sAAABCD + 6*sAAABCD**2 + 8*sAAAAAA*sAABCDE + 10*sAAAAAB*sAABCDE + 10*sAAABBC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 12*sAAABBC*sABCDEF + 16*sAAABCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + sAABCDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 2*sAAABBC*sAAABCD + 2*sAAABBC*sAABCDE + 2*sAAABBC*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABBC + sAAABCD) + d*(2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCDE**2 + 2*sAAABBC*sABCDEF + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAABBC*sAABCDE + 2*sAAABCD*sAABCDE) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBC**2 + 2*sAAABBC*sAAABCD + sAAABCD**2 + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAAAB*sAABCDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAB*sAAABBC + 2*sAAAAAB*sAAABCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABBC + 2*sAAAAAA*sAAABCD) + alpha_10 = d*(sAAAAAB**2) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_3_unique = function(raaaaab, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taaabcd = (raaaaaa+raaaaab+raaabbc+raaabcd)**k + taabcde = (raaaaaa+raaaaab+raaabbc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAAABCD = taaabcd-taaabbc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAAAAB + sAAABBC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + sAABCDE) + alpha_3_unique = (1-d)*(sAAABBC + sAAABCD) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAAB) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raabccd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_4 = function(raaaaab, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raabccd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taabccd = (raaaaaa+raaaaab+raaabbc+raabccd)**k + taabcde = (raaaaaa+raaaaab+raaabbc+raabccd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAABCCD = taabccd-taaabbc + sAABCDE = taabcde-taabccd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAAAAB + sAAABBC + 2*sAABCCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 2*sAAAAAA*sAAABBC + 4*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 4*sAAAAAA*sAABCCD + 6*sAAAAAB*sAABCCD + 6*sAAABBC*sAABCCD + 4*sAABCCD**2 + 8*sAAAAAA*sAABCDE + 10*sAAAAAB*sAABCDE + 10*sAAABBC*sAABCDE + 12*sAABCCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 12*sAAABBC*sABCDEF + 14*sAABCCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + 2*sAABCCD + sAABCDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 2*sAAAAAA*sAABCCD + 2*sAAAAAB*sAABCCD + 4*sAAABBC*sAABCCD + 2*sAABCCD**2 + 2*sAAABBC*sAABCDE + 2*sAABCCD*sAABCDE + 2*sAAABBC*sABCDEF + 2*sAABCCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABBC) + d*(2*sAABCCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCCD**2 + 2*sAABCCD*sAABCDE + sAABCDE**2 + 2*sAAABBC*sABCDEF) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAABBC*sAABCCD + 2*sAAABBC*sAABCDE) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBC**2 + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAAAB*sAABCCD + 2*sAAAAAB*sAABCDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAB*sAAABBC + 2*sAAAAAA*sAABCCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABBC) + alpha_10 = d*(sAAAAAB**2) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raabccd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_4_unique = function(raaaaab, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raabccd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taabccd = (raaaaaa+raaaaab+raaabbc+raabccd)**k + taabcde = (raaaaaa+raaaaab+raaabbc+raabccd+raabcde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAABCCD = taabccd-taaabbc + sAABCDE = taabcde-taabccd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAAAAB + sAAABBC + 2*sAABCCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + 2*sAABCCD + sAABCDE) + alpha_3_unique = (1-d)*(sAAABBC) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAAB) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raabccd,rabcdde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, abcdde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_5 = function(raaaaab, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raabccd-rabcdde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taabccd = (raaaaaa+raaaaab+raaabbc+raabccd)**k + tabcdde = (raaaaaa+raaaaab+raaabbc+raabccd+rabcdde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAABCCD = taabccd-taaabbc + sABCDDE = tabcdde-taabccd + sABCDEF = 1-tabcdde + alpha_1 = (1-d)*(sAAAAAB + sAAABBC + 2*sAABCCD + 4*sABCDDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAAAAB + 2*sAAAAAB**2 + 2*sAAAAAA*sAAABBC + 4*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 4*sAAAAAA*sAABCCD + 6*sAAAAAB*sAABCCD + 6*sAAABBC*sAABCCD + 4*sAABCCD**2 + 6*sAAAAAA*sABCDDE + 8*sAAAAAB*sABCDDE + 8*sAAABBC*sABCDDE + 10*sAABCCD*sABCDDE + 6*sABCDDE**2 + 10*sAAAAAA*sABCDEF + 12*sAAAAAB*sABCDEF + 12*sAAABBC*sABCDEF + 14*sAABCCD*sABCDEF + 16*sABCDDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + 2*sAABCCD + sABCDDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAAAAB*sAAABBC + 2*sAAABBC**2 + 2*sAAAAAA*sAABCCD + 2*sAAAAAB*sAABCCD + 4*sAAABBC*sAABCCD + 2*sAABCCD**2 + 2*sAAAAAA*sABCDDE + 2*sAAAAAB*sABCDDE + 4*sAAABBC*sABCDDE + 4*sAABCCD*sABCDDE + 3*sABCDDE**2 + 2*sAAABBC*sABCDEF + 2*sAABCCD*sABCDEF + 4*sABCDDE*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABBC) + d*(2*sAABCCD*sABCDDE + 2*sAABCCD*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCCD**2 + 2*sAAABBC*sABCDDE + 2*sAAABBC*sABCDEF) + alpha_5 = (1-d)*(sAAAAAB) + d*(2*sAAABBC*sAABCCD) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBC**2 + 2*sAAAAAB*sABCDDE + 2*sAAAAAB*sABCDEF) + alpha_7 = d*(2*sAAAAAB*sAABCCD + 2*sAAAAAA*sABCDDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAB*sAAABBC + 2*sAAAAAA*sAABCCD) + alpha_9 = d*(2*sAAAAAA*sAAABBC) + alpha_10 = d*(sAAAAAB**2) + alpha_11 = d*(2*sAAAAAA*sAAAAAB) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaaab,raaabbc,raabccd,rabcdde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, abcdde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_5_unique = function(raaaaab, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaaab-raaabbc-raabccd-rabcdde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaaab = (raaaaaa+raaaaab)**k + taaabbc = (raaaaaa+raaaaab+raaabbc)**k + taabccd = (raaaaaa+raaaaab+raaabbc+raabccd)**k + tabcdde = (raaaaaa+raaaaab+raaabbc+raabccd+rabcdde)**k + sAAAAAA = taaaaaa + sAAAAAB = taaaaab-taaaaaa + sAAABBC = taaabbc-taaaaab + sAABCCD = taabccd-taaabbc + sABCDDE = tabcdde-taabccd + sABCDEF = 1-tabcdde + alpha_1_unique = (1-d)*(sAAAAAB + sAAABBC + 2*sAABCCD + 4*sABCDDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + 2*sAABCCD + sABCDDE) + alpha_3_unique = (1-d)*(sAAABBC) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(sAAAAAB) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=6) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaaabc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_6 = function(raaaabb, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaaabc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaaabc = (raaaaaa+raaaabb+raaaabc)**k + taaabcd = (raaaaaa+raaaabb+raaaabc+raaabcd)**k + taabcde = (raaaaaa+raaaabb+raaaabc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAAABC = taaaabc-taaaabb + sAAABCD = taaabcd-taaaabc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(2*sAAAABC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + d*(4*sAAAAAA*sAAAABC + 4*sAAAABB*sAAAABC + 4*sAAAABC**2 + 6*sAAAAAA*sAAABCD + 6*sAAAABB*sAAABCD + 10*sAAAABC*sAAABCD + 6*sAAABCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 12*sAAAABC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 14*sAAAABC*sABCDEF + 16*sAAABCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 2*sAAAABB*sAAAABC + 2*sAAAABB*sAAABCD + 2*sAAAABB*sAABCDE + 2*sAAAABB*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABCD) + d*(2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB + sAAAABC) + d*(sAABCDE**2 + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABCD*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAAAABC*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABCD**2 + 2*sAAAABB*sAABCDE + 2*sAAAABC*sAABCDE) + alpha_7 = d*(2*sAAAABB*sAAABCD + 2*sAAAABC*sAAABCD + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAABB*sAAAABC + sAAAABC**2 + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABCD) + alpha_10 = d*(2*sAAAAAA*sAAAABB + 2*sAAAAAA*sAAAABC) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=6, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaaabc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_6_unique = function(raaaabb, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaaabc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaaabc = (raaaaaa+raaaabb+raaaabc)**k + taaabcd = (raaaaaa+raaaabb+raaaabc+raaabcd)**k + taabcde = (raaaaaa+raaaabb+raaaabc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAAABC = taaaabc-taaaabb + sAAABCD = taaabcd-taaaabc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(2*sAAAABC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + sAABCDE) + alpha_3_unique = (1-d)*(sAAABCD) + alpha_4_unique = (1-d)*(sAAAABB + sAAAABC) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=7) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaaabc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_7 = function(raaaabb, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaaabc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaaabc = (raaaaaa+raaaabb+raaaabc)**k + taabbcd = (raaaaaa+raaaabb+raaaabc+raabbcd)**k + taabcde = (raaaaaa+raaaabb+raaaabc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAAABC = taaaabc-taaaabb + sAABBCD = taabbcd-taaaabc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(2*sAAAABC + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + d*(4*sAAAAAA*sAAAABC + 4*sAAAABB*sAAAABC + 4*sAAAABC**2 + 4*sAAAAAA*sAABBCD + 4*sAAAABB*sAABBCD + 8*sAAAABC*sAABBCD + 4*sAABBCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 12*sAAAABC*sAABCDE + 12*sAABBCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 14*sAAAABC*sABCDEF + 14*sAABBCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + 2*sAABBCD + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 2*sAAAABB*sAAAABC + 2*sAAAAAA*sAABBCD + 4*sAAAABB*sAABBCD + 2*sAAAABC*sAABBCD + 2*sAABBCD**2 + 2*sAAAABB*sAABCDE + 2*sAABBCD*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAABBCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB + sAAAABC) + d*(sAABBCD**2 + 2*sAABBCD*sAABCDE + sAABCDE**2) + alpha_5 = (1-d)*(0) + d*(2*sAAAABB*sABCDEF + 2*sAAAABC*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(2*sAAAABB*sAABBCD + 2*sAAAABC*sAABBCD + 2*sAAAABB*sAABCDE + 2*sAAAABC*sAABCDE) + alpha_7 = d*(2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAABB*sAAAABC + sAAAABC**2 + 2*sAAAAAA*sAABBCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(0) + alpha_10 = d*(2*sAAAAAA*sAAAABB + 2*sAAAAAA*sAAAABC) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=7, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaaabc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_7_unique = function(raaaabb, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaaabc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaaabc = (raaaaaa+raaaabb+raaaabc)**k + taabbcd = (raaaaaa+raaaabb+raaaabc+raabbcd)**k + taabcde = (raaaaaa+raaaabb+raaaabc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAAABC = taaaabc-taaaabb + sAABBCD = taabbcd-taaaabc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(2*sAAAABC + 2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + 2*sAABBCD + sAABCDE) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAABB + sAAAABC) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=8) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_8 = function(raaaabb, raaabcc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taaabcd = (raaaaaa+raaaabb+raaabcc+raaabcd)**k + taabcde = (raaaaaa+raaaabb+raaabcc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAAABCD = taaabcd-taaabcc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAABCC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABCC + 2*sAAAABB*sAAABCC + 2*sAAABCC**2 + 6*sAAAAAA*sAAABCD + 6*sAAAABB*sAAABCD + 8*sAAABCC*sAAABCD + 6*sAAABCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 10*sAAABCC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 12*sAAABCC*sABCDEF + 16*sAAABCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + sAAABCC + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 2*sAAAAAA*sAAABCC + 4*sAAAABB*sAAABCC + 2*sAAABCC**2 + 2*sAAAABB*sAAABCD + 2*sAAABCC*sAAABCD + 2*sAAAABB*sAABCDE + 2*sAAABCC*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAAABCC*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABCC + sAAABCD) + d*(2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABCDE**2 + 2*sAAABCC*sABCDEF + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABCC*sAABCDE + 2*sAAABCD*sAABCDE + 2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABCC**2 + 2*sAAABCC*sAAABCD + sAAABCD**2 + 2*sAAAABB*sAABCDE) + alpha_7 = d*(2*sAAAABB*sAAABCC + 2*sAAAABB*sAAABCD + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABCC + 2*sAAAAAA*sAAABCD) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=8, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_8_unique = function(raaaabb, raaabcc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taaabcd = (raaaaaa+raaaabb+raaabcc+raaabcd)**k + taabcde = (raaaaaa+raaaabb+raaabcc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAAABCD = taaabcd-taaabcc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAABCC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + sAAABCC + sAABCDE) + alpha_3_unique = (1-d)*(sAAABCC + sAAABCD) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=9) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raabcdd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_9 = function(raaaabb, raaabcc, raabcdd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raabcdd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taabcdd = (raaaaaa+raaaabb+raaabcc+raabcdd)**k + taabcde = (raaaaaa+raaaabb+raaabcc+raabcdd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAABCDD = taabcdd-taaabcc + sAABCDE = taabcde-taabcdd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAABCC + 2*sAABCDD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABCC + 2*sAAAABB*sAAABCC + 2*sAAABCC**2 + 4*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 6*sAAABCC*sAABCDD + 4*sAABCDD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 10*sAAABCC*sAABCDE + 12*sAABCDD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 12*sAAABCC*sABCDEF + 14*sAABCDD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + sAAABCC + 2*sAABCDD + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 2*sAAAAAA*sAAABCC + 4*sAAAABB*sAAABCC + 2*sAAABCC**2 + 2*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 4*sAAABCC*sAABCDD + 2*sAABCDD**2 + 2*sAAAABB*sAABCDE + 2*sAAABCC*sAABCDE + 2*sAABCDD*sAABCDE + 2*sAAAABB*sABCDEF + 2*sAAABCC*sABCDEF + 2*sAABCDD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABCC) + d*(2*sAABCDD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABCDD**2 + 2*sAABCDD*sAABCDE + sAABCDE**2 + 2*sAAABCC*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABCC*sAABCDD + 2*sAAABCC*sAABCDE + 2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABCC**2 + 2*sAAAABB*sAABCDD + 2*sAAAABB*sAABCDE) + alpha_7 = d*(2*sAAAABB*sAAABCC + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABCDD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABCC) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=9, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raabcdd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_9_unique = function(raaaabb, raaabcc, raabcdd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raabcdd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taabcdd = (raaaaaa+raaaabb+raaabcc+raabcdd)**k + taabcde = (raaaaaa+raaaabb+raaabcc+raabcdd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAABCDD = taabcdd-taaabcc + sAABCDE = taabcde-taabcdd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAABCC + 2*sAABCDD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + sAAABCC + 2*sAABCDD + sAABCDE) + alpha_3_unique = (1-d)*(sAAABCC) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=10) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raabcdd,rabcdee,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, abcdee, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_10 = function(raaaabb, raaabcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raabcdd-rabcdee-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taabcdd = (raaaaaa+raaaabb+raaabcc+raabcdd)**k + tabcdee = (raaaaaa+raaaabb+raaabcc+raabcdd+rabcdee)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAABCDD = taabcdd-taaabcc + sABCDEE = tabcdee-taabcdd + sABCDEF = 1-tabcdee + alpha_1 = (1-d)*(sAAABCC + 2*sAABCDD + 4*sABCDEE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABCC + 2*sAAAABB*sAAABCC + 2*sAAABCC**2 + 4*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 6*sAAABCC*sAABCDD + 4*sAABCDD**2 + 6*sAAAAAA*sABCDEE + 6*sAAAABB*sABCDEE + 8*sAAABCC*sABCDEE + 10*sAABCDD*sABCDEE + 6*sABCDEE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 12*sAAABCC*sABCDEF + 14*sAABCDD*sABCDEF + 16*sABCDEE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + sAAABCC + 2*sAABCDD + sABCDEE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 2*sAAAAAA*sAAABCC + 4*sAAAABB*sAAABCC + 2*sAAABCC**2 + 2*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 4*sAAABCC*sAABCDD + 2*sAABCDD**2 + 2*sAAAAAA*sABCDEE + 4*sAAAABB*sABCDEE + 4*sAAABCC*sABCDEE + 4*sAABCDD*sABCDEE + 3*sABCDEE**2 + 2*sAAAABB*sABCDEF + 2*sAAABCC*sABCDEF + 2*sAABCDD*sABCDEF + 4*sABCDEE*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(sAAABCC) + d*(2*sAABCDD*sABCDEE + 2*sAABCDD*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABCDD**2 + 2*sAAABCC*sABCDEE + 2*sAAABCC*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABCC*sAABCDD + 2*sAAAABB*sABCDEE + 2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABCC**2 + 2*sAAAABB*sAABCDD) + alpha_7 = d*(2*sAAAABB*sAAABCC + 2*sAAAAAA*sABCDEE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABCDD) + alpha_9 = d*(2*sAAAAAA*sAAABCC) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=10, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raaabcc,raabcdd,rabcdee,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, abcdee, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_10_unique = function(raaaabb, raaabcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raaabcc-raabcdd-rabcdee-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taaabcc = (raaaaaa+raaaabb+raaabcc)**k + taabcdd = (raaaaaa+raaaabb+raaabcc+raabcdd)**k + tabcdee = (raaaaaa+raaaabb+raaabcc+raabcdd+rabcdee)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAAABCC = taaabcc-taaaabb + sAABCDD = taabcdd-taaabcc + sABCDEE = tabcdee-taabcdd + sABCDEF = 1-tabcdee + alpha_1_unique = (1-d)*(sAAABCC + 2*sAABCDD + 4*sABCDEE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + sAAABCC + 2*sAABCDD + sABCDEE) + alpha_3_unique = (1-d)*(sAAABCC) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=11) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_11 = function(raaaabb, raabbcc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabbcd = (raaaaaa+raaaabb+raabbcc+raabbcd)**k + taabcde = (raaaaaa+raaaabb+raabbcc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABBCD = taabbcd-taabbcc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + d*(4*sAAAAAA*sAABBCD + 4*sAAAABB*sAABBCD + 4*sAABBCC*sAABBCD + 4*sAABBCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 8*sAABBCC*sAABCDE + 12*sAABBCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 10*sAABBCC*sABCDEF + 14*sAABBCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABBCD + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 4*sAAAAAA*sAABBCC + 6*sAAAABB*sAABBCC + 4*sAABBCC**2 + 2*sAAAAAA*sAABBCD + 4*sAAAABB*sAABBCD + 6*sAABBCC*sAABBCD + 2*sAABBCD**2 + 2*sAAAABB*sAABCDE + 4*sAABBCC*sAABCDE + 2*sAABBCD*sAABCDE + 2*sAAAABB*sABCDEF + 4*sAABBCC*sABCDEF + 2*sAABBCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBCC*sABCDEF + 2*sAABBCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABBCC**2 + 2*sAABBCC*sAABBCD + sAABBCD**2 + 2*sAABBCC*sAABCDE + 2*sAABBCD*sAABCDE + sAABCDE**2) + alpha_5 = (1-d)*(0) + d*(2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(2*sAAAABB*sAABBCC + 2*sAAAABB*sAABBCD + 2*sAAAABB*sAABCDE) + alpha_7 = d*(2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABBCC + 2*sAAAAAA*sAABBCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(0) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=11, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabbcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabbcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_11_unique = function(raaaabb, raabbcc, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabbcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabbcd = (raaaaaa+raaaabb+raabbcc+raabbcd)**k + taabcde = (raaaaaa+raaaabb+raabbcc+raabbcd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABBCD = taabbcd-taabbcc + sAABCDE = taabcde-taabbcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(2*sAABBCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABBCD + sAABCDE) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=12) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabcdd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_12 = function(raaaabb, raabbcc, raabcdd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabcdd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabcdd = (raaaaaa+raaaabb+raabbcc+raabcdd)**k + taabcde = (raaaaaa+raaaabb+raabbcc+raabcdd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABCDD = taabcdd-taabbcc + sAABCDE = taabcde-taabcdd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(2*sAABCDD + 4*sAABCDE + 6*sABCDEF) + d*(4*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 4*sAABBCC*sAABCDD + 4*sAABCDD**2 + 8*sAAAAAA*sAABCDE + 8*sAAAABB*sAABCDE + 8*sAABBCC*sAABCDE + 12*sAABCDD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 10*sAABBCC*sABCDEF + 14*sAABCDD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABCDD + sAABCDE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 4*sAAAAAA*sAABBCC + 6*sAAAABB*sAABBCC + 4*sAABBCC**2 + 2*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 6*sAABBCC*sAABCDD + 2*sAABCDD**2 + 2*sAAAABB*sAABCDE + 4*sAABBCC*sAABCDE + 2*sAABCDD*sAABCDE + 2*sAAAABB*sABCDEF + 4*sAABBCC*sABCDEF + 2*sAABCDD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBCC*sABCDEF + 2*sAABCDD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABBCC**2 + 2*sAABBCC*sAABCDD + sAABCDD**2 + 2*sAABBCC*sAABCDE + 2*sAABCDD*sAABCDE + sAABCDE**2) + alpha_5 = (1-d)*(0) + d*(2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(2*sAAAABB*sAABBCC + 2*sAAAABB*sAABCDD + 2*sAAAABB*sAABCDE) + alpha_7 = d*(2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABBCC + 2*sAAAAAA*sAABCDD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(0) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=12, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabcdd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_12_unique = function(raaaabb, raabbcc, raabcdd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabcdd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabcdd = (raaaaaa+raaaabb+raabbcc+raabcdd)**k + taabcde = (raaaaaa+raaaabb+raabbcc+raabcdd+raabcde)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABCDD = taabcdd-taabbcc + sAABCDE = taabcde-taabcdd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(2*sAABCDD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABCDD + sAABCDE) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=13) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabcdd,rabcdee,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, abcdee, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_13 = function(raaaabb, raabbcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabcdd-rabcdee-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabcdd = (raaaaaa+raaaabb+raabbcc+raabcdd)**k + tabcdee = (raaaaaa+raaaabb+raabbcc+raabcdd+rabcdee)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABCDD = taabcdd-taabbcc + sABCDEE = tabcdee-taabcdd + sABCDEF = 1-tabcdee + alpha_1 = (1-d)*(2*sAABCDD + 4*sABCDEE + 6*sABCDEF) + d*(4*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 4*sAABBCC*sAABCDD + 4*sAABCDD**2 + 6*sAAAAAA*sABCDEE + 6*sAAAABB*sABCDEE + 6*sAABBCC*sABCDEE + 10*sAABCDD*sABCDEE + 6*sABCDEE**2 + 10*sAAAAAA*sABCDEF + 10*sAAAABB*sABCDEF + 10*sAABBCC*sABCDEF + 14*sAABCDD*sABCDEF + 16*sABCDEE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABCDD + sABCDEE) + d*(2*sAAAAAA*sAAAABB + 2*sAAAABB**2 + 4*sAAAAAA*sAABBCC + 6*sAAAABB*sAABBCC + 4*sAABBCC**2 + 2*sAAAAAA*sAABCDD + 4*sAAAABB*sAABCDD + 6*sAABBCC*sAABCDD + 2*sAABCDD**2 + 2*sAAAAAA*sABCDEE + 4*sAAAABB*sABCDEE + 6*sAABBCC*sABCDEE + 4*sAABCDD*sABCDEE + 3*sABCDEE**2 + 2*sAAAABB*sABCDEF + 4*sAABBCC*sABCDEF + 2*sAABCDD*sABCDEF + 4*sABCDEE*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(0) + d*(2*sAABBCC*sABCDEE + 2*sAABCDD*sABCDEE + 2*sAABBCC*sABCDEF + 2*sAABCDD*sABCDEF) + alpha_4 = (1-d)*(sAAAABB) + d*(sAABBCC**2 + 2*sAABBCC*sAABCDD + sAABCDD**2) + alpha_5 = (1-d)*(0) + d*(2*sAAAABB*sABCDEE + 2*sAAAABB*sABCDEF) + alpha_6 = (1-d)*(sAAAAAA) + d*(2*sAAAABB*sAABBCC + 2*sAAAABB*sAABCDD) + alpha_7 = d*(2*sAAAAAA*sABCDEE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(sAAAABB**2 + 2*sAAAAAA*sAABBCC + 2*sAAAAAA*sAABCDD) + alpha_9 = d*(0) + alpha_10 = d*(2*sAAAAAA*sAAAABB) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=13, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaaabb,raabbcc,raabcdd,rabcdee,rabcdef Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, abcdee, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_13_unique = function(raaaabb, raabbcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaaabb-raabbcc-raabcdd-rabcdee-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaaabb = (raaaaaa+raaaabb)**k + taabbcc = (raaaaaa+raaaabb+raabbcc)**k + taabcdd = (raaaaaa+raaaabb+raabbcc+raabcdd)**k + tabcdee = (raaaaaa+raaaabb+raabbcc+raabcdd+rabcdee)**k + sAAAAAA = taaaaaa + sAAAABB = taaaabb-taaaaaa + sAABBCC = taabbcc-taaaabb + sAABCDD = taabcdd-taabbcc + sABCDEE = tabcdee-taabcdd + sABCDEF = 1-tabcdee + alpha_1_unique = (1-d)*(2*sAABCDD + 4*sABCDEE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAAABB + 3*sAABBCC + 2*sAABCDD + sABCDEE) + alpha_3_unique = (1-d)*(0) + alpha_4_unique = (1-d)*(sAAAABB) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=14) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_14 = function(raaabbb, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taaabcd = (raaaaaa+raaabbb+raaabbc+raaabcd)**k + taabcde = (raaaaaa+raaabbb+raaabbc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAAABCD = taaabcd-taaabbc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAABBC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 6*sAAAAAA*sAAABCD + 6*sAAABBB*sAAABCD + 8*sAAABBC*sAAABCD + 6*sAAABCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAABBB*sAABCDE + 10*sAAABBC*sAABCDE + 14*sAAABCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAABBB*sABCDEF + 12*sAAABBC*sABCDEF + 16*sAAABCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + sAABCDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 2*sAAABBC*sAAABCD + 2*sAAABBC*sAABCDE + 2*sAAABBC*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(2*sAAABBB + sAAABBC + sAAABCD) + d*(2*sAAAAAA*sAAABBB + 2*sAAABBB**2 + 2*sAAABBB*sAAABBC + 2*sAAABBB*sAAABCD + 2*sAAABBB*sAABCDE + 2*sAAABBB*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCDE**2 + 2*sAAABBB*sABCDEF + 2*sAAABBC*sABCDEF + 2*sAAABCD*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABBB*sAABCDE + 2*sAAABBC*sAABCDE + 2*sAAABCD*sAABCDE) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBB**2 + 2*sAAABBB*sAAABBC + sAAABBC**2 + 2*sAAABBB*sAAABCD + 2*sAAABBC*sAAABCD + sAAABCD**2) + alpha_7 = d*(2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABBB + 2*sAAAAAA*sAAABBC + 2*sAAAAAA*sAAABCD) + alpha_10 = d*(0) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=14, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raaabcd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aaabcd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_14_unique = function(raaabbb, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raaabcd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taaabcd = (raaaaaa+raaabbb+raaabbc+raaabcd)**k + taabcde = (raaaaaa+raaabbb+raaabbc+raaabcd+raabcde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAAABCD = taaabcd-taaabbc + sAABCDE = taabcde-taaabcd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAABBC + 3*sAAABCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + sAABCDE) + alpha_3_unique = (1-d)*(2*sAAABBB + sAAABBC + sAAABCD) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=15) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raabccd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_15 = function(raaabbb, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raabccd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taabccd = (raaaaaa+raaabbb+raaabbc+raabccd)**k + taabcde = (raaaaaa+raaabbb+raaabbc+raabccd+raabcde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAABCCD = taabccd-taaabbc + sAABCDE = taabcde-taabccd + sABCDEF = 1-taabcde + alpha_1 = (1-d)*(sAAABBC + 2*sAABCCD + 4*sAABCDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 4*sAAAAAA*sAABCCD + 4*sAAABBB*sAABCCD + 6*sAAABBC*sAABCCD + 4*sAABCCD**2 + 8*sAAAAAA*sAABCDE + 8*sAAABBB*sAABCDE + 10*sAAABBC*sAABCDE + 12*sAABCCD*sAABCDE + 8*sAABCDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAABBB*sABCDEF + 12*sAAABBC*sABCDEF + 14*sAABCCD*sABCDEF + 18*sAABCDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + 2*sAABCCD + sAABCDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 2*sAAAAAA*sAABCCD + 2*sAAABBB*sAABCCD + 4*sAAABBC*sAABCCD + 2*sAABCCD**2 + 2*sAAABBC*sAABCDE + 2*sAABCCD*sAABCDE + 2*sAAABBC*sABCDEF + 2*sAABCCD*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(2*sAAABBB + sAAABBC) + d*(2*sAAAAAA*sAAABBB + 2*sAAABBB**2 + 2*sAAABBB*sAAABBC + 2*sAAABBB*sAABCCD + 2*sAAABBB*sAABCDE + 2*sAAABBB*sABCDEF + 2*sAABCCD*sABCDEF + 2*sAABCDE*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCCD**2 + 2*sAABCCD*sAABCDE + sAABCDE**2 + 2*sAAABBB*sABCDEF + 2*sAAABBC*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABBB*sAABCCD + 2*sAAABBC*sAABCCD + 2*sAAABBB*sAABCDE + 2*sAAABBC*sAABCDE) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBB**2 + 2*sAAABBB*sAAABBC + sAAABBC**2) + alpha_7 = d*(2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAA*sAABCCD + 2*sAAAAAA*sAABCDE) + alpha_9 = d*(2*sAAAAAA*sAAABBB + 2*sAAAAAA*sAAABBC) + alpha_10 = d*(0) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=15, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raabccd,raabcde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, aabcde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_15_unique = function(raaabbb, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raabccd-raabcde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taabccd = (raaaaaa+raaabbb+raaabbc+raabccd)**k + taabcde = (raaaaaa+raaabbb+raaabbc+raabccd+raabcde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAABCCD = taabccd-taaabbc + sAABCDE = taabcde-taabccd + sABCDEF = 1-taabcde + alpha_1_unique = (1-d)*(sAAABBC + 2*sAABCCD + 4*sAABCDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + 2*sAABCCD + sAABCDE) + alpha_3_unique = (1-d)*(2*sAAABBB + sAAABBC) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} + +#' Produce model estimated (p=6, topology=16) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raabccd,rabcdde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, abcdde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_16 = function(raaabbb, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raabccd-rabcdde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taabccd = (raaaaaa+raaabbb+raaabbc+raabccd)**k + tabcdde = (raaaaaa+raaabbb+raaabbc+raabccd+rabcdde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAABCCD = taabccd-taaabbc + sABCDDE = tabcdde-taabccd + sABCDEF = 1-tabcdde + alpha_1 = (1-d)*(sAAABBC + 2*sAABCCD + 4*sABCDDE + 6*sABCDEF) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 4*sAAAAAA*sAABCCD + 4*sAAABBB*sAABCCD + 6*sAAABBC*sAABCCD + 4*sAABCCD**2 + 6*sAAAAAA*sABCDDE + 6*sAAABBB*sABCDDE + 8*sAAABBC*sABCDDE + 10*sAABCCD*sABCDDE + 6*sABCDDE**2 + 10*sAAAAAA*sABCDEF + 10*sAAABBB*sABCDEF + 12*sAAABBC*sABCDEF + 14*sAABCCD*sABCDEF + 16*sABCDDE*sABCDEF + 10*sABCDEF**2) + alpha_2 = (1-d)*(sAAABBC + 2*sAABCCD + sABCDDE) + d*(2*sAAAAAA*sAAABBC + 2*sAAABBB*sAAABBC + 2*sAAABBC**2 + 2*sAAAAAA*sAABCCD + 2*sAAABBB*sAABCCD + 4*sAAABBC*sAABCCD + 2*sAABCCD**2 + 2*sAAAAAA*sABCDDE + 2*sAAABBB*sABCDDE + 4*sAAABBC*sABCDDE + 4*sAABCCD*sABCDDE + 3*sABCDDE**2 + 2*sAAABBC*sABCDEF + 2*sAABCCD*sABCDEF + 4*sABCDDE*sABCDEF + sABCDEF**2) + alpha_3 = (1-d)*(2*sAAABBB + sAAABBC) + d*(2*sAAAAAA*sAAABBB + 2*sAAABBB**2 + 2*sAAABBB*sAAABBC + 2*sAAABBB*sAABCCD + 2*sAAABBB*sABCDDE + 2*sAABCCD*sABCDDE + 2*sAAABBB*sABCDEF + 2*sAABCCD*sABCDEF) + alpha_4 = (1-d)*(0) + d*(sAABCCD**2 + 2*sAAABBB*sABCDDE + 2*sAAABBC*sABCDDE + 2*sAAABBB*sABCDEF + 2*sAAABBC*sABCDEF) + alpha_5 = (1-d)*(0) + d*(2*sAAABBB*sAABCCD + 2*sAAABBC*sAABCCD) + alpha_6 = (1-d)*(sAAAAAA) + d*(sAAABBB**2 + 2*sAAABBB*sAAABBC + sAAABBC**2) + alpha_7 = d*(2*sAAAAAA*sABCDDE + 2*sAAAAAA*sABCDEF) + alpha_8 = d*(2*sAAAAAA*sAABCCD) + alpha_9 = d*(2*sAAAAAA*sAAABBB + 2*sAAAAAA*sAAABBC) + alpha_10 = d*(0) + alpha_11 = d*(0) + alpha_12 = d*(sAAAAAA**2) + alpha_1 * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2 * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3 * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4 * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5 * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6 * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6)+ + alpha_7 * dnbinom(x, size = kmercov*7 / bias, mu = kmercov*7)+ + alpha_8 * dnbinom(x, size = kmercov*8 / bias, mu = kmercov*8)+ + alpha_9 * dnbinom(x, size = kmercov*9 / bias, mu = kmercov*9)+ + alpha_10 * dnbinom(x, size = kmercov*10 / bias, mu = kmercov*10)+ + alpha_11 * dnbinom(x, size = kmercov*11 / bias, mu = kmercov*11)+ + alpha_12 * dnbinom(x, size = kmercov*12 / bias, mu = kmercov*12) +} + +#' Produce model estimated (p=6, topology=16, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +#' +#' @param raaabbb,raaabbc,raabccd,rabcdde,rabcdef Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, abcdde, and abcdef respectively. +#' @param k An integer corresponding to the kmer length. +#' @param d A numeric corresponding to the repetitiveness. +#' @param kmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param bias A numeric corresponding to the overdispersion of the negative binomial distribution. +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @return A numeric vector of the model estimated y-coordinates of the kmer spectra. +#' @export +predict6_16_unique = function(raaabbb, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, bias, x) +{ + raaaaaa = 1-raaabbb-raaabbc-raabccd-rabcdde-rabcdef + if (raaaaaa < 0 || d > 1) {return(0)} + taaaaaa = (raaaaaa)**k + taaabbb = (raaaaaa+raaabbb)**k + taaabbc = (raaaaaa+raaabbb+raaabbc)**k + taabccd = (raaaaaa+raaabbb+raaabbc+raabccd)**k + tabcdde = (raaaaaa+raaabbb+raaabbc+raabccd+rabcdde)**k + sAAAAAA = taaaaaa + sAAABBB = taaabbb-taaaaaa + sAAABBC = taaabbc-taaabbb + sAABCCD = taabccd-taaabbc + sABCDDE = tabcdde-taabccd + sABCDEF = 1-tabcdde + alpha_1_unique = (1-d)*(sAAABBC + 2*sAABCCD + 4*sABCDDE + 6*sABCDEF) + alpha_2_unique = (1-d)*(sAAABBC + 2*sAABCCD + sABCDDE) + alpha_3_unique = (1-d)*(2*sAAABBB + sAAABBC) + alpha_4_unique = (1-d)*(0) + alpha_5_unique = (1-d)*(0) + alpha_6_unique = (1-d)*(sAAAAAA) + alpha_1_unique * dnbinom(x, size = kmercov*1 / bias, mu = kmercov*1)+ + alpha_2_unique * dnbinom(x, size = kmercov*2 / bias, mu = kmercov*2)+ + alpha_3_unique * dnbinom(x, size = kmercov*3 / bias, mu = kmercov*3)+ + alpha_4_unique * dnbinom(x, size = kmercov*4 / bias, mu = kmercov*4)+ + alpha_5_unique * dnbinom(x, size = kmercov*5 / bias, mu = kmercov*5)+ + alpha_6_unique * dnbinom(x, size = kmercov*6 / bias, mu = kmercov*6) +} diff --git a/R/nls_peak.R b/R/nls_peak.R new file mode 100644 index 0000000..3508ddf --- /dev/null +++ b/R/nls_peak.R @@ -0,0 +1,130 @@ +#' Uses nlsLM to fit 2p peak model +#' +#' @param x An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @param y A numeric vector of the y-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers). +#' @param k An integer corresponding to the kmer length. +#' @param p An integer corresponding to the ploidy. +#' @param top An integer corresponding to the topology. +#' @param estKmercov A numeric corresponding to the estimated average kmer coverage of the polyploid genome. +#' @param estLength A numeric corresponding to the estimated polyploid genome length. +#' @param max_iterations An integer corresponding to the maximum number iterations to use for nlsLM. +#' @return An nlsLM model object with some additional components. +#' @export +nls_peak<-function(x, y, k, p, top, estKmercov, estLength, max_iterations) { + #Initiate variables + model = NULL + best_deviance = Inf + d_min = 0 + if (d_init!=-1) { + d_initial = d_init + } else { + d_initial = 0.10 + } + d_max = 1 + r_min = 0.00001 + if (top==0) { + p_to_num_r = c(0, 1, 2, 4, 6, 10) + } else { + p_to_num_r = c(0, 1, 2, 3, 4, 5) + } + num_r = p_to_num_r[p] + r_max = 1 + kmercov_min = 0 + kmercov_initial = estKmercov + kmercov_max = Inf + bias_min = 0 + bias_initial = 0.5 + bias_max = Inf + length_min = 0 + length_initial = estLength/p + length_max = Inf + + #Determine what formula to use, based on p + if (p==1) { + r_text = "" + } else { + r_text = paste(paste(lapply(1:(num_r), function(x) paste("r", as.character(x), sep="")), collapse=", "), ", ") + } + x = x[1:min(2000,length(x))] + y = y[1:min(2000,length(y))] + y_transform = as.numeric(x)**transform_exp*as.numeric(y) + formula = as.formula(paste("y_transform ~ x**transform_exp*length*predict",p,"_",top,"(",r_text, "k, d, kmercov, bias, x)",sep="")) + + if (VERBOSE) {cat("trying nlsLM algorithm (Levenberg-Marquardt)\n")} + + if (r_inits!=-1) { + r_initials = unlist(lapply(strsplit(r_inits,","),as.numeric)) + if (length(r_initials)!=num_r) { + stop("Incorrect number of initial rates supplied.") + } + r_initials_list = list(r_initials) + } else { + r_initials_list = list(rep(0.001, num_r), 0.001*(1:num_r), 0.001*(num_r:1), rep(0.01, num_r), 0.01*(1:num_r), 0.01*(num_r:1)) + } + + for (r_initials in r_initials_list) { + + model1 = NULL + r_start = vector("list", num_r) + if (p > 1) { + names(r_start) = paste("r", 1:(num_r), sep="") + for (i in 1:(num_r)) { + r_start[[paste("r",i,sep="")]] = r_initials[i] + } + } + + try(model1 <- nlsLM(formula = formula, + start = c(list(d = d_initial), r_start, list(kmercov = kmercov_initial, bias = bias_initial, length = length_initial)), + lower = c(c(d_min), rep(r_min, num_r), c(kmercov_min, bias_min, length_min)), + upper = c(c(d_max), rep(r_max, num_r), c(kmercov_max, bias_max, length_max)), + control = list(minFactor=1e-12, maxiter=max_iterations, factor=0.1), trace=TRACE_FLAG), silent = TRUE) + + if (!is.null(model1)) { + current_deviance = model1$m$deviance() + #cat("Model deviance: ", current_deviance, "\n") + if (current_deviance < best_deviance) { + model = model1 + best_deviance = current_deviance + } + } else { + #print("Model did not converge.") + } + + } + + if (!is.null(model)) + { + model_sum = summary(model) + model$p = p + model$top = top + if (p==1) { + model$hets = list(c(0, 0)) + } else { + model$hets = lapply(1:(num_r), function(x) min_max1(model_sum$coefficients[paste('r', x, sep=""),])) + } + #model$het = c(1-Reduce("*", 1-unlist(lapply(model$hets, '[[', 1))), 1-Reduce("*", 1-unlist(lapply(model$hets, '[[', 2)))) + model$het = c(sum(sapply(model$hets, '[[', 1)), sum(sapply(model$hets, '[[', 2))) + model$homo = 1-model$het + model$dups = min_max(model_sum$coefficients['bias',]) + model$kcov = min_max(model_sum$coefficients['kmercov',]) + model$mlen = min_max(model_sum$coefficients['length',]) + model$md = min_max1(model_sum$coefficients['d',]) + if (p==1) { + model$ahets = list(c(0)) + } else { + model$ahets = lapply(1:(num_r), function(x) model_sum$coefficients[paste('r', x, sep=""),][[1]]) + } + #model$ahet = 1-Reduce("*", 1-unlist(model$ahets)) + model$ahet = Reduce("+", model$ahets) + model$ahomo = 1-model$ahet + model$adups = model_sum$coefficients['bias',][[1]] + model$akcov = model_sum$coefficients['kmercov',][[1]] + model$amlen = model_sum$coefficients['length',][[1]] + model$amd = model_sum$coefficients['d',][[1]] + } + + #print(model) + #print(model$m$deviance()) + + return(model) +} diff --git a/R/report_results.R b/R/report_results.R new file mode 100644 index 0000000..f384e71 --- /dev/null +++ b/R/report_results.R @@ -0,0 +1,980 @@ +## Format numbers +############################################################################### + +bp_format<-function(num) {paste(formatC(round(num),format="f",big.mark=",", digits=0), "bp",sep=" ")} + +percentage_format<-function(num) {paste(signif(num,6)*100,"%",sep="")} + +X_format<-function(num) {paste(signif(num,4),"X",sep="")} + +#' Report results and make plots +#' +#' @param kmer_hist A data frame of the original histogram data (starting at 1 and going up to the max kmer coverage threshold). +#' @param kmer_hist_orig A data frame of the original histogram data (starting at 1 and with last position removed). +#' @param k An integer corresponding to the kmer length. +#' @param p An integer corresponding to the ploidy. +#' @param container A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +#' and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms). +#' @param foldername A character vector corresponding to the name of the output directory. +#' @param arguments A data frame of the user-specified inputs. +#' @param IN_VERBOSE A boolean flag to designate whether report_results is being called in a VERBOSE block. +#' @export +report_results<-function(kmer_hist,kmer_hist_orig, k, p, container, foldername, arguments, IN_VERBOSE) { + + x=kmer_hist_orig[[1]] + y_orig=kmer_hist_orig[[2]] + y = as.numeric(x)**transform_exp*as.numeric(y_orig) + kmer_hist_transform = kmer_hist_orig + kmer_hist_transform$V2 = as.numeric(kmer_hist_transform$V1)**transform_exp * as.numeric(kmer_hist_transform$V2) + model = container[[1]] + + #automatically zoom into the relevant regions of the plot, ignore first 15 positions + xmax=length(x) + start_orig=which(y_orig == min(y_orig[1:TYPICAL_ERROR])) + start=which(y == min(y[1:TYPICAL_ERROR])) + zoomx=x[start:(xmax-1)] + zoomy_orig=y_orig[start_orig:(xmax-1)] + zoomy=y[start:(xmax-1)] + + ## allow for a little space above max value past the noise + y_limit_orig = max(zoomy_orig[start_orig:length(zoomy_orig)])*1.1 + y_limit = max(zoomy[start:length(zoomy)])*1.1 + + x_limit_orig = which(y_orig == max(y_orig[start_orig:length(zoomx)])) * 3 + x_limit = which(y == max(y[start:length(zoomx)])) * 3 + + if (min(zoomy_orig) > zoomy_orig[1]){ + x_limit_orig=max(which(zoomy_orig zoomy[1]){ + x_limit=max(which(zoomy 1) { + hets = lapply(1:(num_r), function(x) c(-1, -1)) + ahets = lapply(1:(num_r), function(x) -1) + } + amd = -1 + akcov = -1 + adups = -1 + amlen = -1 + atotal_len = -1 + top = -1 + total_len=c(-1,-1) + repeat_len=c(-1,-1) + unique_len=c(-1,-1) + dups=c(-1,-1) + error_rate=c(-1,-1) + model_status="fail" + + model_fit_unique = c(0,0,0) + model_fit_full = c(0,0,0) + model_fit_all = c(0,0,0) + model_fit_allscore = c(0,0,0) + model_fit_fullscore = c(0,0,0) + model_fit_uniquescore = c(0,0,0) + + plot_size=2000 + font_size=1.2 + resolution=300 + + ## Plot the distribution, and hopefully with the model fit + ylabel_orig = "Frequency" + if (transform_exp == 1) { + ylabel_transform = "Coverage*Frequency" + } else { + ylabel_transform = paste("Coverage^", transform_exp, "*Frequency", sep="") + } + png(paste(foldername, "/", arguments$name_prefix, "linear_plot.png", sep=""), + width=plot_size, height=plot_size, res=resolution) + par(mar = c(5.1,4.1,6.1,2.1)) + plot(kmer_hist_orig, type="n", main="GenomeScope Profile\n\n\n", + xlab="Coverage", ylab=ylabel_orig, ylim=c(0,y_limit_orig), xlim=c(0,x_limit_orig), + cex.lab=font_size, cex.axis=font_size, cex.main=font_size, cex.sub=font_size) + #rect(0, 0, max(kmer_hist_orig[[1]])*1.1 , max(kmer_hist_orig[[2]])*1.1, col=COLOR_BGCOLOR) + rect(0, 0, x_limit_orig*1.1 , y_limit_orig*1.1, col=COLOR_BGCOLOR) + points(kmer_hist_orig, type="h", col=COLOR_HIST, lwd=2) +# if(length(kmer_hist[,1])!=length(kmer_hist_orig[,1])){ +# abline(v=length(kmer_hist[,1]),col=COLOR_COVTHRES,lty="dashed", lwd=3) +# } + box(col="black") + + png(paste(foldername, "/", arguments$name_prefix, "transformed_linear_plot.png", sep=""), + width=plot_size, height=plot_size, res=resolution) + par(mar = c(5.1,4.1,6.1,2.1)) + plot(kmer_hist_transform, type="n", main="GenomeScope Profile\n\n\n", + xlab="Coverage", ylab=ylabel_transform, ylim=c(0,y_limit), xlim=c(0,x_limit), + cex.lab=font_size, cex.axis=font_size, cex.main=font_size, cex.sub=font_size) + #rect(0, 0, max(kmer_hist_orig[[1]])*1.1 , max(kmer_hist_orig[[2]])*1.1, col=COLOR_BGCOLOR) + rect(0, 0, x_limit*1.1 , y_limit*1.1, col=COLOR_BGCOLOR) + points(kmer_hist_transform, type="h", col=COLOR_HIST, lwd=2) +# if(length(kmer_hist[,1])!=length(kmer_hist_orig[,1])){ +# abline(v=length(kmer_hist[,1]),col=COLOR_COVTHRES,lty="dashed", lwd=3) +# } + box(col="black") + + ## Make a second plot in log space over entire range + png(paste(foldername, "/", arguments$name_prefix, "log_plot.png", sep=""), + width=plot_size, height=plot_size, res=resolution) + par(mar = c(5.1,4.1,6.1,2.1)) + plot(kmer_hist_orig, type="n", main="GenomeScope Profile\n\n\n", + xlab="Coverage", ylab=ylabel_orig, log="xy", + cex.lab=font_size, cex.axis=font_size, cex.main=font_size, cex.sub=font_size) + rect(1e-10, 1e-10, max(kmer_hist_orig[,1])*10 , max(kmer_hist_orig[,2])*10, col=COLOR_BGCOLOR) + points(kmer_hist_orig, type="h", col=COLOR_HIST, lwd=2) + if(length(kmer_hist[,1])!=length(kmer_hist_orig[,1])){ + abline(v=length(kmer_hist[,1]),col=COLOR_COVTHRES,lty="dashed", lwd=3) + } + box(col="black") + + png(paste(foldername, "/", arguments$name_prefix, "transformed_log_plot.png", sep=""), + width=plot_size, height=plot_size, res=resolution) + par(mar = c(5.1,4.1,6.1,2.1)) + plot(kmer_hist_transform, type="n", main="GenomeScope Profile\n\n\n", + xlab="Coverage", ylab=ylabel_transform, log="xy", + cex.lab=font_size, cex.axis=font_size, cex.main=font_size, cex.sub=font_size) + rect(1e-10, 1e-10, max(kmer_hist_transform[,1])*10 , max(kmer_hist_transform[,2])*10, col=COLOR_BGCOLOR) + points(kmer_hist_transform, type="h", col=COLOR_HIST, lwd=2) + if(length(kmer_hist[,1])!=length(kmer_hist_transform[,1])){ + abline(v=length(kmer_hist[,1]),col=COLOR_COVTHRES,lty="dashed", lwd=3) + } + box(col="black") + + + if(!is.null(model)) + { + x=kmer_hist[[1]] + y=kmer_hist[[2]] + y_transform = as.numeric(x)**transform_exp*as.numeric(y) + + ## The model converged! + pred=predict(model, newdata=data.frame(x)) + + ## Compute the genome characteristics + model_sum=summary(model) + #print(model_sum) + + ## save the model to a file + capture.output(model_sum, file=paste(foldername,"/", arguments$name_prefix, "model.txt", sep="")) + + ## Identify key values + top = model$top + hets = model$hets + het = model$het + ahets = model$ahets + ahet = model$ahet + homo = model$homo + ahomo = model$ahomo + + dups = model$dups + kcov = model$kcov + mlen = model$mlen + md = model$md + + adups = model$adups + akcov = model$akcov + amlen = model$amlen + amd = model$amd + + ## Compute error rate, by counting kmers unexplained by model through first peak + ## truncate errors as soon as it goes to zero, dont allow it to go back up + error_xcutoff = max(1, floor(kcov[1])) + error_xcutoff_ind = tail(which(x<=error_xcutoff),n=1) + if (length(error_xcutoff_ind)==0) {error_xcutoff_ind=1} + + error_kmers = x[1:error_xcutoff_ind]**(-transform_exp)*(y_transform[1:error_xcutoff_ind] - pred[1:error_xcutoff_ind]) + + first_zero = -1 + + for (i in 1:error_xcutoff_ind) + { + if (first_zero == -1) + { + if (error_kmers[i] < 1.0) + { + first_zero = i + if (VERBOSE) {cat(paste("Truncating errors at", i, "\n"))} + } + } + else + { + error_kmers[i] = 0 + } + } + + if (first_zero == -1) + { + first_zero = error_xcutoff_ind + if (VERBOSE) {cat(paste("Truncating errors at", error_xcutoff_ind, "\n"))} + } + + ## Rather than "0", set to be some very small number so log-log plot looks okay + error_kmers = pmax(error_kmers, 1e-10) + + total_error_kmers = sum(as.numeric(error_kmers) * as.numeric(x[1:error_xcutoff_ind])) + + total_kmers = sum(as.numeric(x)*as.numeric(y)) + + error_rate = 1-(1-(total_error_kmers/total_kmers))**(1/k) + error_rate = c(error_rate, error_rate) + + total_len = (total_kmers-total_error_kmers)/(p*kcov) + atotal_len = (total_kmers-total_error_kmers)/(p*akcov) + + ## find kmers that fit the p peak model (no repeats) + if (p==1) + { + unique_hist = amlen*predict1_1_unique(k, amd, akcov, adups, x) + } + if (p==2) + { + unique_hist = amlen*predict2_1_unique(ahets[[1]], k, amd, akcov, adups, x) + } + if (p==3) + { + unique_hist = amlen*predict3_1_unique(ahets[[1]], ahets[[2]], k, amd, akcov, adups, x) + } + if (p==4) + { + if (top==0) { + unique_hist = amlen*predict4_0_unique(ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], k, amd, akcov, adups, x) + } else { + unique_hist = eval(parse(text = paste("amlen*predict4_", top, "_unique(ahets[[1]], ahets[[2]], ahets[[3]], k, amd, akcov, adups, x)", sep=""))) + } + } + if (p==5) + { + if (top==0) { + unique_hist = amlen*predict5_0_unique(ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], k, amd, akcov, adups, x) + } else { + unique_hist = eval(parse(text = paste("amlen*predict5_", top, "_unique(ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], k, amd, akcov, adups, x)", sep=""))) + } + } + if (p==6) + { + if (top==0) { + unique_hist = amlen*predict6_0_unique(ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], ahets[[7]], ahets[[8]], ahets[[9]], ahets[[10]], k, amd, akcov, adups, x) + } else { + unique_hist = eval(parse(text = paste("amlen*predict6_", top, "_unique(ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], k, amd, akcov, adups, x)", sep=""))) + } + } + + r0 = 1-ahet #aa + t0 = r0**k #AA + s0 = t0 #AA + s1 = 1-t0 #AB + alpha_1 = (1-amd)*(2*s1) + amd*(2*s0*s1 + 2*s1**2) + alpha_2 = (1-amd)*(s0) + amd*(s1**2) + alpha_3 = amd*(2*s0*s1) + alpha_4 = amd*(s0**2) + + one_hist = alpha_1 * dnbinom(x, size = akcov*1 / adups, mu = akcov*1) + two_hist = alpha_2 * dnbinom(x, size = akcov*p / adups, mu = akcov*p) + thr_hist = alpha_3 * dnbinom(x, size = akcov*3 / adups, mu = akcov*3) + fou_hist = alpha_4 * dnbinom(x, size = akcov*2*p / adups, mu = akcov*2*p) + + unique_hist_transform = x**transform_exp*unique_hist + + unique_kmers = sum(as.numeric(x)*as.numeric(unique_hist)) + repeat_kmers = max(0, total_kmers - unique_kmers - total_error_kmers) + + repeat_len=repeat_kmers/(p*kcov) + if (repeat_kmers == 0) { + unique_len = total_len + } else { + unique_len=unique_kmers/(p*kcov) + } + + score = container[[2]] + + model_fit_allscore = score$allscore + model_fit_fullscore = score$fullscore + model_fit_uniquescore = score$uniquescore + + model_fit_all = score$all + model_fit_full = score$full + model_fit_unique = score$unique + + residual_transform = y_transform - pred + residual = x**(-transform_exp)*residual_transform + + hetline_simple = paste0("heterozygosity: ", format(100*ahet, digits=3), "%") + + if (p==1) { + hetline = paste0("a:", format(100*ahomo, digits=3), "%") + } + if (p==2) { + hetline = paste0("aa:", format(100*ahomo, digits=3), "% ", + "ab:", format(100*ahets[[1]], digits=3), "%") + } + if (p==3) { + hetline = paste0("aaa:", format(100*ahomo, digits=3), "% ", + "aab:", format(100*ahets[[1]], digits=3), "% ", + "abc:", format(100*ahets[[2]], digits=3), "%") + } + if (p==4) { + if (top==0) { + hetline = paste0("aaaa:", format(100*ahomo, digits=3), "% ", + "aaab:", format(100*ahets[[1]], digits=3), "% ", + "aabb:", format(100*ahets[[2]], digits=3), "% ", + "aabc:", format(100*ahets[[3]], digits=3), "% ", + "abcd:", format(100*ahets[[4]], digits=3), "%") + } else { + hetline = paste0("aaaa:", format(100*ahomo, digits=3), "% ", + switch(top, "aaab:", "aabb:"), format(100*ahets[[1]], digits=3), "% ", + "aabc:", format(100*ahets[[2]], digits=3), "% ", + "abcd:", format(100*ahets[[3]], digits=3), "%") + } + } + if (p==5) { + if (top==0) { + hetline = paste0("aaaaa:", format(100*ahomo, digits=3), "% ", + "aaaab:", format(100*ahets[[1]], digits=3), "% ", + "aaabb:", format(100*ahets[[2]], digits=3), "% ", + "aaabc:", format(100*ahets[[3]], digits=3), "% ",'\n', + "aabbc:", format(100*ahets[[4]], digits=3), "% ", + "aabcd:", format(100*ahets[[5]], digits=3), "% ", + "abcde:", format(100*ahets[[6]], digits=3), "%") + } else { + hetline = paste0("aaaaa:", format(100*ahomo, digits=3), "% ", + switch(top, "aaaab:", "aaaab:", "aaabb:", "aaabb:", "aaabb:"), format(100*ahets[[1]], digits=3), "% ", + switch(top, "aaabc:", "aabbc:", "aaabc:", "aabcc:", "aabcc:"), format(100*ahets[[2]], digits=3), "% ",'\n', + switch(top, "aabcd:", "aabcd:", "aabcd:", "aabcd:", "abcdd:"), format(100*ahets[[3]], digits=3), "% ", + "abcde:", format(100*ahets[[4]], digits=3), "%") + } + } + if (p==6) { + if (top==0) { + hetline = paste0("aaaaaa:", format(100*ahomo, digits=3), "% ", + "aaaaab:", format(100*ahets[[1]], digits=3), "% ", + "aaaabb:", format(100*ahets[[2]], digits=3), "% ", + "aaabbb:", format(100*ahets[[3]], digits=3), "% ",'\n', + "aaaabc:", format(100*ahets[[4]], digits=3), "% ", + "aaabbc:", format(100*ahets[[5]], digits=3), "% ", + "aabbcc:", format(100*ahets[[6]], digits=3), "% ", + "aaabcd:", format(100*ahets[[7]], digits=3), "% ",'\n', + "aabbcd:", format(100*ahets[[8]], digits=3), "% ", + "aabcde:", format(100*ahets[[9]], digits=3), "% ", + "abcdef:", format(100*ahets[[10]], digits=3), "%") + } else { + hetline = paste0("aaaaaa:", format(100*ahomo, digits=3), "% ", + switch(top, "aaaaab:", "aaaaab:", "aaaaab:", "aaaaab:", "aaaaab:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaabbb:", "aaabbb:", "aaabbb:"), format(100*ahets[[1]], digits=3), "% ", + switch(top, "aaaabc:", "aaaabc:", "aaabbc:", "aaabbc:", "aaabbc:", "aaaabc:", "aaaabc:", "aaabcc:", "aaabcc:", "aaabcc:", "aabbcc:", "aabbcc:", "aabbcc:", "aaabbc:", "aaabbc:", "aaabbc:"), format(100*ahets[[2]], digits=3), "% ",'\n', + switch(top, "aaabcd:", "aabbcd:", "aaabcd:", "aabccd:", "aabccd:", "aaabcd:", "aabbcd:", "aaabcd:", "aabcdd:", "aabcdd:", "aabbcd:", "aabcdd:", "aabcdd:", "aaabcd:", "aabccd:", "aabccd:"), format(100*ahets[[3]], digits=3), "% ", + switch(top, "aabcde:", "aabcde:", "aabcde:", "aabcde:", "abcdde:", "aabcde:", "aabcde:", "aabcde:", "aabcde:", "abcdee:", "aabcde:", "aabcde:", "abcdee:", "aabcde:", "aabcde:", "abcdde:"), format(100*ahets[[4]], digits=3), "% ", + "abcdef:", format(100*ahets[[5]], digits=3), "%") + } + } + + if (p >= 5) { + hetline = hetline_simple + } + + if (!IN_VERBOSE) { + cat(paste0(hetline,"\n")) + } + + dev.set(dev.next()) + + ## Finish Linear Plot + title(paste("\n\nlen:", prettyNum(total_len[1], big.mark=","), + "bp", + " uniq:", format(100*(unique_len[1]/total_len[1]), digits=3), + "% ", "\n", + hetline, "\n", + " kcov:", format(akcov, digits=3), + " err:", format(100*error_rate[1], digits=3), + "% ", + " dup:", format(adups, digits=3), + " ", + " k:", format(k, digits=3), + " p:", format(p, digits=3), + sep=""), + cex.main=.85) + + ## Mark the modes of the peaks + abline(v=akcov * (1:(2*p)), col=COLOR_KMERPEAK, lty=2) + + ## Draw just the unique portion of the model + if (!NO_UNIQUE_SEQUENCE) { + lines(x, unique_hist, col=COLOR_pPEAK, lty=1, lwd=3) + } + lines(x, x**(-transform_exp)*pred, col=COLOR_2pPEAK, lwd=3) + lines(x[1:error_xcutoff_ind], error_kmers, lwd=3, col=COLOR_ERRORS) + + if (VERBOSE) { + lines(x, residual, col=COLOR_RESIDUAL, lwd=3) + } + + ## Add legend + if (NO_UNIQUE_SEQUENCE) { + legend(.62 * x_limit_orig, 1.0 * y_limit_orig, + legend=c("observed", "full model", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,2), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } else { + legend(.62 * x_limit_orig, 1.0 * y_limit_orig, + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3,2), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } + + dev.set(dev.next()) + + ## Finish Linear Plot + title(paste("\n\nlen:", prettyNum(total_len[1], big.mark=","), + "bp", + " uniq:", format(100*(unique_len[1]/total_len[1]), digits=3), + "% ", "\n", + hetline, "\n", + " kcov:", format(akcov, digits=3), + " err:", format(100*error_rate[1], digits=3), + "% ", + " dup:", format(adups, digits=3), + " ", + " k:", format(k, digits=3), + " p:", format(p, digits=3), + sep=""), + cex.main=.85) + + ## Mark the modes of the peaks + abline(v=akcov * (1:(2*p)), col=COLOR_KMERPEAK, lty=2) + + ## Draw just the unique portion of the model + if (!NO_UNIQUE_SEQUENCE) { + lines(x, unique_hist_transform, col=COLOR_pPEAK, lty=1, lwd=3) + } + lines(x, pred, col=COLOR_2pPEAK, lwd=3) + lines(x[1:error_xcutoff_ind], (x[1:error_xcutoff_ind]**transform_exp)*error_kmers, lwd=3, col=COLOR_ERRORS) + + if (VERBOSE) { + lines(x, residual_transform, col=COLOR_RESIDUAL, lwd=3) + } + + ## Add legend + if (NO_UNIQUE_SEQUENCE) { + legend(.62 * x_limit, 1.0 * y_limit, + legend=c("observed", "full model", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,2), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } else { + legend(.62 * x_limit, 1.0 * y_limit, + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3,2), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } + + dev.set(dev.next()) + + ## Finish Log plot + title(paste("\n\nlen:", prettyNum(total_len[1], big.mark=","), + "bp", + " uniq:", format(100*(unique_len[1]/total_len[1]), digits=3), + "% ", "\n", + hetline, "\n", + " kcov:", format(akcov, digits=3), + " err:", format(100*error_rate[1], digits=3), + "% ", + " dup:", format(adups, digits=3), + " ", + " k:", format(k, digits=3), + " p:", format(p, digits=3), + sep=""), + cex.main=.85) + + ## Mark the modes of the peaks + abline(v=akcov * (1:(2*p)), col=COLOR_KMERPEAK, lty=2) + + ## Draw just the unique portion of the model + if (!NO_UNIQUE_SEQUENCE) { + lines(x, unique_hist, col=COLOR_pPEAK, lty=1, lwd=3) + } + lines(x, x**(-transform_exp)*pred, col=COLOR_2pPEAK, lwd=3) + lines(x[1:error_xcutoff_ind], error_kmers, lwd=3, col=COLOR_ERRORS) + + if (VERBOSE) { + lines(x, residual, col=COLOR_RESIDUAL, lwd=3) + } + + ## Add legend + if(length(kmer_hist[,1])==length(kmer_hist_orig[,1])) + { + if (NO_UNIQUE_SEQUENCE) { + legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } else { + legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } + } + else + { + if (NO_UNIQUE_SEQUENCE) { + legend("topright", + ##legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "errors", "kmer-peaks","cov-threshold"), + lty=c("solid", "solid", "solid", "dashed", "dashed"), + lwd=c(3,3,3,2,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK, COLOR_COVTHRES), + bg="white") + } else { + legend("topright", + ##legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks","cov-threshold"), + lty=c("solid", "solid", "solid", "solid", "dashed", "dashed"), + lwd=c(3,3,3,3,2,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK, COLOR_COVTHRES), + bg="white") + } + } + + dev.set(dev.next()) + + ## Finish Log plot + title(paste("\n\nlen:", prettyNum(total_len[1], big.mark=","), + "bp", + " uniq:", format(100*(unique_len[1]/total_len[1]), digits=3), + "% ", "\n", + hetline, "\n", + " kcov:", format(akcov, digits=3), + " err:", format(100*error_rate[1], digits=3), + "% ", + " dup:", format(adups, digits=3), + " ", + " k:", format(k, digits=3), + " p:", format(p, digits=3), + sep=""), + cex.main=.85) + + ## Mark the modes of the peaks + abline(v=akcov * (1:(2*p)), col=COLOR_KMERPEAK, lty=2) + + ## Draw just the unique portion of the model + if (!NO_UNIQUE_SEQUENCE) { + lines(x, unique_hist_transform, col=COLOR_pPEAK, lty=1, lwd=3) + } + lines(x, pred, col=COLOR_2pPEAK, lwd=3) + lines(x[1:error_xcutoff_ind], (x[1:error_xcutoff_ind]**transform_exp)*error_kmers, lwd=3, col=COLOR_ERRORS) + + if (VERBOSE) { + lines(x, residual_transform, col=COLOR_RESIDUAL, lwd=3) + } + + ## Add legend + if(length(kmer_hist[,1])==length(kmer_hist_orig[,1])) + { + if (NO_UNIQUE_SEQUENCE) { + legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } else { + legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks"), + lty=c("solid", "solid", "solid", "solid", "dashed"), + lwd=c(3,3,3,3,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK), + bg="white") + } + } + else + { + if (NO_UNIQUE_SEQUENCE) { + legend("topright", + ##legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "errors", "kmer-peaks","cov-threshold"), + lty=c("solid", "solid", "solid", "dashed", "dashed"), + lwd=c(3,3,3,2,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_ERRORS, COLOR_KMERPEAK, COLOR_COVTHRES), + bg="white") + } else { + legend("topright", + ##legend(exp(.62 * log(max(x))), 1.0 * max(y), + legend=c("observed", "full model", "unique sequence", "errors", "kmer-peaks","cov-threshold"), + lty=c("solid", "solid", "solid", "solid", "dashed", "dashed"), + lwd=c(3,3,3,3,2,3), + col=c(COLOR_HIST, COLOR_2pPEAK, COLOR_pPEAK, COLOR_ERRORS, COLOR_KMERPEAK, COLOR_COVTHRES), + bg="white") + } + } + + model_status="done" + + if (!IN_VERBOSE) { + cat(paste("Model converged het:", format(ahet, digits=3), + " kcov:", format(akcov, digits=3), + " err:", format(error_rate[1], digits=3), + " model fit:", format(adups, digits=3), + " len:", round(total_len[1]), "\n", sep="")) + } + } + else + { + title("\nFailed to converge") + dev.set(dev.next()) + title("\nFailed to converge") + cat("Failed to converge.", file=paste(foldername,"/", arguments$name_prefix, "model.txt", sep="")) + cat("Failed to converge.\n") + } + + dev.off() + dev.off() + dev.off() + dev.off() + + ## Write key values to summary file + summaryFile <- paste(foldername,"/", arguments$name_prefix, "summary.txt",sep="") + + format_column_1 = "%-30s" + format_column_2 = "%-18s" + format_column_3 = "%-18s" + + cat(paste("GenomeScope version 2.0", sep=""), file=summaryFile, sep="\n") + cat(paste("input file = ", arguments$input, sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("output directory = ", arguments$output, sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("p = ", p,sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("k = ", k,sep=""), file=summaryFile, sep="\n", append=TRUE) + if (arguments$name_prefix!="") { + cat(paste("name prefix = ", substring(arguments$name_prefix,1,nchar(arguments$name_prefix)-1), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (arguments$lambda!=-1) { + cat(paste("initial kmercov estimate = ", arguments$lambda, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (arguments$max_kmercov!=-1) { + cat(paste("max_kmercov = ", arguments$max_kmercov, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (VERBOSE) { + cat(paste("VERBOSE set to TRUE", sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (NO_UNIQUE_SEQUENCE) { + cat(paste("NO_UNIQUE_SEQUENCE set to TRUE", sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (topology!=0) { + cat(paste("topology = ", topology, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (d_init!=-1) { + cat(paste("initial repetitiveness = ", d_init, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (r_inits!=-1) { + cat(paste("initial heterozygosities = ", r_inits, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (transform_exp != 1) { + cat(paste("TRANSFORM_EXP = ", transform_exp, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (TESTING) { + cat(paste("TESTING set to TRUE", sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (TRUE_PARAMS != -1) { + cat(paste("TRUE_PARAMS = ", TRUE_PARAMS, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (TRACE_FLAG) { + cat(paste("TRACE_FLAG set to TRUE", sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (NUM_ROUNDS != 4) { + cat(paste("NUM_ROUNDS = ", NUM_ROUNDS, sep=""), file=summaryFile, sep="\n", append=TRUE) + } + cat(paste("\n",sprintf(format_column_1,"property"), sprintf(format_column_2,"min"), sprintf(format_column_3,"max"), sep=""), file=summaryFile, sep="\n", append=TRUE) + if (p==1) + { + cat(paste(sprintf(format_column_1,"Homozygous (a)"), sprintf(format_column_2,percentage_format(homo[2])), sprintf(format_column_3,percentage_format(homo[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (p==2) + { + cat(paste(sprintf(format_column_1,"Homozygous (aa)"), sprintf(format_column_2,percentage_format(homo[2])), sprintf(format_column_3,percentage_format(homo[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Heterozygous (ab)"), sprintf(format_column_2,percentage_format(hets[[1]][1])), sprintf(format_column_3,percentage_format(hets[[1]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (p==3) + { + cat(paste(sprintf(format_column_1,"Homozygous (aaa)"), sprintf(format_column_2,percentage_format(homo[2])), sprintf(format_column_3,percentage_format(homo[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Heterozygous (not aaa)"), sprintf(format_column_2,percentage_format(het[1])), sprintf(format_column_3,percentage_format(het[2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"aab"), sprintf(format_column_2,percentage_format(hets[[1]][1])), sprintf(format_column_3,percentage_format(hets[[1]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"abc"), sprintf(format_column_2,percentage_format(hets[[2]][1])), sprintf(format_column_3,percentage_format(hets[[2]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + if (p==4) + { + cat(paste(sprintf(format_column_1,"Homozygous (aaaa)"), sprintf(format_column_2,percentage_format(homo[2])), sprintf(format_column_3,percentage_format(homo[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Heterozygous (not aaaa)"), sprintf(format_column_2,percentage_format(het[1])), sprintf(format_column_3,percentage_format(het[2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1, switch(top+1, "aaab", "aaab", "aabb")), sprintf(format_column_2,percentage_format(hets[[1]][1])), sprintf(format_column_3,percentage_format(hets[[1]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1, switch(top+1, "aabb", "aabc", "aabc")), sprintf(format_column_2,percentage_format(hets[[2]][1])), sprintf(format_column_3,percentage_format(hets[[2]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1, switch(top+1, "aabc", "abcd", "abcd")), sprintf(format_column_2,percentage_format(hets[[3]][1])), sprintf(format_column_3,percentage_format(hets[[3]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + if (top == 0) { + cat(paste(sprintf(format_column_1,"abcd"), sprintf(format_column_2,percentage_format(hets[[4]][1])), sprintf(format_column_3,percentage_format(hets[[4]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + } + if (p==5) + { + cat(paste(sprintf(format_column_1,"Homozygous (aaaaa)"), sprintf(format_column_2,percentage_format(ahomo)), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Heterozygous (not aaaaa)"), sprintf(format_column_2,percentage_format(ahet)), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1,"aaaab", "aaaab", "aaaab", "aaabb", "aaabb", "aaabb")), sprintf(format_column_2,percentage_format(hets[[1]][1])), sprintf(format_column_3,percentage_format(hets[[1]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1,"aaabb", "aaabc", "aabbc", "aaabc", "aabcc", "aabcc")), sprintf(format_column_2,percentage_format(hets[[2]][1])), sprintf(format_column_3,percentage_format(hets[[2]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1,"aaabc", "aabcd", "aabcd", "aabcd", "aabcd", "abcdd")), sprintf(format_column_2,percentage_format(hets[[3]][1])), sprintf(format_column_3,percentage_format(hets[[3]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1,"aabbc", "abcde", "abcde", "abcde", "abcde", "abcde")), sprintf(format_column_2,percentage_format(hets[[4]][1])), sprintf(format_column_3,percentage_format(hets[[4]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + if (top == 0) { + #cat(paste(sprintf(format_column_1,"aabcd"), sprintf(format_column_2,percentage_format(hets[[5]][1])), sprintf(format_column_3,percentage_format(hets[[5]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1,"abcde"), sprintf(format_column_2,percentage_format(hets[[6]][1])), sprintf(format_column_3,percentage_format(hets[[6]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + } + if (p==6) + { + cat(paste(sprintf(format_column_1,"Homozygous (aaaaaa)"), sprintf(format_column_2,percentage_format(ahomo)), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Heterozygous (not aaaaaa)"), sprintf(format_column_2,percentage_format(ahet)), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1, "aaaaab", "aaaaab:", "aaaaab:", "aaaaab:", "aaaaab:", "aaaaab:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaaabb:", "aaabbb:", "aaabbb:", "aaabbb:")), sprintf(format_column_2,percentage_format(hets[[1]][1])), sprintf(format_column_3,percentage_format(hets[[1]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1, "aaaabb", "aaaabc:", "aaaabc:", "aaabbc:", "aaabbc:", "aaabbc:", "aaaabc:", "aaaabc:", "aaabcc:", "aaabcc:", "aaabcc:", "aabbcc:", "aabbcc:", "aabbcc:", "aaabbc:", "aaabbc:", "aaabbc:")), sprintf(format_column_2,percentage_format(hets[[2]][1])), sprintf(format_column_3,percentage_format(hets[[2]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1, "aaabbb", "aaabcd:", "aabbcd:", "aaabcd:", "aabccd:", "aabccd:", "aaabcd:", "aabbcd:", "aaabcd:", "aabcdd:", "aabcdd:", "aabbcd:", "aabcdd:", "aabcdd:", "aaabcd:", "aabccd:", "aabccd:")), sprintf(format_column_2,percentage_format(hets[[3]][1])), sprintf(format_column_3,percentage_format(hets[[3]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1, "aaaabc", "aabcde:", "aabcde:", "aabcde:", "aabcde:", "abcdde:", "aabcde:", "aabcde:", "aabcde:", "aabcde:", "abcdee:", "aabcde:", "aabcde:", "abcdee:", "aabcde:", "aabcde:", "abcdde:")), sprintf(format_column_2,percentage_format(hets[[4]][1])), sprintf(format_column_3,percentage_format(hets[[4]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1, switch(top+1, "aaabbc", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:", "abcdef:")), sprintf(format_column_2,percentage_format(hets[[5]][1])), sprintf(format_column_3,percentage_format(hets[[5]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + if (top==0) { + #cat(paste(sprintf(format_column_1,"aabbcc"), sprintf(format_column_2,percentage_format(hets[[6]][1])), sprintf(format_column_3,percentage_format(hets[[6]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1,"aaabcd"), sprintf(format_column_2,percentage_format(hets[[7]][1])), sprintf(format_column_3,percentage_format(hets[[7]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1,"aabbcd"), sprintf(format_column_2,percentage_format(hets[[8]][1])), sprintf(format_column_3,percentage_format(hets[[8]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1,"aabcde"), sprintf(format_column_2,percentage_format(hets[[9]][1])), sprintf(format_column_3,percentage_format(hets[[9]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + #cat(paste(sprintf(format_column_1,"abcdef"), sprintf(format_column_2,percentage_format(hets[[10]][1])), sprintf(format_column_3,percentage_format(hets[[10]][2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + } + } + cat(paste(sprintf(format_column_1,"Genome Haploid Length"), sprintf(format_column_2,bp_format(total_len[2])), sprintf(format_column_3,bp_format(total_len[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Genome Repeat Length"), sprintf(format_column_2,bp_format(repeat_len[2])), sprintf(format_column_3,bp_format(repeat_len[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Genome Unique Length"), sprintf(format_column_2,bp_format(unique_len[2])), sprintf(format_column_3,bp_format(unique_len[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Model Fit "), sprintf(format_column_2,percentage_format(model_fit_allscore[1])), sprintf(format_column_3,percentage_format(model_fit_fullscore[1])), sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste(sprintf(format_column_1,"Read Error Rate"), sprintf(format_column_2,percentage_format(error_rate[1])), sprintf(format_column_3,percentage_format(error_rate[2])), sep=""), file=summaryFile, sep="\n", append=TRUE) + if (VERBOSE) + { + cat(paste("\nPercent Kmers Modeled (All Kmers) = ", percentage_format(model_fit_allscore[1]), " [", model_fit_allscore[2], ", ", model_fit_allscore[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("Percent Kmers Modeled (Full Model) = ", percentage_format(model_fit_fullscore[1]), " [", model_fit_fullscore[2], ", ", model_fit_fullscore[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("Percent Kmers Modeled (Unique Kmers) = ", percentage_format(model_fit_uniquescore[1]), " [", model_fit_uniquescore[2], ", ", model_fit_uniquescore[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + + cat(paste("\nModel RSSE (All Kmers) = ", model_fit_all[1], " [", model_fit_all[2], ", ", model_fit_all[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("Model RSSE (Full Model) = ", model_fit_full[1], " [", model_fit_full[2], ", ", model_fit_full[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + cat(paste("Model RSSE (Unique Model) = ", model_fit_unique[1], " [", model_fit_unique[2], ", ", model_fit_unique[3], "]", sep=""), file=summaryFile, sep="\n", append=TRUE) + } + ## Finalize the progress + progressFilename=paste(foldername, "/", arguments$name_prefix, "progress.txt",sep="") + cat(model_status, file=progressFilename, sep="\n", append=TRUE) + + ## 0 if NA + ############################################################################### + + na.zero <- function (x) { + x[is.na(x)] <- 0 + return(x) + } + + ## Merfin probabilities + + colors <- c("black","red","green","purple","blue") + + if (p<=2 & FITTED_HIST){ + + if (!(p==1)){ + + fitted_hist=data.frame(cbind(one_hist,two_hist,thr_hist,fou_hist)) + + } else { + + fitted_hist=data.frame(cbind(two_hist,fou_hist)) + + } + + ## Fitted histogram + + png(paste(foldername, "/fitted_hist.png", sep=""), height = plot_size, width = plot_size, res=resolution) + layout(matrix(c(1,2), nrow=2, byrow = TRUE),heights=lcm(c(11,5.5))) + par(mar=c(0,5,1,1)) + + plot(kmer_hist_orig, type="n", xlab=NULL, ylab=ylabel_orig, ylim=c(0,y_limit_orig), xlim=c(0,akcov*(p*2.5)), + cex.main=font_size, cex.sub=font_size, cex.axis=font_size, cex.lab=font_size, + xaxt='n', yaxt='n') + myTicks = axTicks(4) + myTicks[1]<-0 + axis(2, at=myTicks, labels=myTicks, cex.axis=font_size, + cex.lab=font_size) + + peaks<-akcov * 1:6 + + points(kmer_hist, type="h", col=COLOR_HIST, lwd=2) + lines(error_kmers, col="black", lwd=1.5) + + abline(v=peaks, col="black", lty=2, lwd=0.3) + + for (i in 1:ncol(fitted_hist)) { + lines(fitted_hist[,i]*amlen, type="l", lwd=1.5, col=colors[i+1]) + } + + lines(rowSums(fitted_hist*amlen), col="darkgray", lwd=2, lty=2) + + legend_names=c("0-copy", "1-copy", "2-copy", "3-copy", "4-copy") + legend_lty=c("solid", "solid", "solid", "solid", "solid") + legend_lwd=c(3,3,3,3,3) + + legend("topright", + ##legend(exp(.65 * log(max(x))), 1.0 * max(y), + legend=c("Observed",legend_names[1:(ncol(fitted_hist)+1)],"Full model"), + lty=c("solid",legend_lty[1:(ncol(fitted_hist)+1)], "dashed"), + lwd=c(2, legend_lwd[1:(ncol(fitted_hist)+1)], 3), + col=c(COLOR_HIST,colors[1:(ncol(fitted_hist)+1)], "darkgray"), + bg="white") + + ## Generate lookup_table + + lookup_table <- NULL + plot_table <- NULL + + fitted_hist[(akcov*(p*2.5)):length(one_hist),1:ncol(fitted_hist)] <- 0 + + fitted_hist <- na.zero(fitted_hist) + + for (i in 1:(akcov*(p*2.5)-1)){ + + totalP<-sum(na.zero(error_kmers[i]), rowSums(fitted_hist[i,]*amlen)) + + prob<-c(na.zero(error_kmers[i]/totalP),as.numeric(fitted_hist[i,]*amlen)/totalP) + + plot_table<-rbind(plot_table,prob) + + max.p<-max(prob) + readK<-which.max(prob)-1 + + lookup_table<-rbind(lookup_table,c(readK,max.p)) + + } + + lookup_table<-data.frame(lookup_table) + rownames(plot_table) <- make.names(plot_table[,1], unique = TRUE) + + write.table(lookup_table, paste(foldername, "/lookup_table.txt", sep=""), sep=",", row.names = FALSE, col.names = FALSE) + + ## Plot lookup values + + par(mar=c(5,5,0,1)) + + plot_table<-data.frame(plot_table) + plot(plot_table$X1,type="n", xlab="Coverage", ylab="Probability",xlim=c(0,akcov*(p*2.5)), ylim=c(0,1), cex.lab=font_size, cex.axis=font_size, cex.main=font_size, cex.sub=font_size, yaxt='n') + + abline(v=peaks, col="black", lty=2, lwd=0.3) + + for (i in 1:(ncol(fitted_hist)+1)) { + lines(plot_table[,i], type="l", lwd=1.5, col=colors[i]) + } + axis(2, at=c(0,0.5,1), labels=c(0,0.5,1), cex.axis=font_size, + cex.lab=font_size) + + dev.off() + + } + + if (TESTING) { + if (TRUE_PARAMS!=-1) { + testingFile <- paste(foldername, "/", arguments$name_prefix, "SIMULATED_testing.tsv",sep="") + } else { + testingFile <- paste(foldername,"/SIMULATED_testing.tsv",sep="") + } + if (p==1) { + cat(paste(amd, akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + if (p==2) { + cat(paste(amd, ahets[[1]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + if (p==3) { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, ahets[[1]], ahets[[2]], akcov, adups, atotal_len, top, true_params[1], true_params[2], true_params[3], true_params[4], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } + if (p==4) { + if (topology==0) { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], akcov, adups, atotal_len, top, true_params[1], true_params[2], true_params[3], true_params[4], true_params[5], true_params[6], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } else { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, switch(top, ahets[[1]], 0), switch(top, 0, ahets[[1]]), ahets[[2]], ahets[[3]], akcov, adups, atotal_len, top, true_params[1], switch(true_params[5], true_params[2], 0), switch(true_params[5], 0, true_params[2]), true_params[3], true_params[4], true_params[5], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } + } + if (p==5) { + if (topology==0) { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], akcov, adups, atotal_len, top, true_params[1], true_params[2], true_params[3], true_params[4], true_params[5], true_params[6], true_params[7], true_params[8], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } else { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, switch(top, ahets[[1]], ahets[[1]], 0, 0, 0), switch(top, 0, 0, ahets[[1]], ahets[[1]], ahets[[1]]), switch(top, ahets[[2]], 0, ahets[[2]], 0, 0), switch(top, 0, ahets[[2]], 0, 0, 0), switch(top, 0, 0, 0, ahets[[2]], ahets[[2]]), switch(top, ahets[[3]], ahets[[3]], ahets[[3]], ahets[[3]], 0), switch(top, 0, 0, 0, 0, ahets[[3]]), ahets[[4]], akcov, adups, atotal_len, top, true_params[1], switch(true_params[6], true_params[2], true_params[2], 0, 0, 0), switch(true_params[6], 0, 0, true_params[2], true_params[2], true_params[2]), switch(true_params[6], true_params[3], 0, true_params[3], 0, 0), switch(true_params[6], 0, true_params[3], 0, 0, 0), switch(true_params[6], 0, 0, 0, true_params[3], true_params[3]), switch(true_params[6], true_params[4], true_params[4], true_params[4], true_params[4], 0), switch(true_params[6], 0, 0, 0, 0, true_params[4]), true_params[5], true_params[6], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } + } + if (p==6) { + if (topology==0) { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], ahets[[7]], ahets[[8]], ahets[[9]], ahets[[10]], akcov, adups, atotal_len, top, true_params[1], true_params[2], true_params[3], true_params[4], true_params[5], true_params[6], true_params[7], true_params[8], true_params[9], true_params[10], true_params[11], true_params[12], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], ahets[[6]], ahets[[7]], ahets[[8]], ahets[[9]], ahets[[10]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } else { + if (TRUE_PARAMS!=-1) { + true_params = unlist(lapply(strsplit(TRUE_PARAMS, ","), as.numeric)) + cat(paste(amd, ifelse(top %in% c(1,2,3,4,5), ahets[[1]], 0), ifelse(top %in% c(6,7,8,9,10,11,12,13), ahets[[1]], 0), ifelse(top %in% c(14,15,16), ahets[[1]], 0), ifelse(top %in% c(1,2,6,7), ahets[[2]], 0), ifelse(top %in% c(3,4,5,14,15,16), ahets[[2]], 0), ifelse(top %in% c(8,9,10), ahets[[2]], 0), ifelse(top %in% c(11,12,13), ahets[[2]], 0), ifelse(top %in% c(1,3,6,8,14), ahets[[3]], 0), ifelse(top %in% c(2,7,11), ahets[[3]], 0), ifelse(top %in% c(4,5,15,16), ahets[[3]], 0), ifelse(top %in% c(9,10,12,13), ahets[[3]], 0), ifelse(top %in% c(1,2,3,4,6,7,8,9,11,12,14,15), ahets[[4]], 0), ifelse(top %in% c(5,16), ahets[[4]], 0), ifelse(top %in% c(10,13), ahets[[4]], 0), ahets[[5]], akcov, adups, atotal_len, top, true_params[1], ifelse(true_params[7] %in% c(1,2,3,4,5), true_params[2], 0), ifelse(true_params[7] %in% c(6,7,8,9,10,11,12,13), true_params[2], 0), ifelse(true_params[7] %in% c(14,15,16), true_params[2], 0), ifelse(true_params[7] %in% c(1,2,6,7), true_params[3], 0), ifelse(true_params[7] %in% c(3,4,5,14,15,16), true_params[3], 0), ifelse(true_params[7] %in% c(8,9,10), true_params[3], 0), ifelse(true_params[7] %in% c(11,12,13), true_params[3], 0), ifelse(true_params[7] %in% c(1,3,6,8,14), true_params[4], 0), ifelse(true_params[7] %in% c(2,7,11), true_params[4], 0), ifelse(true_params[7] %in% c(4,5,15,16), true_params[4], 0), ifelse(true_params[7] %in% c(9,10,12,13), true_params[4], 0), ifelse(true_params[7] %in% c(1,2,3,4,6,7,8,9,11,12,14,15), true_params[5], 0), ifelse(true_params[7] %in% c(5,16), true_params[5], 0), ifelse(true_params[7] %in% c(10,13), true_params[5], 0), true_params[6], true_params[7], sep="\t"), file=testingFile, sep="\n", append=FALSE) + } else { + cat(paste(amd, ahets[[1]], ahets[[2]], ahets[[3]], ahets[[4]], ahets[[5]], akcov, adups, atotal_len, top, sep="\t"), file=testingFile, sep="\n", append=TRUE) + } + } + } + } +} diff --git a/R/score_model.R b/R/score_model.R new file mode 100644 index 0000000..50225ab --- /dev/null +++ b/R/score_model.R @@ -0,0 +1,69 @@ +#' Score nlsLM model by number and percent of residual errors after excluding sequencing errors +#' +#' @param kmer_hist_orig A data frame of the original histogram data (starting at 1 and with last position removed). +#' @param nls An nlsLM model object. +#' @param round An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process. +#' @param foldername A character vector corresponding to the name of the output directory. +#' @return A data frame where the variables "all", "full", and "unique" correspond to the model residual sum of square error (excluding sequencing error) +#' including x-values up to the end of kmer_hist_orig, up to (2p+1)*lambda, and up to (p+1)*lambda respectively. +#' Additionally, the variables "allscore", "fullscore", and "uniquescore" are the +#' corresponding percentage of kmers that are correctly modeled. +#' @export +score_model<-function(kmer_hist_orig, nls, round, foldername) { + x = kmer_hist_orig[[1]] + y = kmer_hist_orig[[2]] + y_transform = as.numeric(x)**transform_exp*as.numeric(y) + + pred=predict(nls, newdata=data.frame(x)) + model_sum=summary(nls) + p=nls$p + kcovfloor = max(1, floor(min_max(model_sum$coefficients['kmercov',])[[1]])) + + ## Compute error rate, by counting kmers unexplained by model through first peak + ## truncate errors as soon as it goes to zero, dont allow it to go back up + error_xcutoff = kcovfloor + error_xcutoff_ind = tail(which(x<=error_xcutoff),n=1) + if (length(error_xcutoff_ind)==0) {error_xcutoff_ind=1} + + error_kmers = x[1:error_xcutoff_ind]**(-transform_exp)*(y_transform[1:error_xcutoff_ind] - pred[1:error_xcutoff_ind]) + + first_zero = -1 + + for (i in 1:error_xcutoff_ind) { + if (first_zero == -1) { + if (error_kmers[i] < 1.0) { + first_zero = i + } + } + else { + error_kmers[i] = 0 + } + } + + if (first_zero == -1) { + first_zero = error_xcutoff_ind + } + + #if (TRANSFORM) { + # y_fit = y_transform + #} else { + # y_fit = y + #} + y_fit = y_transform + + ## The fit is residual sum of square error, excluding sequencing errors + model_fit_all = c(sum(as.numeric(y_fit[first_zero:length(y_fit)] - pred[first_zero:length(y_fit)]) ** 2), first_zero, x[length(y_fit)]) + model_fit_full = c(sum(as.numeric(y_fit[first_zero:(min(length(y_fit),(2*p+1)*kcovfloor))] - pred[first_zero:(min(length(y_fit), (2*p+1)*kcovfloor))]) ** 2), first_zero, (min(length(y_fit), (2*p+1)*kcovfloor))) + model_fit_unique = c(sum(as.numeric(y_fit[first_zero:((p+1)*kcovfloor)] - pred[first_zero:((p+1)*kcovfloor)]) ** 2), first_zero, ((p+1)*kcovfloor)) + + ## The score is the percentage of kmers correctly modeled, excluding sequencing errors + model_fit_allscore = c(1-sum(abs(as.numeric(y_fit[first_zero:length(y_fit)] - pred[first_zero:length(y_fit)]))) / sum(as.numeric(y_fit[first_zero:length(y_fit)])), first_zero, x[length(y_fit)]) + model_fit_fullscore = c(1-sum(abs(as.numeric(y_fit[first_zero:(min(length(y_fit), (2*p+1)*kcovfloor))] - pred[first_zero:(min(length(y_fit), (2*p+1)*kcovfloor))]))) / sum(as.numeric(y_fit[first_zero:(min(length(y_fit), (2*p+1)*kcovfloor))])), first_zero, (min(length(y_fit), (2*p+1)*kcovfloor))) + model_fit_uniquescore = c(1-sum(abs(as.numeric(y_fit[first_zero:((p+1)*kcovfloor)] - pred[first_zero:((p+1)*kcovfloor)]))) / sum(as.numeric(y_fit[first_zero:((p+1)*kcovfloor)])), first_zero, ((p+1)*kcovfloor)) + + fit = data.frame(all = model_fit_all, allscore = model_fit_allscore, + full = model_fit_full, fullscore = model_fit_fullscore, + unique = model_fit_unique, uniquescore = model_fit_uniquescore) + + return (fit) +} diff --git a/README.md b/README.md index 6101acc..bdf5646 100644 --- a/README.md +++ b/README.md @@ -1,92 +1,115 @@ -# GenomeScope: Fast genome analysis from unassembled short reads -## Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) *Bioinformatics* doi: https://doi.org/10.1093/bioinformatics/btx153 +# GenomeScope 2.0: Reference-free profiling of polyploid genomes +## T. Rhyker Ranallo-Benavidez, Kamil S. Jaron, and Michael C. Schatz -Current developments in de novo assembly technologies have been focused on relatively simple genomes. Even the human genome, with a heterozygosity rate of only ~0.1% and 2n diploid structure, is significantly simpler than many other species, especially plants. However, genomics is rapidly advancing towards sequencing more complex species such as pineapple, sugarcane, or wheat that have much higher rates of heterozygosity (>1% for pineapple), much higher ploidy (8n for sugarcane), and much larger genomes (16Gbp for wheat). +Many genomics analyses require first establishing a reference genome. However, *de novo* genome assembly is a complicated and computationally intensive process with many assumptions hidden to the user. A popular assessment prior to genome assembly is genome profiling, where the k-mer frequencies within the sequencing reads are analyzed to efficiently estimate major genome characteristics such as genome size, heterozygosity, and repetitiveness. However, current genome profiling tools are suited only for diploid genomes and use heuristic approaches. -One of the first goals when sequencing a new species is determining the overall characteristics of the genome structure, including the genome size, abundance of repetitive elements, and the rate of heterozygosity. These features are needed to study trends in genome evolution, and can inform the parameters that should be used for the individual assembly steps. They can also serve as an independent quality control during any analysis, such as quantifying the quality of an assembly, or measuring the expected number of heterozygous bases in the genome before mapping any variants. - -We have developed an analytical model and open-source software package GenomeScope that can infer the global properties of a genome from unassembled sequenced data. GenomeScope uses the k-mer count distribution, e.g. from Jellyfish, and within seconds produces a report and several informative plots describing the genome properties. We validate the approach on simulated heterozygous genomes, as well as synthetic crosses of related strains of microbial and eukaryotic genomes with known reference genomes. GenomeScope was also applied to study the characteristics of several novel species, including pineapple, pear, the regenerative flatworm Macrostomum lignano, and the Asian sea bass. +We have developed GenomeScope 2.0, which applies classical insights from combinatorial theory to establish a detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes. GenomeScope 2.0 employs a polyploid-aware mixture model that, within seconds, accurately infers genome properties from unassembled sequencing data. GenomeScope 2.0 uses the k-mer count distribution, e.g. from KMC or Jellyfish, and produces a report and several informative plots describing the genome properties. We validate the approach on simulated polyploid data created using a generative model with parameters for genome size, heterozygosity, repetitiveness, ploidy, and sequencing coverage, and find GenomeScope 2.0 retains accuracy across a broad range of realistic and extreme parameter values. We also validate GenomeScope 2.0 by analyzing genuine sequence data from 11 diverse polyploid genomes with known genome characteristics. ## Getting Started -Before running GenomeScope, you must first compute the histogram of k-mer frequencies. We recommend the tool [jellyfish](https://academic.oup.com/bioinformatics/article/27/6/764/234905/A-fast-lock-free-approach-for-efficient-parallel) that is available here: http://www.genome.umd.edu/jellyfish.html. After compiling jellyfish, you can run it like this: +Before running GenomeScope 2.0, you must first compute the histogram of k-mer frequencies. We recommend [KMC](https://academic.oup.com/bioinformatics/article/33/17/2759/3796399) that is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=download, or [jellyfish](https://academic.oup.com/bioinformatics/article/27/6/764/234905/A-fast-lock-free-approach-for-efficient-parallel) that is available at http://www.genome.umd.edu/jellyfish.html. + +After compiling KMC, you can count the k-mers with these commands: + + $ mkdir tmp + $ ls *.fastq > FILES + $ kmc -k21 -t10 -m64 -ci1 -cs10000 @FILES reads tmp/ + +Note you should adjust the memory (-m) and threads (-t) parameters according to your server. This example will use 10 threads and 64GB of RAM. The k-mer length (-k) may need to be scaled if you have low coverage or high error rate. The lower (-ci) and upper (-cs) bounds exclude k-mers with counts outside these boundaries. FILES is a file with a list of input files. + +After compiling jellyfish, you can count the k-mers with this command: $ jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf -Note you should adjust the memory (-s) and threads (-t) parameter according to your server. This example will use 10 threads and 1GB of RAM. The kmer length (-m) may need to be scaled if you have low coverage or a high error rate. We recommend using a kmer length of 21 (m=21) for most genomes, as this length is sufficiently long that most k-mers are not repetitive and is short enough that the analysis will be more robust to sequencing errors. Extremely large (haploid size >>10GB) and/or very repetitive genomes may benefit from larger kmer lengths to increase the number of unique k-mers. Accurate inferences requires a minimum amount of coverage, at least 25x coverage of the haploid genome or greater, otherwise the model fit will be poor or not converge. GenomeScope also requires relatively low error rate sequencing, such as Illumina sequencing, so that most k-mers do not have errors in them. For example, a 2% error corresponds to an error every 50bp on average, which is greater than the typical k-mer size used (k=21). Notably, raw single molecule sequencing reads from Oxford Nanopore or Pacific Biosciences, which currently average 5-15% error, are not supported as an error will occur on average every 6 to 20 bp. You should always use "canonical kmers" (-C) since the sequencing reads will come from both the forward and reverse strand of DNA. +Note you should adjust the memory (-s) and threads (-t) parameters according to your server. This example will use 10 threads and 1GB of RAM. The k-mer length (-m) may need to be scaled if you have low coverage or a high error rate. You should always use "canonical k-mers" (-C) since the sequencing reads will come from both the forward and reverse strand of DNA. + +We recommend using a k-mer length of 21 for most genomes, as this length is sufficiently long that most k-mers are not repetitive and is short enough that the analysis will be more robust to sequencing errors. Extremely large (haploid size >>10GB) and/or very repetitive genomes may benefit from larger k-mer lengths to increase the number of unique k-mers. Accurate inferences requires a minimum amount of coverage, at least 15x coverage of the haploid genome or greater, otherwise the model fit will be poor or not converge. GenomeScope also requires relatively low error rate sequencing, such as Illumina sequencing, so that most k-mers do not have errors in them. For example, a 2% error corresponds to an error every 50bp on average, which is greater than the typical k-mer size used (k=21). Notably, raw single molecule sequencing reads from Oxford Nanopore or Pacific Biosciences, which currently average 5-15% error, are not supported as an error will occur on average every 6 to 20 bp. -Then export the kmer count histogram +After counting the k-mers, you then export the k-mer count histogram. With KMC: + + $ kmc_tools transform reads histogram reads.histo -cx10000 + +The upper bound (-cx) gives the cutoff for the histogram. + +With jellyfish: $ jellyfish histo -t 10 reads.jf > reads.histo -Again the thread count (-t) should be scaled according to your server. After you have the jellyfish histogram file, you can run GenomeScope within the online web tool, or at the command line. +Again the thread count (-t) should be scaled according to your server. + +After you have the histogram file, you can run GenomeScope within the online web tool, or at the command line. ### Running GenomeScope Online Users may prefer to use the online version, which offers all of the same functionality within an easy to use web interface: -http://genomescope.org/ +http://genomescope.org/genomescope2.0 ### Running GenomeScope on the Command Line -Command line users can run the modeling with the R script genomescope.R, making sure that Rscript is in your PATH (alternatively, edit the shebang line to point to the Rscript location) +First we need to download GenomeScope 2.0 and enter its directory: + + $ git clone https://github.com/tbenavi1/genomescope2.0.git + $ cd genomescope2.0/ + +Then we need to install GenomeScope 2.0. + +If you already have write access to a specific path for R libraries that your R installation is set up to use, please set the local_lib_path variable in the install.R file equal to this path. Then we can run: + + $ Rscript install.R + +For most users, it is instead easiest to install GenomeScope 2.0 in a local directory. In this example we create an "R_libs" folder located in the home directory to use for local R libraries: - $ Rscript genomescope.R histogram_file k-mer_length read_length output_dir [kmer_max] [verbose] + $ mkdir ~/R_libs -The histogram_file (from jellyfish), k-mer_length, read_length, and output_dir are required parameters. The optional parameter kmer_max specifies the cutoff for excluding high frequency kmers from the analysis. We recommend setting kmer_max=1000, but it depends on the specific characteristics of your data. If the optional parameter verbose is set to 1, then GenomeScope will output more details on the model fitting as different parameters are used. The output plots and a text file of the inferred genome characteristics will be output to the specified output_dir directory. +In order for R to load libraries from this location, we have to create and/or edit the .Renviron file in the home directory: + + $ echo "R_LIBS=~/R_libs/" >> ~/.Renviron + +Now we can install GenomeScope 2.0: + + $ Rscript install.R + +After installation, command line users can run the modeling with the R script genomescope.R, making sure that genomescope.R is in your PATH. + + $ genomescope.R -i histogram_file -o output_dir -k k-mer_length + +The input histogram_file (from KMC or jellyfish), output_dir, and k-mer_length are required parameters. The optional parameter *-p ploidy* sets the ploidy of the model for GenomeScope to use. The optional parameter *-l lambda* sets the initial guess for the average k-mer coverage of the sequencing. The optional parameter *-n 'name_prefix'* sets the prefix for the output files. The optional parameter *-m max_kmercov* specifies the cutoff for excluding high frequence k-mers from the analysis. The output plots and a text file of the inferred genome characteristics will be output to the specified output_dir directory. For example, you can download the histogram from the Arabidopsis F1 described in the manuscript here: https://raw.githubusercontent.com/schatzlab/genomescope/master/analysis/real_data/ara_F1_21.hist Then run GenomeScope like this: - $ /PATH/TO/Rscript /PATH/TO/genomescope.R ara_F1_21.hist 21 150 output + $ /PATH/TO/genomescope.R -i ara_F1_21.hist -o output -k 21 This should complete in less than 1 minute, and report: - Model converged het:0.0104 kcov:22.2 err:0.0035 model fit:0.446 len:151975724 + Model converged het:0.0104 kcov:22.2 err:0.0035 model fit:0.458 len:151978519 -The plots and the full results will be in output directory, showing the estimated genome size to be 151.9Mbp and a 1.04% heterozygosity rate (the exact values may slightly differ due to the randomization within the modeling) +The plots and the full results will be in output directory, showing the estimated genome size to be 151.9Mbp and a 1.04% heterozygosity rate (the exact values may slightly differ due to the randomization within the modeling). ## Tutorial -A tutorial by Andrew Severin on running GenomeScope is available here http://gif.biotech.iastate.edu/genomescope +A tutorial by Andrew Severin on running GenomeScope 1.0 is available here: http://gif.biotech.iastate.edu/genomescope ## Frequently Asked Questions (FAQ) -**> Q: Why didnt the model converge, or why does it give very different results than expected?** +**> Q: Why didn't the model converge, or why does it give very different results than expected?** -A: The most common problem is you have too low of coverage for the model to confidently identify the peaks corresponding to the homozygous kmers. This can be recognized by a lack of any peaks in the kmer plots or that the model fit doesnt match the observed kmer profile very well. To correct this problem, first make sure that you have used the cannonically kmer counting mode (-C if you are using jellyfish). If this still fails, you can try slightly decreasing the kmer size used to 17 or 19. If all of these attempts still fail you will unfortunately need to generate additional sequencing data. +A: The most common problem is that you have too low of coverage for the model to confidently identify the peaks corresponding to the homozygous k-mers. This can be recognized by a lack of any peaks in the k-mer plots or that the model fit doesn't match the observed k-mer profile very well. To correct this problem, first make sure that you have used the canonical k-mer counting mode (-C if you are using jellyfish). If this still fails, you can try slightly decreasing the k-mer size used to 19 or 17. If all of these attempts still fail you will unfortunately need to generate additional sequencing data. -**> Q: As mentioned in the Supplementary Notes and Figures 1.3.2 Genome Size Estimation, the haploid genome size is estimated by: "This estimate is revised by summing the total number of k-mers, except presumptive sequencing errors identified as in section 1.3.1, and dividing by the 2*λ, the estimated coverage for homozygous k-mers". If I understand it correctly, λ is the mean of a distribution, the estimated coverage for homozygous k-mers; and in the genomescope profile, kcov is the estimated coverage for heterozygous kmers. -Could you explain how genomescope estimates haploid genome size, specifically why dividing by 2 times of the estimated coverage for homozygous k-mers?** +**> Q: As mentioned in the Supplementary Notes in Section 1.3.2 Genome Size Estimation in the GenomeScope 1.0 paper, the haploid genome size estimate "is revised by summing the total number of k-mers, except presumptive sequencing errors identified as in section 1.3.1, and dividing by 2λ, the estimated coverage for homozygous k-mers." If I understand it correctly, λ is the mean of a distribution, the estimated coverage for homozygous k-mers; and in the genomescope profile, kcov is the estimated coverage for heterozygous k-mers. Could you explain how genomescope estimates haploid genome size, specifically why dividing by 2 times of the estimated coverage for homozygous k-mers?** -A: Thank you for writing. I think there is a bit of confusion over the variable names and how they relate to each other. The first thing to note is λ and kcov refer to the same value, just that we use λ in the written document and kcov in the code. The modeling tries to identify 4 peaks centered at λ, 2*λ, 3*λ, and 4*λ. These 4 peaks correspond to the mean coverage levels of the unique heterozygous, unique homozygous, repetitive heterozygous and repetitive homozygous sequences, respectively. So when it estimates the haploid genome size, it divides by the 2*λ, which is the average homozygous coverage, not "2 times the estimated coverage for homozygous k-mers" as you write. +A: Thank you for writing. I think there is a bit of confusion over the variable names and how they relate to each other. The first thing to note is λ and kcov refer to the same value, just that we use λ in the written document and kcov in the code. The modeling tries to identify 4 peaks centered at λ, 2λ, 3λ, and 4λ. These 4 peaks correspond to the mean coverage levels of the unique heterozygous, unique homozygous, repetitive heterozygous and repetitive homozygous sequences, respectively. So when it estimates the haploid genome size, it divides by 2λ, which is the average homozygous coverage, not "2 times the estimated coverage for homozygous k-mers" as you write. -The other potentially confusing aspect is what is meant by haploid genome size versus diploid genome size. We consider the haploid genome size to mean the span of one complete set of haploid chromosomes and the diploid genome size to be the span of both haploid copies (total DNA content in one diploid cell). In particular, in a human cell, the haploid genome size is about 3Gbp and the diploid genome size is about 6Gbp. If you sequence a total of 300Gbp for a human genome, that would be about 150Gbp (50x coverage) of the maternal haplotype and about 150Gbp (50x coverage) of the paternal haplotype. But since the heterozygosity rate in humans is so low, the main peak in the distribution would be centered around 100x. However, GenomeScope will still try to fit the 4 peaks, so should set the heterozygous kmer coverage λ equal to 50x, and thus the homozygous coverage to 2*λ = 100x. From this GenomeScope will compute the haploid genome size as the total amount of sequence data (300GB) divided by the homozygous coverage (100x) to report 3Gbp as expected. Kmers with higher coverage are naturally scaled as well: kmers that occur 200 or 300 times in the kmer profile (and thus are 2 or 3 copy repeats in the diploid genome, 4 or 6 times in the haploid sequences) are still scaled by 100x to contribute 2 or 3 copies to the estimate. Finally, note that if the two haplotypes have significantly different lengths, then the reported haploid genome size will be the average of the two. +The other potentially confusing aspect is what is meant by haploid genome size versus diploid genome size. We consider the haploid genome size to mean the span of one complete set of haploid chromosomes and the diploid genome size to be the span of both haploid copies (total DNA content in one diploid cell). In particular, in a human cell, the haploid genome size is about 3Gbp and the diploid genome size is about 6Gbp. If you sequence a total of 300Gbp for a human genome, that would be about 150Gbp (50x coverage) of the maternal haplotype and about 150Gbp (50x coverage) of the paternal haplotype. But since the heterozygosity rate in humans is so low, the main peak in the distribution would be centered around 100x. However, GenomeScope will still try to fit the 4 peaks, and will set the heterozygous k-mer coverage λ equal to 50x, and thus the homozygous coverage to 2λ = 100x. From this GenomeScope will compute the haploid genome size as the total amount of sequence data (300GB) divided by the homozygous coverage (100x) to report 3Gbp as expected. K-mers with higher coverage are naturally scaled as well: k-mers that occur 200 or 300 times in the k-mer profile (and thus are 2 or 3 copy repeats in the diploid genome, 4 or 6 times in the haploid sequences) are still scaled by 100x to contribute 2 or 3 copies to the estimate. Finally, note that if the two haplotypes have significantly different lengths, then the reported haploid genome size will be the average of the two. **> Q: Can GenomeScope be used to estimate ploidy, or used with genomes with higher ploidy?** -A: No, GenomeScope is only appropriate for diploid genomes. In principle the model could be extend to higher levels of polyploidy by extending the model to consider additional peaks in the k-mer profile, but this is not currently supported. GenomeScope also does not support genomes that have uneven copy number of their chromosomes, such as aneuploid cancer genomes or even unequal numbers of sex chromosomes. In these scenarios the reported heterozygosity rate will represent the fraction of bases that are haploid (copy number 1) versus diploid (copy number 2) as well as any heterozygous positions in the other chromosomes. - +A: Yes, GenomeScope 2.0 is appropriate for genomes up to a hexaploid (6) ploidy level. To estimate ploidy, you can use [Smudgeplot](https://github.com/KamilSJaron/smudgeplot), which is another tool we developed. GenomeScope currently does not support genomes that have uneven copy number of their chromosomes, however, such as aneuploid cancer genomes or even unequal numbers of sex chromosomes. In these scenarios the reported heterozygosity rate will represent the fraction of bases that are haploid (copy number 1) versus diploid (copy number 2) as well as any heterozygous positions in the other chromosomes. **> Q: I tried out GenomeScope in order to obtain a genome size estimate for an organism that I am working on. Using the widely-used and cited k-mer method and calculation outlined in the XXX paper, I got an estimate of 869 - 919 Mbp and this is somewhat consistent with a c-value of 0.83pg from a different published study. However, with GenomeScope, I got an estimate of 650 Mbp instead. Would you or your team have any insights into why I am observing this discrepancy of more than 200Mbp in my estimations?** -While GenomeScope can automate most of the analysis, it does have one critical parameter on which high frequency kmers should be filtered out. This parameter is needed because we often see in real samples that kmers that occur 10,000 times or 100,000 times or greater are artifacts such as phiX sequencing, or organelle sequencing (or other contamination). To account for these, GenomeScope will by default exclude any kmers that occur more than 1000 times from the analysis, which lead to a genome size estimate of 649Mbp. If you increase this cutoff to 10,000, then the new size estimate is 697Mbp. You could perhaps raise this limit even higher, but it looks like your histogram is truncated at 10,000 (which is the default for jellyfish). If you want to include these ultrahigh frequency kmers, then you will have to regenerate the histogram from jellyfish and then set the max coverage threshold to 100,000 or perhaps even 1,000,000. This will likely increase the estimated genome size, but also make the analysis even more sensitive to any artifacts in the data. Unfortunately every project is a little bit different on how to best remove those artifacts. Please see the paper for details (especially the section in the supplement on characterizing the high frequency kmers in Arabidopsis) - -**> Q: I sequenced the gDNA of two closely related fish samples, and GenomeScope reports the heterozygosity rate of each separately at 0.103% and 0.113%. However, when I merge the reads together, GenomeScope reports an overall rate of heterozygosity to be lower at 0.056%. Why is that?** - -The short answer is by mixing the samples together, this becomes a tetraploid sample, but GenomeScope currently doesnt work with ploidy > 2. Ive been doing some simulations to further understand this: I randomly generate a 1Mbp maternal sequence m1, and then introduce heterozygous variants to create the paternal sequence p1 at a given rate of heterozygosity r1. In parallel, I create a second maternal genome m2 that differs from m1 by a separate rate of heterozygosity rM. From m2, I derive the paternal genome p2 using the rate of heterozygosity r2. Note that there are 3 rates of heterozygosity that can be adjusted (r1, r2, and rM), and from your data we know that r1 and r2 are around 0.1% but rM is unknown, although is assumed to be very low because the mitochondrial genomes are identical. From this framework, I tried several values of rM, and see that when rM is set to 0.02% then GenomeScope infers the overall rate of heterozygosity at about 0.05%, similar to your data (see attached results). In the joint GenomeScope plot, there is a new peak of heterozygous kmers centered at around 10x coverage (below the expected coverage for heterozygous variants), but GenomeScope incorrectly assumes these are errors just because it doesnt understand how to deal with higher levels of ploidy. We are working on extended the model to consider situations like this, but for now if you want to demonstrate this further, you'd have to align the reads to your assembly, and then you should detect variants that occur at about 50% allele frequency (where m1 and m2 are different), plus variants that occur at about 25% allele frequency (where there is further heterozygosity in p1 or p2). If you would like to run additional simulations, the code is available in the repo at [https://github.com/schatzlab/genomescope/tree/master/analysis/genomesim/polyploid](https://github.com/schatzlab/genomescope/tree/master/analysis/genomesim/polyploid) - - -**> Q: Can you please define the terms on the plot:** - -The published paper, and especially the supplemental methods defines the terms more completely but briefly: - -len: inferred total genome length
-uniq: percent of the genome that is unique (not repetitive)
-het: overall rate of heterozygosity
-kcov: mean kmer coverage for heterozygous bases. note the top of the peak will not intersect the kcov line because of the over dispersion in real data
-err: error rate of the reads +While GenomeScope can automate most of the analysis, it does have an optional parameter (--max_kmercov) to filter out high frequency k-mers. This parameter is sometimes needed because we see in real samples that k-mers that occur 10,000 times or 100,000 times or greater may be artifacts such as phiX sequencing, or organelle sequencing (or other contamination). To account for these, the user will have to specify a cutoff value for GenomeScope to exclude any k-mers that occur above this threshold. On the other hand, for highly repetitive or huge genomes you may need to expand your k-mer histogram to include higher counter k-mers (jellyfish histograms are truncated at 10,000 by default). If you want to include these ultrahigh frequency k-mers, then you will have to regenerate the histogram from jellyfish or KMC with a higher upper bound (perhaps 100,000, 1 million, or even higher). This will likely increase the estimated genome size, but could also make the analysis more sensitive to any artifacts in the data. Unfortunately every project is a little bit different on how to best remove those artifacts. Please see the GenomeScope 1.0 paper for details (especially the section in the supplement on characterizing the high frequency k-mers in Arabidopsis). ## Resources @@ -95,4 +118,6 @@ VCF files of the variants identified in the larger genomes are available here: http://labshare.cshl.edu/shares/schatzlab/www-data/genomescope/vcf/ ## References: +Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. *Nature Communications* **11**, 1432 (2020). https://doi.org/10.1038/s41467-020-14998-3 + Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) *Bioinformatics* doi: https://doi.org/10.1093/bioinformatics/btx153 diff --git a/analysis.php b/analysis.php index 756dd7d..5ec25d2 100755 --- a/analysis.php +++ b/analysis.php @@ -25,6 +25,15 @@ +
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"; ?> diff --git a/analysis/._.DS_Store b/analysis/._.DS_Store deleted file mode 100644 index e03770c..0000000 Binary files a/analysis/._.DS_Store and /dev/null differ diff --git a/analysis/COMMANDS b/analysis/COMMANDS new file mode 100644 index 0000000..aff540e --- /dev/null +++ b/analysis/COMMANDS @@ -0,0 +1,15 @@ +python make_random_genome.py 1000000000 random_genome_001Gbp.fa +head -n 100000000 random_genome_001Gbp.fa > random_genome.fa +head -n 100000000 random_genome_001Gbp.fa > random_genome_100Mbp.fa +head -n 10000000 random_genome_001Gbp.fa > random_genome_010Mbp.fa +head -n 1000000 random_genome_001Gbp.fa > random_genome_001Mbp.fa +python heterozygosity_commands.py +bash HETEROZYGOSITY_COMMANDS +python repetitiveness_commands.py +bash REPETITIVENESS_COMMANDS +python length_commands.py +bash LENGTH_COMMANDS +python heterozygosity_smudgeplot_commands.py +bash HETEROZYGOSITY_smudgeplot_COMMANDS +python repetitiveness_smudgeplot_commands.py +bash REPETITIVENESS_smudgeplot_COMMANDS diff --git a/analysis/chromosomeMutator.py b/analysis/chromosomeMutator.py new file mode 100644 index 0000000..f898117 --- /dev/null +++ b/analysis/chromosomeMutator.py @@ -0,0 +1,257 @@ +def chromosomeMutator(chromosome,heterozygosities,p, topology_model, top): #"Partition", p=1 to p=6 + import random + mutate = {"A": "ACGTAC", "C": "CGTACG", "G": "GTACGT", "T": "TACGTA"} + mutatedchromosomes = {} + length = len(chromosome) + if topology_model == "Partition": + if p == 1: + mutatedchromosomes[1] = chromosome + if p == 2: + mutatedchromosomes[1] = list(chromosome) + mutatedchromosomes[2] = list(chromosome) + r = [1-heterozygosities[0]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= r[0]: + nums = [0, 0] + else: + nums = [0, 1] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[1] = "".join(mutatedchromosomes[1]) + mutatedchromosomes[2] = "".join(mutatedchromosomes[2]) + if p == 3: + mutatedchromosomes[1] = list(chromosome) + mutatedchromosomes[2] = list(chromosome) + mutatedchromosomes[3] = list(chromosome) + r = [1-heterozygosities[0]-heterozygosities[1]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= r[0]: + nums = [0, 0, 0] #how to mutate + elif chance <= r[0] + r[1]: + nums = [0, 0, 1] + else: + nums = [0, 1, 2] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[1] = "".join(mutatedchromosomes[1]) + mutatedchromosomes[2] = "".join(mutatedchromosomes[2]) + mutatedchromosomes[3] = "".join(mutatedchromosomes[3]) + if p == 4: + mutatedchromosomes[1] = list(chromosome) + mutatedchromosomes[2] = list(chromosome) + mutatedchromosomes[3] = list(chromosome) + mutatedchromosomes[4] = list(chromosome) + if top != 0: + r = [1 - heterozygosities[0] - heterozygosities[1] - heterozygosities[2]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= r[0]: + nums = [0, 0, 0, 0] + elif chance <= r[0] + r[1]: + if top == 1: + nums = [0, 0, 0, 1] + if top == 2: + nums = [0, 0, 1, 1] + elif chance <= r[0] + r[1] + r[2]: + nums = [0, 0, 1, 2] + else: + nums = [0, 1, 2, 3] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + else: + r = [1 - heterozygosities[0] - heterozygosities[1] - heterozygosities[2] - heterozygosities[3]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= r[0]: + nums = [0, 0, 0, 0] + elif chance <= r[0] + r[1]: + nums = [0, 0, 0, 1] + elif chance <= r[0] + r[1] + r[2]: + nums = [0, 0, 1, 1] + elif chance <= r[0] + r[1] + r[2] + r[3]: + nums = [0, 0, 1, 2] + else: + nums = [0, 1, 2, 3] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + mutatedchromosomes[1] = "".join(mutatedchromosomes[1]) + mutatedchromosomes[2] = "".join(mutatedchromosomes[2]) + mutatedchromosomes[3] = "".join(mutatedchromosomes[3]) + mutatedchromosomes[4] = "".join(mutatedchromosomes[4]) + if p == 5: + mutatedchromosomes[1] = list(chromosome) + mutatedchromosomes[2] = list(chromosome) + mutatedchromosomes[3] = list(chromosome) + mutatedchromosomes[4] = list(chromosome) + mutatedchromosomes[5] = list(chromosome) + if top!=0: + r = [1 - heterozygosities[0] - heterozygosities[1] - heterozygosities[2] - heterozygosities[3]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= sum(r[:1]): + nums = [0, 0, 0, 0, 0] + elif chance <= sum(r[:2]): + if top in [1, 2]: + nums = [0, 0, 0, 0, 1] + if top in [3, 4, 5]: + nums = [0, 0, 0, 1, 1] + elif chance <= sum(r[:3]): + if top in [1,3]: + nums = [0, 0, 0, 1, 2] + if top in [2]: + nums = [0, 0, 1, 1, 2] + if top in [4, 5]: + nums = [0, 0, 1, 2, 2] + elif chance <= sum(r[:4]): + if top in [1, 2, 3, 4]: + nums = [0, 0, 1, 2, 3] + if top in [5]: + nums = [0, 1, 2, 3, 3] + else: + nums = [0, 1, 2, 3, 0] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + mutatedchromosomes[5][i] = mutate[mutatedchromosomes[5][i]][nums[4]] + else: + r = [1 - sum(heterozygosities)] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= sum(r[:1]): + nums = [0, 0, 0, 0, 0] + elif chance <= sum(r[:2]): + nums = [0, 0, 0, 0, 1] + elif chance <= sum(r[:3]): + nums = [0, 0, 0, 1, 1] + elif chance <= sum(r[:4]): + nums = [0, 0, 0, 1, 2] + elif chance <= sum(r[:5]): + nums = [0, 0, 1, 1, 2] + elif chance <= sum(r[:6]): + nums = [0, 0, 1, 2, 3] #nums = [0, 0, 1, 2, 2] + #elif chance <= sum(r[:7]): + # nums = [0, 0, 1, 2, 3] + #elif chance <= sum(r[:8]): + # nums = [0, 1, 2, 3, 3] + else: + nums = [0, 1, 2, 3, 4] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + mutatedchromosomes[5][i] = mutate[mutatedchromosomes[5][i]][nums[4]] + mutatedchromosomes[1] = "".join(mutatedchromosomes[1]) + mutatedchromosomes[2] = "".join(mutatedchromosomes[2]) + mutatedchromosomes[3] = "".join(mutatedchromosomes[3]) + mutatedchromosomes[4] = "".join(mutatedchromosomes[4]) + mutatedchromosomes[5] = "".join(mutatedchromosomes[5]) + if p == 6: + mutatedchromosomes[1] = list(chromosome) + mutatedchromosomes[2] = list(chromosome) + mutatedchromosomes[3] = list(chromosome) + mutatedchromosomes[4] = list(chromosome) + mutatedchromosomes[5] = list(chromosome) + mutatedchromosomes[6] = list(chromosome) + if top!=0: + r = [1 - heterozygosities[0] - heterozygosities[1] - heterozygosities[2] - heterozygosities[3] - heterozygosities[4]] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= sum(r[:1]): + nums = [0, 0, 0, 0, 0, 0] + elif chance <= sum(r[:2]): + if top in [1, 2, 3, 4, 5]: + nums = [0, 0, 0, 0, 0, 1] + if top in [6, 7, 8, 9, 10, 11, 12, 13]: + nums = [0, 0, 0, 0, 1, 1] + if top in [14, 15, 16]: + nums = [0, 0, 0, 1, 1, 1] + elif chance <= sum(r[:3]): + if top in [1, 2, 6, 7]: + nums = [0, 0, 0, 0, 1, 2] + if top in [3, 4, 5, 14, 15, 16]: + nums = [0, 0, 0, 1, 1, 2] + if top in [8, 9, 10]: + nums = [0, 0, 0, 1, 2, 2] + if top in [11, 12, 13]: + nums = [0, 0, 1, 1, 2, 2] + elif chance <= sum(r[:4]): + if top in [1, 3, 6, 8, 14]: + nums = [0, 0, 0, 1, 2, 3] + if top in [2, 7, 11]: + nums = [0, 0, 1, 1, 2, 3] + if top in [4, 5, 15, 16]: + nums = [0, 0, 1, 2, 2, 3] + if top in [9, 10, 12, 13]: + nums = [0, 0, 1, 2, 3, 3] + elif chance <= sum(r[:5]): + if top in [1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 14, 15]: + nums = [0, 0, 1, 2, 3, 0] + if top in [5, 16]: + nums = [0, 1, 2, 3, 3, 0] + if top in [10, 13]: + nums = [0, 1, 2, 3, 0, 0] + else: + nums = [0, 1, 2, 3, 0, 1] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + mutatedchromosomes[5][i] = mutate[mutatedchromosomes[5][i]][nums[4]] + mutatedchromosomes[6][i] = mutate[mutatedchromosomes[6][i]][nums[5]] + else: + r = [1 - sum(heterozygosities)] + heterozygosities + for i in range(length): + chance = random.random() + if chance <= sum(r[:1]): + nums = [0, 0, 0, 0, 0, 0] + elif chance <= sum(r[:2]): + nums = [0, 0, 0, 0, 0, 1] + elif chance <= sum(r[:3]): + nums = [0, 0, 0, 0, 1, 1] + elif chance <= sum(r[:4]): + nums = [0, 0, 0, 1, 1, 1] + elif chance <= sum(r[:5]): + nums = [0, 0, 0, 0, 1, 2] + elif chance <= sum(r[:6]): + nums = [0, 0, 0, 1, 1, 2] + elif chance <= sum(r[:7]): + nums = [0, 0, 1, 1, 2, 2] #nums = [0, 0, 0, 1, 2, 2] + elif chance <= sum(r[:8]): + nums = [0, 0, 0, 1, 2, 3] #nums = [0, 0, 1, 1, 2, 2] + elif chance <= sum(r[:9]): + nums = [0, 0, 1, 1, 2, 3] #nums = [0, 0, 0, 1, 2, 3] + elif chance <= sum(r[:10]): + nums = [0, 0, 1, 2, 3, 4] #nums = [0, 0, 1, 1, 2, 3] + #elif chance <= sum(r[:11]): + # nums = [0, 0, 1, 2, 2, 3] + #elif chance <= sum(r[:12]): + # nums = [0, 0, 1, 2, 3, 3] + #elif chance <= sum(r[:13]): + # nums = [0, 0, 1, 2, 3, 4] + #elif chance <= sum(r[:14]): + # nums = [0, 1, 2, 3, 3, 4] + #elif chance <= sum(r[:15]): + # nums = [0, 1, 2, 3, 4, 4] + else: + nums = [0, 1, 2, 3, 4, 5] + mutatedchromosomes[1][i] = mutate[mutatedchromosomes[1][i]][nums[0]] + mutatedchromosomes[2][i] = mutate[mutatedchromosomes[2][i]][nums[1]] + mutatedchromosomes[3][i] = mutate[mutatedchromosomes[3][i]][nums[2]] + mutatedchromosomes[4][i] = mutate[mutatedchromosomes[4][i]][nums[3]] + mutatedchromosomes[5][i] = mutate[mutatedchromosomes[5][i]][nums[4]] + mutatedchromosomes[6][i] = mutate[mutatedchromosomes[6][i]][nums[5]] + mutatedchromosomes[1] = "".join(mutatedchromosomes[1]) + mutatedchromosomes[2] = "".join(mutatedchromosomes[2]) + mutatedchromosomes[3] = "".join(mutatedchromosomes[3]) + mutatedchromosomes[4] = "".join(mutatedchromosomes[4]) + mutatedchromosomes[5] = "".join(mutatedchromosomes[5]) + mutatedchromosomes[6] = "".join(mutatedchromosomes[6]) + return mutatedchromosomes diff --git a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist b/analysis/ecoli_mix/ERR351256_ERR687900_21.hist deleted file mode 100644 index 1953cbb..0000000 --- a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist +++ /dev/null @@ -1,1062 +0,0 @@ -1 9326807 -2 272412 -3 42998 -4 18885 -5 10979 -6 6992 -7 5078 -8 4021 -9 3310 -10 3195 -11 2963 -12 3073 -13 3452 -14 4234 -15 5466 -16 7237 -17 9115 -18 11937 -19 16068 -20 20651 -21 26946 -22 34333 -23 43908 -24 55020 -25 68619 -26 82515 -27 99063 -28 116724 -29 135583 -30 154214 -31 173316 -32 191136 -33 207473 -34 219937 -35 230341 -36 234876 -37 236071 -38 234001 -39 229489 -40 220286 -41 208853 -42 195160 -43 177812 -44 161794 -45 146372 -46 130134 -47 115298 -48 99962 -49 88402 -50 77310 -51 68181 -52 60050 -53 54458 -54 49958 -55 46951 -56 44959 -57 44588 -58 44920 -59 46259 -60 47237 -61 49589 -62 52288 -63 56092 -64 59260 -65 62793 -66 66979 -67 69871 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a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.824e-03 1.618e-03 4.836 1.58e-06 *** -r 3.156e-02 4.584e-05 688.444 < 2e-16 *** -kmercov 3.802e+01 8.224e-03 4622.543 < 2e-16 *** -bias 7.425e-01 3.344e-03 222.009 < 2e-16 *** -length 4.832e+06 5.101e+03 947.298 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 654 on 835 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.799e-06 - diff --git a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.log.png b/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.log.png deleted file mode 100644 index f9349d1..0000000 Binary files a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.png b/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.png deleted file mode 100644 index ed23674..0000000 Binary files a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/progress.txt b/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/progress.txt deleted file mode 100644 index 8806050..0000000 --- a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 386716976.746704 -round 1 trimming to 16 trying 4peak model... converged. score: 385394047.188395 -round 2 trimming to 21 trying 4peak model... converged. score: 370786324.949783 -round 3 trimming to 26 trying 4peak model... converged. score: 357156310.194421 -done diff --git a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/summary.txt b/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/summary.txt deleted file mode 100644 index 735fe28..0000000 --- a/analysis/ecoli_mix/ERR351256_ERR687900_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.14655% 3.16488% -Genome Haploid Length 4,927,737 bp 4,932,003 bp -Genome Repeat Length 126,457 bp 126,566 bp -Genome Unique Length 4,801,280 bp 4,805,437 bp -Model Fit 97.8724% 98.0054% -Read Error Rate 0.144979% 0.144979% diff --git a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist b/analysis/ecoli_mix/ERR351256_SRR530851_21.hist deleted file mode 100644 index 7f375bb..0000000 --- a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist +++ /dev/null @@ -1,1198 +0,0 @@ -1 12601822 -2 396584 -3 66950 -4 28517 -5 15808 -6 10224 -7 7209 -8 5988 -9 5142 -10 5035 -11 4835 -12 5227 -13 6011 -14 7314 -15 9744 -16 12443 -17 15307 -18 19081 -19 23119 -20 28536 -21 35475 -22 42882 -23 51217 -24 60381 -25 70550 -26 80295 -27 91534 -28 102009 -29 113570 -30 122639 -31 131528 -32 141287 -33 147099 -34 151942 -35 154791 -36 156334 -37 156925 -38 154319 -39 150019 -40 146378 -41 140233 -42 133521 -43 124735 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* 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.833e-03 7.720e-04 12.74 <2e-16 *** -r 2.164e-02 1.863e-05 1161.73 <2e-16 *** -kmercov 3.796e+01 6.147e-03 6175.73 <2e-16 *** -bias 1.276e+00 2.731e-03 467.11 <2e-16 *** -length 4.910e+06 2.951e+03 1663.59 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 327.3 on 905 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.323e-06 - diff --git a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.log.png b/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.log.png deleted file mode 100644 index 7a0c3ae..0000000 Binary files a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.png b/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.png deleted file mode 100644 index 5ca5cca..0000000 Binary files a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/progress.txt b/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/progress.txt deleted file mode 100644 index f98696c..0000000 --- a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 169115831.14402 -round 1 trimming to 16 trying 4peak model... converged. score: 202754444.320522 -round 2 trimming to 21 trying 4peak model... converged. score: 139038233.644842 -round 3 trimming to 26 trying 4peak model... converged. score: 57271215.0050469 -done diff --git a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/summary.txt b/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/summary.txt deleted file mode 100644 index 36e639f..0000000 --- a/analysis/ecoli_mix/ERR351256_SRR530851_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.16049% 2.16794% -Genome Haploid Length 5,097,143 bp 5,100,446 bp -Genome Repeat Length 230,836 bp 230,986 bp -Genome Unique Length 4,866,307 bp 4,869,460 bp -Model Fit 98.3953% 98.8914% -Read Error Rate 0.198456% 0.198456% diff --git a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist deleted file mode 100644 index 91c73b6..0000000 --- a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist +++ /dev/null @@ -1,1160 +0,0 @@ -1 9301246 -2 264174 -3 53326 -4 23153 -5 12899 -6 7768 -7 5377 -8 4241 -9 3537 -10 3373 -11 3463 -12 3961 -13 4698 -14 5811 -15 7738 -16 9548 -17 12300 -18 15070 -19 18769 -20 23975 -21 29647 -22 36954 -23 46113 -24 58132 -25 72043 -26 87219 -27 104590 -28 125144 -29 145419 -30 166225 -31 187168 -32 206734 -33 224536 -34 239734 -35 251686 -36 257336 -37 262058 -38 261691 -39 256505 -40 247815 -41 233779 -42 218804 -43 200174 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a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/model.txt b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/model.txt deleted file mode 100644 index cd28590..0000000 --- a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.549e-02 1.114e-03 13.9 <2e-16 *** -r 3.290e-02 3.245e-05 1013.7 <2e-16 *** -kmercov 3.821e+01 5.324e-03 7177.8 <2e-16 *** -bias 6.826e-01 2.100e-03 325.0 <2e-16 *** -length 5.142e+06 3.662e+03 1404.3 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 476.9 on 925 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.092e-07 - diff --git a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.log.png deleted file mode 100644 index 168aad5..0000000 Binary files a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.png b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.png deleted file mode 100644 index 12a54b0..0000000 Binary files a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/progress.txt deleted file mode 100644 index a6e99ee..0000000 --- a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 264494231.96864 -round 1 trimming to 15 trying 4peak model... converged. score: 263185649.971863 -round 2 trimming to 20 trying 4peak model... converged. score: 236686046.321763 -round 3 trimming to 25 trying 4peak model... converged. score: 179044535.185591 -done diff --git a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/summary.txt deleted file mode 100644 index a5d801b..0000000 --- a/analysis/ecoli_mix/SRR530851_ERR687900_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.28356% 3.29654% -Genome Haploid Length 5,354,397 bp 5,357,382 bp -Genome Repeat Length 272,754 bp 272,906 bp -Genome Unique Length 5,081,643 bp 5,084,476 bp -Model Fit 98.3617% 98.7015% -Read Error Rate 0.142695% 0.142695% diff --git a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist b/analysis/ecoli_mix/SRR733088_ERR351256_21.hist deleted file mode 100644 index bfc0317..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist +++ /dev/null @@ -1,1588 +0,0 @@ -1 18754048 -2 751114 -3 114444 -4 42630 -5 20568 -6 11461 -7 7731 -8 5679 -9 4133 -10 3749 -11 2937 -12 2724 -13 2820 -14 2955 -15 3877 -16 4921 -17 5902 -18 7425 -19 9350 -20 12008 -21 15602 -22 19512 -23 24036 -24 29307 -25 35239 -26 41012 -27 47869 -28 53224 -29 59847 -30 65593 -31 71419 -32 76238 -33 79074 -34 81469 -35 82591 -36 82660 -37 81301 -38 79552 -39 76438 -40 72736 -41 69784 -42 66002 -43 61319 -44 57634 -45 53941 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((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.047e-03 8.511e-04 8.279 4.11e-16 *** -r 1.076e-02 1.551e-05 693.621 < 2e-16 *** -kmercov 3.695e+01 7.162e-03 5159.488 < 2e-16 *** -bias 1.300e+00 3.697e-03 351.538 < 2e-16 *** -length 4.495e+06 3.865e+03 1163.094 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 375.4 on 964 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 5.755e-07 - diff --git a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.log.png deleted file mode 100644 index 9b8acf4..0000000 Binary files a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.png b/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.png deleted file mode 100644 index 6a0aa8e..0000000 Binary files a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/progress.txt deleted file mode 100644 index 77438de..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 134797248.05048 -round 1 trimming to 17 trying 4peak model... converged. score: 134716401.197328 -round 2 trimming to 22 trying 4peak model... converged. score: 134802484.524294 -round 3 trimming to 27 trying 4peak model... converged. score: 143190623.999057 -done diff --git a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/summary.txt deleted file mode 100644 index 4b4bf9a..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR351256_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.07248% 1.07868% -Genome Haploid Length 4,682,848 bp 4,686,480 bp -Genome Repeat Length 219,942 bp 220,112 bp -Genome Unique Length 4,462,906 bp 4,466,367 bp -Model Fit 98.0214% 98.4742% -Read Error Rate 0.283004% 0.283004% diff --git a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist deleted file mode 100644 index 40e3609..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist +++ /dev/null @@ -1,1399 +0,0 @@ -1 15596391 -2 575317 -3 91411 -4 33941 -5 16288 -6 8929 -7 5551 -8 3741 -9 2702 -10 2147 -11 1828 -12 1760 -13 1809 -14 2064 -15 2684 -16 3605 -17 5074 -18 7403 -19 10465 -20 14964 -21 20592 -22 27886 -23 37341 -24 50044 -25 64332 -26 80637 -27 99136 -28 120717 -29 141437 -30 164591 -31 185627 -32 205346 -33 221775 -34 235837 -35 246510 -36 250412 -37 250143 -38 245227 -39 237430 -40 224092 -41 208142 -42 190491 -43 171880 -44 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b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/model.txt deleted file mode 100644 index e9535d9..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.424e-03 1.098e-03 5.853 6.63e-09 *** -r 3.099e-02 3.051e-05 1015.532 < 2e-16 *** -kmercov 3.730e+01 4.932e-03 7561.871 < 2e-16 *** -bias 4.679e-01 1.969e-03 237.643 < 2e-16 *** -length 4.760e+06 3.524e+03 1350.734 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 455.9 on 949 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 7.531e-07 - diff --git a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.log.png deleted file mode 100644 index 07d1565..0000000 Binary files a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.png b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.png deleted file mode 100644 index f97747f..0000000 Binary files a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/progress.txt deleted file mode 100644 index bc8f990..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 205392168.038413 -round 1 trimming to 17 trying 4peak model... converged. score: 205011973.390525 -round 2 trimming to 22 trying 4peak model... converged. score: 200339333.619266 -round 3 trimming to 27 trying 4peak model... converged. score: 197270900.979701 -done diff --git a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/summary.txt deleted file mode 100644 index 49f44f5..0000000 --- a/analysis/ecoli_mix/SRR733088_ERR687900_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.09252% 3.10473% -Genome Haploid Length 4,929,484 bp 4,932,092 bp -Genome Repeat Length 194,413 bp 194,516 bp -Genome Unique Length 4,735,071 bp 4,737,576 bp -Model Fit 98.1426% 98.4244% -Read Error Rate 0.231131% 0.231131% diff --git a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist deleted file mode 100644 index ffce328..0000000 --- a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist +++ /dev/null @@ -1,1377 +0,0 @@ -1 18840049 -2 705143 -3 118154 -4 44317 -5 21303 -6 12163 -7 7932 -8 5880 -9 4726 -10 4120 -11 3865 -12 4166 -13 4614 -14 5855 -15 7924 -16 9856 -17 12642 -18 15677 -19 19507 -20 24883 -21 31067 -22 39157 -23 47792 -24 57854 -25 69294 -26 81142 -27 94226 -28 107499 -29 120923 -30 132705 -31 144267 -32 155834 -33 162568 -34 168704 -35 172348 -36 173130 -37 171657 -38 167013 -39 161088 -40 153069 -41 143757 -42 133635 -43 123464 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b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/model.txt deleted file mode 100644 index a97d019..0000000 --- a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.149e-02 6.318e-04 18.18 <2e-16 *** -r 2.198e-02 1.515e-05 1450.69 <2e-16 *** -kmercov 3.714e+01 4.207e-03 8828.19 <2e-16 *** -bias 9.076e-01 1.798e-03 504.74 <2e-16 *** -length 4.835e+06 2.421e+03 1997.04 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 274.8 on 970 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.119e-07 - diff --git a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.log.png deleted file mode 100644 index 94c8cb6..0000000 Binary files a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.png b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.png deleted file mode 100644 index 0f51071..0000000 Binary files a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/progress.txt deleted file mode 100644 index eac36bf..0000000 --- a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 141469379.098963 -round 1 trimming to 16 trying 4peak model... converged. score: 136718018.266762 -round 2 trimming to 21 trying 4peak model... converged. score: 101285321.579319 -round 3 trimming to 26 trying 4peak model... converged. score: 59168237.8511684 -done diff --git a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/summary.txt deleted file mode 100644 index f67e818..0000000 --- a/analysis/ecoli_mix/SRR733088_SRR530851_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.19467% 2.20073% -Genome Haploid Length 5,118,042 bp 5,120,362 bp -Genome Repeat Length 332,427 bp 332,577 bp -Genome Unique Length 4,785,616 bp 4,787,784 bp -Model Fit 98.168% 98.8168% -Read Error Rate 0.277878% 0.277878% diff --git a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist b/analysis/ecoli_mix/SRR941832_ERR351256_21.hist deleted file mode 100644 index 3e7f256..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist +++ /dev/null @@ -1,1488 +0,0 @@ -1 13496660 -2 377320 -3 55145 -4 22265 -5 11557 -6 7173 -7 5066 -8 3739 -9 2969 -10 2896 -11 2618 -12 2714 -13 3080 -14 3446 -15 4498 -16 5775 -17 7428 -18 9106 -19 11207 -20 14059 -21 17222 -22 20899 -23 25238 -24 29480 -25 33997 -26 38389 -27 43274 -28 47488 -29 51940 -30 56108 -31 59724 -32 63978 -33 66477 -34 68213 -35 69812 -36 70730 -37 69998 -38 69428 -39 69001 -40 68032 -41 67323 -42 65284 -43 62954 -44 60797 -45 60100 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(1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.058e-03 1.617e-03 2.51 0.0123 * -r 1.052e-02 3.073e-05 342.19 <2e-16 *** -kmercov 3.785e+01 1.782e-02 2124.62 <2e-16 *** -bias 2.161e+00 1.076e-02 200.84 <2e-16 *** -length 4.526e+06 7.034e+03 643.47 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 658.8 on 829 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 4.485e-06 - diff --git a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.log.png deleted file mode 100644 index 3bc4bb8..0000000 Binary files a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.png b/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.png deleted file mode 100644 index f5d63ee..0000000 Binary files a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/progress.txt deleted file mode 100644 index 801c6d9..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 359773210.597075 -round 1 trimming to 16 trying 4peak model... converged. score: 359756661.193556 -round 2 trimming to 21 trying 4peak model... converged. score: 360936725.389763 -round 3 trimming to 26 trying 4peak model... converged. score: 386566334.44475 -done diff --git a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/summary.txt deleted file mode 100644 index aa7005f..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR351256_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04552% 1.05781% -Genome Haploid Length 4,618,530 bp 4,627,234 bp -Genome Repeat Length 114,095 bp 114,310 bp -Genome Unique Length 4,504,435 bp 4,512,924 bp -Model Fit 97.096% 97.3708% -Read Error Rate 0.198405% 0.198405% diff --git a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist b/analysis/ecoli_mix/SRR941832_ERR687900_21.hist deleted file mode 100644 index 169f4b1..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist +++ /dev/null @@ -1,1198 +0,0 @@ -1 10224458 -2 231350 -3 39882 -4 16174 -5 8473 -6 4838 -7 3175 -8 2272 -9 2072 -10 1824 -11 1847 -12 2489 -13 3226 -14 4432 -15 5522 -16 7512 -17 10219 -18 13251 -19 17452 -20 21803 -21 27238 -22 35035 -23 44037 -24 54884 -25 65941 -26 78788 -27 93499 -28 109842 -29 125577 -30 142543 -31 159738 -32 176257 -33 190650 -34 202730 -35 212896 -36 217947 -37 219798 -38 218119 -39 215143 -40 206755 -41 195953 -42 182789 -43 168739 -44 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4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.772e-02 3.150e-03 5.625 2.63e-08 *** -r 3.106e-02 9.020e-05 344.375 < 2e-16 *** -kmercov 3.827e+01 1.769e-02 2164.138 < 2e-16 *** -bias 9.267e-01 7.263e-03 127.599 < 2e-16 *** -length 4.720e+06 9.733e+03 484.993 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 1227 on 747 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.061e-06 - diff --git a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.log.png deleted file mode 100644 index 7dfdc58..0000000 Binary files a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.png b/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.png deleted file mode 100644 index 72bbf5f..0000000 Binary files a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/progress.txt deleted file mode 100644 index f392319..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 1141067189.27313 -round 1 trimming to 15 trying 4peak model... converged. score: 1140414862.74338 -round 2 trimming to 20 trying 4peak model... converged. score: 1131579559.43164 -round 3 trimming to 25 trying 4peak model... converged. score: 1124702919.62465 -done diff --git a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/summary.txt deleted file mode 100644 index fd4ace5..0000000 --- a/analysis/ecoli_mix/SRR941832_ERR687900_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.08815% 3.12423% -Genome Haploid Length 4,844,913 bp 4,853,876 bp -Genome Repeat Length 192,917 bp 193,274 bp -Genome Unique Length 4,651,996 bp 4,660,602 bp -Model Fit 95.8036% 95.9431% -Read Error Rate 0.151645% 0.151645% diff --git a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist b/analysis/ecoli_mix/SRR941832_SRR530851_21.hist deleted file mode 100644 index 3050cdd..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist +++ /dev/null @@ -1,1383 +0,0 @@ -1 13427649 -2 364005 -3 67782 -4 27205 -5 14355 -6 8665 -7 5874 -8 4492 -9 3941 -10 3727 -11 3910 -12 4694 -13 5747 -14 7476 -15 9834 -16 12664 -17 16135 -18 20018 -19 24253 -20 29825 -21 35729 -22 43502 -23 51442 -24 60684 -25 69978 -26 78816 -27 89358 -28 99488 -29 108832 -30 116260 -31 124604 -32 134619 -33 139974 -34 145640 -35 148751 -36 151335 -37 151383 -38 149486 -39 147322 -40 143653 -41 138331 -42 131762 -43 125258 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index 70ba642..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.331e-02 1.285e-03 18.14 <2e-16 *** -r 2.405e-02 3.449e-05 697.37 <2e-16 *** -kmercov 3.861e+01 1.257e-02 3073.06 <2e-16 *** -bias 1.829e+00 5.862e-03 312.07 <2e-16 *** -length 4.758e+06 4.409e+03 1078.96 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 491.9 on 926 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 5.015e-07 - diff --git a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.log.png deleted file mode 100644 index 5c74376..0000000 Binary files a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.png b/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.png deleted file mode 100644 index fe5b05b..0000000 Binary files a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/progress.txt deleted file mode 100644 index e41642a..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 237270584.49706 -round 1 trimming to 15 trying 4peak model... converged. score: 234444907.569743 -round 2 trimming to 20 trying 4peak model... converged. score: 225452728.071815 -round 3 trimming to 25 trying 4peak model... converged. score: 224097206.735722 -done diff --git a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/summary.txt deleted file mode 100644 index 52c0272..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR530851_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.39834% 2.41214% -Genome Haploid Length 4,981,954 bp 4,988,442 bp -Genome Repeat Length 320,436 bp 320,853 bp -Genome Unique Length 4,661,517 bp 4,667,589 bp -Model Fit 97.5663% 97.9677% -Read Error Rate 0.188027% 0.188027% diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist deleted file mode 100644 index ad14a38..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist +++ /dev/null @@ -1,1573 +0,0 @@ -1 19600996 -2 737087 -3 114443 -4 40184 -5 18606 -6 9906 -7 6022 -8 3919 -9 2509 -10 1957 -11 1429 -12 1074 -13 1042 -14 877 -15 797 -16 779 -17 831 -18 980 -19 1256 -20 1722 -21 2097 -22 2586 -23 3175 -24 3936 -25 4634 -26 5274 -27 6461 -28 7109 -29 8113 -30 8964 -31 9554 -32 10229 -33 10590 -34 11016 -35 11497 -36 11690 -37 12025 -38 12391 -39 12526 -40 13203 -41 13719 -42 13906 -43 14673 -44 15752 -45 17643 -46 19561 -47 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1 -3847 1 -3852 1 -3856 1 -3867 1 -3871 1 -3872 1 -3873 1 -3874 1 -3877 1 -3878 1 -3896 1 -3899 1 -3909 1 -3932 1 -3935 1 -3936 1 -3962 1 -3990 1 -4012 1 -4029 1 -4049 1 -4063 1 -4071 1 -4091 1 -4093 1 -4119 1 -4182 1 -4191 1 -4213 1 -4241 1 -4732 1 -4828 1 -5044 1 -5089 1 -5446 1 -5609 1 -5801 1 -5828 1 -5888 1 -6815 1 -10817 1 diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/model.txt b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/model.txt deleted file mode 100644 index 3ac29ee..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.093e-03 3.669e-04 19.33 <2e-16 *** -r 1.352e-03 6.383e-06 211.89 <2e-16 *** -kmercov 3.699e+01 3.194e-03 11580.59 <2e-16 *** -bias 1.618e+00 2.355e-03 687.00 <2e-16 *** -length 4.436e+06 2.206e+03 2010.68 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 189.2 on 978 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.339e-06 - diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.log.png b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.log.png deleted file mode 100644 index 1e7e7ab..0000000 Binary files a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.png b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.png deleted file mode 100644 index 2c0acc6..0000000 Binary files a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/progress.txt b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/progress.txt deleted file mode 100644 index 7dcc22b..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 34882032.0114038 -round 1 trimming to 20 trying 4peak model... converged. score: 34882673.1851225 -round 2 trimming to 25 trying 4peak model... converged. score: 34995623.6821361 -round 3 trimming to 30 trying 4peak model... converged. score: 36075239.6628756 -done diff --git a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/summary.txt b/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/summary.txt deleted file mode 100644 index 525f5ee..0000000 --- a/analysis/ecoli_mix/SRR941832_SRR733088_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.133973% 0.136526% -Genome Haploid Length 4,629,781 bp 4,631,380 bp -Genome Repeat Length 226,265 bp 226,343 bp -Genome Unique Length 4,403,516 bp 4,405,037 bp -Model Fit 98.2513% 98.7377% -Read Error Rate 0.29447% 0.29447% diff --git a/analysis/eval_datasets.sh b/analysis/eval_datasets.sh deleted file mode 100755 index 3bc742c..0000000 --- a/analysis/eval_datasets.sh +++ /dev/null @@ -1,35 +0,0 @@ -#!/bin/sh - -K=21 -READLEN=100 -MODELBIN=../genomescope.R - - -#for INDIR in simulation_results -#for INDIR in real_data -for INDIR in simulation_results_100x simulation_results_50x simulation_results_25x simulation_results_15x simulation_results_10x real_data ecoli_mix -do - echo "Processing $INDIR" - - if [ $(which parallel) ] - then - echo "Running results in parallel" - #/bin/ls $INDIR/seabass*.hist | parallel -t Rscript $MODELBIN {} $K $READLEN {} - #/bin/ls $INDIR/D*.hist | parallel -t Rscript $MODELBIN {} $K $READLEN {} - /bin/ls $INDIR/*.hist | parallel -t Rscript $MODELBIN {} $K $READLEN {}_results 1000 - - else - for hist in `/bin/ls $INDIR/*21.hist` - do - echo "Processing $hist" - Rscript $MODELBIN $hist $K $READLEN ${hist}_results - done - fi -done - - - - - - - diff --git a/analysis/genome_sizes.txt b/analysis/genome_sizes.txt deleted file mode 100644 index 42e507f..0000000 --- a/analysis/genome_sizes.txt +++ /dev/null @@ -1,4 +0,0 @@ -genome GenomeHaploidLen GenomeUniqueLen GenomeRepeatLen -Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa 119481543 107213570 12267973 -Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa 142573017 116913468 25659549 -Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa 4646332 4525311 121021 diff --git a/analysis/genomesim/eval_err.pl b/analysis/genomesim/eval_err.pl deleted file mode 100755 index e5e5126..0000000 --- a/analysis/genomesim/eval_err.pl +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/perl -w -use strict; - -my $filename = shift @ARGV or die "eval_err.pl simhisto.out\n"; - -open FILE, $filename or die "Cant open $filename ($!)\n"; - -my @model = (0,0,0,0); -my @obs = (0,0,0,0); - -my $inobs = 0; - -while() -{ - chomp; - - if (/^Model:/) - { - # The next 4 lines are the model output - my $aline = ; chomp $aline; $model[0] = (split/ /, $aline)[1]; - my $bline = ; chomp $bline; $model[1] = (split/ /, $bline)[1]; - my $cline = ; chomp $cline; $model[2] = (split/ /, $cline)[1]; - my $dline = ; chomp $dline; $model[3] = (split/ /, $dline)[1]; - } - elsif (/^Observed Counts:/) - { - # The next few lines are the jellyfish output - $inobs = 1; - } - elsif ($inobs) - { - my ($f, $c) = split / /, $_; - $obs[$f-1] = $c; - } -} - -print "model:\t$model[0]\t$model[1]\t$model[2]\t$model[3]\n"; -print "obs:\t$obs[0]\t$obs[1]\t$obs[2]\t$obs[3]\n"; - -my @diff = (0,0,0,0); # count of differences -my @diffp = (0,0,0,0); # percent of differences - -my $sumkmer = 0; -my $sumdiff = 0; - -for (my $i = 0; $i < 4; $i++) -{ - $diff[$i] = $model[$i] - $obs[$i]; - $diffp[$i] = sprintf("%0.02f", ($obs[$i]) ? (100*$diff[$i] / $obs[$i]) : 0); - $sumdiff += $diff[$i]; - $sumkmer += $obs[$i]; -} - -my $score = sprintf("%.03f", 100.0*(1-($sumdiff / $sumkmer))); - -print "diff:\t$diff[0]\t$diff[1]\t$diff[2]\t$diff[3]\n"; -print "diffp:\t$diffp[0]\t$diffp[1]\t$diffp[2]\t$diffp[3]\n"; -print "#$filename\tsumkmer\t$sumkmer\tsumdiff:\t$sumdiff\tscore:\t$score\n"; diff --git a/analysis/genomesim/polyploid/simhisto.sh b/analysis/genomesim/polyploid/simhisto.sh deleted file mode 100755 index 3f2f032..0000000 --- a/analysis/genomesim/polyploid/simhisto.sh +++ /dev/null @@ -1,32 +0,0 @@ -#!/bin/sh - -if [[ $# != 6 ]] -then - echo "simhist.sh LEN DUP HET1 HET2 HETZ KMER\n"; - exit -fi - -LEN=$1 -DUP=$2 -HET1=$3 -HET2=$4 -HETZ=$5 -KMER=$6 - -dir=pp-$LEN-$DUP-$HET1-$HET2-$HETZ-$KMER -mkdir -p $dir -cd $dir - -../simpolyploid.pl $LEN $DUP $HET1 $HET2 $HETZ $KMER > genome.fa - -echo "\n" -echo "Observed Counts:" - -jellyfish count -t 2 -m $KMER -s 100000000 -C genome.fa -jellyfish histo mer_counts.jf - - -dwgsim -r 0 -F 0 -y 0 -C 10 -e 0 -E 0 genome.fa reads -jellyfish count -m 21 -s 1000000 -t 4 -C -o reads.jf reads.bwa.read* -jellyfish histo reads.jf > reads.histo -~/build/genomescope/genomescope.R reads.histo 21 100 reads.gs diff --git a/analysis/genomesim/polyploid/simpolyploid.pl b/analysis/genomesim/polyploid/simpolyploid.pl deleted file mode 100755 index c26e91d..0000000 --- a/analysis/genomesim/polyploid/simpolyploid.pl +++ /dev/null @@ -1,135 +0,0 @@ -#!/usr/bin/perl -w -use strict; - -my $USAGE = "simgenome.pl GENOME_LEN DUP_RATE HET_RATE1 HET_RATE2 HET_RATE_ACROSS KMER_LEN > genome.fa\n"; - -die $USAGE if (scalar @ARGV != 6); - -my $GENOME_LEN = shift @ARGV or die $USAGE; -my $DUP_RATE = shift @ARGV; -my $HET_RATE1 = shift @ARGV; -my $HET_RATE2 = shift @ARGV; -my $HET_RATE_ACROSS = shift @ARGV; -my $KMER_LEN = shift @ARGV; - -die "Dup rate cant be > 1\n" if ($DUP_RATE > 1.0); -die "Hetrate1 cant be > 1\n" if ($HET_RATE1 > 1.0); -die "Hetrate2 cant be > 1\n" if ($HET_RATE2 > 1.0); -die "HetrateZ cant be > 1\n" if ($HET_RATE_ACROSS > 1.0); - -print STDERR "Simulating G=$GENOME_LEN, d=$DUP_RATE, r1=$HET_RATE1, r2=$HET_RATE2, rZ=$HET_RATE_ACROSS k=$KMER_LEN\n"; - - - -## Initialize DNA coding table: 0<->A, 1<->C, 2<->G, 3<->T -############################################################################### -my @DNA = ("A", "C", "G", "T"); -my %DNAIDX; -for (my $i = 0; $i < scalar @DNA; $i++) { $DNAIDX{$DNA[$i]} = $i; } - - -## Function for mutating a genome string -############################################################################### -sub mutate -{ - my $orig = shift; - my $hetrate = shift; - - my $new = $orig; - my $l = length($new); - - for (my $i = 0; $i < $l; $i++) - { - my $r = rand(); - if ($r <= $hetrate) - { - my $b = substr($new, $i, 1); - my $n = $DNA[($DNAIDX{$b}+1)%4]; - substr($new, $i, 1) = $n; - } - } - - return $new; -} - - -## Simutate a random genome of length GENOME_LEN -############################################################################### - -print STDERR " ... simulating progenitor\n"; - -my $matgenome1 = ""; - -for (my $i = 0; $i < $GENOME_LEN; $i++) -{ - my $z = int(rand(4)); - my $b = $DNA[$z]; - $matgenome1 .= $b; -} - - -## Now duplicate the first $DUP_RATE percent of the genome -############################################################################### - -my $dup = substr($matgenome1, 0, $DUP_RATE * $GENOME_LEN); -$matgenome1 .= $dup; -my $newlen = length($matgenome1); - -print STDERR " ... duplicated $DUP_RATE, newlen=$newlen\n"; - - - -## Now create the heterozygous alleles -############################################################################### - -print STDERR "generating paternal genome1 (r1=$HET_RATE1)\n"; -my $patgenome1 = mutate($matgenome1, $HET_RATE1); - -print STDERR "generating maternal genome2 (rZ=$HET_RATE_ACROSS)\n"; -my $matgenome2 = mutate($matgenome1, $HET_RATE_ACROSS); - -print STDERR "generating paternal genome2 (r2=$HET_RATE2)\n"; -my $patgenome2 = mutate($matgenome2, $HET_RATE2); - - - - -## Print the genome sequences -############################################################################### - -print ">mat1\n"; -print $matgenome1; -print "\n"; - -print ">pat1\n"; -print $patgenome1; -print "\n"; - -print ">mat2\n"; -print $matgenome2; -print "\n"; - -print ">pat2\n"; -print $patgenome2; -print "\n"; - - - - - - -# ## Print expected # kmers in each peak -# ############################################################################### -# -# print STDERR "\n"; -# print STDERR "Model:\n"; -# -# my $delta = int($GENOME_LEN * $DUP_RATE * (1.0-$HET_RATE)**(2*$KMER_LEN)); -# my $gamma = int($GENOME_LEN * 2 * $DUP_RATE * (1.0-$HET_RATE)**($KMER_LEN) * (1-(1-$HET_RATE)**($KMER_LEN))); -# my $alpha = int($GENOME_LEN * (2 * (1-$DUP_RATE)*(1.0-(1.0-$HET_RATE)**($KMER_LEN)) + 2*$DUP_RATE*(1-(1-$HET_RATE)**($KMER_LEN))**(2)) + $gamma); -# my $beta = int($GENOME_LEN * ((1-$DUP_RATE)*((1.0-$HET_RATE)**($KMER_LEN)) + $DUP_RATE * (1-(1-$HET_RATE)**($KMER_LEN))**(2))); -# -# print STDERR "1 $alpha\n"; -# print STDERR "2 $beta\n"; -# print STDERR "3 $gamma\n"; -# print STDERR "4 $delta\n"; diff --git a/analysis/genomesim/run_eval.sh b/analysis/genomesim/run_eval.sh deleted file mode 100755 index 4df2d0c..0000000 --- a/analysis/genomesim/run_eval.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/sh - -if [[ $# != 1 ]] -then - echo run_eval.sh dir - exit -fi - -DIR=$1 - -for i in `/bin/ls $DIR/*-out`; -do - ./eval_err.pl $i > $i.eval -done - -grep "#" $DIR/*.eval | sort -nk7 diff --git a/analysis/genomesim/run_sweep.sh b/analysis/genomesim/run_sweep.sh deleted file mode 100755 index c9b22ba..0000000 --- a/analysis/genomesim/run_sweep.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/sh - -if [[ $# != 1 ]] -then - echo "run_sweep.sh KMER_LEN" - exit -fi - -k=$1 -g=1000000 - -outdir="sweep.k$k" - -mkdir -p $outdir - -for d in 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 -do - for r in 0.00 .001 .010 .050 .100 .200 .300 - do - echo "eval d=$d r=$r k=$k g=$g" - ./simhisto.sh $g $d $r $k >& $outdir/sim-d${d}-r${r}-k${k}-g${g}-out - done -done - diff --git a/analysis/genomesim/simgenome.pl b/analysis/genomesim/simgenome.pl deleted file mode 100755 index a57e35c..0000000 --- a/analysis/genomesim/simgenome.pl +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/perl -w -use strict; - -my $USAGE = "simgenome.pl GENOME_LEN DUP_RATE HET_RATE KMER_LEN > genome.fa\n"; - -die $USAGE if (scalar @ARGV != 4); - -my $GENOME_LEN = shift @ARGV or die $USAGE; -my $DUP_RATE = shift @ARGV; -my $HET_RATE = shift @ARGV; -my $KMER_LEN = shift @ARGV; - -die "Dup rate cant be > 1\n" if ($DUP_RATE > 1.0); -die "Het rate cant be > 1\n" if ($HET_RATE > 1.0); - -print STDERR "Simulating G=$GENOME_LEN, d=$DUP_RATE, r=$HET_RATE, k=$KMER_LEN\n"; - - - -## Initialize DNA coding table: 0<->A, 1<->C, 2<->G, 3<->T -############################################################################### -my @DNA = ("A", "C", "G", "T"); -my %DNAIDX; -for (my $i = 0; $i < scalar @DNA; $i++) { $DNAIDX{$DNA[$i]} = $i; } - - -## Simutate a random genome of length GENOME_LEN -############################################################################### - -print STDERR " ... simulating progenitor\n"; - -my $matgenome = ""; - -for (my $i = 0; $i < $GENOME_LEN; $i++) -{ - my $z = int(rand(4)); - my $b = $DNA[$z]; - $matgenome .= $b; -} - - -## Now duplicate the first $DUP_RATE percent of the genome -############################################################################### - -my $dup = substr($matgenome, 0, $DUP_RATE * $GENOME_LEN); -$matgenome .= $dup; -my $newlen = length($matgenome); - -print STDERR " ... duplicated $DUP_RATE, newlen=$newlen\n"; - -## Print the maternal haplotype -############################################################################### - -print ">mat\n"; -print $matgenome; -print "\n"; - - -## Add random heterozygosity to the paternal haplotype -############################################################################### - -print STDERR " ... add heterozygosity r=$HET_RATE\n"; - -my $nummut = 0; -my $patgenome = $matgenome; - -for (my $i = 0; $i < $newlen; $i++) -{ - my $r = rand(); - if ($r <= $HET_RATE) - { - $nummut++; - my $b = substr($patgenome, $i, 1); - my $n = $DNA[($DNAIDX{$b}+1)%4]; - substr($patgenome, $i, 1) = $n; - } -} - - -## Print the paternal haplotype -############################################################################### - -print ">pat\n"; -print $patgenome; -print "\n"; - -my $mutrate = sprintf("%0.02f", 100*($nummut / $newlen)); -print STDERR "Simulated $newlen total bases, $nummut mutations ($mutrate%), G=$GENOME_LEN, d=$DUP_RATE, r=$HET_RATE\n"; - - - -## Print expected # kmers in each peak -############################################################################### - -print STDERR "\n"; -print STDERR "Model:\n"; - -my $delta = int($GENOME_LEN * $DUP_RATE * (1.0-$HET_RATE)**(2*$KMER_LEN)); -my $gamma = int($GENOME_LEN * 2 * $DUP_RATE * (1.0-$HET_RATE)**($KMER_LEN) * (1-(1-$HET_RATE)**($KMER_LEN))); -my $alpha = int($GENOME_LEN * (2 * (1-$DUP_RATE)*(1.0-(1.0-$HET_RATE)**($KMER_LEN)) + 2*$DUP_RATE*(1-(1-$HET_RATE)**($KMER_LEN))**(2)) + $gamma); -my $beta = int($GENOME_LEN * ((1-$DUP_RATE)*((1.0-$HET_RATE)**($KMER_LEN)) + $DUP_RATE * (1-(1-$HET_RATE)**($KMER_LEN))**(2))); - -print STDERR "1 $alpha\n"; -print STDERR "2 $beta\n"; -print STDERR "3 $gamma\n"; -print STDERR "4 $delta\n"; diff --git a/analysis/genomesim/simhisto.sh b/analysis/genomesim/simhisto.sh deleted file mode 100755 index 97d0783..0000000 --- a/analysis/genomesim/simhisto.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/sh - -if [[ $# != 4 ]] -then - echo "simhist.sh LEN DUP HET KMER\n"; - exit -fi - -LEN=$1 -DUP=$2 -HET=$3 -KMER=$4 - -./simgenome.pl $LEN $DUP $HET $KMER > genome.fa - - -echo "\n" -echo "Observed Counts:" - -jellyfish count -t 2 -m $KMER -s 100000000 -C genome.fa -jellyfish histo mer_counts.jf diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out deleted file mode 100644 index 29c7340..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.001 -Simulated 1000000 total bases, 1072 mutations (0.11%), G=1000000, d=0.00, r=.001 - -Model: -1 192225 -2 903887 -3 0 -4 0 - - -Observed Counts: -1 205868 -2 896966 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out.eval deleted file mode 100644 index a3cfe8b..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 903887 0 0 -obs: 205868 896966 0 0 -diff: -13643 6921 0 0 -diffp: -6.63 0.77 0.00 0.00 -#sweep.k101//sim-d0.00-r.001-k101-g1000000-out sumkmer 1102834 sumdiff: -6722 score: 100.610 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out deleted file mode 100644 index c6f4ded..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.010 -Simulated 1000000 total bases, 9983 mutations (1.00%), G=1000000, d=0.00, r=.010 - -Model: -1 1275255 -2 362372 -3 0 -4 0 - - -Observed Counts: -1 1277738 -2 361031 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out.eval deleted file mode 100644 index b0f03ec..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 362372 0 0 -obs: 1277738 361031 0 0 -diff: -2483 1341 0 0 -diffp: -0.19 0.37 0.00 0.00 -#sweep.k101//sim-d0.00-r.010-k101-g1000000-out sumkmer 1638769 sumdiff: -1142 score: 100.070 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out deleted file mode 100644 index b33f2d8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.050 -Simulated 1000000 total bases, 50242 mutations (5.02%), G=1000000, d=0.00, r=.050 - -Model: -1 1988750 -2 5624 -3 0 -4 0 - - -Observed Counts: -1 1988278 -2 5761 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out.eval deleted file mode 100644 index cac36e8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 5624 0 0 -obs: 1988278 5761 0 0 -diff: 472 -137 0 0 -diffp: 0.02 -2.38 0.00 0.00 -#sweep.k101//sim-d0.00-r.050-k101-g1000000-out sumkmer 1994039 sumdiff: 335 score: 99.983 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out deleted file mode 100644 index 4e5ac40..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.100 -Simulated 1000000 total bases, 99619 mutations (9.96%), G=1000000, d=0.00, r=.100 - -Model: -1 1999952 -2 23 -3 0 -4 0 - - -Observed Counts: -1 1999792 -2 4 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out.eval deleted file mode 100644 index 6832565..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999952 23 0 0 -obs: 1999792 4 0 0 -diff: 160 19 0 0 -diffp: 0.01 475.00 0.00 0.00 -#sweep.k101//sim-d0.00-r.100-k101-g1000000-out sumkmer 1999796 sumdiff: 179 score: 99.991 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out deleted file mode 100644 index 7ac4648..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.200 -Simulated 1000000 total bases, 200488 mutations (20.05%), G=1000000, d=0.00, r=.200 - -Model: -1 1999999 -2 0 -3 0 -4 0 - - -Observed Counts: -1 1999800 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out.eval deleted file mode 100644 index 992e972..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 0 0 0 -obs: 1999800 0 0 0 -diff: 199 0 0 0 -diffp: 0.01 0.00 0.00 0.00 -#sweep.k101//sim-d0.00-r.200-k101-g1000000-out sumkmer 1999800 sumdiff: 199 score: 99.990 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out deleted file mode 100644 index 056ce03..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.300 -Simulated 1000000 total bases, 299240 mutations (29.92%), G=1000000, d=0.00, r=.300 - -Model: -1 1999999 -2 0 -3 0 -4 0 - - -Observed Counts: -1 1999800 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out.eval deleted file mode 100644 index 91389ac..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 0 0 0 -obs: 1999800 0 0 0 -diff: 199 0 0 0 -diffp: 0.01 0.00 0.00 0.00 -#sweep.k101//sim-d0.00-r.300-k101-g1000000-out sumkmer 1999800 sumdiff: 199 score: 99.990 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out deleted file mode 100644 index 622efc2..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=0.00 -Simulated 1000000 total bases, 0 mutations (0.00%), G=1000000, d=0.00, r=0.00 - -Model: -1 0 -2 1000000 -3 0 -4 0 - - -Observed Counts: -2 999900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 9b8ac06..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.00-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 1000000 0 0 -obs: 0 999900 0 0 -diff: 0 100 0 0 -diffp: 0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.00-r0.00-k101-g1000000-out sumkmer 999900 sumdiff: 100 score: 99.990 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out deleted file mode 100644 index fc40c4a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.001 -Simulated 1100000 total bases, 1141 mutations (0.10%), G=1000000, d=0.10, r=.001 - -Model: -1 192225 -2 814422 -3 17375 -4 81701 - - -Observed Counts: -1 198895 -2 811416 -3 17035 -4 81742 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out.eval deleted file mode 100644 index 8786cce..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 814422 17375 81701 -obs: 198895 811416 17035 81742 -diff: -6670 3006 340 -41 -diffp: -3.35 0.37 2.00 -0.05 -#sweep.k101//sim-d0.10-r.001-k101-g1000000-out sumkmer 1109088 sumdiff: -3365 score: 100.303 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out deleted file mode 100644 index 3630c4d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.010 -Simulated 1100000 total bases, 11045 mutations (1.00%), G=1000000, d=0.10, r=.010 - -Model: -1 1275255 -2 366791 -3 46211 -4 13131 - - -Observed Counts: -1 1271553 -2 364767 -3 46979 -4 14444 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out.eval deleted file mode 100644 index 883b754..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 366791 46211 13131 -obs: 1271553 364767 46979 14444 -diff: 3702 2024 -768 -1313 -diffp: 0.29 0.55 -1.63 -9.09 -#sweep.k101//sim-d0.10-r.010-k101-g1000000-out sumkmer 1697743 sumdiff: 3645 score: 99.785 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out deleted file mode 100644 index ed318ff..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.10, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.050 -Simulated 1100000 total bases, 55033 mutations (5.00%), G=1000000, d=0.10, r=.050 - -Model: -1 1988750 -2 103940 -3 1118 -4 3 - - -Observed Counts: -1 1987674 -2 104221 -3 1228 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out.eval deleted file mode 100644 index a907976..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 103940 1118 3 -obs: 1987674 104221 1228 0 -diff: 1076 -281 -110 3 -diffp: 0.05 -0.27 -8.96 0.00 -#sweep.k101//sim-d0.10-r.050-k101-g1000000-out sumkmer 2093123 sumdiff: 688 score: 99.967 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out deleted file mode 100644 index f28b10c..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.100 -Simulated 1100000 total bases, 109872 mutations (9.99%), G=1000000, d=0.10, r=.100 - -Model: -1 1999951 -2 100016 -3 4 -4 0 - - -Observed Counts: -1 1999958 -2 99921 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out.eval deleted file mode 100644 index e06b3df..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 100016 4 0 -obs: 1999958 99921 0 0 -diff: -7 95 4 0 -diffp: -0.00 0.10 0.00 0.00 -#sweep.k101//sim-d0.10-r.100-k101-g1000000-out sumkmer 2099879 sumdiff: 92 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out deleted file mode 100644 index 6e8fcc8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.200 -Simulated 1100000 total bases, 220447 mutations (20.04%), G=1000000, d=0.10, r=.200 - -Model: -1 1999999 -2 100000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 99900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out.eval deleted file mode 100644 index 95477a6..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 100000 0 0 -obs: 2000000 99900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.10 0.00 0.00 -#sweep.k101//sim-d0.10-r.200-k101-g1000000-out sumkmer 2099900 sumdiff: 99 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out deleted file mode 100644 index 2d0c92c..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.300 -Simulated 1100000 total bases, 329774 mutations (29.98%), G=1000000, d=0.10, r=.300 - -Model: -1 1999999 -2 100000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 99900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out.eval deleted file mode 100644 index cee651f..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 100000 0 0 -obs: 2000000 99900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.10 0.00 0.00 -#sweep.k101//sim-d0.10-r.300-k101-g1000000-out sumkmer 2099900 sumdiff: 99 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out deleted file mode 100644 index 8ed282a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=0.00 -Simulated 1100000 total bases, 0 mutations (0.00%), G=1000000, d=0.10, r=0.00 - -Model: -1 0 -2 900000 -3 0 -4 100000 - - -Observed Counts: -2 900100 -4 99900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 8ede44a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.10-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 900000 0 100000 -obs: 0 900100 0 99900 -diff: 0 -100 0 100 -diffp: 0.00 -0.01 0.00 0.10 -#sweep.k101//sim-d0.10-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out deleted file mode 100644 index 9fce14b..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.001 -Simulated 1200000 total bases, 1220 mutations (0.10%), G=1000000, d=0.20, r=.001 - -Model: -1 192225 -2 724957 -3 34750 -4 163402 - - -Observed Counts: -1 198052 -2 720652 -3 31260 -4 166666 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out.eval deleted file mode 100644 index 0a07b76..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 724957 34750 163402 -obs: 198052 720652 31260 166666 -diff: -5827 4305 3490 -3264 -diffp: -2.94 0.60 11.16 -1.96 -#sweep.k101//sim-d0.20-r.001-k101-g1000000-out sumkmer 1116630 sumdiff: -1296 score: 100.116 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out deleted file mode 100644 index e38b5ec..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.010 -Simulated 1200000 total bases, 12014 mutations (1.00%), G=1000000, d=0.20, r=.010 - -Model: -1 1275255 -2 371211 -3 92423 -4 26262 - - -Observed Counts: -1 1271254 -2 374470 -3 91558 -4 26233 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out.eval deleted file mode 100644 index 0168ebc..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 371211 92423 26262 -obs: 1271254 374470 91558 26233 -diff: 4001 -3259 865 29 -diffp: 0.31 -0.87 0.94 0.11 -#sweep.k101//sim-d0.20-r.010-k101-g1000000-out sumkmer 1763515 sumdiff: 1636 score: 99.907 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out deleted file mode 100644 index 4e13a19..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.050 -Simulated 1200000 total bases, 59884 mutations (4.99%), G=1000000, d=0.20, r=.050 - -Model: -1 1988750 -2 202256 -3 2237 -4 6 - - -Observed Counts: -1 1988986 -2 202092 -3 2182 -4 21 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out.eval deleted file mode 100644 index 8632be3..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 202256 2237 6 -obs: 1988986 202092 2182 21 -diff: -236 164 55 -15 -diffp: -0.01 0.08 2.52 -71.43 -#sweep.k101//sim-d0.20-r.050-k101-g1000000-out sumkmer 2193281 sumdiff: -32 score: 100.001 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out deleted file mode 100644 index dfc3090..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.100 -Simulated 1200000 total bases, 120126 mutations (10.01%), G=1000000, d=0.20, r=.100 - -Model: -1 1999951 -2 200009 -3 9 -4 0 - - -Observed Counts: -1 1999980 -2 199910 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out.eval deleted file mode 100644 index 6dc2fb8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 200009 9 0 -obs: 1999980 199910 0 0 -diff: -29 99 9 0 -diffp: -0.00 0.05 0.00 0.00 -#sweep.k101//sim-d0.20-r.100-k101-g1000000-out sumkmer 2199890 sumdiff: 79 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out deleted file mode 100644 index 1785683..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.200 -Simulated 1200000 total bases, 239163 mutations (19.93%), G=1000000, d=0.20, r=.200 - -Model: -1 1999999 -2 200000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 199900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out.eval deleted file mode 100644 index 43847a7..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 200000 0 0 -obs: 2000000 199900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.05 0.00 0.00 -#sweep.k101//sim-d0.20-r.200-k101-g1000000-out sumkmer 2199900 sumdiff: 99 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out deleted file mode 100644 index 1cff889..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.300 -Simulated 1200000 total bases, 360241 mutations (30.02%), G=1000000, d=0.20, r=.300 - -Model: -1 1999999 -2 200000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 199900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out.eval deleted file mode 100644 index 17e3f58..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 200000 0 0 -obs: 2000000 199900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.05 0.00 0.00 -#sweep.k101//sim-d0.20-r.300-k101-g1000000-out sumkmer 2199900 sumdiff: 99 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out deleted file mode 100644 index d4480aa..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=0.00 -Simulated 1200000 total bases, 0 mutations (0.00%), G=1000000, d=0.20, r=0.00 - -Model: -1 0 -2 800000 -3 0 -4 200000 - - -Observed Counts: -2 800100 -4 199900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 020842d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.20-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 800000 0 200000 -obs: 0 800100 0 199900 -diff: 0 -100 0 100 -diffp: 0.00 -0.01 0.00 0.05 -#sweep.k101//sim-d0.20-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out deleted file mode 100644 index b067c91..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.001 -Simulated 1300000 total bases, 1288 mutations (0.10%), G=1000000, d=0.30, r=.001 - -Model: -1 192225 -2 635492 -3 52125 -4 245103 - - -Observed Counts: -1 191595 -2 634774 -3 50927 -4 246469 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out.eval deleted file mode 100644 index b653e58..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 635492 52125 245103 -obs: 191595 634774 50927 246469 -diff: 630 718 1198 -1366 -diffp: 0.33 0.11 2.35 -0.55 -#sweep.k101//sim-d0.30-r.001-k101-g1000000-out sumkmer 1123765 sumdiff: 1180 score: 99.895 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out deleted file mode 100644 index d5ef26b..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.010 -Simulated 1300000 total bases, 13136 mutations (1.01%), G=1000000, d=0.30, r=.010 - -Model: -1 1275255 -2 375631 -3 138635 -4 39394 - - -Observed Counts: -1 1271762 -2 385059 -3 137324 -4 36487 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out.eval deleted file mode 100644 index 21ffa3f..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 375631 138635 39394 -obs: 1271762 385059 137324 36487 -diff: 3493 -9428 1311 2907 -diffp: 0.27 -2.45 0.95 7.97 -#sweep.k101//sim-d0.30-r.010-k101-g1000000-out sumkmer 1830632 sumdiff: -1717 score: 100.094 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out deleted file mode 100644 index fc235e4..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.30, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.050 -Simulated 1300000 total bases, 65194 mutations (5.01%), G=1000000, d=0.30, r=.050 - -Model: -1 1988750 -2 300571 -3 3355 -4 9 - - -Observed Counts: -1 1988916 -2 300324 -3 3412 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out.eval deleted file mode 100644 index e9dce89..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 300571 3355 9 -obs: 1988916 300324 3412 0 -diff: -166 247 -57 9 -diffp: -0.01 0.08 -1.67 0.00 -#sweep.k101//sim-d0.30-r.050-k101-g1000000-out sumkmer 2292652 sumdiff: 33 score: 99.999 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out deleted file mode 100644 index 965e777..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.30, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.100 -Simulated 1300000 total bases, 129555 mutations (9.97%), G=1000000, d=0.30, r=.100 - -Model: -1 1999951 -2 300002 -3 14 -4 0 - - -Observed Counts: -1 1999951 -2 299893 -3 21 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out.eval deleted file mode 100644 index 8b3015f..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 300002 14 0 -obs: 1999951 299893 21 0 -diff: 0 109 -7 0 -diffp: 0.00 0.04 -33.33 0.00 -#sweep.k101//sim-d0.30-r.100-k101-g1000000-out sumkmer 2299865 sumdiff: 102 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out deleted file mode 100644 index 624e034..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.200 -Simulated 1300000 total bases, 259990 mutations (20.00%), G=1000000, d=0.30, r=.200 - -Model: -1 1999999 -2 300000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 299900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out.eval deleted file mode 100644 index 3f7b46a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 300000 0 0 -obs: 2000000 299900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.03 0.00 0.00 -#sweep.k101//sim-d0.30-r.200-k101-g1000000-out sumkmer 2299900 sumdiff: 99 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out deleted file mode 100644 index b903d8e..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.300 -Simulated 1300000 total bases, 389729 mutations (29.98%), G=1000000, d=0.30, r=.300 - -Model: -1 1999999 -2 300000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 299900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out.eval deleted file mode 100644 index 177129f..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 300000 0 0 -obs: 2000000 299900 0 0 -diff: -1 100 0 0 -diffp: -0.00 0.03 0.00 0.00 -#sweep.k101//sim-d0.30-r.300-k101-g1000000-out sumkmer 2299900 sumdiff: 99 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out deleted file mode 100644 index 82a9e28..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=0.00 -Simulated 1300000 total bases, 0 mutations (0.00%), G=1000000, d=0.30, r=0.00 - -Model: -1 0 -2 700000 -3 0 -4 300000 - - -Observed Counts: -2 700100 -4 299900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 7b890c1..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.30-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 700000 0 300000 -obs: 0 700100 0 299900 -diff: 0 -100 0 100 -diffp: 0.00 -0.01 0.00 0.03 -#sweep.k101//sim-d0.30-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out deleted file mode 100644 index bc49182..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.001 -Simulated 1400000 total bases, 1353 mutations (0.10%), G=1000000, d=0.40, r=.001 - -Model: -1 192225 -2 546027 -3 69500 -4 326804 - - -Observed Counts: -1 185435 -2 547646 -3 67963 -4 328796 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out.eval deleted file mode 100644 index eaaf236..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 546027 69500 326804 -obs: 185435 547646 67963 328796 -diff: 6790 -1619 1537 -1992 -diffp: 3.66 -0.30 2.26 -0.61 -#sweep.k101//sim-d0.40-r.001-k101-g1000000-out sumkmer 1129840 sumdiff: 4716 score: 99.583 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out deleted file mode 100644 index fd0f5e3..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.010 -Simulated 1400000 total bases, 14024 mutations (1.00%), G=1000000, d=0.40, r=.010 - -Model: -1 1275255 -2 380050 -3 184846 -4 52525 - - -Observed Counts: -1 1272349 -2 372613 -3 185443 -4 56474 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out.eval deleted file mode 100644 index db7b663..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 380050 184846 52525 -obs: 1272349 372613 185443 56474 -diff: 2906 7437 -597 -3949 -diffp: 0.23 2.00 -0.32 -6.99 -#sweep.k101//sim-d0.40-r.010-k101-g1000000-out sumkmer 1886879 sumdiff: 5797 score: 99.693 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out deleted file mode 100644 index a04259a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.40, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.050 -Simulated 1400000 total bases, 70152 mutations (5.01%), G=1000000, d=0.40, r=.050 - -Model: -1 1988750 -2 398887 -3 4474 -4 12 - - -Observed Counts: -1 1988737 -2 398576 -3 4637 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out.eval deleted file mode 100644 index f8d08fe..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 398887 4474 12 -obs: 1988737 398576 4637 0 -diff: 13 311 -163 12 -diffp: 0.00 0.08 -3.52 0.00 -#sweep.k101//sim-d0.40-r.050-k101-g1000000-out sumkmer 2391950 sumdiff: 173 score: 99.993 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out deleted file mode 100644 index e37c9ac..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.100 -Simulated 1400000 total bases, 140432 mutations (10.03%), G=1000000, d=0.40, r=.100 - -Model: -1 1999952 -2 399995 -3 19 -4 0 - - -Observed Counts: -1 1999992 -2 399904 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out.eval deleted file mode 100644 index 459e3a7..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999952 399995 19 0 -obs: 1999992 399904 0 0 -diff: -40 91 19 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.40-r.100-k101-g1000000-out sumkmer 2399896 sumdiff: 70 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out deleted file mode 100644 index ea63aec..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.200 -Simulated 1400000 total bases, 278841 mutations (19.92%), G=1000000, d=0.40, r=.200 - -Model: -1 1999999 -2 399999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 399900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out.eval deleted file mode 100644 index 3d32436..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 399999 0 0 -obs: 2000000 399900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.40-r.200-k101-g1000000-out sumkmer 2399900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out deleted file mode 100644 index ff751dd..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.300 -Simulated 1400000 total bases, 419233 mutations (29.95%), G=1000000, d=0.40, r=.300 - -Model: -1 1999999 -2 399999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 399900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out.eval deleted file mode 100644 index 9a838fe..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 399999 0 0 -obs: 2000000 399900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.40-r.300-k101-g1000000-out sumkmer 2399900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out deleted file mode 100644 index c83e757..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=0.00 -Simulated 1400000 total bases, 0 mutations (0.00%), G=1000000, d=0.40, r=0.00 - -Model: -1 0 -2 600000 -3 0 -4 400000 - - -Observed Counts: -2 600100 -4 399900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 5f919b0..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.40-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 600000 0 400000 -obs: 0 600100 0 399900 -diff: 0 -100 0 100 -diffp: 0.00 -0.02 0.00 0.03 -#sweep.k101//sim-d0.40-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out deleted file mode 100644 index 735926d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.001 -Simulated 1500000 total bases, 1508 mutations (0.10%), G=1000000, d=0.50, r=.001 - -Model: -1 192225 -2 456562 -3 86875 -4 408506 - - -Observed Counts: -1 192946 -2 457083 -3 87164 -4 407799 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out.eval deleted file mode 100644 index e0daa18..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 456562 86875 408506 -obs: 192946 457083 87164 407799 -diff: -721 -521 -289 707 -diffp: -0.37 -0.11 -0.33 0.17 -#sweep.k101//sim-d0.50-r.001-k101-g1000000-out sumkmer 1144992 sumdiff: -824 score: 100.072 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out deleted file mode 100644 index 066749d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.010 -Simulated 1500000 total bases, 15009 mutations (1.00%), G=1000000, d=0.50, r=.010 - -Model: -1 1275255 -2 384470 -3 231058 -4 65656 - - -Observed Counts: -1 1275953 -2 376679 -3 235447 -4 66037 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out.eval deleted file mode 100644 index 1664317..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 384470 231058 65656 -obs: 1275953 376679 235447 66037 -diff: -698 7791 -4389 -381 -diffp: -0.05 2.07 -1.86 -0.58 -#sweep.k101//sim-d0.50-r.010-k101-g1000000-out sumkmer 1954116 sumdiff: 2323 score: 99.881 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out deleted file mode 100644 index 13c3fbb..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.050 -Simulated 1500000 total bases, 74838 mutations (4.99%), G=1000000, d=0.50, r=.050 - -Model: -1 1988750 -2 497203 -3 5592 -4 15 - - -Observed Counts: -1 1989445 -2 497207 -3 5259 -4 41 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out.eval deleted file mode 100644 index 836a541..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 497203 5592 15 -obs: 1989445 497207 5259 41 -diff: -695 -4 333 -26 -diffp: -0.03 -0.00 6.33 -63.41 -#sweep.k101//sim-d0.50-r.050-k101-g1000000-out sumkmer 2491952 sumdiff: -392 score: 100.016 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out deleted file mode 100644 index 3f8b935..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.50, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.100 -Simulated 1500000 total bases, 149414 mutations (9.96%), G=1000000, d=0.50, r=.100 - -Model: -1 1999951 -2 499988 -3 23 -4 0 - - -Observed Counts: -1 1999999 -2 499899 -3 1 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out.eval deleted file mode 100644 index bac1ab9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 499988 23 0 -obs: 1999999 499899 1 0 -diff: -48 89 22 0 -diffp: -0.00 0.02 2200.00 0.00 -#sweep.k101//sim-d0.50-r.100-k101-g1000000-out sumkmer 2499899 sumdiff: 63 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out deleted file mode 100644 index f142fae..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.200 -Simulated 1500000 total bases, 299561 mutations (19.97%), G=1000000, d=0.50, r=.200 - -Model: -1 1999999 -2 499999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 499900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out.eval deleted file mode 100644 index 790d6d9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 499999 0 0 -obs: 2000000 499900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.50-r.200-k101-g1000000-out sumkmer 2499900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out deleted file mode 100644 index 9dd8ca9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.300 -Simulated 1500000 total bases, 450439 mutations (30.03%), G=1000000, d=0.50, r=.300 - -Model: -1 1999999 -2 499999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 499900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out.eval deleted file mode 100644 index b3bf797..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 499999 0 0 -obs: 2000000 499900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.50-r.300-k101-g1000000-out sumkmer 2499900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out deleted file mode 100644 index ce52c2a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=0.00 -Simulated 1500000 total bases, 0 mutations (0.00%), G=1000000, d=0.50, r=0.00 - -Model: -1 0 -2 500000 -3 0 -4 500000 - - -Observed Counts: -2 500100 -4 499900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 14ac407..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.50-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 500000 0 500000 -obs: 0 500100 0 499900 -diff: 0 -100 0 100 -diffp: 0.00 -0.02 0.00 0.02 -#sweep.k101//sim-d0.50-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out deleted file mode 100644 index e9f9bc4..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.001 -Simulated 1600000 total bases, 1597 mutations (0.10%), G=1000000, d=0.60, r=.001 - -Model: -1 192225 -2 367097 -3 104250 -4 490207 - - -Observed Counts: -1 192146 -2 365474 -3 104974 -4 490446 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out.eval deleted file mode 100644 index 0a97d01..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 367097 104250 490207 -obs: 192146 365474 104974 490446 -diff: 79 1623 -724 -239 -diffp: 0.04 0.44 -0.69 -0.05 -#sweep.k101//sim-d0.60-r.001-k101-g1000000-out sumkmer 1153040 sumdiff: 739 score: 99.936 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out deleted file mode 100644 index 95f41e3..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.010 -Simulated 1600000 total bases, 15947 mutations (1.00%), G=1000000, d=0.60, r=.010 - -Model: -1 1275255 -2 388890 -3 277270 -4 78788 - - -Observed Counts: -1 1270224 -2 392077 -3 271630 -4 82633 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out.eval deleted file mode 100644 index 5a3b129..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 388890 277270 78788 -obs: 1270224 392077 271630 82633 -diff: 5031 -3187 5640 -3845 -diffp: 0.40 -0.81 2.08 -4.65 -#sweep.k101//sim-d0.60-r.010-k101-g1000000-out sumkmer 2016564 sumdiff: 3639 score: 99.820 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out deleted file mode 100644 index 93c9f27..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.050 -Simulated 1600000 total bases, 80394 mutations (5.02%), G=1000000, d=0.60, r=.050 - -Model: -1 1988750 -2 595519 -3 6711 -4 18 - - -Observed Counts: -1 1989848 -2 595569 -3 6270 -4 1 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out.eval deleted file mode 100644 index 145ab8d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 595519 6711 18 -obs: 1989848 595569 6270 1 -diff: -1098 -50 441 17 -diffp: -0.06 -0.01 7.03 1700.00 -#sweep.k101//sim-d0.60-r.050-k101-g1000000-out sumkmer 2591688 sumdiff: -690 score: 100.027 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out deleted file mode 100644 index ed5273e..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.60, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.100 -Simulated 1600000 total bases, 160053 mutations (10.00%), G=1000000, d=0.60, r=.100 - -Model: -1 1999951 -2 599980 -3 28 -4 0 - - -Observed Counts: -1 1999962 -2 599862 -3 38 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out.eval deleted file mode 100644 index 95af2fd..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 599980 28 0 -obs: 1999962 599862 38 0 -diff: -11 118 -10 0 -diffp: -0.00 0.02 -26.32 0.00 -#sweep.k101//sim-d0.60-r.100-k101-g1000000-out sumkmer 2599862 sumdiff: 97 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out deleted file mode 100644 index fc4bcfe..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.200 -Simulated 1600000 total bases, 320142 mutations (20.01%), G=1000000, d=0.60, r=.200 - -Model: -1 1999999 -2 599999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 599900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out.eval deleted file mode 100644 index 5f9df7c..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 599999 0 0 -obs: 2000000 599900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.60-r.200-k101-g1000000-out sumkmer 2599900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out deleted file mode 100644 index 79d57e6..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.300 -Simulated 1600000 total bases, 480079 mutations (30.00%), G=1000000, d=0.60, r=.300 - -Model: -1 1999999 -2 599999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 599900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out.eval deleted file mode 100644 index ffbf9eb..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 599999 0 0 -obs: 2000000 599900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k101//sim-d0.60-r.300-k101-g1000000-out sumkmer 2599900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out deleted file mode 100644 index 06afd79..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=0.00 -Simulated 1600000 total bases, 0 mutations (0.00%), G=1000000, d=0.60, r=0.00 - -Model: -1 0 -2 400000 -3 0 -4 600000 - - -Observed Counts: -2 400100 -4 599900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out.eval deleted file mode 100644 index e232960..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.60-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 400000 0 600000 -obs: 0 400100 0 599900 -diff: 0 -100 0 100 -diffp: 0.00 -0.02 0.00 0.02 -#sweep.k101//sim-d0.60-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out deleted file mode 100644 index bdfa00f..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.001 -Simulated 1700000 total bases, 1677 mutations (0.10%), G=1000000, d=0.70, r=.001 - -Model: -1 192225 -2 277632 -3 121625 -4 571908 - - -Observed Counts: -1 186583 -2 281559 -3 122205 -4 570871 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out.eval deleted file mode 100644 index b8f675a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 277632 121625 571908 -obs: 186583 281559 122205 570871 -diff: 5642 -3927 -580 1037 -diffp: 3.02 -1.39 -0.47 0.18 -#sweep.k101//sim-d0.70-r.001-k101-g1000000-out sumkmer 1161218 sumdiff: 2172 score: 99.813 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out deleted file mode 100644 index dc967cd..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.010 -Simulated 1700000 total bases, 16930 mutations (1.00%), G=1000000, d=0.70, r=.010 - -Model: -1 1275255 -2 393310 -3 323481 -4 91919 - - -Observed Counts: -1 1272786 -2 397493 -3 321600 -4 91807 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out.eval deleted file mode 100644 index 96cbae1..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 393310 323481 91919 -obs: 1272786 397493 321600 91807 -diff: 2469 -4183 1881 112 -diffp: 0.19 -1.05 0.58 0.12 -#sweep.k101//sim-d0.70-r.010-k101-g1000000-out sumkmer 2083686 sumdiff: 279 score: 99.987 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out deleted file mode 100644 index 74c9abc..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.050 -Simulated 1700000 total bases, 85013 mutations (5.00%), G=1000000, d=0.70, r=.050 - -Model: -1 1988750 -2 693835 -3 7830 -4 22 - - -Observed Counts: -1 1989224 -2 694191 -3 7342 -4 42 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out.eval deleted file mode 100644 index 4c68710..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 693835 7830 22 -obs: 1989224 694191 7342 42 -diff: -474 -356 488 -20 -diffp: -0.02 -0.05 6.65 -47.62 -#sweep.k101//sim-d0.70-r.050-k101-g1000000-out sumkmer 2690799 sumdiff: -362 score: 100.013 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out deleted file mode 100644 index 65a1fce..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.100 -Simulated 1700000 total bases, 170066 mutations (10.00%), G=1000000, d=0.70, r=.100 - -Model: -1 1999951 -2 699973 -3 33 -4 0 - - -Observed Counts: -1 1999925 -2 699903 -3 23 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out.eval deleted file mode 100644 index 4286a6a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 699973 33 0 -obs: 1999925 699903 23 0 -diff: 26 70 10 0 -diffp: 0.00 0.01 43.48 0.00 -#sweep.k101//sim-d0.70-r.100-k101-g1000000-out sumkmer 2699851 sumdiff: 106 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out deleted file mode 100644 index 731a013..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.200 -Simulated 1700000 total bases, 340107 mutations (20.01%), G=1000000, d=0.70, r=.200 - -Model: -1 1999999 -2 699999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 699900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out.eval deleted file mode 100644 index 1042037..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 699999 0 0 -obs: 2000000 699900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.70-r.200-k101-g1000000-out sumkmer 2699900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out deleted file mode 100644 index 415ed7a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.300 -Simulated 1700000 total bases, 509947 mutations (30.00%), G=1000000, d=0.70, r=.300 - -Model: -1 1999999 -2 699999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 699900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out.eval deleted file mode 100644 index ef05569..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 699999 0 0 -obs: 2000000 699900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.70-r.300-k101-g1000000-out sumkmer 2699900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out deleted file mode 100644 index 1b8fc48..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=0.00 -Simulated 1700000 total bases, 0 mutations (0.00%), G=1000000, d=0.70, r=0.00 - -Model: -1 0 -2 300000 -3 0 -4 700000 - - -Observed Counts: -2 300100 -4 699900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out.eval deleted file mode 100644 index e631dbc..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.70-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 300000 0 700000 -obs: 0 300100 0 699900 -diff: 0 -100 0 100 -diffp: 0.00 -0.03 0.00 0.01 -#sweep.k101//sim-d0.70-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out deleted file mode 100644 index b54fd59..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.001 -Simulated 1800000 total bases, 1838 mutations (0.10%), G=1000000, d=0.80, r=.001 - -Model: -1 192225 -2 188167 -3 139000 -4 653609 - - -Observed Counts: -1 195406 -2 189855 -3 140160 -4 651051 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out.eval deleted file mode 100644 index 7eb9ca1..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 188167 139000 653609 -obs: 195406 189855 140160 651051 -diff: -3181 -1688 -1160 2558 -diffp: -1.63 -0.89 -0.83 0.39 -#sweep.k101//sim-d0.80-r.001-k101-g1000000-out sumkmer 1176472 sumdiff: -3471 score: 100.295 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out deleted file mode 100644 index 1994e46..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.010 -Simulated 1800000 total bases, 17982 mutations (1.00%), G=1000000, d=0.80, r=.010 - -Model: -1 1275255 -2 397729 -3 369693 -4 105050 - - -Observed Counts: -1 1268226 -2 396070 -3 373506 -4 104729 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out.eval deleted file mode 100644 index bdf0fb1..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 397729 369693 105050 -obs: 1268226 396070 373506 104729 -diff: 7029 1659 -3813 321 -diffp: 0.55 0.42 -1.02 0.31 -#sweep.k101//sim-d0.80-r.010-k101-g1000000-out sumkmer 2142531 sumdiff: 5196 score: 99.757 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out deleted file mode 100644 index 55f87e8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.050 -Simulated 1800000 total bases, 89999 mutations (5.00%), G=1000000, d=0.80, r=.050 - -Model: -1 1988750 -2 792151 -3 8948 -4 25 - - -Observed Counts: -1 1989250 -2 792250 -3 8650 -4 25 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out.eval deleted file mode 100644 index 130ba96..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 792151 8948 25 -obs: 1989250 792250 8650 25 -diff: -500 -99 298 0 -diffp: -0.03 -0.01 3.45 0.00 -#sweep.k101//sim-d0.80-r.050-k101-g1000000-out sumkmer 2790175 sumdiff: -301 score: 100.011 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out deleted file mode 100644 index 578c2a4..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.100 -Simulated 1800000 total bases, 179813 mutations (9.99%), G=1000000, d=0.80, r=.100 - -Model: -1 1999951 -2 799966 -3 38 -4 0 - - -Observed Counts: -1 1999934 -2 799834 -3 66 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out.eval deleted file mode 100644 index 2db900c..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 799966 38 0 -obs: 1999934 799834 66 0 -diff: 17 132 -28 0 -diffp: 0.00 0.02 -42.42 0.00 -#sweep.k101//sim-d0.80-r.100-k101-g1000000-out sumkmer 2799834 sumdiff: 121 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out deleted file mode 100644 index bc2e1e8..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.200 -Simulated 1800000 total bases, 360767 mutations (20.04%), G=1000000, d=0.80, r=.200 - -Model: -1 1999999 -2 799999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 799900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out.eval deleted file mode 100644 index ac8c969..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 799999 0 0 -obs: 2000000 799900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.80-r.200-k101-g1000000-out sumkmer 2799900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out deleted file mode 100644 index 540d893..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.300 -Simulated 1800000 total bases, 540618 mutations (30.03%), G=1000000, d=0.80, r=.300 - -Model: -1 1999999 -2 799999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 799900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out.eval deleted file mode 100644 index 21d1206..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 799999 0 0 -obs: 2000000 799900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.80-r.300-k101-g1000000-out sumkmer 2799900 sumdiff: 98 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out deleted file mode 100644 index 3eb4573..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=0.00 -Simulated 1800000 total bases, 0 mutations (0.00%), G=1000000, d=0.80, r=0.00 - -Model: -1 0 -2 199999 -3 0 -4 800000 - - -Observed Counts: -2 200100 -4 799900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out.eval deleted file mode 100644 index 5500cd9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.80-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 199999 0 800000 -obs: 0 200100 0 799900 -diff: 0 -101 0 100 -diffp: 0.00 -0.05 0.00 0.01 -#sweep.k101//sim-d0.80-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out deleted file mode 100644 index 6ceeb5a..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.001, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.001 -Simulated 1900000 total bases, 1965 mutations (0.10%), G=1000000, d=0.90, r=.001 - -Model: -1 192225 -2 98702 -3 156375 -4 735311 - - -Observed Counts: -1 199418 -2 98677 -3 160636 -4 730280 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out.eval deleted file mode 100644 index 84aa629..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 98702 156375 735311 -obs: 199418 98677 160636 730280 -diff: -7193 25 -4261 5031 -diffp: -3.61 0.03 -2.65 0.69 -#sweep.k101//sim-d0.90-r.001-k101-g1000000-out sumkmer 1189011 sumdiff: -6398 score: 100.538 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out deleted file mode 100644 index 305b28e..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.010, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.010 -Simulated 1900000 total bases, 19086 mutations (1.00%), G=1000000, d=0.90, r=.010 - -Model: -1 1275255 -2 402149 -3 415905 -4 118182 - - -Observed Counts: -1 1271711 -2 408471 -3 411085 -4 119473 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out.eval deleted file mode 100644 index 4001b6e..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 402149 415905 118182 -obs: 1271711 408471 411085 119473 -diff: 3544 -6322 4820 -1291 -diffp: 0.28 -1.55 1.17 -1.08 -#sweep.k101//sim-d0.90-r.010-k101-g1000000-out sumkmer 2210740 sumdiff: 751 score: 99.966 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out deleted file mode 100644 index 7870f5d..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.050, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.050 -Simulated 1900000 total bases, 95188 mutations (5.01%), G=1000000, d=0.90, r=.050 - -Model: -1 1988750 -2 890466 -3 10067 -4 28 - - -Observed Counts: -1 1988175 -2 889808 -3 10627 -4 32 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out.eval deleted file mode 100644 index 400619e..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 890466 10067 28 -obs: 1988175 889808 10627 32 -diff: 575 658 -560 -4 -diffp: 0.03 0.07 -5.27 -12.50 -#sweep.k101//sim-d0.90-r.050-k101-g1000000-out sumkmer 2888642 sumdiff: 669 score: 99.977 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out deleted file mode 100644 index 41f9b71..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.90, r=.100, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.100 -Simulated 1900000 total bases, 189971 mutations (10.00%), G=1000000, d=0.90, r=.100 - -Model: -1 1999952 -2 899959 -3 43 -4 0 - - -Observed Counts: -1 1999913 -2 899813 -3 87 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out.eval deleted file mode 100644 index b5c6d04..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999952 899959 43 0 -obs: 1999913 899813 87 0 -diff: 39 146 -44 0 -diffp: 0.00 0.02 -50.57 0.00 -#sweep.k101//sim-d0.90-r.100-k101-g1000000-out sumkmer 2899813 sumdiff: 141 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out deleted file mode 100644 index 7b89da1..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=.200, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.200 -Simulated 1900000 total bases, 379684 mutations (19.98%), G=1000000, d=0.90, r=.200 - -Model: -1 1999999 -2 899999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 899900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out.eval deleted file mode 100644 index 77f52a3..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 899999 0 0 -obs: 2000000 899900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.90-r.200-k101-g1000000-out sumkmer 2899900 sumdiff: 98 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out deleted file mode 100644 index aa76c3c..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=.300, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.300 -Simulated 1900000 total bases, 570166 mutations (30.01%), G=1000000, d=0.90, r=.300 - -Model: -1 1999999 -2 899999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 899900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out.eval deleted file mode 100644 index 216d4f2..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 899999 0 0 -obs: 2000000 899900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d0.90-r.300-k101-g1000000-out sumkmer 2899900 sumdiff: 98 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out deleted file mode 100644 index e188210..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=0.00, k=101 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=0.00 -Simulated 1900000 total bases, 0 mutations (0.00%), G=1000000, d=0.90, r=0.00 - -Model: -1 0 -2 99999 -3 0 -4 900000 - - -Observed Counts: -2 100100 -4 899900 diff --git a/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out.eval deleted file mode 100644 index da80cad..0000000 --- a/analysis/genomesim/sweep.k101/sim-d0.90-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 99999 0 900000 -obs: 0 100100 0 899900 -diff: 0 -101 0 100 -diffp: 0.00 -0.10 0.00 0.01 -#sweep.k101//sim-d0.90-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out deleted file mode 100644 index dd2c727..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.001, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.001 -Simulated 2000000 total bases, 2020 mutations (0.10%), G=1000000, d=1.00, r=.001 - -Model: -1 192225 -2 9237 -3 173750 -4 817012 - - -Observed Counts: -1 193691 -2 8401 -3 177149 -4 814465 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out.eval deleted file mode 100644 index 324e6c0..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.001-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 192225 9237 173750 817012 -obs: 193691 8401 177149 814465 -diff: -1466 836 -3399 2547 -diffp: -0.76 9.95 -1.92 0.31 -#sweep.k101//sim-d1.00-r.001-k101-g1000000-out sumkmer 1193706 sumdiff: -1482 score: 100.124 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out deleted file mode 100644 index 69f6bf9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.010, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.010 -Simulated 2000000 total bases, 19963 mutations (1.00%), G=1000000, d=1.00, r=.010 - -Model: -1 1275255 -2 406569 -3 462117 -4 131313 - - -Observed Counts: -1 1267037 -2 406247 -3 461387 -4 134027 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out.eval deleted file mode 100644 index a2d63e6..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.010-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1275255 406569 462117 131313 -obs: 1267037 406247 461387 134027 -diff: 8218 322 730 -2714 -diffp: 0.65 0.08 0.16 -2.02 -#sweep.k101//sim-d1.00-r.010-k101-g1000000-out sumkmer 2268698 sumdiff: 6556 score: 99.711 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out deleted file mode 100644 index b170738..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.050, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.050 -Simulated 2000000 total bases, 99623 mutations (4.98%), G=1000000, d=1.00, r=.050 - -Model: -1 1988750 -2 988782 -3 11185 -4 31 - - -Observed Counts: -1 1988707 -2 988665 -3 11217 -4 28 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out.eval deleted file mode 100644 index 6367a53..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.050-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1988750 988782 11185 31 -obs: 1988707 988665 11217 28 -diff: 43 117 -32 3 -diffp: 0.00 0.01 -0.29 10.71 -#sweep.k101//sim-d1.00-r.050-k101-g1000000-out sumkmer 2988617 sumdiff: 131 score: 99.996 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out deleted file mode 100644 index 094b891..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=1.00, r=.100, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.100 -Simulated 2000000 total bases, 200838 mutations (10.04%), G=1000000, d=1.00, r=.100 - -Model: -1 1999951 -2 999952 -3 47 -4 0 - - -Observed Counts: -1 1999895 -2 999795 -3 105 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out.eval deleted file mode 100644 index e94ee36..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.100-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999951 999952 47 0 -obs: 1999895 999795 105 0 -diff: 56 157 -58 0 -diffp: 0.00 0.02 -55.24 0.00 -#sweep.k101//sim-d1.00-r.100-k101-g1000000-out sumkmer 2999795 sumdiff: 155 score: 99.995 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out deleted file mode 100644 index 5331811..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=.200, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.200 -Simulated 2000000 total bases, 400077 mutations (20.00%), G=1000000, d=1.00, r=.200 - -Model: -1 1999999 -2 999999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 999900 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out.eval deleted file mode 100644 index ef5b392..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.200-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 999999 0 0 -obs: 2000000 999900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d1.00-r.200-k101-g1000000-out sumkmer 2999900 sumdiff: 98 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out deleted file mode 100644 index e5359c9..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=.300, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.300 -Simulated 2000000 total bases, 599978 mutations (30.00%), G=1000000, d=1.00, r=.300 - -Model: -1 1999999 -2 999999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 999900 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out.eval deleted file mode 100644 index 7c202a0..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r.300-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 999999 0 0 -obs: 2000000 999900 0 0 -diff: -1 99 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k101//sim-d1.00-r.300-k101-g1000000-out sumkmer 2999900 sumdiff: 98 score: 99.997 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out b/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out deleted file mode 100644 index 5648c70..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=0.00, k=101 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=0.00 -Simulated 2000000 total bases, 0 mutations (0.00%), G=1000000, d=1.00, r=0.00 - -Model: -1 0 -2 0 -3 0 -4 1000000 - - -Observed Counts: -2 100 -4 999900 diff --git a/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out.eval b/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out.eval deleted file mode 100644 index ef60a31..0000000 --- a/analysis/genomesim/sweep.k101/sim-d1.00-r0.00-k101-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 0 0 1000000 -obs: 0 100 0 999900 -diff: 0 -100 0 100 -diffp: 0.00 -100.00 0.00 0.01 -#sweep.k101//sim-d1.00-r0.00-k101-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out deleted file mode 100644 index 95acc36..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.00, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.001 -Simulated 1000000 total bases, 1071 mutations (0.11%), G=1000000, d=0.00, r=.001 - -Model: -1 21890 -2 989054 -3 0 -4 0 - - -Observed Counts: -1 14363 -2 608244 -3 6854 -4 144092 -5 1701 -6 22751 -7 253 -8 2769 -9 29 -10 269 -11 2 -12 22 -14 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out.eval deleted file mode 100644 index 7267270..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21890 989054 0 0 -obs: 14363 608244 6854 144092 -diff: 7527 380810 -6854 -144092 -diffp: 52.41 62.61 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.001-k11-g1000000-out sumkmer 773553 sumdiff: 237391 score: 69.312 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out deleted file mode 100644 index 05f452a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.00, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.010 -Simulated 1000000 total bases, 9856 mutations (0.99%), G=1000000, d=0.00, r=.010 - -Model: -1 209323 -2 895338 -3 0 -4 0 - - -Observed Counts: -1 122275 -2 536229 -3 52215 -4 115669 -5 11113 -6 16901 -7 1600 -8 1744 -9 190 -10 177 -11 15 -12 12 -14 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out.eval deleted file mode 100644 index f67f834..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 895338 0 0 -obs: 122275 536229 52215 115669 -diff: 87048 359109 -52215 -115669 -diffp: 71.19 66.97 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.010-k11-g1000000-out sumkmer 826388 sumdiff: 278273 score: 66.327 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out deleted file mode 100644 index 151a1d4..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.00, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.050 -Simulated 1000000 total bases, 50366 mutations (5.04%), G=1000000, d=0.00, r=.050 - -Model: -1 862399 -2 568800 -3 0 -4 0 - - -Observed Counts: -1 438265 -2 375559 -3 130961 -4 64122 -5 19563 -6 7169 -7 1932 -8 601 -9 176 -10 41 -11 2 -12 3 -13 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out.eval deleted file mode 100644 index 1539f04..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 568800 0 0 -obs: 438265 375559 130961 64122 -diff: 424134 193241 -130961 -64122 -diffp: 96.78 51.45 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.050-k11-g1000000-out sumkmer 1008907 sumdiff: 422292 score: 58.144 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out deleted file mode 100644 index edad1d2..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.00, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.100 -Simulated 1000000 total bases, 99646 mutations (9.96%), G=1000000, d=0.00, r=.100 - -Model: -1 1372378 -2 313810 -3 0 -4 0 - - -Observed Counts: -1 614333 -2 341164 -3 135833 -4 47486 -5 14437 -6 4050 -7 945 -8 262 -9 57 -10 12 -11 1 -12 3 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out.eval deleted file mode 100644 index 8abce9a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 313810 0 0 -obs: 614333 341164 135833 47486 -diff: 758045 -27354 -135833 -47486 -diffp: 123.39 -8.02 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.100-k11-g1000000-out sumkmer 1138816 sumdiff: 547372 score: 51.935 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out deleted file mode 100644 index 83b527f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out +++ /dev/null @@ -1,23 +0,0 @@ -Simulating G=1000000, d=0.00, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.200 -Simulated 1000000 total bases, 200140 mutations (20.01%), G=1000000, d=0.00, r=.200 - -Model: -1 1828201 -2 85899 -3 0 -4 0 - - -Observed Counts: -1 734935 -2 353968 -3 122744 -4 34163 -5 7970 -6 1665 -7 264 -8 57 -9 9 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out.eval deleted file mode 100644 index fa54a6b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 85899 0 0 -obs: 734935 353968 122744 34163 -diff: 1093266 -268069 -122744 -34163 -diffp: 148.76 -75.73 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.200-k11-g1000000-out sumkmer 1245810 sumdiff: 668290 score: 46.357 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out deleted file mode 100644 index dbc3a64..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out +++ /dev/null @@ -1,23 +0,0 @@ -Simulating G=1000000, d=0.00, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.300 -Simulated 1000000 total bases, 300329 mutations (30.03%), G=1000000, d=0.00, r=.300 - -Model: -1 1960453 -2 19773 -3 0 -4 0 - - -Observed Counts: -1 762177 -2 363742 -3 118288 -4 29515 -5 6055 -6 985 -7 147 -8 17 -9 5 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out.eval deleted file mode 100644 index 72fa4e1..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 19773 0 0 -obs: 762177 363742 118288 29515 -diff: 1198276 -343969 -118288 -29515 -diffp: 157.22 -94.56 -100.00 -100.00 -#sweep.k11//sim-d0.00-r.300-k11-g1000000-out sumkmer 1273722 sumdiff: 706504 score: 44.532 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out deleted file mode 100644 index be79698..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out +++ /dev/null @@ -1,20 +0,0 @@ -Simulating G=1000000, d=0.00, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=0.00 -Simulated 1000000 total bases, 0 mutations (0.00%), G=1000000, d=0.00, r=0.00 - -Model: -1 0 -2 1000000 -3 0 -4 0 - - -Observed Counts: -2 621246 -4 147734 -6 23453 -8 2841 -10 283 -12 23 diff --git a/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 2d7a960..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.00-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 1000000 0 0 -obs: 0 621246 0 147734 -diff: 0 378754 0 -147734 -diffp: 0.00 60.97 0.00 -100.00 -#sweep.k11//sim-d0.00-r0.00-k11-g1000000-out sumkmer 768980 sumdiff: 231020 score: 69.958 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out deleted file mode 100644 index 11aa99d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=0.10, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.001 -Simulated 1100000 total bases, 1113 mutations (0.10%), G=1000000, d=0.10, r=.001 - -Model: -1 21890 -2 890161 -3 2165 -4 97822 - - -Observed Counts: -1 13516 -2 550134 -3 7198 -4 176576 -5 2472 -6 41930 -7 703 -8 8705 -9 134 -10 1486 -11 22 -12 230 -13 2 -14 41 -15 1 -16 6 -18 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out.eval deleted file mode 100644 index 32119c8..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21890 890161 2165 97822 -obs: 13516 550134 7198 176576 -diff: 8374 340027 -5033 -78754 -diffp: 61.96 61.81 -69.92 -44.60 -#sweep.k11//sim-d0.10-r.001-k11-g1000000-out sumkmer 747424 sumdiff: 264614 score: 64.597 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out deleted file mode 100644 index 5a8e2c3..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=0.10, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.010 -Simulated 1100000 total bases, 10960 mutations (1.00%), G=1000000, d=0.10, r=.010 - -Model: -1 209322 -2 806899 -3 18741 -4 80163 - - -Observed Counts: -1 122308 -2 478424 -3 58532 -4 142316 -5 18363 -6 31024 -7 4294 -8 5853 -9 856 -10 945 -11 157 -12 145 -13 19 -14 16 -15 1 -16 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out.eval deleted file mode 100644 index 11a4ae1..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209322 806899 18741 80163 -obs: 122308 478424 58532 142316 -diff: 87014 328475 -39791 -62153 -diffp: 71.14 68.66 -67.98 -43.67 -#sweep.k11//sim-d0.10-r.010-k11-g1000000-out sumkmer 801580 sumdiff: 313545 score: 60.884 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out deleted file mode 100644 index 0685463..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.10, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.050 -Simulated 1100000 total bases, 54786 mutations (4.98%), G=1000000, d=0.10, r=.050 - -Model: -1 862399 -2 530513 -3 49053 -4 32353 - - -Observed Counts: -1 426203 -2 351187 -3 143750 -4 82730 -5 31607 -6 14456 -7 5171 -8 2146 -9 744 -10 271 -11 92 -12 25 -13 12 -14 8 -15 4 -16 1 -17 1 -18 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out.eval deleted file mode 100644 index a61bc8b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 530513 49053 32353 -obs: 426203 351187 143750 82730 -diff: 436196 179326 -94697 -50377 -diffp: 102.34 51.06 -65.88 -60.89 -#sweep.k11//sim-d0.10-r.050-k11-g1000000-out sumkmer 1003870 sumdiff: 470448 score: 53.137 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out deleted file mode 100644 index 77950b9..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.10, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.100 -Simulated 1100000 total bases, 110307 mutations (10.03%), G=1000000, d=0.10, r=.100 - -Model: -1 1372378 -2 329515 -3 43066 -4 9847 - - -Observed Counts: -1 594197 -2 337706 -3 154070 -4 65528 -5 24566 -6 8653 -7 2908 -8 896 -9 278 -10 87 -11 28 -12 7 -13 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out.eval deleted file mode 100644 index 6bfb341..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 329515 43066 9847 -obs: 594197 337706 154070 65528 -diff: 778181 -8191 -111004 -55681 -diffp: 130.96 -2.43 -72.05 -84.97 -#sweep.k11//sim-d0.10-r.100-k11-g1000000-out sumkmer 1151501 sumdiff: 603305 score: 47.607 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out deleted file mode 100644 index ea92e23..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.10, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.200 -Simulated 1100000 total bases, 220300 mutations (20.03%), G=1000000, d=0.10, r=.200 - -Model: -1 1828201 -2 160867 -3 15704 -4 737 - - -Observed Counts: -1 701502 -2 368644 -3 149004 -4 51048 -5 15046 -6 4125 -7 1082 -8 235 -9 43 -10 12 -11 3 -12 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out.eval deleted file mode 100644 index 0fc9365..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 160867 15704 737 -obs: 701502 368644 149004 51048 -diff: 1126699 -207777 -133300 -50311 -diffp: 160.61 -56.36 -89.46 -98.56 -#sweep.k11//sim-d0.10-r.200-k11-g1000000-out sumkmer 1270198 sumdiff: 735311 score: 42.111 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out deleted file mode 100644 index add1ba5..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out +++ /dev/null @@ -1,25 +0,0 @@ -Simulating G=1000000, d=0.10, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.300 -Simulated 1100000 total bases, 329957 mutations (30.00%), G=1000000, d=0.10, r=.300 - -Model: -1 1960453 -2 113880 -3 3876 -4 39 - - -Observed Counts: -1 726483 -2 381879 -3 146837 -4 46077 -5 12418 -6 2878 -7 599 -8 140 -9 23 -10 3 -12 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out.eval deleted file mode 100644 index c7998ce..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 113880 3876 39 -obs: 726483 381879 146837 46077 -diff: 1233970 -267999 -142961 -46038 -diffp: 169.86 -70.18 -97.36 -99.92 -#sweep.k11//sim-d0.10-r.300-k11-g1000000-out sumkmer 1301276 sumdiff: 776972 score: 40.292 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out deleted file mode 100644 index 14d5df0..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out +++ /dev/null @@ -1,23 +0,0 @@ -Simulating G=1000000, d=0.10, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=0.00 -Simulated 1100000 total bases, 0 mutations (0.00%), G=1000000, d=0.10, r=0.00 - -Model: -1 0 -2 900000 -3 0 -4 100000 - - -Observed Counts: -2 556915 -4 182524 -6 43744 -8 9080 -10 1707 -12 264 -14 46 -16 3 -20 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 2a327d1..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.10-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 900000 0 100000 -obs: 0 556915 0 182524 -diff: 0 343085 0 -82524 -diffp: 0.00 61.60 0.00 -45.21 -#sweep.k11//sim-d0.10-r0.00-k11-g1000000-out sumkmer 739439 sumdiff: 260561 score: 64.762 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out deleted file mode 100644 index c1738c0..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.20, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.001 -Simulated 1200000 total bases, 1174 mutations (0.10%), G=1000000, d=0.20, r=.001 - -Model: -1 21890 -2 791267 -3 4330 -4 195645 - - -Observed Counts: -1 13188 -2 489130 -3 7681 -4 213014 -5 3125 -6 57026 -7 1027 -8 15300 -9 263 -10 3212 -11 58 -12 725 -13 16 -14 109 -15 2 -16 25 -18 2 -19 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out.eval deleted file mode 100644 index 71c5116..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21890 791267 4330 195645 -obs: 13188 489130 7681 213014 -diff: 8702 302137 -3351 -17369 -diffp: 65.98 61.77 -43.63 -8.15 -#sweep.k11//sim-d0.20-r.001-k11-g1000000-out sumkmer 723013 sumdiff: 290119 score: 59.874 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out deleted file mode 100644 index 4cd9556..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.20, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.010 -Simulated 1200000 total bases, 11984 mutations (1.00%), G=1000000, d=0.20, r=.010 - -Model: -1 209323 -2 718461 -3 37483 -4 160326 - - -Observed Counts: -1 121311 -2 426704 -3 64053 -4 169440 -5 24458 -6 42450 -7 7052 -8 10271 -9 1696 -10 2011 -11 361 -12 417 -13 85 -14 59 -15 13 -16 16 -17 1 -18 4 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out.eval deleted file mode 100644 index e373690..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 718461 37483 160326 -obs: 121311 426704 64053 169440 -diff: 88012 291757 -26570 -9114 -diffp: 72.55 68.37 -41.48 -5.38 -#sweep.k11//sim-d0.20-r.010-k11-g1000000-out sumkmer 781508 sumdiff: 344085 score: 55.972 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out deleted file mode 100644 index 87ee746..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.20, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.050 -Simulated 1200000 total bases, 60232 mutations (5.02%), G=1000000, d=0.20, r=.050 - -Model: -1 862399 -2 492226 -3 98106 -4 64706 - - -Observed Counts: -1 418449 -2 325172 -3 156618 -4 100550 -5 42747 -6 21043 -7 8887 -8 3935 -9 1575 -10 644 -11 263 -12 103 -13 34 -14 12 -15 2 -16 2 -17 1 -18 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out.eval deleted file mode 100644 index b5bb4e7..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 492226 98106 64706 -obs: 418449 325172 156618 100550 -diff: 443950 167054 -58512 -35844 -diffp: 106.09 51.37 -37.36 -35.65 -#sweep.k11//sim-d0.20-r.050-k11-g1000000-out sumkmer 1000789 sumdiff: 516648 score: 48.376 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out deleted file mode 100644 index 4e8d09d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out +++ /dev/null @@ -1,28 +0,0 @@ -Simulating G=1000000, d=0.20, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.100 -Simulated 1200000 total bases, 120654 mutations (10.05%), G=1000000, d=0.20, r=.100 - -Model: -1 1372378 -2 345219 -3 86133 -4 19695 - - -Observed Counts: -1 575296 -2 333575 -3 171436 -4 80921 -5 34766 -6 13906 -7 5334 -8 1972 -9 630 -10 227 -11 74 -12 23 -13 8 -14 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out.eval deleted file mode 100644 index 6e0ff35..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 345219 86133 19695 -obs: 575296 333575 171436 80921 -diff: 797082 11644 -85303 -61226 -diffp: 138.55 3.49 -49.76 -75.66 -#sweep.k11//sim-d0.20-r.100-k11-g1000000-out sumkmer 1161228 sumdiff: 662197 score: 42.974 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out deleted file mode 100644 index ec61d0c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.20, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.200 -Simulated 1200000 total bases, 240575 mutations (20.05%), G=1000000, d=0.20, r=.200 - -Model: -1 1828201 -2 235835 -3 31408 -4 1475 - - -Observed Counts: -1 671624 -2 381110 -3 172104 -4 66782 -5 23497 -6 7262 -7 2135 -8 608 -9 158 -10 34 -11 4 -12 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out.eval deleted file mode 100644 index 88da7ea..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 235835 31408 1475 -obs: 671624 381110 172104 66782 -diff: 1156577 -145275 -140696 -65307 -diffp: 172.21 -38.12 -81.75 -97.79 -#sweep.k11//sim-d0.20-r.200-k11-g1000000-out sumkmer 1291620 sumdiff: 805299 score: 37.652 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out deleted file mode 100644 index 5162df1..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.20, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.300 -Simulated 1200000 total bases, 359325 mutations (29.94%), G=1000000, d=0.20, r=.300 - -Model: -1 1960452 -2 207987 -3 7752 -4 78 - - -Observed Counts: -1 692768 -2 398609 -3 173200 -4 61775 -5 19453 -6 5441 -7 1404 -8 326 -9 78 -10 20 -11 3 -12 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out.eval deleted file mode 100644 index 6780e0c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960452 207987 7752 78 -obs: 692768 398609 173200 61775 -diff: 1267684 -190622 -165448 -61697 -diffp: 182.99 -47.82 -95.52 -99.87 -#sweep.k11//sim-d0.20-r.300-k11-g1000000-out sumkmer 1326352 sumdiff: 849917 score: 35.921 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out deleted file mode 100644 index 5eabbb9..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out +++ /dev/null @@ -1,24 +0,0 @@ -Simulating G=1000000, d=0.20, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=0.00 -Simulated 1200000 total bases, 0 mutations (0.00%), G=1000000, d=0.20, r=0.00 - -Model: -1 0 -2 800000 -3 0 -4 200000 - - -Observed Counts: -2 496511 -4 219306 -6 59074 -8 16154 -10 3531 -12 699 -14 138 -16 22 -18 2 -20 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out.eval deleted file mode 100644 index d13d26e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.20-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 800000 0 200000 -obs: 0 496511 0 219306 -diff: 0 303489 0 -19306 -diffp: 0.00 61.12 0.00 -8.80 -#sweep.k11//sim-d0.20-r0.00-k11-g1000000-out sumkmer 715817 sumdiff: 284183 score: 60.299 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out deleted file mode 100644 index fd5f68d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.30, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.001 -Simulated 1300000 total bases, 1267 mutations (0.10%), G=1000000, d=0.30, r=.001 - -Model: -1 21890 -2 692374 -3 6495 -4 293468 - - -Observed Counts: -1 13229 -2 425992 -3 8281 -4 251999 -5 3777 -6 67509 -7 1471 -8 23447 -9 418 -10 5290 -11 133 -12 1367 -13 27 -14 289 -15 8 -16 52 -17 2 -18 9 -20 1 -22 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out.eval deleted file mode 100644 index 0d2d622..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21890 692374 6495 293468 -obs: 13229 425992 8281 251999 -diff: 8661 266382 -1786 41469 -diffp: 65.47 62.53 -21.57 16.46 -#sweep.k11//sim-d0.30-r.001-k11-g1000000-out sumkmer 699501 sumdiff: 314726 score: 55.007 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out deleted file mode 100644 index 3757de5..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out +++ /dev/null @@ -1,35 +0,0 @@ -Simulating G=1000000, d=0.30, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.010 -Simulated 1300000 total bases, 12882 mutations (0.99%), G=1000000, d=0.30, r=.010 - -Model: -1 209322 -2 630023 -3 56224 -4 240489 - - -Observed Counts: -1 119982 -2 373021 -3 69468 -4 201154 -5 29147 -6 49694 -7 10172 -8 15686 -9 2653 -10 3364 -11 675 -12 789 -13 160 -14 181 -15 36 -16 30 -17 3 -18 7 -20 3 -21 2 -22 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out.eval deleted file mode 100644 index 6f7186c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209322 630023 56224 240489 -obs: 119982 373021 69468 201154 -diff: 89340 257002 -13244 39335 -diffp: 74.46 68.90 -19.06 19.55 -#sweep.k11//sim-d0.30-r.010-k11-g1000000-out sumkmer 763625 sumdiff: 372433 score: 51.228 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out deleted file mode 100644 index 85ef223..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.30, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.050 -Simulated 1300000 total bases, 65520 mutations (5.04%), G=1000000, d=0.30, r=.050 - -Model: -1 862398 -2 453940 -3 147159 -4 97060 - - -Observed Counts: -1 409087 -2 300886 -3 170791 -4 116758 -5 52253 -6 27367 -7 12838 -8 6176 -9 2620 -10 1184 -11 476 -12 210 -13 80 -14 33 -15 13 -16 2 -17 3 -19 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out.eval deleted file mode 100644 index bdce76b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862398 453940 147159 97060 -obs: 409087 300886 170791 116758 -diff: 453311 153054 -23632 -19698 -diffp: 110.81 50.87 -13.84 -16.87 -#sweep.k11//sim-d0.30-r.050-k11-g1000000-out sumkmer 997522 sumdiff: 563035 score: 43.557 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out deleted file mode 100644 index d200a09..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=0.30, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.100 -Simulated 1300000 total bases, 130105 mutations (10.01%), G=1000000, d=0.30, r=.100 - -Model: -1 1372378 -2 360924 -3 129200 -4 29543 - - -Observed Counts: -1 554595 -2 328876 -3 187198 -4 96767 -5 44316 -6 19348 -7 8100 -8 3243 -9 1221 -10 470 -11 170 -12 59 -13 17 -14 10 -15 1 -16 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out.eval deleted file mode 100644 index 564ba93..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 360924 129200 29543 -obs: 554595 328876 187198 96767 -diff: 817783 32048 -57998 -67224 -diffp: 147.46 9.74 -30.98 -69.47 -#sweep.k11//sim-d0.30-r.100-k11-g1000000-out sumkmer 1167436 sumdiff: 724609 score: 37.932 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out deleted file mode 100644 index fd7f5be..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.30, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.200 -Simulated 1300000 total bases, 260306 mutations (20.02%), G=1000000, d=0.30, r=.200 - -Model: -1 1828200 -2 310803 -3 47112 -4 2213 - - -Observed Counts: -1 642313 -2 390128 -3 193697 -4 82868 -5 31797 -6 11184 -7 3631 -8 1080 -9 364 -10 104 -11 23 -12 10 -13 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out.eval deleted file mode 100644 index 9a157cd..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828200 310803 47112 2213 -obs: 642313 390128 193697 82868 -diff: 1185887 -79325 -146585 -80655 -diffp: 184.63 -20.33 -75.68 -97.33 -#sweep.k11//sim-d0.30-r.200-k11-g1000000-out sumkmer 1309006 sumdiff: 879322 score: 32.825 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out deleted file mode 100644 index 9cbde82..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.30, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.300 -Simulated 1300000 total bases, 390019 mutations (30.00%), G=1000000, d=0.30, r=.300 - -Model: -1 1960453 -2 302094 -3 11629 -4 117 - - -Observed Counts: -1 661926 -2 412287 -3 196384 -4 78137 -5 27246 -6 8619 -7 2375 -8 678 -9 155 -10 28 -11 9 -13 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out.eval deleted file mode 100644 index f6b3c65..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 302094 11629 117 -obs: 661926 412287 196384 78137 -diff: 1298527 -110193 -184755 -78020 -diffp: 196.17 -26.73 -94.08 -99.85 -#sweep.k11//sim-d0.30-r.300-k11-g1000000-out sumkmer 1348734 sumdiff: 925559 score: 31.376 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out deleted file mode 100644 index 16b531a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out +++ /dev/null @@ -1,25 +0,0 @@ -Simulating G=1000000, d=0.30, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=0.00 -Simulated 1300000 total bases, 0 mutations (0.00%), G=1000000, d=0.30, r=0.00 - -Model: -1 0 -2 700000 -3 0 -4 300000 - - -Observed Counts: -2 434979 -4 259240 -6 70015 -8 24158 -10 5686 -12 1491 -14 257 -16 67 -18 9 -20 5 -24 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 8fad384..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.30-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 700000 0 300000 -obs: 0 434979 0 259240 -diff: 0 265021 0 40760 -diffp: 0.00 60.93 0.00 15.72 -#sweep.k11//sim-d0.30-r0.00-k11-g1000000-out sumkmer 694219 sumdiff: 305781 score: 55.953 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out deleted file mode 100644 index 0b0da4a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out +++ /dev/null @@ -1,35 +0,0 @@ -Simulating G=1000000, d=0.40, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.001 -Simulated 1400000 total bases, 1411 mutations (0.10%), G=1000000, d=0.40, r=.001 - -Model: -1 21890 -2 593480 -3 8660 -4 391291 - - -Observed Counts: -1 13730 -2 365083 -3 9038 -4 292535 -5 4621 -6 73013 -7 2019 -8 32900 -9 652 -10 7344 -11 214 -12 2386 -13 51 -14 481 -15 17 -16 114 -17 6 -18 15 -20 4 -22 2 -24 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out.eval deleted file mode 100644 index a19f754..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21890 593480 8660 391291 -obs: 13730 365083 9038 292535 -diff: 8160 228397 -378 98756 -diffp: 59.43 62.56 -4.18 33.76 -#sweep.k11//sim-d0.40-r.001-k11-g1000000-out sumkmer 680386 sumdiff: 334935 score: 50.773 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out deleted file mode 100644 index cf6475b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out +++ /dev/null @@ -1,36 +0,0 @@ -Simulating G=1000000, d=0.40, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.010 -Simulated 1400000 total bases, 14123 mutations (1.01%), G=1000000, d=0.40, r=.010 - -Model: -1 209323 -2 541584 -3 74966 -4 320652 - - -Observed Counts: -1 121427 -2 319115 -3 75196 -4 232088 -5 33986 -6 54281 -7 13560 -8 21913 -9 3970 -10 4601 -11 1189 -12 1293 -13 274 -14 276 -15 78 -16 63 -17 10 -18 14 -19 3 -20 3 -21 1 -22 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out.eval deleted file mode 100644 index 57a98b2..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 541584 74966 320652 -obs: 121427 319115 75196 232088 -diff: 87896 222469 -230 88564 -diffp: 72.39 69.71 -0.31 38.16 -#sweep.k11//sim-d0.40-r.010-k11-g1000000-out sumkmer 747826 sumdiff: 398699 score: 46.686 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out deleted file mode 100644 index d01853c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.40, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.050 -Simulated 1400000 total bases, 69616 mutations (4.97%), G=1000000, d=0.40, r=.050 - -Model: -1 862399 -2 415653 -3 196213 -4 129413 - - -Observed Counts: -1 397759 -2 276429 -3 182268 -4 134388 -5 60738 -6 32802 -7 17414 -8 8950 -9 3892 -10 1864 -11 807 -12 390 -13 171 -14 62 -15 31 -16 5 -17 3 -18 2 -19 1 -20 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out.eval deleted file mode 100644 index 84e794e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 415653 196213 129413 -obs: 397759 276429 182268 134388 -diff: 464640 139224 13945 -4975 -diffp: 116.81 50.37 7.65 -3.70 -#sweep.k11//sim-d0.40-r.050-k11-g1000000-out sumkmer 990844 sumdiff: 612834 score: 38.150 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out deleted file mode 100644 index 40a0a68..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=0.40, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.100 -Simulated 1400000 total bases, 140248 mutations (10.02%), G=1000000, d=0.40, r=.100 - -Model: -1 1372378 -2 376628 -3 172266 -4 39390 - - -Observed Counts: -1 535326 -2 325122 -3 203651 -4 111156 -5 53196 -6 24780 -7 11041 -8 4679 -9 1913 -10 715 -11 267 -12 124 -13 33 -14 11 -15 2 -16 2 -17 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out.eval deleted file mode 100644 index 8546e03..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 376628 172266 39390 -obs: 535326 325122 203651 111156 -diff: 837052 51506 -31385 -71766 -diffp: 156.36 15.84 -15.41 -64.56 -#sweep.k11//sim-d0.40-r.100-k11-g1000000-out sumkmer 1175255 sumdiff: 785407 score: 33.171 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out deleted file mode 100644 index 0aca404..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out +++ /dev/null @@ -1,28 +0,0 @@ -Simulating G=1000000, d=0.40, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.200 -Simulated 1400000 total bases, 279833 mutations (19.99%), G=1000000, d=0.40, r=.200 - -Model: -1 1828200 -2 385771 -3 62816 -4 2951 - - -Observed Counts: -1 614520 -2 398264 -3 213372 -4 97729 -5 40761 -6 15455 -7 5548 -8 1827 -9 604 -10 162 -11 50 -12 20 -13 3 -14 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out.eval deleted file mode 100644 index b7debfc..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828200 385771 62816 2951 -obs: 614520 398264 213372 97729 -diff: 1213680 -12493 -150556 -94778 -diffp: 197.50 -3.14 -70.56 -96.98 -#sweep.k11//sim-d0.40-r.200-k11-g1000000-out sumkmer 1323885 sumdiff: 955853 score: 27.799 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out deleted file mode 100644 index 6cbaca3..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.40, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.300 -Simulated 1400000 total bases, 419986 mutations (30.00%), G=1000000, d=0.40, r=.300 - -Model: -1 1960452 -2 396201 -3 15505 -4 156 - - -Observed Counts: -1 632749 -2 422899 -3 216272 -4 94121 -5 36289 -6 12317 -7 3963 -8 1154 -9 316 -10 69 -11 22 -12 2 -13 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out.eval deleted file mode 100644 index b9cd8d1..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960452 396201 15505 156 -obs: 632749 422899 216272 94121 -diff: 1327703 -26698 -200767 -93965 -diffp: 209.83 -6.31 -92.83 -99.83 -#sweep.k11//sim-d0.40-r.300-k11-g1000000-out sumkmer 1366041 sumdiff: 1006273 score: 26.337 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out deleted file mode 100644 index 805f6d6..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out +++ /dev/null @@ -1,25 +0,0 @@ -Simulating G=1000000, d=0.40, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=0.00 -Simulated 1400000 total bases, 0 mutations (0.00%), G=1000000, d=0.40, r=0.00 - -Model: -1 0 -2 600000 -3 0 -4 400000 - - -Observed Counts: -2 372555 -4 301401 -6 75796 -8 34434 -10 7775 -12 2538 -14 543 -16 156 -18 34 -20 4 -22 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 5d27eac..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.40-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 600000 0 400000 -obs: 0 372555 0 301401 -diff: 0 227445 0 98599 -diffp: 0.00 61.05 0.00 32.71 -#sweep.k11//sim-d0.40-r0.00-k11-g1000000-out sumkmer 673956 sumdiff: 326044 score: 51.622 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out deleted file mode 100644 index 9853c98..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.50, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.001 -Simulated 1500000 total bases, 1498 mutations (0.10%), G=1000000, d=0.50, r=.001 - -Model: -1 21889 -2 494587 -3 10825 -4 489114 - - -Observed Counts: -1 13253 -2 305734 -3 9890 -4 337195 -5 5066 -6 73415 -7 2586 -8 43773 -9 838 -10 8978 -11 305 -12 3747 -13 89 -14 748 -15 27 -16 242 -17 6 -18 36 -19 3 -20 14 -22 1 -23 1 -24 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out.eval deleted file mode 100644 index a34d4ab..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 494587 10825 489114 -obs: 13253 305734 9890 337195 -diff: 8636 188853 935 151919 -diffp: 65.16 61.77 9.45 45.05 -#sweep.k11//sim-d0.50-r.001-k11-g1000000-out sumkmer 666072 sumdiff: 350343 score: 47.402 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out deleted file mode 100644 index 17489b7..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.50, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.010 -Simulated 1500000 total bases, 15144 mutations (1.01%), G=1000000, d=0.50, r=.010 - -Model: -1 209322 -2 453146 -3 93707 -4 400815 - - -Observed Counts: -1 121379 -2 266034 -3 80454 -4 265647 -5 37809 -6 55397 -7 16990 -8 29345 -9 5249 -10 5836 -11 1788 -12 2120 -13 450 -14 431 -15 130 -16 113 -17 25 -18 22 -19 6 -20 9 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out.eval deleted file mode 100644 index 45ee8c3..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209322 453146 93707 400815 -obs: 121379 266034 80454 265647 -diff: 87943 187112 13253 135168 -diffp: 72.45 70.33 16.47 50.88 -#sweep.k11//sim-d0.50-r.010-k11-g1000000-out sumkmer 733514 sumdiff: 423476 score: 42.267 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out deleted file mode 100644 index 725f10e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out +++ /dev/null @@ -1,36 +0,0 @@ -Simulating G=1000000, d=0.50, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.050 -Simulated 1500000 total bases, 74698 mutations (4.98%), G=1000000, d=0.50, r=.050 - -Model: -1 862399 -2 377366 -3 245266 -4 161766 - - -Observed Counts: -1 388492 -2 253606 -3 193613 -4 151118 -5 68124 -6 38265 -7 21693 -8 12040 -9 5189 -10 2607 -11 1310 -12 560 -13 265 -14 122 -15 60 -16 20 -17 8 -18 3 -19 3 -20 1 -21 1 -22 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out.eval deleted file mode 100644 index 10490d6..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 377366 245266 161766 -obs: 388492 253606 193613 151118 -diff: 473907 123760 51653 10648 -diffp: 121.99 48.80 26.68 7.05 -#sweep.k11//sim-d0.50-r.050-k11-g1000000-out sumkmer 986829 sumdiff: 659968 score: 33.122 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out deleted file mode 100644 index 1be3bad..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.50, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.100 -Simulated 1500000 total bases, 149768 mutations (9.98%), G=1000000, d=0.50, r=.100 - -Model: -1 1372378 -2 392333 -3 215333 -4 49238 - - -Observed Counts: -1 518323 -2 320350 -3 216216 -4 124567 -5 62158 -6 30549 -7 14608 -8 6568 -9 2752 -10 1169 -11 438 -12 199 -13 69 -14 22 -15 10 -16 4 -17 1 -18 1 -19 1 -20 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out.eval deleted file mode 100644 index f632454..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 392333 215333 49238 -obs: 518323 320350 216216 124567 -diff: 854055 71983 -883 -75329 -diffp: 164.77 22.47 -0.41 -60.47 -#sweep.k11//sim-d0.50-r.100-k11-g1000000-out sumkmer 1179456 sumdiff: 849826 score: 27.948 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out deleted file mode 100644 index ebaf745..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out +++ /dev/null @@ -1,29 +0,0 @@ -Simulating G=1000000, d=0.50, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.200 -Simulated 1500000 total bases, 300861 mutations (20.06%), G=1000000, d=0.50, r=.200 - -Model: -1 1828200 -2 460739 -3 78520 -4 3689 - - -Observed Counts: -1 588146 -2 406655 -3 230116 -4 112586 -5 49621 -6 20018 -7 7710 -8 2798 -9 975 -10 298 -11 91 -12 31 -13 5 -14 3 -15 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out.eval deleted file mode 100644 index e26830a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828200 460739 78520 3689 -obs: 588146 406655 230116 112586 -diff: 1240054 54084 -151596 -108897 -diffp: 210.84 13.30 -65.88 -96.72 -#sweep.k11//sim-d0.50-r.200-k11-g1000000-out sumkmer 1337503 sumdiff: 1033645 score: 22.718 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out deleted file mode 100644 index b7baa5b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.50, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.300 -Simulated 1500000 total bases, 449978 mutations (30.00%), G=1000000, d=0.50, r=.300 - -Model: -1 1960453 -2 490308 -3 19382 -4 195 - - -Observed Counts: -1 604168 -2 432270 -3 235376 -4 109469 -5 45013 -6 16791 -7 5767 -8 1792 -9 525 -10 140 -11 38 -12 12 -13 5 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out.eval deleted file mode 100644 index f0af3c2..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 490308 19382 195 -obs: 604168 432270 235376 109469 -diff: 1356285 58038 -215994 -109274 -diffp: 224.49 13.43 -91.77 -99.82 -#sweep.k11//sim-d0.50-r.300-k11-g1000000-out sumkmer 1381283 sumdiff: 1089055 score: 21.156 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out deleted file mode 100644 index 827f549..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.50, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=0.00 -Simulated 1500000 total bases, 0 mutations (0.00%), G=1000000, d=0.50, r=0.00 - -Model: -1 0 -2 500000 -3 0 -4 500000 - - -Observed Counts: -2 310142 -4 347072 -6 76792 -8 46182 -10 9591 -12 4052 -14 765 -16 286 -18 56 -20 14 -22 2 -24 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 423f6ce..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.50-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 500000 0 500000 -obs: 0 310142 0 347072 -diff: 0 189858 0 152928 -diffp: 0.00 61.22 0.00 44.06 -#sweep.k11//sim-d0.50-r0.00-k11-g1000000-out sumkmer 657214 sumdiff: 342786 score: 47.843 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out deleted file mode 100644 index 415cbc3..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.60, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.001 -Simulated 1600000 total bases, 1621 mutations (0.10%), G=1000000, d=0.60, r=.001 - -Model: -1 21889 -2 395693 -3 12990 -4 586937 - - -Observed Counts: -1 13582 -2 243428 -3 10812 -4 383578 -5 5536 -6 69699 -7 3247 -8 57227 -9 1013 -10 9888 -11 457 -12 5703 -13 132 -14 960 -15 46 -16 446 -17 10 -18 56 -19 6 -20 21 -21 1 -22 8 -24 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out.eval deleted file mode 100644 index 637dd4d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 395693 12990 586937 -obs: 13582 243428 10812 383578 -diff: 8307 152265 2178 203359 -diffp: 61.16 62.55 20.14 53.02 -#sweep.k11//sim-d0.60-r.001-k11-g1000000-out sumkmer 651400 sumdiff: 366109 score: 43.797 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out deleted file mode 100644 index 1862c3a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out +++ /dev/null @@ -1,40 +0,0 @@ -Simulating G=1000000, d=0.60, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.010 -Simulated 1600000 total bases, 16133 mutations (1.01%), G=1000000, d=0.60, r=.010 - -Model: -1 209323 -2 364707 -3 112449 -4 480978 - - -Observed Counts: -1 119700 -2 216467 -3 86360 -4 300153 -5 40879 -6 53361 -7 20993 -8 38041 -9 6156 -10 6514 -11 2534 -12 3187 -13 666 -14 580 -15 203 -16 212 -17 32 -18 30 -19 17 -20 15 -21 4 -22 1 -23 2 -24 1 -26 1 -28 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out.eval deleted file mode 100644 index 118ab1c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 364707 112449 480978 -obs: 119700 216467 86360 300153 -diff: 89623 148240 26089 180825 -diffp: 74.87 68.48 30.21 60.24 -#sweep.k11//sim-d0.60-r.010-k11-g1000000-out sumkmer 722680 sumdiff: 444777 score: 38.455 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out deleted file mode 100644 index 8c44f1f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out +++ /dev/null @@ -1,35 +0,0 @@ -Simulating G=1000000, d=0.60, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.050 -Simulated 1600000 total bases, 80106 mutations (5.01%), G=1000000, d=0.60, r=.050 - -Model: -1 862398 -2 339080 -3 294319 -4 194120 - - -Observed Counts: -1 380567 -2 232242 -3 205249 -4 166580 -5 74988 -6 42664 -7 26984 -8 14807 -9 6756 -10 3422 -11 1810 -12 833 -13 396 -14 176 -15 76 -16 30 -17 10 -18 9 -19 2 -20 2 -22 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out.eval deleted file mode 100644 index a6afbfe..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862398 339080 294319 194120 -obs: 380567 232242 205249 166580 -diff: 481831 106838 89070 27540 -diffp: 126.61 46.00 43.40 16.53 -#sweep.k11//sim-d0.60-r.050-k11-g1000000-out sumkmer 984638 sumdiff: 705279 score: 28.372 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out deleted file mode 100644 index d76a174..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=0.60, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.100 -Simulated 1600000 total bases, 159790 mutations (9.99%), G=1000000, d=0.60, r=.100 - -Model: -1 1372378 -2 408037 -3 258400 -4 59086 - - -Observed Counts: -1 500711 -2 314685 -3 230067 -4 136509 -5 70097 -6 36993 -7 18457 -8 8223 -9 3896 -10 1737 -11 717 -12 294 -13 111 -14 36 -15 12 -16 12 -17 4 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out.eval deleted file mode 100644 index 2c1bac7..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 408037 258400 59086 -obs: 500711 314685 230067 136509 -diff: 871667 93352 28333 -77423 -diffp: 174.09 29.67 12.32 -56.72 -#sweep.k11//sim-d0.60-r.100-k11-g1000000-out sumkmer 1181972 sumdiff: 915929 score: 22.508 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out deleted file mode 100644 index f023c19..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=0.60, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.200 -Simulated 1600000 total bases, 320436 mutations (20.03%), G=1000000, d=0.60, r=.200 - -Model: -1 1828200 -2 535707 -3 94224 -4 4427 - - -Observed Counts: -1 563104 -2 411633 -3 244619 -4 126346 -5 59288 -6 25585 -7 10362 -8 3859 -9 1517 -10 498 -11 158 -12 40 -13 9 -14 1 -15 1 -16 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out.eval deleted file mode 100644 index e6a1cdd..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828200 535707 94224 4427 -obs: 563104 411633 244619 126346 -diff: 1265096 124074 -150395 -121919 -diffp: 224.66 30.14 -61.48 -96.50 -#sweep.k11//sim-d0.60-r.200-k11-g1000000-out sumkmer 1345702 sumdiff: 1116856 score: 17.006 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out deleted file mode 100644 index e410ef0..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out +++ /dev/null @@ -1,28 +0,0 @@ -Simulating G=1000000, d=0.60, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.300 -Simulated 1600000 total bases, 479219 mutations (29.95%), G=1000000, d=0.60, r=.300 - -Model: -1 1960452 -2 584415 -3 23258 -4 234 - - -Observed Counts: -1 575456 -2 441097 -3 250395 -4 125380 -5 54772 -6 21426 -7 7867 -8 2633 -9 812 -10 265 -11 76 -12 18 -13 4 -14 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out.eval deleted file mode 100644 index e90a08e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960452 584415 23258 234 -obs: 575456 441097 250395 125380 -diff: 1384996 143318 -227137 -125146 -diffp: 240.68 32.49 -90.71 -99.81 -#sweep.k11//sim-d0.60-r.300-k11-g1000000-out sumkmer 1392328 sumdiff: 1176031 score: 15.535 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out deleted file mode 100644 index 8180c13..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.60, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=0.00 -Simulated 1600000 total bases, 0 mutations (0.00%), G=1000000, d=0.60, r=0.00 - -Model: -1 0 -2 400000 -3 0 -4 600000 - - -Observed Counts: -2 248998 -4 395721 -6 72370 -8 60416 -10 10608 -12 5992 -14 1019 -16 470 -18 57 -20 30 -22 6 -24 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 4c6d119..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.60-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 400000 0 600000 -obs: 0 248998 0 395721 -diff: 0 151002 0 204279 -diffp: 0.00 60.64 0.00 51.62 -#sweep.k11//sim-d0.60-r0.00-k11-g1000000-out sumkmer 644719 sumdiff: 355281 score: 44.894 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out deleted file mode 100644 index 33324f6..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.70, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.001 -Simulated 1700000 total bases, 1672 mutations (0.10%), G=1000000, d=0.70, r=.001 - -Model: -1 21889 -2 296800 -3 15155 -4 684760 - - -Observed Counts: -1 13138 -2 182555 -3 11141 -4 434551 -5 5854 -6 60429 -7 3654 -8 72780 -9 1208 -10 9942 -11 655 -12 8297 -13 142 -14 1134 -15 63 -16 722 -17 20 -18 88 -19 4 -20 49 -21 1 -22 3 -24 4 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out.eval deleted file mode 100644 index 3f50b37..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 296800 15155 684760 -obs: 13138 182555 11141 434551 -diff: 8751 114245 4014 250209 -diffp: 66.61 62.58 36.03 57.58 -#sweep.k11//sim-d0.70-r.001-k11-g1000000-out sumkmer 641385 sumdiff: 377219 score: 41.187 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out deleted file mode 100644 index 03189ba..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out +++ /dev/null @@ -1,40 +0,0 @@ -Simulating G=1000000, d=0.70, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.010 -Simulated 1700000 total bases, 17170 mutations (1.01%), G=1000000, d=0.70, r=.010 - -Model: -1 209322 -2 276269 -3 131190 -4 561141 - - -Observed Counts: -1 119853 -2 163873 -3 90503 -4 338682 -5 42895 -6 47265 -7 25146 -8 48310 -9 7367 -10 6973 -11 3560 -12 4705 -13 857 -14 673 -15 337 -16 320 -17 65 -18 55 -19 19 -20 17 -21 4 -22 8 -23 1 -24 2 -26 1 -33 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out.eval deleted file mode 100644 index e42db2a..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209322 276269 131190 561141 -obs: 119853 163873 90503 338682 -diff: 89469 112396 40687 222459 -diffp: 74.65 68.59 44.96 65.68 -#sweep.k11//sim-d0.70-r.010-k11-g1000000-out sumkmer 712911 sumdiff: 465011 score: 34.773 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out deleted file mode 100644 index ad2519f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.70, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.050 -Simulated 1700000 total bases, 84612 mutations (4.98%), G=1000000, d=0.70, r=.050 - -Model: -1 862399 -2 300793 -3 343373 -4 226473 - - -Observed Counts: -1 372437 -2 209101 -3 214767 -4 182674 -5 80596 -6 47159 -7 32231 -8 18304 -9 8385 -10 4509 -11 2525 -12 1146 -13 522 -14 290 -15 116 -16 59 -17 18 -18 17 -19 6 -23 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out.eval deleted file mode 100644 index f19bbcf..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 300793 343373 226473 -obs: 372437 209101 214767 182674 -diff: 489962 91692 128606 43799 -diffp: 131.56 43.85 59.88 23.98 -#sweep.k11//sim-d0.70-r.050-k11-g1000000-out sumkmer 978979 sumdiff: 754059 score: 22.975 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out deleted file mode 100644 index d69c30b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.70, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.100 -Simulated 1700000 total bases, 170607 mutations (10.04%), G=1000000, d=0.70, r=.100 - -Model: -1 1372377 -2 423742 -3 301466 -4 68933 - - -Observed Counts: -1 484558 -2 310821 -3 241812 -4 147845 -5 78655 -6 42647 -7 22211 -8 10583 -9 5090 -10 2192 -11 965 -12 432 -13 185 -14 72 -15 33 -16 11 -17 1 -18 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out.eval deleted file mode 100644 index cf0a62e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372377 423742 301466 68933 -obs: 484558 310821 241812 147845 -diff: 887819 112921 59654 -78912 -diffp: 183.22 36.33 24.67 -53.37 -#sweep.k11//sim-d0.70-r.100-k11-g1000000-out sumkmer 1185036 sumdiff: 981482 score: 17.177 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out deleted file mode 100644 index 2036097..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=0.70, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.200 -Simulated 1700000 total bases, 339295 mutations (19.96%), G=1000000, d=0.70, r=.200 - -Model: -1 1828200 -2 610675 -3 109928 -4 5165 - - -Observed Counts: -1 538965 -2 415813 -3 257788 -4 139617 -5 68522 -6 31342 -7 13274 -8 5366 -9 2112 -10 761 -11 249 -12 91 -13 33 -14 10 -15 1 -16 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out.eval deleted file mode 100644 index 4f120d5..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828200 610675 109928 5165 -obs: 538965 415813 257788 139617 -diff: 1289235 194862 -147860 -134452 -diffp: 239.21 46.86 -57.36 -96.30 -#sweep.k11//sim-d0.70-r.200-k11-g1000000-out sumkmer 1352183 sumdiff: 1201785 score: 11.123 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out deleted file mode 100644 index 1732314..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=0.70, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.300 -Simulated 1700000 total bases, 509407 mutations (29.97%), G=1000000, d=0.70, r=.300 - -Model: -1 1960453 -2 678523 -3 27135 -4 273 - - -Observed Counts: -1 548582 -2 446457 -3 265210 -4 140497 -5 64322 -6 26689 -7 10344 -8 3711 -9 1226 -10 412 -11 129 -12 24 -13 7 -14 3 -15 1 -17 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out.eval deleted file mode 100644 index 579f974..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 678523 27135 273 -obs: 548582 446457 265210 140497 -diff: 1411871 232066 -238075 -140224 -diffp: 257.37 51.98 -89.77 -99.81 -#sweep.k11//sim-d0.70-r.300-k11-g1000000-out sumkmer 1400746 sumdiff: 1265638 score: 9.645 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out deleted file mode 100644 index 17d0175..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out +++ /dev/null @@ -1,26 +0,0 @@ -Simulating G=1000000, d=0.70, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=0.00 -Simulated 1700000 total bases, 0 mutations (0.00%), G=1000000, d=0.70, r=0.00 - -Model: -1 0 -2 300000 -3 0 -4 700000 - - -Observed Counts: -2 186358 -4 447653 -6 62895 -8 77164 -10 10533 -12 8851 -14 1145 -16 706 -18 106 -20 47 -22 5 -24 6 diff --git a/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out.eval deleted file mode 100644 index ae07537..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.70-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 300000 0 700000 -obs: 0 186358 0 447653 -diff: 0 113642 0 252347 -diffp: 0.00 60.98 0.00 56.37 -#sweep.k11//sim-d0.70-r0.00-k11-g1000000-out sumkmer 634011 sumdiff: 365989 score: 42.274 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out deleted file mode 100644 index 8659f75..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.80, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.001 -Simulated 1800000 total bases, 1750 mutations (0.10%), G=1000000, d=0.80, r=.001 - -Model: -1 21889 -2 197906 -3 17320 -4 782583 - - -Observed Counts: -1 13269 -2 121553 -3 11557 -4 487106 -5 5909 -6 45648 -7 4291 -8 91946 -9 1324 -10 8621 -11 827 -12 11794 -13 187 -14 1088 -15 106 -16 1208 -17 22 -18 87 -19 8 -20 89 -21 2 -22 7 -24 3 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out.eval deleted file mode 100644 index 536e387..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 197906 17320 782583 -obs: 13269 121553 11557 487106 -diff: 8620 76353 5763 295477 -diffp: 64.96 62.81 49.87 60.66 -#sweep.k11//sim-d0.80-r.001-k11-g1000000-out sumkmer 633485 sumdiff: 386213 score: 39.034 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out deleted file mode 100644 index 9705c87..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out +++ /dev/null @@ -1,38 +0,0 @@ -Simulating G=1000000, d=0.80, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.010 -Simulated 1800000 total bases, 17863 mutations (0.99%), G=1000000, d=0.80, r=.010 - -Model: -1 209323 -2 187830 -3 149932 -4 641304 - - -Observed Counts: -1 116571 -2 112840 -3 96069 -4 377829 -5 44329 -6 38612 -7 30010 -8 60398 -9 8278 -10 6539 -11 4643 -12 6392 -13 965 -14 772 -15 484 -16 543 -17 95 -18 64 -19 34 -20 40 -21 5 -22 4 -23 5 -24 6 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out.eval deleted file mode 100644 index c5cf85f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 187830 149932 641304 -obs: 116571 112840 96069 377829 -diff: 92752 74990 53863 263475 -diffp: 79.57 66.46 56.07 69.73 -#sweep.k11//sim-d0.80-r.010-k11-g1000000-out sumkmer 703309 sumdiff: 485080 score: 31.029 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out deleted file mode 100644 index e64fa04..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out +++ /dev/null @@ -1,36 +0,0 @@ -Simulating G=1000000, d=0.80, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.050 -Simulated 1800000 total bases, 90503 mutations (5.03%), G=1000000, d=0.80, r=.050 - -Model: -1 862399 -2 262506 -3 392426 -4 258826 - - -Observed Counts: -1 365134 -2 190163 -3 226532 -4 196773 -5 84690 -6 51058 -7 37839 -8 21960 -9 9866 -10 5586 -11 3183 -12 1531 -13 709 -14 356 -15 196 -16 75 -17 29 -18 13 -19 12 -20 3 -21 3 -23 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out.eval deleted file mode 100644 index 9e7f38d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 262506 392426 258826 -obs: 365134 190163 226532 196773 -diff: 497265 72343 165894 62053 -diffp: 136.19 38.04 73.23 31.54 -#sweep.k11//sim-d0.80-r.050-k11-g1000000-out sumkmer 978602 sumdiff: 797555 score: 18.501 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out deleted file mode 100644 index e10b954..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out +++ /dev/null @@ -1,32 +0,0 @@ -Simulating G=1000000, d=0.80, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.100 -Simulated 1800000 total bases, 179953 mutations (10.00%), G=1000000, d=0.80, r=.100 - -Model: -1 1372378 -2 439446 -3 344533 -4 78781 - - -Observed Counts: -1 466254 -2 306796 -3 251319 -4 158560 -5 86335 -6 48858 -7 26539 -8 13029 -9 6501 -10 3002 -11 1425 -12 601 -13 224 -14 122 -15 43 -16 16 -17 8 -18 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out.eval deleted file mode 100644 index 517c792..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 439446 344533 78781 -obs: 466254 306796 251319 158560 -diff: 906124 132650 93214 -79779 -diffp: 194.34 43.24 37.09 -50.31 -#sweep.k11//sim-d0.80-r.100-k11-g1000000-out sumkmer 1182929 sumdiff: 1052209 score: 11.051 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out deleted file mode 100644 index dc68d03..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=0.80, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.200 -Simulated 1800000 total bases, 360901 mutations (20.05%), G=1000000, d=0.80, r=.200 - -Model: -1 1828201 -2 685643 -3 125633 -4 5902 - - -Observed Counts: -1 515454 -2 419869 -3 270950 -4 152233 -5 78276 -6 37069 -7 16266 -8 6787 -9 2692 -10 1014 -11 368 -12 138 -13 50 -14 17 -15 4 -16 1 -18 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out.eval deleted file mode 100644 index 572a85e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 685643 125633 5902 -obs: 515454 419869 270950 152233 -diff: 1312747 265774 -145317 -146331 -diffp: 254.68 63.30 -53.63 -96.12 -#sweep.k11//sim-d0.80-r.200-k11-g1000000-out sumkmer 1358506 sumdiff: 1286873 score: 5.273 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out deleted file mode 100644 index bfbbc4f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out +++ /dev/null @@ -1,29 +0,0 @@ -Simulating G=1000000, d=0.80, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.300 -Simulated 1800000 total bases, 540420 mutations (30.02%), G=1000000, d=0.80, r=.300 - -Model: -1 1960452 -2 772630 -3 31011 -4 312 - - -Observed Counts: -1 523305 -2 452017 -3 278257 -4 153831 -5 73663 -6 32737 -7 13242 -8 5018 -9 1743 -10 609 -11 211 -12 47 -13 15 -14 7 -16 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out.eval deleted file mode 100644 index ac5f211..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960452 772630 31011 312 -obs: 523305 452017 278257 153831 -diff: 1437147 320613 -247246 -153519 -diffp: 274.63 70.93 -88.86 -99.80 -#sweep.k11//sim-d0.80-r.300-k11-g1000000-out sumkmer 1407410 sumdiff: 1356995 score: 3.582 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out deleted file mode 100644 index 7a8423c..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.80, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=0.00 -Simulated 1800000 total bases, 0 mutations (0.00%), G=1000000, d=0.80, r=0.00 - -Model: -1 0 -2 199999 -3 0 -4 800000 - - -Observed Counts: -2 124164 -4 502440 -6 47382 -8 97209 -10 9013 -12 12608 -14 1139 -16 1170 -18 99 -20 83 -22 8 -24 8 -26 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 3c38583..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.80-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 199999 0 800000 -obs: 0 124164 0 502440 -diff: 0 75835 0 297560 -diffp: 0.00 61.08 0.00 59.22 -#sweep.k11//sim-d0.80-r0.00-k11-g1000000-out sumkmer 626604 sumdiff: 373395 score: 40.410 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out deleted file mode 100644 index ec768bf..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.90, r=.001, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.001 -Simulated 1900000 total bases, 1799 mutations (0.09%), G=1000000, d=0.90, r=.001 - -Model: -1 21889 -2 99013 -3 19485 -4 880406 - - -Observed Counts: -1 12939 -2 61036 -3 12010 -4 542998 -5 5958 -6 25571 -7 4900 -8 114856 -9 1349 -10 5395 -11 991 -12 16246 -13 203 -14 747 -15 136 -16 1730 -17 28 -18 88 -19 7 -20 159 -21 5 -22 8 -24 7 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out.eval deleted file mode 100644 index 6ab4f8e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 99013 19485 880406 -obs: 12939 61036 12010 542998 -diff: 8950 37977 7475 337408 -diffp: 69.17 62.22 62.24 62.14 -#sweep.k11//sim-d0.90-r.001-k11-g1000000-out sumkmer 628983 sumdiff: 391810 score: 37.707 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out deleted file mode 100644 index 4911b42..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out +++ /dev/null @@ -1,39 +0,0 @@ -Simulating G=1000000, d=0.90, r=.010, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.010 -Simulated 1900000 total bases, 18989 mutations (1.00%), G=1000000, d=0.90, r=.010 - -Model: -1 209322 -2 99392 -3 168673 -4 721467 - - -Observed Counts: -1 117519 -2 62121 -3 101295 -4 418290 -5 45507 -6 25877 -7 35418 -8 74253 -9 8767 -10 5128 -11 6126 -12 8764 -13 1190 -14 705 -15 691 -16 773 -17 110 -18 67 -19 59 -20 51 -21 7 -22 4 -23 5 -24 1 -26 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out.eval deleted file mode 100644 index 5d8b0f6..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209322 99392 168673 721467 -obs: 117519 62121 101295 418290 -diff: 91803 37271 67378 303177 -diffp: 78.12 60.00 66.52 72.48 -#sweep.k11//sim-d0.90-r.010-k11-g1000000-out sumkmer 699225 sumdiff: 499629 score: 28.545 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out deleted file mode 100644 index afc2402..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=0.90, r=.050, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.050 -Simulated 1900000 total bases, 94752 mutations (4.99%), G=1000000, d=0.90, r=.050 - -Model: -1 862399 -2 224220 -3 441479 -4 291180 - - -Observed Counts: -1 355545 -2 170631 -3 234067 -4 212454 -5 88348 -6 54291 -7 43760 -8 25726 -9 11679 -10 6784 -11 4186 -12 2115 -13 956 -14 521 -15 236 -16 119 -17 56 -18 25 -19 18 -20 5 -21 1 -22 4 -23 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out.eval deleted file mode 100644 index 5fb3d0f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 224220 441479 291180 -obs: 355545 170631 234067 212454 -diff: 506854 53589 207412 78726 -diffp: 142.56 31.41 88.61 37.06 -#sweep.k11//sim-d0.90-r.050-k11-g1000000-out sumkmer 972697 sumdiff: 846581 score: 12.966 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out deleted file mode 100644 index 5fc7d2f..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=0.90, r=.100, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.100 -Simulated 1900000 total bases, 190442 mutations (10.02%), G=1000000, d=0.90, r=.100 - -Model: -1 1372378 -2 455151 -3 387600 -4 88629 - - -Observed Counts: -1 451331 -2 301947 -3 261659 -4 168218 -5 93725 -6 55459 -7 30435 -8 15665 -9 7920 -10 3784 -11 1766 -12 822 -13 355 -14 166 -15 71 -16 29 -17 9 -18 4 -19 2 -21 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out.eval deleted file mode 100644 index 8f43717..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 455151 387600 88629 -obs: 451331 301947 261659 168218 -diff: 921047 153204 125941 -79589 -diffp: 204.07 50.74 48.13 -47.31 -#sweep.k11//sim-d0.90-r.100-k11-g1000000-out sumkmer 1183155 sumdiff: 1120603 score: 5.287 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out deleted file mode 100644 index a017449..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=0.90, r=.200, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.200 -Simulated 1900000 total bases, 380161 mutations (20.01%), G=1000000, d=0.90, r=.200 - -Model: -1 1828201 -2 760611 -3 141337 -4 6640 - - -Observed Counts: -1 494297 -2 422230 -3 280822 -4 164536 -5 87784 -6 43132 -7 19644 -8 8679 -9 3648 -10 1358 -11 530 -12 221 -13 46 -14 16 -15 12 -16 3 -17 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out.eval deleted file mode 100644 index 9d1ff07..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 760611 141337 6640 -obs: 494297 422230 280822 164536 -diff: 1333904 338381 -139485 -157896 -diffp: 269.86 80.14 -49.67 -95.96 -#sweep.k11//sim-d0.90-r.200-k11-g1000000-out sumkmer 1361885 sumdiff: 1374904 score: -0.956 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out deleted file mode 100644 index aeed650..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out +++ /dev/null @@ -1,29 +0,0 @@ -Simulating G=1000000, d=0.90, r=.300, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.300 -Simulated 1900000 total bases, 569763 mutations (29.99%), G=1000000, d=0.90, r=.300 - -Model: -1 1960453 -2 866737 -3 34888 -4 351 - - -Observed Counts: -1 500177 -2 454521 -3 289059 -4 168029 -5 83500 -6 38680 -7 16358 -8 6485 -9 2460 -10 842 -11 285 -12 102 -13 35 -14 7 -15 2 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out.eval deleted file mode 100644 index e66af26..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960453 866737 34888 351 -obs: 500177 454521 289059 168029 -diff: 1460276 412216 -254171 -167678 -diffp: 291.95 90.69 -87.93 -99.79 -#sweep.k11//sim-d0.90-r.300-k11-g1000000-out sumkmer 1411786 sumdiff: 1450643 score: -2.752 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out deleted file mode 100644 index c2abfe6..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out +++ /dev/null @@ -1,27 +0,0 @@ -Simulating G=1000000, d=0.90, r=0.00, k=11 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=0.00 -Simulated 1900000 total bases, 0 mutations (0.00%), G=1000000, d=0.90, r=0.00 - -Model: -1 0 -2 99999 -3 0 -4 900000 - - -Observed Counts: -2 61632 -4 559232 -6 26887 -8 120579 -10 5737 -12 17508 -14 828 -16 1864 -18 89 -20 142 -22 10 -24 11 -26 1 diff --git a/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 35323f0..0000000 --- a/analysis/genomesim/sweep.k11/sim-d0.90-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 99999 0 900000 -obs: 0 61632 0 559232 -diff: 0 38367 0 340768 -diffp: 0.00 62.25 0.00 60.93 -#sweep.k11//sim-d0.90-r0.00-k11-g1000000-out sumkmer 620864 sumdiff: 379135 score: 38.934 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out deleted file mode 100644 index f9e1493..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out +++ /dev/null @@ -1,37 +0,0 @@ -Simulating G=1000000, d=1.00, r=.001, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.001 -Simulated 2000000 total bases, 2025 mutations (0.10%), G=1000000, d=1.00, r=.001 - -Model: -1 21889 -2 119 -3 21650 -4 978229 - - -Observed Counts: -1 13690 -2 170 -3 13250 -4 601123 -5 6328 -6 152 -7 6368 -8 139938 -9 1427 -10 53 -11 1528 -12 21712 -13 223 -14 12 -15 233 -16 2554 -17 21 -18 3 -19 34 -20 255 -23 4 -24 27 -28 1 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out.eval deleted file mode 100644 index f665054..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.001-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 21889 119 21650 978229 -obs: 13690 170 13250 601123 -diff: 8199 -51 8400 377106 -diffp: 59.89 -30.00 63.40 62.73 -#sweep.k11//sim-d1.00-r.001-k11-g1000000-out sumkmer 628233 sumdiff: 393654 score: 37.339 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out deleted file mode 100644 index 7f5073b..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out +++ /dev/null @@ -1,40 +0,0 @@ -Simulating G=1000000, d=1.00, r=.010, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.010 -Simulated 2000000 total bases, 19916 mutations (1.00%), G=1000000, d=1.00, r=.010 - -Model: -1 209323 -2 10954 -3 187415 -4 801630 - - -Observed Counts: -1 116407 -2 12524 -3 105680 -4 461930 -5 45133 -6 9569 -7 41124 -8 90201 -9 8852 -10 2818 -11 8030 -12 11746 -13 1193 -14 450 -15 1062 -16 1176 -17 127 -18 56 -19 102 -20 80 -21 8 -22 9 -23 9 -24 7 -25 1 -27 2 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out.eval deleted file mode 100644 index 8fb9b76..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.010-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 209323 10954 187415 801630 -obs: 116407 12524 105680 461930 -diff: 92916 -1570 81735 339700 -diffp: 79.82 -12.54 77.34 73.54 -#sweep.k11//sim-d1.00-r.010-k11-g1000000-out sumkmer 696541 sumdiff: 512781 score: 26.382 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out deleted file mode 100644 index c3a0120..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out +++ /dev/null @@ -1,40 +0,0 @@ -Simulating G=1000000, d=1.00, r=.050, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.050 -Simulated 2000000 total bases, 99866 mutations (4.99%), G=1000000, d=1.00, r=.050 - -Model: -1 862399 -2 185933 -3 490533 -4 323533 - - -Observed Counts: -1 348492 -2 150255 -3 243948 -4 226372 -5 91774 -6 56748 -7 50074 -8 29518 -9 13438 -10 8042 -11 5166 -12 2691 -13 1244 -14 658 -15 391 -16 199 -17 67 -18 39 -19 20 -20 11 -21 6 -22 1 -23 2 -24 1 -26 1 -28 1 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out.eval deleted file mode 100644 index 6e000bf..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.050-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 862399 185933 490533 323533 -obs: 348492 150255 243948 226372 -diff: 513907 35678 246585 97161 -diffp: 147.47 23.74 101.08 42.92 -#sweep.k11//sim-d1.00-r.050-k11-g1000000-out sumkmer 969067 sumdiff: 893331 score: 7.815 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out deleted file mode 100644 index 714d2b5..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out +++ /dev/null @@ -1,34 +0,0 @@ -Simulating G=1000000, d=1.00, r=.100, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.100 -Simulated 2000000 total bases, 199537 mutations (9.98%), G=1000000, d=1.00, r=.100 - -Model: -1 1372378 -2 470855 -3 430667 -4 98477 - - -Observed Counts: -1 437277 -2 297988 -3 270148 -4 177743 -5 100851 -6 61273 -7 34914 -8 17935 -9 9587 -10 4832 -11 2325 -12 1094 -13 503 -14 221 -15 93 -16 42 -17 16 -18 10 -20 2 -21 2 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out.eval deleted file mode 100644 index 9dd1a35..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.100-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1372378 470855 430667 98477 -obs: 437277 297988 270148 177743 -diff: 935101 172867 160519 -79266 -diffp: 213.85 58.01 59.42 -44.60 -#sweep.k11//sim-d1.00-r.100-k11-g1000000-out sumkmer 1183156 sumdiff: 1189221 score: -0.513 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out deleted file mode 100644 index 05b509e..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out +++ /dev/null @@ -1,31 +0,0 @@ -Simulating G=1000000, d=1.00, r=.200, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.200 -Simulated 2000000 total bases, 399325 mutations (19.97%), G=1000000, d=1.00, r=.200 - -Model: -1 1828201 -2 835580 -3 157041 -4 7378 - - -Observed Counts: -1 472636 -2 423035 -3 289443 -4 175990 -5 97550 -6 49707 -7 23752 -8 10665 -9 4417 -10 1776 -11 717 -12 313 -13 112 -14 38 -15 9 -16 7 -18 1 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out.eval deleted file mode 100644 index af1ed11..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.200-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1828201 835580 157041 7378 -obs: 472636 423035 289443 175990 -diff: 1355565 412545 -132402 -168612 -diffp: 286.81 97.52 -45.74 -95.81 -#sweep.k11//sim-d1.00-r.200-k11-g1000000-out sumkmer 1361104 sumdiff: 1467096 score: -7.787 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out deleted file mode 100644 index 8ce7041..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out +++ /dev/null @@ -1,30 +0,0 @@ -Simulating G=1000000, d=1.00, r=.300, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.300 -Simulated 2000000 total bases, 599644 mutations (29.98%), G=1000000, d=1.00, r=.300 - -Model: -1 1960452 -2 960844 -3 38764 -4 390 - - -Observed Counts: -1 477827 -2 456909 -3 296396 -4 181581 -5 93385 -6 45468 -7 19862 -8 8318 -9 3219 -10 1159 -11 398 -12 149 -13 39 -14 9 -15 8 -16 2 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out.eval deleted file mode 100644 index 5c00e2d..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r.300-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1960452 960844 38764 390 -obs: 477827 456909 296396 181581 -diff: 1482625 503935 -257632 -181191 -diffp: 310.28 110.29 -86.92 -99.79 -#sweep.k11//sim-d1.00-r.300-k11-g1000000-out sumkmer 1412713 sumdiff: 1547737 score: -9.558 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out b/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out deleted file mode 100644 index 4c901fb..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out +++ /dev/null @@ -1,24 +0,0 @@ -Simulating G=1000000, d=1.00, r=0.00, k=11 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=0.00 -Simulated 2000000 total bases, 0 mutations (0.00%), G=1000000, d=1.00, r=0.00 - -Model: -1 0 -2 0 -3 0 -4 1000000 - - -Observed Counts: -2 6 -4 620123 -6 3 -8 147899 -12 23748 -14 1 -16 2809 -20 278 -24 31 -28 1 diff --git a/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out.eval b/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out.eval deleted file mode 100644 index 41eb2fd..0000000 --- a/analysis/genomesim/sweep.k11/sim-d1.00-r0.00-k11-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 0 0 1000000 -obs: 0 6 0 620123 -diff: 0 -6 0 379877 -diffp: 0.00 -100.00 0.00 61.26 -#sweep.k11//sim-d1.00-r0.00-k11-g1000000-out sumkmer 620129 sumdiff: 379871 score: 38.743 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out deleted file mode 100644 index 0fe2b8c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.001 -Simulated 1000000 total bases, 1021 mutations (0.10%), G=1000000, d=0.00, r=.001 - -Model: -1 41582 -2 979208 -3 0 -4 0 - - -Observed Counts: -1 42364 -2 978798 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out.eval deleted file mode 100644 index 9d8bad2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 979208 0 0 -obs: 42364 978798 0 0 -diff: -782 410 0 0 -diffp: -1.85 0.04 0.00 0.00 -#sweep.k21//sim-d0.00-r.001-k21-g1000000-out sumkmer 1021162 sumdiff: -372 score: 100.036 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out deleted file mode 100644 index 8a88658..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.010 -Simulated 1000000 total bases, 9973 mutations (1.00%), G=1000000, d=0.00, r=.010 - -Model: -1 380544 -2 809727 -3 0 -4 0 - - -Observed Counts: -1 379522 -2 810219 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out.eval deleted file mode 100644 index 449e384..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380544 809727 0 0 -obs: 379522 810219 0 0 -diff: 1022 -492 0 0 -diffp: 0.27 -0.06 0.00 0.00 -#sweep.k21//sim-d0.00-r.010-k21-g1000000-out sumkmer 1189741 sumdiff: 530 score: 99.955 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out deleted file mode 100644 index 2eab41c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.050 -Simulated 1000000 total bases, 50008 mutations (5.00%), G=1000000, d=0.00, r=.050 - -Model: -1 1318876 -2 340561 -3 0 -4 0 - - -Observed Counts: -1 1321252 -2 339354 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out.eval deleted file mode 100644 index e9532ef..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 340561 0 0 -obs: 1321252 339354 0 0 -diff: -2376 1207 0 0 -diffp: -0.18 0.36 0.00 0.00 -#sweep.k21//sim-d0.00-r.050-k21-g1000000-out sumkmer 1660606 sumdiff: -1169 score: 100.070 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out deleted file mode 100644 index 639694a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.100 -Simulated 1000000 total bases, 99939 mutations (9.99%), G=1000000, d=0.00, r=.100 - -Model: -1 1781162 -2 109418 -3 0 -4 0 - - -Observed Counts: -1 1778096 -2 110932 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out.eval deleted file mode 100644 index 7c80dad..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781162 109418 0 0 -obs: 1778096 110932 0 0 -diff: 3066 -1514 0 0 -diffp: 0.17 -1.36 0.00 0.00 -#sweep.k21//sim-d0.00-r.100-k21-g1000000-out sumkmer 1889028 sumdiff: 1552 score: 99.918 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out deleted file mode 100644 index 0987b62..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.200 -Simulated 1000000 total bases, 200207 mutations (20.02%), G=1000000, d=0.00, r=.200 - -Model: -1 1981553 -2 9223 -3 0 -4 0 - - -Observed Counts: -1 1982146 -2 8907 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out.eval deleted file mode 100644 index 88c9ed8..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981553 9223 0 0 -obs: 1982146 8907 0 0 -diff: -593 316 0 0 -diffp: -0.03 3.55 0.00 0.00 -#sweep.k21//sim-d0.00-r.200-k21-g1000000-out sumkmer 1991053 sumdiff: -277 score: 100.014 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out deleted file mode 100644 index 0e8405e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.300 -Simulated 1000000 total bases, 300641 mutations (30.06%), G=1000000, d=0.00, r=.300 - -Model: -1 1998882 -2 558 -3 0 -4 0 - - -Observed Counts: -1 1998704 -2 628 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out.eval deleted file mode 100644 index df25975..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 558 0 0 -obs: 1998704 628 0 0 -diff: 178 -70 0 0 -diffp: 0.01 -11.15 0.00 0.00 -#sweep.k21//sim-d0.00-r.300-k21-g1000000-out sumkmer 1999332 sumdiff: 108 score: 99.995 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out deleted file mode 100644 index 06e7af2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=0.00 -Simulated 1000000 total bases, 0 mutations (0.00%), G=1000000, d=0.00, r=0.00 - -Model: -1 0 -2 1000000 -3 0 -4 0 - - -Observed Counts: -2 999976 -4 2 diff --git a/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out.eval deleted file mode 100644 index cfe2f14..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.00-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 1000000 0 0 -obs: 0 999976 0 2 -diff: 0 24 0 -2 -diffp: 0.00 0.00 0.00 -100.00 -#sweep.k21//sim-d0.00-r0.00-k21-g1000000-out sumkmer 999978 sumdiff: 22 score: 99.998 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out deleted file mode 100644 index 87daf0e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.001 -Simulated 1100000 total bases, 1088 mutations (0.10%), G=1000000, d=0.10, r=.001 - -Model: -1 41581 -2 881331 -3 4071 -4 95884 - - -Observed Counts: -1 41217 -2 881427 -3 3875 -4 96066 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out.eval deleted file mode 100644 index 025609f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41581 881331 4071 95884 -obs: 41217 881427 3875 96066 -diff: 364 -96 196 -182 -diffp: 0.88 -0.01 5.06 -0.19 -#sweep.k21//sim-d0.10-r.001-k21-g1000000-out sumkmer 1022585 sumdiff: 282 score: 99.972 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out deleted file mode 100644 index cf3be01..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.010 -Simulated 1100000 total bases, 10911 mutations (0.99%), G=1000000, d=0.10, r=.010 - -Model: -1 380543 -2 732375 -3 30813 -4 65565 - - -Observed Counts: -1 378172 -2 732989 -3 31150 -4 65590 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out.eval deleted file mode 100644 index 4878dda..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 732375 30813 65565 -obs: 378172 732989 31150 65590 -diff: 2371 -614 -337 -25 -diffp: 0.63 -0.08 -1.08 -0.04 -#sweep.k21//sim-d0.10-r.010-k21-g1000000-out sumkmer 1207901 sumdiff: 1395 score: 99.885 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out deleted file mode 100644 index 7320bf6..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.050 -Simulated 1100000 total bases, 55136 mutations (5.01%), G=1000000, d=0.10, r=.050 - -Model: -1 1318875 -2 349991 -3 44915 -4 11598 - - -Observed Counts: -1 1320774 -2 350648 -3 44050 -4 11435 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out.eval deleted file mode 100644 index bc9fa1f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318875 349991 44915 11598 -obs: 1320774 350648 44050 11435 -diff: -1899 -657 865 163 -diffp: -0.14 -0.19 1.96 1.43 -#sweep.k21//sim-d0.10-r.050-k21-g1000000-out sumkmer 1726907 sumdiff: -1528 score: 100.088 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out deleted file mode 100644 index 01b63e2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.100 -Simulated 1100000 total bases, 109906 mutations (9.99%), G=1000000, d=0.10, r=.100 - -Model: -1 1781161 -2 177790 -3 19489 -4 1197 - - -Observed Counts: -1 1778567 -2 179005 -3 19517 -4 1208 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out.eval deleted file mode 100644 index 022e9a3..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 177790 19489 1197 -obs: 1778567 179005 19517 1208 -diff: 2594 -1215 -28 -11 -diffp: 0.15 -0.68 -0.14 -0.91 -#sweep.k21//sim-d0.10-r.100-k21-g1000000-out sumkmer 1978297 sumdiff: 1340 score: 99.932 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out deleted file mode 100644 index 4079261..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.200 -Simulated 1100000 total bases, 220545 mutations (20.05%), G=1000000, d=0.10, r=.200 - -Model: -1 1981552 -2 106464 -3 1827 -4 8 - - -Observed Counts: -1 1981301 -2 106608 -3 1805 -4 7 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out.eval deleted file mode 100644 index a0337c6..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 106464 1827 8 -obs: 1981301 106608 1805 7 -diff: 251 -144 22 1 -diffp: 0.01 -0.14 1.22 14.29 -#sweep.k21//sim-d0.10-r.200-k21-g1000000-out sumkmer 2089721 sumdiff: 130 score: 99.994 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out deleted file mode 100644 index 0e7ceef..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.10, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.300 -Simulated 1100000 total bases, 330370 mutations (30.03%), G=1000000, d=0.10, r=.300 - -Model: -1 1998882 -2 100391 -3 111 -4 0 - - -Observed Counts: -1 1998904 -2 100369 -3 106 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out.eval deleted file mode 100644 index 123eeee..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 100391 111 0 -obs: 1998904 100369 106 0 -diff: -22 22 5 0 -diffp: -0.00 0.02 4.72 0.00 -#sweep.k21//sim-d0.10-r.300-k21-g1000000-out sumkmer 2099379 sumdiff: 5 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out deleted file mode 100644 index b37c5f0..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=0.00 -Simulated 1100000 total bases, 0 mutations (0.00%), G=1000000, d=0.10, r=0.00 - -Model: -1 0 -2 900000 -3 0 -4 100000 - - -Observed Counts: -2 900020 -4 99980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out.eval deleted file mode 100644 index bc48050..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.10-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 900000 0 100000 -obs: 0 900020 0 99980 -diff: 0 -20 0 20 -diffp: 0.00 -0.00 0.00 0.02 -#sweep.k21//sim-d0.10-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out deleted file mode 100644 index 810ac7a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.001 -Simulated 1200000 total bases, 1152 mutations (0.10%), G=1000000, d=0.20, r=.001 - -Model: -1 41582 -2 783453 -3 8143 -4 191769 - - -Observed Counts: -1 40172 -2 783875 -3 7642 -4 192278 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out.eval deleted file mode 100644 index 6eac45f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 783453 8143 191769 -obs: 40172 783875 7642 192278 -diff: 1410 -422 501 -509 -diffp: 3.51 -0.05 6.56 -0.26 -#sweep.k21//sim-d0.20-r.001-k21-g1000000-out sumkmer 1023967 sumdiff: 980 score: 99.904 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out deleted file mode 100644 index 0cc6d1d..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.010 -Simulated 1200000 total bases, 12166 mutations (1.01%), G=1000000, d=0.20, r=.010 - -Model: -1 380543 -2 655022 -3 61627 -4 131131 - - -Observed Counts: -1 385430 -2 652407 -3 61164 -4 131556 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out.eval deleted file mode 100644 index b23e972..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 655022 61627 131131 -obs: 385430 652407 61164 131556 -diff: -4887 2615 463 -425 -diffp: -1.27 0.40 0.76 -0.32 -#sweep.k21//sim-d0.20-r.010-k21-g1000000-out sumkmer 1230557 sumdiff: -2234 score: 100.182 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out deleted file mode 100644 index c498291..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.050 -Simulated 1200000 total bases, 60080 mutations (5.01%), G=1000000, d=0.20, r=.050 - -Model: -1 1318875 -2 359421 -3 89831 -4 23196 - - -Observed Counts: -1 1317000 -2 362638 -3 88772 -4 22842 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out.eval deleted file mode 100644 index c862c0d..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318875 359421 89831 23196 -obs: 1317000 362638 88772 22842 -diff: 1875 -3217 1059 354 -diffp: 0.14 -0.89 1.19 1.55 -#sweep.k21//sim-d0.20-r.050-k21-g1000000-out sumkmer 1791252 sumdiff: 71 score: 99.996 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out deleted file mode 100644 index 14f5745..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.100 -Simulated 1200000 total bases, 119471 mutations (9.96%), G=1000000, d=0.20, r=.100 - -Model: -1 1781161 -2 246162 -3 38978 -4 2394 - - -Observed Counts: -1 1780506 -2 244642 -3 40178 -4 2409 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out.eval deleted file mode 100644 index 0babce7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 246162 38978 2394 -obs: 1780506 244642 40178 2409 -diff: 655 1520 -1200 -15 -diffp: 0.04 0.62 -2.99 -0.62 -#sweep.k21//sim-d0.20-r.100-k21-g1000000-out sumkmer 2067735 sumdiff: 960 score: 99.954 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out deleted file mode 100644 index b48a3e7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.200 -Simulated 1200000 total bases, 238595 mutations (19.88%), G=1000000, d=0.20, r=.200 - -Model: -1 1981552 -2 203706 -3 3655 -4 17 - - -Observed Counts: -1 1981474 -2 203918 -3 3534 -4 12 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out.eval deleted file mode 100644 index abcb7d2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 203706 3655 17 -obs: 1981474 203918 3534 12 -diff: 78 -212 121 5 -diffp: 0.00 -0.10 3.42 41.67 -#sweep.k21//sim-d0.20-r.200-k21-g1000000-out sumkmer 2188938 sumdiff: -8 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out deleted file mode 100644 index 96777fa..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.20, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.300 -Simulated 1200000 total bases, 360010 mutations (30.00%), G=1000000, d=0.20, r=.300 - -Model: -1 1998882 -2 200223 -3 223 -4 0 - - -Observed Counts: -1 1998963 -2 200128 -3 247 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out.eval deleted file mode 100644 index 6c33544..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 200223 223 0 -obs: 1998963 200128 247 0 -diff: -81 95 -24 0 -diffp: -0.00 0.05 -9.72 0.00 -#sweep.k21//sim-d0.20-r.300-k21-g1000000-out sumkmer 2199338 sumdiff: -10 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out deleted file mode 100644 index 3e57188..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=0.00 -Simulated 1200000 total bases, 0 mutations (0.00%), G=1000000, d=0.20, r=0.00 - -Model: -1 0 -2 800000 -3 0 -4 200000 - - -Observed Counts: -2 800020 -4 199980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out.eval deleted file mode 100644 index 1350cd5..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.20-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 800000 0 200000 -obs: 0 800020 0 199980 -diff: 0 -20 0 20 -diffp: 0.00 -0.00 0.00 0.01 -#sweep.k21//sim-d0.20-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out deleted file mode 100644 index 2717890..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.001 -Simulated 1300000 total bases, 1229 mutations (0.09%), G=1000000, d=0.30, r=.001 - -Model: -1 41582 -2 685575 -3 12215 -4 287654 - - -Observed Counts: -1 39627 -2 686002 -3 11255 -4 288641 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out.eval deleted file mode 100644 index 24b44b2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 685575 12215 287654 -obs: 39627 686002 11255 288641 -diff: 1955 -427 960 -987 -diffp: 4.93 -0.06 8.53 -0.34 -#sweep.k21//sim-d0.30-r.001-k21-g1000000-out sumkmer 1025525 sumdiff: 1501 score: 99.854 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out deleted file mode 100644 index 3c0534d..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.010 -Simulated 1300000 total bases, 12974 mutations (1.00%), G=1000000, d=0.30, r=.010 - -Model: -1 380544 -2 577670 -3 92441 -4 196697 - - -Observed Counts: -1 378840 -2 578802 -3 92612 -4 196420 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out.eval deleted file mode 100644 index 8909396..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380544 577670 92441 196697 -obs: 378840 578802 92612 196420 -diff: 1704 -1132 -171 277 -diffp: 0.45 -0.20 -0.18 0.14 -#sweep.k21//sim-d0.30-r.010-k21-g1000000-out sumkmer 1246674 sumdiff: 678 score: 99.946 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out deleted file mode 100644 index b3aeafc..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.050 -Simulated 1300000 total bases, 64691 mutations (4.98%), G=1000000, d=0.30, r=.050 - -Model: -1 1318876 -2 368850 -3 134747 -4 34794 - - -Observed Counts: -1 1311958 -2 371530 -3 134806 -4 35131 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out.eval deleted file mode 100644 index 8a351d3..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 368850 134747 34794 -obs: 1311958 371530 134806 35131 -diff: 6918 -2680 -59 -337 -diffp: 0.53 -0.72 -0.04 -0.96 -#sweep.k21//sim-d0.30-r.050-k21-g1000000-out sumkmer 1853425 sumdiff: 3842 score: 99.793 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out deleted file mode 100644 index 1665cee..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.100 -Simulated 1300000 total bases, 130335 mutations (10.03%), G=1000000, d=0.30, r=.100 - -Model: -1 1781161 -2 314533 -3 58467 -4 3591 - - -Observed Counts: -1 1779154 -2 317792 -3 57302 -4 3329 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out.eval deleted file mode 100644 index bf9a621..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 314533 58467 3591 -obs: 1779154 317792 57302 3329 -diff: 2007 -3259 1165 262 -diffp: 0.11 -1.03 2.03 7.87 -#sweep.k21//sim-d0.30-r.100-k21-g1000000-out sumkmer 2157577 sumdiff: 175 score: 99.992 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out deleted file mode 100644 index 635f7a7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.200 -Simulated 1300000 total bases, 260607 mutations (20.05%), G=1000000, d=0.30, r=.200 - -Model: -1 1981552 -2 300947 -3 5482 -4 25 - - -Observed Counts: -1 1981764 -2 301334 -3 5144 -4 24 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out.eval deleted file mode 100644 index 866c780..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 300947 5482 25 -obs: 1981764 301334 5144 24 -diff: -212 -387 338 1 -diffp: -0.01 -0.13 6.57 4.17 -#sweep.k21//sim-d0.30-r.200-k21-g1000000-out sumkmer 2288266 sumdiff: -260 score: 100.011 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out deleted file mode 100644 index e70b38e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.30, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.300 -Simulated 1300000 total bases, 389797 mutations (29.98%), G=1000000, d=0.30, r=.300 - -Model: -1 1998881 -2 300055 -3 334 -4 0 - - -Observed Counts: -1 1998780 -2 300146 -3 296 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out.eval deleted file mode 100644 index 954ac56..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998881 300055 334 0 -obs: 1998780 300146 296 0 -diff: 101 -91 38 0 -diffp: 0.01 -0.03 12.84 0.00 -#sweep.k21//sim-d0.30-r.300-k21-g1000000-out sumkmer 2299222 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out deleted file mode 100644 index a486445..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=0.00 -Simulated 1300000 total bases, 0 mutations (0.00%), G=1000000, d=0.30, r=0.00 - -Model: -1 0 -2 700000 -3 0 -4 300000 - - -Observed Counts: -2 700020 -4 299980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out.eval deleted file mode 100644 index 8305f34..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.30-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 700000 0 300000 -obs: 0 700020 0 299980 -diff: 0 -20 0 20 -diffp: 0.00 -0.00 0.00 0.01 -#sweep.k21//sim-d0.30-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out deleted file mode 100644 index b65a426..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.001 -Simulated 1400000 total bases, 1418 mutations (0.10%), G=1000000, d=0.40, r=.001 - -Model: -1 41582 -2 587698 -3 16287 -4 383539 - - -Observed Counts: -1 42173 -2 587661 -3 16435 -4 383290 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out.eval deleted file mode 100644 index e4b9011..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 587698 16287 383539 -obs: 42173 587661 16435 383290 -diff: -591 37 -148 249 -diffp: -1.40 0.01 -0.90 0.06 -#sweep.k21//sim-d0.40-r.001-k21-g1000000-out sumkmer 1029559 sumdiff: -453 score: 100.044 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out deleted file mode 100644 index 8c70003..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out +++ /dev/null @@ -1,20 +0,0 @@ -Simulating G=1000000, d=0.40, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.010 -Simulated 1400000 total bases, 13887 mutations (0.99%), G=1000000, d=0.40, r=.010 - -Model: -1 380543 -2 500318 -3 123254 -4 262263 - - -Observed Counts: -1 375522 -2 503138 -3 123392 -4 261992 -5 2 -8 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out.eval deleted file mode 100644 index e504a13..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 500318 123254 262263 -obs: 375522 503138 123392 261992 -diff: 5021 -2820 -138 271 -diffp: 1.34 -0.56 -0.11 0.10 -#sweep.k21//sim-d0.40-r.010-k21-g1000000-out sumkmer 1264044 sumdiff: 2334 score: 99.815 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out deleted file mode 100644 index 827fd8b..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.40, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.050 -Simulated 1400000 total bases, 70050 mutations (5.00%), G=1000000, d=0.40, r=.050 - -Model: -1 1318876 -2 378280 -3 179663 -4 46392 - - -Observed Counts: -1 1310921 -2 377322 -3 182159 -4 46978 -6 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out.eval deleted file mode 100644 index 439b86b..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 378280 179663 46392 -obs: 1310921 377322 182159 46978 -diff: 7955 958 -2496 -586 -diffp: 0.61 0.25 -1.37 -1.25 -#sweep.k21//sim-d0.40-r.050-k21-g1000000-out sumkmer 1917380 sumdiff: 5831 score: 99.696 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out deleted file mode 100644 index dc59901..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.100 -Simulated 1400000 total bases, 140032 mutations (10.00%), G=1000000, d=0.40, r=.100 - -Model: -1 1781161 -2 382905 -3 77957 -4 4789 - - -Observed Counts: -1 1777606 -2 384554 -3 78314 -4 4576 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out.eval deleted file mode 100644 index 5c2fdcb..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 382905 77957 4789 -obs: 1777606 384554 78314 4576 -diff: 3555 -1649 -357 213 -diffp: 0.20 -0.43 -0.46 4.65 -#sweep.k21//sim-d0.40-r.100-k21-g1000000-out sumkmer 2245050 sumdiff: 1762 score: 99.922 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out deleted file mode 100644 index 312026c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.200 -Simulated 1400000 total bases, 279653 mutations (19.98%), G=1000000, d=0.40, r=.200 - -Model: -1 1981552 -2 398189 -3 7310 -4 34 - - -Observed Counts: -1 1981626 -2 398044 -3 7374 -4 31 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out.eval deleted file mode 100644 index 39ee1f2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 398189 7310 34 -obs: 1981626 398044 7374 31 -diff: -74 145 -64 3 -diffp: -0.00 0.04 -0.87 9.68 -#sweep.k21//sim-d0.40-r.200-k21-g1000000-out sumkmer 2387075 sumdiff: 10 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out deleted file mode 100644 index 6c0caf9..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.40, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.300 -Simulated 1400000 total bases, 418864 mutations (29.92%), G=1000000, d=0.40, r=.300 - -Model: -1 1998882 -2 399888 -3 446 -4 0 - - -Observed Counts: -1 1998731 -2 399797 -3 545 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out.eval deleted file mode 100644 index caa7c97..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 399888 446 0 -obs: 1998731 399797 545 0 -diff: 151 91 -99 0 -diffp: 0.01 0.02 -18.17 0.00 -#sweep.k21//sim-d0.40-r.300-k21-g1000000-out sumkmer 2399073 sumdiff: 143 score: 99.994 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out deleted file mode 100644 index 4f38368..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=0.00 -Simulated 1400000 total bases, 0 mutations (0.00%), G=1000000, d=0.40, r=0.00 - -Model: -1 0 -2 600000 -3 0 -4 400000 - - -Observed Counts: -2 600018 -4 399981 diff --git a/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out.eval deleted file mode 100644 index ed68e4f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.40-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 600000 0 400000 -obs: 0 600018 0 399981 -diff: 0 -18 0 19 -diffp: 0.00 -0.00 0.00 0.00 -#sweep.k21//sim-d0.40-r0.00-k21-g1000000-out sumkmer 999999 sumdiff: 1 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out deleted file mode 100644 index b064cfc..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.001 -Simulated 1500000 total bases, 1477 mutations (0.10%), G=1000000, d=0.50, r=.001 - -Model: -1 41582 -2 489820 -3 20359 -4 479424 - - -Observed Counts: -1 41287 -2 489715 -3 19865 -4 479912 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out.eval deleted file mode 100644 index 33c5b0d..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 489820 20359 479424 -obs: 41287 489715 19865 479912 -diff: 295 105 494 -488 -diffp: 0.71 0.02 2.49 -0.10 -#sweep.k21//sim-d0.50-r.001-k21-g1000000-out sumkmer 1030779 sumdiff: 406 score: 99.961 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out deleted file mode 100644 index 50ee480..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.010 -Simulated 1500000 total bases, 15130 mutations (1.01%), G=1000000, d=0.50, r=.010 - -Model: -1 380543 -2 422965 -3 154068 -4 327829 - - -Observed Counts: -1 382418 -2 423026 -3 154746 -4 326813 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out.eval deleted file mode 100644 index 7dd2f8a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 422965 154068 327829 -obs: 382418 423026 154746 326813 -diff: -1875 -61 -678 1016 -diffp: -0.49 -0.01 -0.44 0.31 -#sweep.k21//sim-d0.50-r.010-k21-g1000000-out sumkmer 1287003 sumdiff: -1598 score: 100.124 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out deleted file mode 100644 index 51ab24b..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.50, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.050 -Simulated 1500000 total bases, 74881 mutations (4.99%), G=1000000, d=0.50, r=.050 - -Model: -1 1318876 -2 387710 -3 224579 -4 57991 - - -Observed Counts: -1 1312904 -2 389677 -3 225790 -4 57580 -6 2 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out.eval deleted file mode 100644 index b187c9c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 387710 224579 57991 -obs: 1312904 389677 225790 57580 -diff: 5972 -1967 -1211 411 -diffp: 0.45 -0.50 -0.54 0.71 -#sweep.k21//sim-d0.50-r.050-k21-g1000000-out sumkmer 1985951 sumdiff: 3205 score: 99.839 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out deleted file mode 100644 index bc5b02c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.100 -Simulated 1500000 total bases, 149589 mutations (9.97%), G=1000000, d=0.50, r=.100 - -Model: -1 1781161 -2 451276 -3 97446 -4 5986 - - -Observed Counts: -1 1776135 -2 452392 -3 98187 -4 6120 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out.eval deleted file mode 100644 index 176cf0a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 451276 97446 5986 -obs: 1776135 452392 98187 6120 -diff: 5026 -1116 -741 -134 -diffp: 0.28 -0.25 -0.75 -2.19 -#sweep.k21//sim-d0.50-r.100-k21-g1000000-out sumkmer 2332834 sumdiff: 3035 score: 99.870 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out deleted file mode 100644 index 5956808..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.200 -Simulated 1500000 total bases, 300531 mutations (20.04%), G=1000000, d=0.50, r=.200 - -Model: -1 1981552 -2 495430 -3 9138 -4 42 - - -Observed Counts: -1 1981212 -2 496346 -3 8628 -4 43 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out.eval deleted file mode 100644 index 46f96a0..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 495430 9138 42 -obs: 1981212 496346 8628 43 -diff: 340 -916 510 -1 -diffp: 0.02 -0.18 5.91 -2.33 -#sweep.k21//sim-d0.50-r.200-k21-g1000000-out sumkmer 2486229 sumdiff: -67 score: 100.003 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out deleted file mode 100644 index 1918c59..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.50, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.300 -Simulated 1500000 total bases, 449954 mutations (30.00%), G=1000000, d=0.50, r=.300 - -Model: -1 1998882 -2 499720 -3 558 -4 0 - - -Observed Counts: -1 1998710 -2 499779 -3 564 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out.eval deleted file mode 100644 index 2216744..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 499720 558 0 -obs: 1998710 499779 564 0 -diff: 172 -59 -6 0 -diffp: 0.01 -0.01 -1.06 0.00 -#sweep.k21//sim-d0.50-r.300-k21-g1000000-out sumkmer 2499053 sumdiff: 107 score: 99.996 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out deleted file mode 100644 index 0429096..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=0.00 -Simulated 1500000 total bases, 0 mutations (0.00%), G=1000000, d=0.50, r=0.00 - -Model: -1 0 -2 500000 -3 0 -4 500000 - - -Observed Counts: -2 500020 -4 499980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out.eval deleted file mode 100644 index 5bc5a70..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.50-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 500000 0 500000 -obs: 0 500020 0 499980 -diff: 0 -20 0 20 -diffp: 0.00 -0.00 0.00 0.00 -#sweep.k21//sim-d0.50-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out deleted file mode 100644 index 3f5852a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.60, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.001 -Simulated 1600000 total bases, 1635 mutations (0.10%), G=1000000, d=0.60, r=.001 - -Model: -1 41581 -2 391942 -3 24430 -4 575309 - - -Observed Counts: -1 42155 -2 391906 -3 25101 -4 574668 -6 3 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out.eval deleted file mode 100644 index da7a12e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41581 391942 24430 575309 -obs: 42155 391906 25101 574668 -diff: -574 36 -671 641 -diffp: -1.36 0.01 -2.67 0.11 -#sweep.k21//sim-d0.60-r.001-k21-g1000000-out sumkmer 1033830 sumdiff: -568 score: 100.055 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out deleted file mode 100644 index 26944bf..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out +++ /dev/null @@ -1,21 +0,0 @@ -Simulating G=1000000, d=0.60, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.010 -Simulated 1600000 total bases, 15984 mutations (1.00%), G=1000000, d=0.60, r=.010 - -Model: -1 380543 -2 345613 -3 184882 -4 393395 - - -Observed Counts: -1 375226 -2 349509 -3 185136 -4 392569 -5 2 -6 1 -8 2 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out.eval deleted file mode 100644 index 7f34cc7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 345613 184882 393395 -obs: 375226 349509 185136 392569 -diff: 5317 -3896 -254 826 -diffp: 1.42 -1.11 -0.14 0.21 -#sweep.k21//sim-d0.60-r.010-k21-g1000000-out sumkmer 1302440 sumdiff: 1993 score: 99.847 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out deleted file mode 100644 index b7b43bc..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.050 -Simulated 1600000 total bases, 79831 mutations (4.99%), G=1000000, d=0.60, r=.050 - -Model: -1 1318876 -2 397140 -3 269495 -4 69589 - - -Observed Counts: -1 1308206 -2 401853 -3 268856 -4 70370 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out.eval deleted file mode 100644 index 69f9da6..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 397140 269495 69589 -obs: 1308206 401853 268856 70370 -diff: 10670 -4713 639 -781 -diffp: 0.82 -1.17 0.24 -1.11 -#sweep.k21//sim-d0.60-r.050-k21-g1000000-out sumkmer 2049285 sumdiff: 5815 score: 99.716 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out deleted file mode 100644 index 3d9dec0..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.100 -Simulated 1600000 total bases, 159848 mutations (9.99%), G=1000000, d=0.60, r=.100 - -Model: -1 1781161 -2 519648 -3 116935 -4 7183 - - -Observed Counts: -1 1773491 -2 520567 -3 119113 -4 6999 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out.eval deleted file mode 100644 index b3b97ec..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 519648 116935 7183 -obs: 1773491 520567 119113 6999 -diff: 7670 -919 -2178 184 -diffp: 0.43 -0.18 -1.83 2.63 -#sweep.k21//sim-d0.60-r.100-k21-g1000000-out sumkmer 2420170 sumdiff: 4757 score: 99.803 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out deleted file mode 100644 index eeaaa15..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.200 -Simulated 1600000 total bases, 319544 mutations (19.97%), G=1000000, d=0.60, r=.200 - -Model: -1 1981552 -2 592672 -3 10965 -4 51 - - -Observed Counts: -1 1981006 -2 592319 -3 11360 -4 59 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out.eval deleted file mode 100644 index 40379f2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 592672 10965 51 -obs: 1981006 592319 11360 59 -diff: 546 353 -395 -8 -diffp: 0.03 0.06 -3.48 -13.56 -#sweep.k21//sim-d0.60-r.200-k21-g1000000-out sumkmer 2584744 sumdiff: 496 score: 99.981 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out deleted file mode 100644 index b3cee5c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.60, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.300 -Simulated 1600000 total bases, 480295 mutations (30.02%), G=1000000, d=0.60, r=.300 - -Model: -1 1998882 -2 599553 -3 669 -4 0 - - -Observed Counts: -1 1998901 -2 599646 -3 589 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out.eval deleted file mode 100644 index 16996a1..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 599553 669 0 -obs: 1998901 599646 589 0 -diff: -19 -93 80 0 -diffp: -0.00 -0.02 13.58 0.00 -#sweep.k21//sim-d0.60-r.300-k21-g1000000-out sumkmer 2599136 sumdiff: -32 score: 100.001 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out deleted file mode 100644 index 87555ef..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=0.00 -Simulated 1600000 total bases, 0 mutations (0.00%), G=1000000, d=0.60, r=0.00 - -Model: -1 0 -2 400000 -3 0 -4 600000 - - -Observed Counts: -2 400020 -4 599980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out.eval deleted file mode 100644 index d23f798..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.60-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 400000 0 600000 -obs: 0 400020 0 599980 -diff: 0 -20 0 20 -diffp: 0.00 -0.00 0.00 0.00 -#sweep.k21//sim-d0.60-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out deleted file mode 100644 index 2cd7507..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.001 -Simulated 1700000 total bases, 1712 mutations (0.10%), G=1000000, d=0.70, r=.001 - -Model: -1 41581 -2 294065 -3 28502 -4 671194 - - -Observed Counts: -1 41860 -2 293863 -3 28978 -4 670860 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out.eval deleted file mode 100644 index 969c31f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41581 294065 28502 671194 -obs: 41860 293863 28978 670860 -diff: -279 202 -476 334 -diffp: -0.67 0.07 -1.64 0.05 -#sweep.k21//sim-d0.70-r.001-k21-g1000000-out sumkmer 1035561 sumdiff: -219 score: 100.021 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out deleted file mode 100644 index 2d1ddd4..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.70, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.010 -Simulated 1700000 total bases, 17124 mutations (1.01%), G=1000000, d=0.70, r=.010 - -Model: -1 380544 -2 268260 -3 215696 -4 458961 - - -Observed Counts: -1 379956 -2 270477 -3 216106 -4 457677 -8 3 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out.eval deleted file mode 100644 index b44b721..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380544 268260 215696 458961 -obs: 379956 270477 216106 457677 -diff: 588 -2217 -410 1284 -diffp: 0.15 -0.82 -0.19 0.28 -#sweep.k21//sim-d0.70-r.010-k21-g1000000-out sumkmer 1324216 sumdiff: -755 score: 100.057 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out deleted file mode 100644 index 545a114..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.050 -Simulated 1700000 total bases, 85364 mutations (5.02%), G=1000000, d=0.70, r=.050 - -Model: -1 1318876 -2 406569 -3 314411 -4 81187 - - -Observed Counts: -1 1310312 -2 413849 -3 314358 -4 79719 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out.eval deleted file mode 100644 index cfa0721..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 406569 314411 81187 -obs: 1310312 413849 314358 79719 -diff: 8564 -7280 53 1468 -diffp: 0.65 -1.76 0.02 1.84 -#sweep.k21//sim-d0.70-r.050-k21-g1000000-out sumkmer 2118238 sumdiff: 2805 score: 99.868 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out deleted file mode 100644 index a71dba0..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.100 -Simulated 1700000 total bases, 170092 mutations (10.01%), G=1000000, d=0.70, r=.100 - -Model: -1 1781161 -2 588019 -3 136425 -4 8380 - - -Observed Counts: -1 1774132 -2 592178 -3 135960 -4 8398 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out.eval deleted file mode 100644 index 5ad9c22..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 588019 136425 8380 -obs: 1774132 592178 135960 8398 -diff: 7029 -4159 465 -18 -diffp: 0.40 -0.70 0.34 -0.21 -#sweep.k21//sim-d0.70-r.100-k21-g1000000-out sumkmer 2510668 sumdiff: 3317 score: 99.868 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out deleted file mode 100644 index 0e563af..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.200 -Simulated 1700000 total bases, 339181 mutations (19.95%), G=1000000, d=0.70, r=.200 - -Model: -1 1981552 -2 689913 -3 12793 -4 59 - - -Observed Counts: -1 1980696 -2 689544 -3 13356 -4 27 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out.eval deleted file mode 100644 index f8938d5..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 689913 12793 59 -obs: 1980696 689544 13356 27 -diff: 856 369 -563 32 -diffp: 0.04 0.05 -4.22 118.52 -#sweep.k21//sim-d0.70-r.200-k21-g1000000-out sumkmer 2683623 sumdiff: 694 score: 99.974 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out deleted file mode 100644 index e583644..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.300 -Simulated 1700000 total bases, 509424 mutations (29.97%), G=1000000, d=0.70, r=.300 - -Model: -1 1998882 -2 699385 -3 781 -4 0 - - -Observed Counts: -1 1998863 -2 699383 -3 777 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out.eval deleted file mode 100644 index 9e274c7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 699385 781 0 -obs: 1998863 699383 777 0 -diff: 19 2 4 0 -diffp: 0.00 0.00 0.51 0.00 -#sweep.k21//sim-d0.70-r.300-k21-g1000000-out sumkmer 2699023 sumdiff: 25 score: 99.999 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out deleted file mode 100644 index 0fefc91..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=0.00 -Simulated 1700000 total bases, 0 mutations (0.00%), G=1000000, d=0.70, r=0.00 - -Model: -1 0 -2 300000 -3 0 -4 700000 - - -Observed Counts: -2 300020 -4 699978 -8 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out.eval deleted file mode 100644 index 27de31c..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.70-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 300000 0 700000 -obs: 0 300020 0 699978 -diff: 0 -20 0 22 -diffp: 0.00 -0.01 0.00 0.00 -#sweep.k21//sim-d0.70-r0.00-k21-g1000000-out sumkmer 999998 sumdiff: 2 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out deleted file mode 100644 index 2440923..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.80, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.001 -Simulated 1800000 total bases, 1797 mutations (0.10%), G=1000000, d=0.80, r=.001 - -Model: -1 41582 -2 196187 -3 32574 -4 767079 - - -Observed Counts: -1 41501 -2 196419 -3 32541 -4 766996 -7 2 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out.eval deleted file mode 100644 index 848958a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 196187 32574 767079 -obs: 41501 196419 32541 766996 -diff: 81 -232 33 83 -diffp: 0.20 -0.12 0.10 0.01 -#sweep.k21//sim-d0.80-r.001-k21-g1000000-out sumkmer 1037457 sumdiff: -35 score: 100.003 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out deleted file mode 100644 index b63a8c4..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.80, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.010 -Simulated 1800000 total bases, 17997 mutations (1.00%), G=1000000, d=0.80, r=.010 - -Model: -1 380543 -2 190908 -3 246509 -4 524527 - - -Observed Counts: -1 379267 -2 192616 -3 247140 -4 523509 -5 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out.eval deleted file mode 100644 index e626270..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 190908 246509 524527 -obs: 379267 192616 247140 523509 -diff: 1276 -1708 -631 1018 -diffp: 0.34 -0.89 -0.26 0.19 -#sweep.k21//sim-d0.80-r.010-k21-g1000000-out sumkmer 1342532 sumdiff: -45 score: 100.003 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out deleted file mode 100644 index e5ad2ff..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.050 -Simulated 1800000 total bases, 90112 mutations (5.01%), G=1000000, d=0.80, r=.050 - -Model: -1 1318876 -2 415999 -3 359327 -4 92785 - - -Observed Counts: -1 1307525 -2 423590 -3 357301 -4 93338 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out.eval deleted file mode 100644 index 1ed303e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318876 415999 359327 92785 -obs: 1307525 423590 357301 93338 -diff: 11351 -7591 2026 -553 -diffp: 0.87 -1.79 0.57 -0.59 -#sweep.k21//sim-d0.80-r.050-k21-g1000000-out sumkmer 2181754 sumdiff: 5233 score: 99.760 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out deleted file mode 100644 index eab024b..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.100 -Simulated 1800000 total bases, 180111 mutations (10.01%), G=1000000, d=0.80, r=.100 - -Model: -1 1781161 -2 656391 -3 155914 -4 9578 - - -Observed Counts: -1 1774834 -2 659008 -3 155978 -4 9794 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out.eval deleted file mode 100644 index 12c8f93..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 656391 155914 9578 -obs: 1774834 659008 155978 9794 -diff: 6327 -2617 -64 -216 -diffp: 0.36 -0.40 -0.04 -2.21 -#sweep.k21//sim-d0.80-r.100-k21-g1000000-out sumkmer 2599614 sumdiff: 3430 score: 99.868 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out deleted file mode 100644 index ab14a2f..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.200 -Simulated 1800000 total bases, 359308 mutations (19.96%), G=1000000, d=0.80, r=.200 - -Model: -1 1981552 -2 787155 -3 14621 -4 68 - - -Observed Counts: -1 1981017 -2 786997 -3 14887 -4 72 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out.eval deleted file mode 100644 index 68852c7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 787155 14621 68 -obs: 1981017 786997 14887 72 -diff: 535 158 -266 -4 -diffp: 0.03 0.02 -1.79 -5.56 -#sweep.k21//sim-d0.80-r.200-k21-g1000000-out sumkmer 2782973 sumdiff: 423 score: 99.985 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out deleted file mode 100644 index 0cdd453..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.300 -Simulated 1800000 total bases, 538572 mutations (29.92%), G=1000000, d=0.80, r=.300 - -Model: -1 1998882 -2 799218 -3 893 -4 0 - - -Observed Counts: -1 1998798 -2 799171 -3 940 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out.eval deleted file mode 100644 index 32ac01a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 799218 893 0 -obs: 1998798 799171 940 0 -diff: 84 47 -47 0 -diffp: 0.00 0.01 -5.00 0.00 -#sweep.k21//sim-d0.80-r.300-k21-g1000000-out sumkmer 2798909 sumdiff: 84 score: 99.997 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out deleted file mode 100644 index b418afc..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=0.00 -Simulated 1800000 total bases, 0 mutations (0.00%), G=1000000, d=0.80, r=0.00 - -Model: -1 0 -2 199999 -3 0 -4 800000 - - -Observed Counts: -2 200020 -4 799978 -8 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out.eval deleted file mode 100644 index 9fba566..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.80-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 199999 0 800000 -obs: 0 200020 0 799978 -diff: 0 -21 0 22 -diffp: 0.00 -0.01 0.00 0.00 -#sweep.k21//sim-d0.80-r0.00-k21-g1000000-out sumkmer 999998 sumdiff: 1 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out deleted file mode 100644 index 313c271..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.001, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.001 -Simulated 1900000 total bases, 1965 mutations (0.10%), G=1000000, d=0.90, r=.001 - -Model: -1 41582 -2 98309 -3 36646 -4 862964 - - -Observed Counts: -1 43111 -2 98057 -3 37721 -4 861893 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out.eval deleted file mode 100644 index 77700ae..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 98309 36646 862964 -obs: 43111 98057 37721 861893 -diff: -1529 252 -1075 1071 -diffp: -3.55 0.26 -2.85 0.12 -#sweep.k21//sim-d0.90-r.001-k21-g1000000-out sumkmer 1040782 sumdiff: -1281 score: 100.123 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out deleted file mode 100644 index d8a58cb..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.010, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.010 -Simulated 1900000 total bases, 19074 mutations (1.00%), G=1000000, d=0.90, r=.010 - -Model: -1 380543 -2 113555 -3 277323 -4 590093 - - -Observed Counts: -1 380112 -2 115365 -3 278486 -4 588415 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out.eval deleted file mode 100644 index 1007991..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 113555 277323 590093 -obs: 380112 115365 278486 588415 -diff: 431 -1810 -1163 1678 -diffp: 0.11 -1.57 -0.42 0.29 -#sweep.k21//sim-d0.90-r.010-k21-g1000000-out sumkmer 1362378 sumdiff: -864 score: 100.063 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out deleted file mode 100644 index 4931da7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.050, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.050 -Simulated 1900000 total bases, 95390 mutations (5.02%), G=1000000, d=0.90, r=.050 - -Model: -1 1318875 -2 425429 -3 404242 -4 104383 - - -Observed Counts: -1 1309201 -2 434151 -3 403019 -4 103350 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out.eval deleted file mode 100644 index 07c1c01..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318875 425429 404242 104383 -obs: 1309201 434151 403019 103350 -diff: 9674 -8722 1223 1033 -diffp: 0.74 -2.01 0.30 1.00 -#sweep.k21//sim-d0.90-r.050-k21-g1000000-out sumkmer 2249721 sumdiff: 3208 score: 99.857 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out deleted file mode 100644 index 851d1c7..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.100, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.100 -Simulated 1900000 total bases, 190135 mutations (10.01%), G=1000000, d=0.90, r=.100 - -Model: -1 1781161 -2 724762 -3 175403 -4 10775 - - -Observed Counts: -1 1777054 -2 729509 -3 173948 -4 10511 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out.eval deleted file mode 100644 index 0ac78eb..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 724762 175403 10775 -obs: 1777054 729509 173948 10511 -diff: 4107 -4747 1455 264 -diffp: 0.23 -0.65 0.84 2.51 -#sweep.k21//sim-d0.90-r.100-k21-g1000000-out sumkmer 2691022 sumdiff: 1079 score: 99.960 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out deleted file mode 100644 index eb076a0..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=0.90, r=.200, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.200 -Simulated 1900000 total bases, 380535 mutations (20.03%), G=1000000, d=0.90, r=.200 - -Model: -1 1981552 -2 884396 -3 16448 -4 76 - - -Observed Counts: -1 1981890 -2 885017 -3 15914 -4 72 -6 1 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out.eval deleted file mode 100644 index 41d6a08..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 884396 16448 76 -obs: 1981890 885017 15914 72 -diff: -338 -621 534 4 -diffp: -0.02 -0.07 3.36 5.56 -#sweep.k21//sim-d0.90-r.200-k21-g1000000-out sumkmer 2882893 sumdiff: -421 score: 100.015 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out deleted file mode 100644 index 73ae9ad..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.90, r=.300, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.300 -Simulated 1900000 total bases, 568578 mutations (29.93%), G=1000000, d=0.90, r=.300 - -Model: -1 1998882 -2 899050 -3 1004 -4 0 - - -Observed Counts: -1 1998765 -2 898928 -3 1113 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out.eval deleted file mode 100644 index 813678e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 899050 1004 0 -obs: 1998765 898928 1113 0 -diff: 117 122 -109 0 -diffp: 0.01 0.01 -9.79 0.00 -#sweep.k21//sim-d0.90-r.300-k21-g1000000-out sumkmer 2898806 sumdiff: 130 score: 99.996 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out deleted file mode 100644 index be04ba2..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=0.00, k=21 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=0.00 -Simulated 1900000 total bases, 0 mutations (0.00%), G=1000000, d=0.90, r=0.00 - -Model: -1 0 -2 99999 -3 0 -4 900000 - - -Observed Counts: -2 100020 -4 899980 diff --git a/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out.eval deleted file mode 100644 index a8d45cb..0000000 --- a/analysis/genomesim/sweep.k21/sim-d0.90-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 99999 0 900000 -obs: 0 100020 0 899980 -diff: 0 -21 0 20 -diffp: 0.00 -0.02 0.00 0.00 -#sweep.k21//sim-d0.90-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out deleted file mode 100644 index 014dd2d..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out +++ /dev/null @@ -1,19 +0,0 @@ -Simulating G=1000000, d=1.00, r=.001, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.001 -Simulated 2000000 total bases, 2023 mutations (0.10%), G=1000000, d=1.00, r=.001 - -Model: -1 41582 -2 432 -3 40718 -4 958849 - - -Observed Counts: -1 42139 -2 446 -3 41287 -4 958265 -8 1 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out.eval deleted file mode 100644 index 166150e..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.001-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 41582 432 40718 958849 -obs: 42139 446 41287 958265 -diff: -557 -14 -569 584 -diffp: -1.32 -3.14 -1.38 0.06 -#sweep.k21//sim-d1.00-r.001-k21-g1000000-out sumkmer 1042137 sumdiff: -556 score: 100.053 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out deleted file mode 100644 index d80c0e4..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.010, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.010 -Simulated 2000000 total bases, 19976 mutations (1.00%), G=1000000, d=1.00, r=.010 - -Model: -1 380543 -2 36203 -3 308137 -4 655659 - - -Observed Counts: -1 376972 -2 37852 -3 307796 -4 655974 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out.eval deleted file mode 100644 index 78289ed..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.010-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 380543 36203 308137 655659 -obs: 376972 37852 307796 655974 -diff: 3571 -1649 341 -315 -diffp: 0.95 -4.36 0.11 -0.05 -#sweep.k21//sim-d1.00-r.010-k21-g1000000-out sumkmer 1378594 sumdiff: 1948 score: 99.859 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out deleted file mode 100644 index d513a52..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.050, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.050 -Simulated 2000000 total bases, 99947 mutations (5.00%), G=1000000, d=1.00, r=.050 - -Model: -1 1318875 -2 434858 -3 449158 -4 115982 - - -Observed Counts: -1 1304954 -2 441918 -3 448546 -4 116383 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out.eval deleted file mode 100644 index 5c6d186..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.050-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1318875 434858 449158 115982 -obs: 1304954 441918 448546 116383 -diff: 13921 -7060 612 -401 -diffp: 1.07 -1.60 0.14 -0.34 -#sweep.k21//sim-d1.00-r.050-k21-g1000000-out sumkmer 2311801 sumdiff: 7072 score: 99.694 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out deleted file mode 100644 index a5f6f99..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.100, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.100 -Simulated 2000000 total bases, 200441 mutations (10.02%), G=1000000, d=1.00, r=.100 - -Model: -1 1781161 -2 793134 -3 194892 -4 11972 - - -Observed Counts: -1 1777752 -2 800263 -3 191838 -4 11542 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out.eval deleted file mode 100644 index e0b160a..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.100-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1781161 793134 194892 11972 -obs: 1777752 800263 191838 11542 -diff: 3409 -7129 3054 430 -diffp: 0.19 -0.89 1.59 3.73 -#sweep.k21//sim-d1.00-r.100-k21-g1000000-out sumkmer 2781395 sumdiff: -236 score: 100.008 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out deleted file mode 100644 index 2626bbf..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.200, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.200 -Simulated 2000000 total bases, 399775 mutations (19.99%), G=1000000, d=1.00, r=.200 - -Model: -1 1981552 -2 981638 -3 18276 -4 85 - - -Observed Counts: -1 1981302 -2 981900 -3 18186 -4 75 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out.eval deleted file mode 100644 index f9fbccf..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.200-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1981552 981638 18276 85 -obs: 1981302 981900 18186 75 -diff: 250 -262 90 10 -diffp: 0.01 -0.03 0.49 13.33 -#sweep.k21//sim-d1.00-r.200-k21-g1000000-out sumkmer 2981463 sumdiff: 88 score: 99.997 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out deleted file mode 100644 index 98b9153..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.300, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.300 -Simulated 2000000 total bases, 600247 mutations (30.01%), G=1000000, d=1.00, r=.300 - -Model: -1 1998882 -2 998883 -3 1116 -4 0 - - -Observed Counts: -1 1998838 -2 998854 -3 1130 -4 6 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out.eval deleted file mode 100644 index 7cdd4e4..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r.300-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998882 998883 1116 0 -obs: 1998838 998854 1130 6 -diff: 44 29 -14 -6 -diffp: 0.00 0.00 -1.24 -100.00 -#sweep.k21//sim-d1.00-r.300-k21-g1000000-out sumkmer 2998828 sumdiff: 53 score: 99.998 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out b/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out deleted file mode 100644 index 0e01c7b..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=0.00, k=21 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=0.00 -Simulated 2000000 total bases, 0 mutations (0.00%), G=1000000, d=1.00, r=0.00 - -Model: -1 0 -2 0 -3 0 -4 1000000 - - -Observed Counts: -2 20 -4 999980 diff --git a/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out.eval b/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out.eval deleted file mode 100644 index b6ae228..0000000 --- a/analysis/genomesim/sweep.k21/sim-d1.00-r0.00-k21-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 0 0 1000000 -obs: 0 20 0 999980 -diff: 0 -20 0 20 -diffp: 0.00 -100.00 0.00 0.00 -#sweep.k21//sim-d1.00-r0.00-k21-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out deleted file mode 100644 index dce4b5e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.001 -Simulated 1000000 total bases, 965 mutations (0.10%), G=1000000, d=0.00, r=.001 - -Model: -1 61078 -2 969460 -3 0 -4 0 - - -Observed Counts: -1 59108 -2 970416 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out.eval deleted file mode 100644 index 43f5cdc..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 969460 0 0 -obs: 59108 970416 0 0 -diff: 1970 -956 0 0 -diffp: 3.33 -0.10 0.00 0.00 -#sweep.k31//sim-d0.00-r.001-k31-g1000000-out sumkmer 1029524 sumdiff: 1014 score: 99.902 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out deleted file mode 100644 index 1b0810f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.010 -Simulated 1000000 total bases, 9930 mutations (0.99%), G=1000000, d=0.00, r=.010 - -Model: -1 535393 -2 732303 -3 0 -4 0 - - -Observed Counts: -1 532100 -2 733920 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out.eval deleted file mode 100644 index 4de1d3c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 732303 0 0 -obs: 532100 733920 0 0 -diff: 3293 -1617 0 0 -diffp: 0.62 -0.22 0.00 0.00 -#sweep.k31//sim-d0.00-r.010-k31-g1000000-out sumkmer 1266020 sumdiff: 1676 score: 99.868 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out deleted file mode 100644 index 263f677..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.050 -Simulated 1000000 total bases, 49968 mutations (5.00%), G=1000000, d=0.00, r=.050 - -Model: -1 1592186 -2 203906 -3 0 -4 0 - - -Observed Counts: -1 1592650 -2 203645 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out.eval deleted file mode 100644 index f69fd5d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592186 203906 0 0 -obs: 1592650 203645 0 0 -diff: -464 261 0 0 -diffp: -0.03 0.13 0.00 0.00 -#sweep.k31//sim-d0.00-r.050-k31-g1000000-out sumkmer 1796295 sumdiff: -203 score: 100.011 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out deleted file mode 100644 index 623561d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.100 -Simulated 1000000 total bases, 99960 mutations (10.00%), G=1000000, d=0.00, r=.100 - -Model: -1 1923695 -2 38152 -3 0 -4 0 - - -Observed Counts: -1 1922998 -2 38471 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out.eval deleted file mode 100644 index b972204..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 38152 0 0 -obs: 1922998 38471 0 0 -diff: 697 -319 0 0 -diffp: 0.04 -0.83 0.00 0.00 -#sweep.k31//sim-d0.00-r.100-k31-g1000000-out sumkmer 1961469 sumdiff: 378 score: 99.981 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out deleted file mode 100644 index f899b67..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.200 -Simulated 1000000 total bases, 199862 mutations (19.99%), G=1000000, d=0.00, r=.200 - -Model: -1 1998019 -2 990 -3 0 -4 0 - - -Observed Counts: -1 1997794 -2 1073 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out.eval deleted file mode 100644 index 6e08814..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998019 990 0 0 -obs: 1997794 1073 0 0 -diff: 225 -83 0 0 -diffp: 0.01 -7.74 0.00 0.00 -#sweep.k31//sim-d0.00-r.200-k31-g1000000-out sumkmer 1998867 sumdiff: 142 score: 99.993 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out deleted file mode 100644 index 5c48e92..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.300 -Simulated 1000000 total bases, 299659 mutations (29.97%), G=1000000, d=0.00, r=.300 - -Model: -1 1999968 -2 15 -3 0 -4 0 - - -Observed Counts: -1 1999922 -2 9 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out.eval deleted file mode 100644 index 5900786..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 15 0 0 -obs: 1999922 9 0 0 -diff: 46 6 0 0 -diffp: 0.00 66.67 0.00 0.00 -#sweep.k31//sim-d0.00-r.300-k31-g1000000-out sumkmer 1999931 sumdiff: 52 score: 99.997 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out deleted file mode 100644 index f9f8466..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=0.00 -Simulated 1000000 total bases, 0 mutations (0.00%), G=1000000, d=0.00, r=0.00 - -Model: -1 0 -2 1000000 -3 0 -4 0 - - -Observed Counts: -2 999970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out.eval deleted file mode 100644 index bcad31b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.00-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 1000000 0 0 -obs: 0 999970 0 0 -diff: 0 30 0 0 -diffp: 0.00 0.00 0.00 0.00 -#sweep.k31//sim-d0.00-r0.00-k31-g1000000-out sumkmer 999970 sumdiff: 30 score: 99.997 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out deleted file mode 100644 index e812cad..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.001 -Simulated 1100000 total bases, 1122 mutations (0.10%), G=1000000, d=0.10, r=.001 - -Model: -1 61078 -2 872607 -3 5921 -4 93985 - - -Observed Counts: -1 63566 -2 870692 -3 4702 -4 95221 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out.eval deleted file mode 100644 index 2252d59..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 872607 5921 93985 -obs: 63566 870692 4702 95221 -diff: -2488 1915 1219 -1236 -diffp: -3.91 0.22 25.93 -1.30 -#sweep.k31//sim-d0.10-r.001-k31-g1000000-out sumkmer 1034181 sumdiff: -590 score: 100.057 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out deleted file mode 100644 index f84bf3d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.010 -Simulated 1100000 total bases, 11198 mutations (1.02%), G=1000000, d=0.10, r=.010 - -Model: -1 535393 -2 666239 -3 39207 -4 53626 - - -Observed Counts: -1 545454 -2 660951 -3 40428 -4 52825 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out.eval deleted file mode 100644 index c8b0fa8..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 666239 39207 53626 -obs: 545454 660951 40428 52825 -diff: -10061 5288 -1221 801 -diffp: -1.84 0.80 -3.02 1.52 -#sweep.k31//sim-d0.10-r.010-k31-g1000000-out sumkmer 1299658 sumdiff: -5193 score: 100.400 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out deleted file mode 100644 index 8473569..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.050 -Simulated 1100000 total bases, 54447 mutations (4.95%), G=1000000, d=0.10, r=.050 - -Model: -1 1592185 -2 246892 -3 32465 -4 4157 - - -Observed Counts: -1 1583567 -2 248725 -3 34073 -4 4176 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out.eval deleted file mode 100644 index ac505d5..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 246892 32465 4157 -obs: 1583567 248725 34073 4176 -diff: 8618 -1833 -1608 -19 -diffp: 0.54 -0.74 -4.72 -0.45 -#sweep.k31//sim-d0.10-r.050-k31-g1000000-out sumkmer 1870541 sumdiff: 5158 score: 99.724 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out deleted file mode 100644 index 6ab0a0b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.100 -Simulated 1100000 total bases, 110007 mutations (10.00%), G=1000000, d=0.10, r=.100 - -Model: -1 1923695 -2 126851 -3 7339 -4 145 - - -Observed Counts: -1 1924143 -2 126663 -3 7357 -4 100 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out.eval deleted file mode 100644 index cdc0b3c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 126851 7339 145 -obs: 1924143 126663 7357 100 -diff: -448 188 -18 45 -diffp: -0.02 0.15 -0.24 45.00 -#sweep.k31//sim-d0.10-r.100-k31-g1000000-out sumkmer 2058263 sumdiff: -233 score: 100.011 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out deleted file mode 100644 index c0265ba..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.10, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.200 -Simulated 1100000 total bases, 219369 mutations (19.94%), G=1000000, d=0.10, r=.200 - -Model: -1 1998018 -2 100693 -3 197 -4 0 - - -Observed Counts: -1 1997911 -2 100692 -3 215 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out.eval deleted file mode 100644 index 8ba4888..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 100693 197 0 -obs: 1997911 100692 215 0 -diff: 107 1 -18 0 -diffp: 0.01 0.00 -8.37 0.00 -#sweep.k31//sim-d0.10-r.200-k31-g1000000-out sumkmer 2098818 sumdiff: 90 score: 99.996 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out deleted file mode 100644 index 7203da9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.10, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.300 -Simulated 1100000 total bases, 330912 mutations (30.08%), G=1000000, d=0.10, r=.300 - -Model: -1 1999968 -2 100011 -3 3 -4 0 - - -Observed Counts: -1 1999951 -2 99993 -3 1 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out.eval deleted file mode 100644 index 1be524b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 100011 3 0 -obs: 1999951 99993 1 0 -diff: 17 18 2 0 -diffp: 0.00 0.02 200.00 0.00 -#sweep.k31//sim-d0.10-r.300-k31-g1000000-out sumkmer 2099945 sumdiff: 37 score: 99.998 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out deleted file mode 100644 index 1d10e4e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=0.00 -Simulated 1100000 total bases, 0 mutations (0.00%), G=1000000, d=0.10, r=0.00 - -Model: -1 0 -2 900000 -3 0 -4 100000 - - -Observed Counts: -2 900030 -4 99970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out.eval deleted file mode 100644 index b2c180e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.10-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 900000 0 100000 -obs: 0 900030 0 99970 -diff: 0 -30 0 30 -diffp: 0.00 -0.00 0.00 0.03 -#sweep.k31//sim-d0.10-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out deleted file mode 100644 index d439f97..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.001 -Simulated 1200000 total bases, 1200 mutations (0.10%), G=1000000, d=0.20, r=.001 - -Model: -1 61078 -2 775754 -3 11842 -4 187970 - - -Observed Counts: -1 60933 -2 775805 -3 11975 -4 187868 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out.eval deleted file mode 100644 index 43c2abe..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 775754 11842 187970 -obs: 60933 775805 11975 187868 -diff: 145 -51 -133 102 -diffp: 0.24 -0.01 -1.11 0.05 -#sweep.k31//sim-d0.20-r.001-k31-g1000000-out sumkmer 1036581 sumdiff: 63 score: 99.994 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out deleted file mode 100644 index 1fbf2a2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.010 -Simulated 1200000 total bases, 12012 mutations (1.00%), G=1000000, d=0.20, r=.010 - -Model: -1 535393 -2 600174 -3 78414 -4 107253 - - -Observed Counts: -1 535509 -2 599406 -3 77385 -4 108366 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out.eval deleted file mode 100644 index 82663e6..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 600174 78414 107253 -obs: 535509 599406 77385 108366 -diff: -116 768 1029 -1113 -diffp: -0.02 0.13 1.33 -1.03 -#sweep.k31//sim-d0.20-r.010-k31-g1000000-out sumkmer 1320666 sumdiff: 568 score: 99.957 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out deleted file mode 100644 index 95b7777..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.050 -Simulated 1200000 total bases, 59893 mutations (4.99%), G=1000000, d=0.20, r=.050 - -Model: -1 1592185 -2 289878 -3 64931 -4 8315 - - -Observed Counts: -1 1589382 -2 291356 -3 65082 -4 8150 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out.eval deleted file mode 100644 index 9c9366e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 289878 64931 8315 -obs: 1589382 291356 65082 8150 -diff: 2803 -1478 -151 165 -diffp: 0.18 -0.51 -0.23 2.02 -#sweep.k31//sim-d0.20-r.050-k31-g1000000-out sumkmer 1953970 sumdiff: 1339 score: 99.931 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out deleted file mode 100644 index c2df68c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.100 -Simulated 1200000 total bases, 119866 mutations (9.99%), G=1000000, d=0.20, r=.100 - -Model: -1 1923695 -2 215551 -3 14678 -4 291 - - -Observed Counts: -1 1923326 -2 215088 -3 15098 -4 286 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out.eval deleted file mode 100644 index c669cb9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 215551 14678 291 -obs: 1923326 215088 15098 286 -diff: 369 463 -420 5 -diffp: 0.02 0.22 -2.78 1.75 -#sweep.k31//sim-d0.20-r.100-k31-g1000000-out sumkmer 2153798 sumdiff: 417 score: 99.981 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out deleted file mode 100644 index 696de05..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.20, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.200 -Simulated 1200000 total bases, 240770 mutations (20.06%), G=1000000, d=0.20, r=.200 - -Model: -1 1998018 -2 200396 -3 395 -4 0 - - -Observed Counts: -1 1998032 -2 200369 -3 390 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out.eval deleted file mode 100644 index 28d9ea2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 200396 395 0 -obs: 1998032 200369 390 0 -diff: -14 27 5 0 -diffp: -0.00 0.01 1.28 0.00 -#sweep.k31//sim-d0.20-r.200-k31-g1000000-out sumkmer 2198791 sumdiff: 18 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out deleted file mode 100644 index 4095efc..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.20, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.300 -Simulated 1200000 total bases, 359373 mutations (29.95%), G=1000000, d=0.20, r=.300 - -Model: -1 1999968 -2 200006 -3 6 -4 0 - - -Observed Counts: -1 1999933 -2 199990 -3 9 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out.eval deleted file mode 100644 index 66f3744..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 200006 6 0 -obs: 1999933 199990 9 0 -diff: 35 16 -3 0 -diffp: 0.00 0.01 -33.33 0.00 -#sweep.k31//sim-d0.20-r.300-k31-g1000000-out sumkmer 2199932 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out deleted file mode 100644 index 4fae610..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=0.00 -Simulated 1200000 total bases, 0 mutations (0.00%), G=1000000, d=0.20, r=0.00 - -Model: -1 0 -2 800000 -3 0 -4 200000 - - -Observed Counts: -2 800030 -4 199970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out.eval deleted file mode 100644 index d8e78ab..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.20-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 800000 0 200000 -obs: 0 800030 0 199970 -diff: 0 -30 0 30 -diffp: 0.00 -0.00 0.00 0.02 -#sweep.k31//sim-d0.20-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out deleted file mode 100644 index 8400a89..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.001 -Simulated 1300000 total bases, 1299 mutations (0.10%), G=1000000, d=0.30, r=.001 - -Model: -1 61078 -2 678902 -3 17764 -4 281956 - - -Observed Counts: -1 60098 -2 679838 -3 18498 -4 281168 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out.eval deleted file mode 100644 index d1c25db..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 678902 17764 281956 -obs: 60098 679838 18498 281168 -diff: 980 -936 -734 788 -diffp: 1.63 -0.14 -3.97 0.28 -#sweep.k31//sim-d0.30-r.001-k31-g1000000-out sumkmer 1039602 sumdiff: 98 score: 99.991 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out deleted file mode 100644 index 5a5af2b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.010 -Simulated 1300000 total bases, 12973 mutations (1.00%), G=1000000, d=0.30, r=.010 - -Model: -1 535393 -2 534110 -3 117621 -4 160880 - - -Observed Counts: -1 535671 -2 533377 -3 115213 -4 162969 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out.eval deleted file mode 100644 index ee05eba..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 534110 117621 160880 -obs: 535671 533377 115213 162969 -diff: -278 733 2408 -2089 -diffp: -0.05 0.14 2.09 -1.28 -#sweep.k31//sim-d0.30-r.010-k31-g1000000-out sumkmer 1347230 sumdiff: 774 score: 99.943 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out deleted file mode 100644 index 32e12c0..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.050 -Simulated 1300000 total bases, 65119 mutations (5.01%), G=1000000, d=0.30, r=.050 - -Model: -1 1592186 -2 332864 -3 97397 -4 12473 - - -Observed Counts: -1 1597005 -2 329730 -3 97653 -4 12629 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out.eval deleted file mode 100644 index 9cba2a2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592186 332864 97397 12473 -obs: 1597005 329730 97653 12629 -diff: -4819 3134 -256 -156 -diffp: -0.30 0.95 -0.26 -1.24 -#sweep.k31//sim-d0.30-r.050-k31-g1000000-out sumkmer 2037017 sumdiff: -2097 score: 100.103 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out deleted file mode 100644 index a76afc6..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.100 -Simulated 1300000 total bases, 129337 mutations (9.95%), G=1000000, d=0.30, r=.100 - -Model: -1 1923695 -2 304251 -3 22017 -4 436 - - -Observed Counts: -1 1923736 -2 302793 -3 22910 -4 472 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out.eval deleted file mode 100644 index 76fb32d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 304251 22017 436 -obs: 1923736 302793 22910 472 -diff: -41 1458 -893 -36 -diffp: -0.00 0.48 -3.90 -7.63 -#sweep.k31//sim-d0.30-r.100-k31-g1000000-out sumkmer 2249911 sumdiff: 488 score: 99.978 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out deleted file mode 100644 index c43f4d2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.30, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.200 -Simulated 1300000 total bases, 260343 mutations (20.03%), G=1000000, d=0.30, r=.200 - -Model: -1 1998018 -2 300099 -3 593 -4 0 - - -Observed Counts: -1 1997955 -2 300139 -3 569 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out.eval deleted file mode 100644 index e266d8b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 300099 593 0 -obs: 1997955 300139 569 0 -diff: 63 -40 24 0 -diffp: 0.00 -0.01 4.22 0.00 -#sweep.k31//sim-d0.30-r.200-k31-g1000000-out sumkmer 2298663 sumdiff: 47 score: 99.998 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out deleted file mode 100644 index 4f8ac04..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.300 -Simulated 1300000 total bases, 389441 mutations (29.96%), G=1000000, d=0.30, r=.300 - -Model: -1 1999967 -2 300001 -3 9 -4 0 - - -Observed Counts: -1 1999980 -2 299980 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out.eval deleted file mode 100644 index bdcfeba..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999967 300001 9 0 -obs: 1999980 299980 0 0 -diff: -13 21 9 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k31//sim-d0.30-r.300-k31-g1000000-out sumkmer 2299960 sumdiff: 17 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out deleted file mode 100644 index 1d11718..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=0.00 -Simulated 1300000 total bases, 0 mutations (0.00%), G=1000000, d=0.30, r=0.00 - -Model: -1 0 -2 700000 -3 0 -4 300000 - - -Observed Counts: -2 700030 -4 299970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out.eval deleted file mode 100644 index 5a55995..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.30-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 700000 0 300000 -obs: 0 700030 0 299970 -diff: 0 -30 0 30 -diffp: 0.00 -0.00 0.00 0.01 -#sweep.k31//sim-d0.30-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out deleted file mode 100644 index a476b0a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.001 -Simulated 1400000 total bases, 1317 mutations (0.09%), G=1000000, d=0.40, r=.001 - -Model: -1 61078 -2 582049 -3 23685 -4 375941 - - -Observed Counts: -1 57995 -2 582608 -3 21551 -4 378019 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out.eval deleted file mode 100644 index b3c0d8a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 582049 23685 375941 -obs: 57995 582608 21551 378019 -diff: 3083 -559 2134 -2078 -diffp: 5.32 -0.10 9.90 -0.55 -#sweep.k31//sim-d0.40-r.001-k31-g1000000-out sumkmer 1040173 sumdiff: 2580 score: 99.752 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out deleted file mode 100644 index 44c6205..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.010 -Simulated 1400000 total bases, 13966 mutations (1.00%), G=1000000, d=0.40, r=.010 - -Model: -1 535393 -2 468046 -3 156828 -4 214507 - - -Observed Counts: -1 532253 -2 467782 -3 156221 -4 215865 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out.eval deleted file mode 100644 index 0e9a9b1..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 468046 156828 214507 -obs: 532253 467782 156221 215865 -diff: 3140 264 607 -1358 -diffp: 0.59 0.06 0.39 -0.63 -#sweep.k31//sim-d0.40-r.010-k31-g1000000-out sumkmer 1372121 sumdiff: 2653 score: 99.807 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out deleted file mode 100644 index 9fc2e20..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.050 -Simulated 1400000 total bases, 70150 mutations (5.01%), G=1000000, d=0.40, r=.050 - -Model: -1 1592186 -2 375849 -3 129863 -4 16631 - - -Observed Counts: -1 1593205 -2 377152 -3 129049 -4 16321 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out.eval deleted file mode 100644 index 98e4784..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592186 375849 129863 16631 -obs: 1593205 377152 129049 16321 -diff: -1019 -1303 814 310 -diffp: -0.06 -0.35 0.63 1.90 -#sweep.k31//sim-d0.40-r.050-k31-g1000000-out sumkmer 2115727 sumdiff: -1198 score: 100.057 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out deleted file mode 100644 index daa1821..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.100 -Simulated 1400000 total bases, 139947 mutations (10.00%), G=1000000, d=0.40, r=.100 - -Model: -1 1923695 -2 392951 -3 29357 -4 582 - - -Observed Counts: -1 1923299 -2 393807 -3 28873 -4 602 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out.eval deleted file mode 100644 index 7d450e3..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 392951 29357 582 -obs: 1923299 393807 28873 602 -diff: 396 -856 484 -20 -diffp: 0.02 -0.22 1.68 -3.32 -#sweep.k31//sim-d0.40-r.100-k31-g1000000-out sumkmer 2346581 sumdiff: 4 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out deleted file mode 100644 index cffeb18..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.200 -Simulated 1400000 total bases, 279719 mutations (19.98%), G=1000000, d=0.40, r=.200 - -Model: -1 1998018 -2 399802 -3 791 -4 0 - - -Observed Counts: -1 1997907 -2 399844 -3 771 -4 8 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out.eval deleted file mode 100644 index 642151a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 399802 791 0 -obs: 1997907 399844 771 8 -diff: 111 -42 20 -8 -diffp: 0.01 -0.01 2.59 -100.00 -#sweep.k31//sim-d0.40-r.200-k31-g1000000-out sumkmer 2398530 sumdiff: 81 score: 99.997 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out deleted file mode 100644 index a32def1..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.40, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.300 -Simulated 1400000 total bases, 420298 mutations (30.02%), G=1000000, d=0.40, r=.300 - -Model: -1 1999967 -2 399996 -3 12 -4 0 - - -Observed Counts: -1 1999968 -2 399953 -3 22 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out.eval deleted file mode 100644 index 5a39fba..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999967 399996 12 0 -obs: 1999968 399953 22 0 -diff: -1 43 -10 0 -diffp: -0.00 0.01 -45.45 0.00 -#sweep.k31//sim-d0.40-r.300-k31-g1000000-out sumkmer 2399943 sumdiff: 32 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out deleted file mode 100644 index 9fb16b9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=0.00 -Simulated 1400000 total bases, 0 mutations (0.00%), G=1000000, d=0.40, r=0.00 - -Model: -1 0 -2 600000 -3 0 -4 400000 - - -Observed Counts: -2 600030 -4 399970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out.eval deleted file mode 100644 index f9bc90d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.40-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 600000 0 400000 -obs: 0 600030 0 399970 -diff: 0 -30 0 30 -diffp: 0.00 -0.00 0.00 0.01 -#sweep.k31//sim-d0.40-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out deleted file mode 100644 index ed2bb83..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.001 -Simulated 1500000 total bases, 1539 mutations (0.10%), G=1000000, d=0.50, r=.001 - -Model: -1 61078 -2 485196 -3 29606 -4 469926 - - -Observed Counts: -1 61545 -2 486059 -3 31555 -4 467903 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out.eval deleted file mode 100644 index f3180f8..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 485196 29606 469926 -obs: 61545 486059 31555 467903 -diff: -467 -863 -1949 2023 -diffp: -0.76 -0.18 -6.18 0.43 -#sweep.k31//sim-d0.50-r.001-k31-g1000000-out sumkmer 1047062 sumdiff: -1256 score: 100.120 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out deleted file mode 100644 index fd60d8a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.010 -Simulated 1500000 total bases, 14976 mutations (1.00%), G=1000000, d=0.50, r=.010 - -Model: -1 535393 -2 401982 -3 196035 -4 268134 - - -Observed Counts: -1 533411 -2 400961 -3 194217 -4 270489 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out.eval deleted file mode 100644 index 4a3f568..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 401982 196035 268134 -obs: 533411 400961 194217 270489 -diff: 1982 1021 1818 -2355 -diffp: 0.37 0.25 0.94 -0.87 -#sweep.k31//sim-d0.50-r.010-k31-g1000000-out sumkmer 1399078 sumdiff: 2466 score: 99.824 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out deleted file mode 100644 index ae46eab..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.050 -Simulated 1500000 total bases, 74996 mutations (5.00%), G=1000000, d=0.50, r=.050 - -Model: -1 1592185 -2 418835 -3 162328 -4 20788 - - -Observed Counts: -1 1586464 -2 420261 -3 163054 -4 20948 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out.eval deleted file mode 100644 index 01a2af4..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 418835 162328 20788 -obs: 1586464 420261 163054 20948 -diff: 5721 -1426 -726 -160 -diffp: 0.36 -0.34 -0.45 -0.76 -#sweep.k31//sim-d0.50-r.050-k31-g1000000-out sumkmer 2190727 sumdiff: 3409 score: 99.844 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out deleted file mode 100644 index d4ee8fb..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.100 -Simulated 1500000 total bases, 150225 mutations (10.02%), G=1000000, d=0.50, r=.100 - -Model: -1 1923695 -2 481651 -3 36696 -4 727 - - -Observed Counts: -1 1924074 -2 481495 -3 36824 -4 601 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out.eval deleted file mode 100644 index 7fb7d5d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 481651 36696 727 -obs: 1924074 481495 36824 601 -diff: -379 156 -128 126 -diffp: -0.02 0.03 -0.35 20.97 -#sweep.k31//sim-d0.50-r.100-k31-g1000000-out sumkmer 2442994 sumdiff: -225 score: 100.009 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out deleted file mode 100644 index dcbf880..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.200 -Simulated 1500000 total bases, 299477 mutations (19.97%), G=1000000, d=0.50, r=.200 - -Model: -1 1998018 -2 499505 -3 989 -4 0 - - -Observed Counts: -1 1997849 -2 499200 -3 1229 -4 1 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out.eval deleted file mode 100644 index ab3e68f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 499505 989 0 -obs: 1997849 499200 1229 1 -diff: 169 305 -240 -1 -diffp: 0.01 0.06 -19.53 -100.00 -#sweep.k31//sim-d0.50-r.200-k31-g1000000-out sumkmer 2498279 sumdiff: 233 score: 99.991 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out deleted file mode 100644 index 0ceed8b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.50, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.300 -Simulated 1500000 total bases, 450019 mutations (30.00%), G=1000000, d=0.50, r=.300 - -Model: -1 1999967 -2 499992 -3 15 -4 0 - - -Observed Counts: -1 1999964 -2 499967 -3 14 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out.eval deleted file mode 100644 index fda62aa..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999967 499992 15 0 -obs: 1999964 499967 14 0 -diff: 3 25 1 0 -diffp: 0.00 0.01 7.14 0.00 -#sweep.k31//sim-d0.50-r.300-k31-g1000000-out sumkmer 2499945 sumdiff: 29 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out deleted file mode 100644 index 9995169..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=0.00 -Simulated 1500000 total bases, 0 mutations (0.00%), G=1000000, d=0.50, r=0.00 - -Model: -1 0 -2 500000 -3 0 -4 500000 - - -Observed Counts: -2 500030 -4 499970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out.eval deleted file mode 100644 index c3f6d42..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.50-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 500000 0 500000 -obs: 0 500030 0 499970 -diff: 0 -30 0 30 -diffp: 0.00 -0.01 0.00 0.01 -#sweep.k31//sim-d0.50-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out deleted file mode 100644 index 8b3a31d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.001 -Simulated 1600000 total bases, 1611 mutations (0.10%), G=1000000, d=0.60, r=.001 - -Model: -1 61078 -2 388343 -3 35528 -4 563912 - - -Observed Counts: -1 61544 -2 388129 -3 35722 -4 563743 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out.eval deleted file mode 100644 index 8de2af5..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 388343 35528 563912 -obs: 61544 388129 35722 563743 -diff: -466 214 -194 169 -diffp: -0.76 0.06 -0.54 0.03 -#sweep.k31//sim-d0.60-r.001-k31-g1000000-out sumkmer 1049138 sumdiff: -277 score: 100.026 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out deleted file mode 100644 index 76e7cc7..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.010 -Simulated 1600000 total bases, 15923 mutations (1.00%), G=1000000, d=0.60, r=.010 - -Model: -1 535393 -2 335918 -3 235242 -4 321760 - - -Observed Counts: -1 531531 -2 337396 -3 234347 -4 322644 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out.eval deleted file mode 100644 index 96e4ea9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 335918 235242 321760 -obs: 531531 337396 234347 322644 -diff: 3862 -1478 895 -884 -diffp: 0.73 -0.44 0.38 -0.27 -#sweep.k31//sim-d0.60-r.010-k31-g1000000-out sumkmer 1425918 sumdiff: 2395 score: 99.832 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out deleted file mode 100644 index f2cc25c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.050 -Simulated 1600000 total bases, 79940 mutations (5.00%), G=1000000, d=0.60, r=.050 - -Model: -1 1592185 -2 461821 -3 194794 -4 24946 - - -Observed Counts: -1 1589311 -2 464606 -3 193215 -4 25443 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out.eval deleted file mode 100644 index f5ab27c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 461821 194794 24946 -obs: 1589311 464606 193215 25443 -diff: 2874 -2785 1579 -497 -diffp: 0.18 -0.60 0.82 -1.95 -#sweep.k31//sim-d0.60-r.050-k31-g1000000-out sumkmer 2272575 sumdiff: 1171 score: 99.948 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out deleted file mode 100644 index 2f4219e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.100 -Simulated 1600000 total bases, 159834 mutations (9.99%), G=1000000, d=0.60, r=.100 - -Model: -1 1923695 -2 570351 -3 44035 -4 873 - - -Observed Counts: -1 1922244 -2 570710 -3 44184 -4 931 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out.eval deleted file mode 100644 index 797b182..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 570351 44035 873 -obs: 1922244 570710 44184 931 -diff: 1451 -359 -149 -58 -diffp: 0.08 -0.06 -0.34 -6.23 -#sweep.k31//sim-d0.60-r.100-k31-g1000000-out sumkmer 2538069 sumdiff: 885 score: 99.965 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out deleted file mode 100644 index 2d5fae3..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.60, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.200 -Simulated 1600000 total bases, 319755 mutations (19.98%), G=1000000, d=0.60, r=.200 - -Model: -1 1998019 -2 599208 -3 1187 -4 0 - - -Observed Counts: -1 1998175 -2 599030 -3 1235 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out.eval deleted file mode 100644 index ce4d84f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998019 599208 1187 0 -obs: 1998175 599030 1235 0 -diff: -156 178 -48 0 -diffp: -0.01 0.03 -3.89 0.00 -#sweep.k31//sim-d0.60-r.200-k31-g1000000-out sumkmer 2598440 sumdiff: -26 score: 100.001 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out deleted file mode 100644 index 102312a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.60, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.300 -Simulated 1600000 total bases, 480268 mutations (30.02%), G=1000000, d=0.60, r=.300 - -Model: -1 1999967 -2 599987 -3 18 -4 0 - - -Observed Counts: -1 1999985 -2 599967 -3 7 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out.eval deleted file mode 100644 index 889c96c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999967 599987 18 0 -obs: 1999985 599967 7 0 -diff: -18 20 11 0 -diffp: -0.00 0.00 157.14 0.00 -#sweep.k31//sim-d0.60-r.300-k31-g1000000-out sumkmer 2599959 sumdiff: 13 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out deleted file mode 100644 index 08a5ed9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=0.00 -Simulated 1600000 total bases, 0 mutations (0.00%), G=1000000, d=0.60, r=0.00 - -Model: -1 0 -2 400000 -3 0 -4 600000 - - -Observed Counts: -2 400030 -4 599970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out.eval deleted file mode 100644 index c75ce37..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.60-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 400000 0 600000 -obs: 0 400030 0 599970 -diff: 0 -30 0 30 -diffp: 0.00 -0.01 0.00 0.01 -#sweep.k31//sim-d0.60-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out deleted file mode 100644 index 1ece0c3..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.001 -Simulated 1700000 total bases, 1713 mutations (0.10%), G=1000000, d=0.70, r=.001 - -Model: -1 61078 -2 291491 -3 41449 -4 657897 - - -Observed Counts: -1 60731 -2 292294 -3 42783 -4 656568 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out.eval deleted file mode 100644 index 7a12a06..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 291491 41449 657897 -obs: 60731 292294 42783 656568 -diff: 347 -803 -1334 1329 -diffp: 0.57 -0.27 -3.12 0.20 -#sweep.k31//sim-d0.70-r.001-k31-g1000000-out sumkmer 1052376 sumdiff: -461 score: 100.044 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out deleted file mode 100644 index 8f62c30..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.010 -Simulated 1700000 total bases, 16902 mutations (0.99%), G=1000000, d=0.70, r=.010 - -Model: -1 535393 -2 269854 -3 274449 -4 375387 - - -Observed Counts: -1 529425 -2 270854 -3 276305 -4 374973 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out.eval deleted file mode 100644 index 1d4b12c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 269854 274449 375387 -obs: 529425 270854 276305 374973 -diff: 5968 -1000 -1856 414 -diffp: 1.13 -0.37 -0.67 0.11 -#sweep.k31//sim-d0.70-r.010-k31-g1000000-out sumkmer 1451557 sumdiff: 3526 score: 99.757 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out deleted file mode 100644 index 295da88..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.050 -Simulated 1700000 total bases, 85074 mutations (5.00%), G=1000000, d=0.70, r=.050 - -Model: -1 1592185 -2 504807 -3 227260 -4 29104 - - -Observed Counts: -1 1586730 -2 505465 -3 228260 -4 29375 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out.eval deleted file mode 100644 index 6ed4789..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 504807 227260 29104 -obs: 1586730 505465 228260 29375 -diff: 5455 -658 -1000 -271 -diffp: 0.34 -0.13 -0.44 -0.92 -#sweep.k31//sim-d0.70-r.050-k31-g1000000-out sumkmer 2349830 sumdiff: 3526 score: 99.850 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out deleted file mode 100644 index c2910a5..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.100 -Simulated 1700000 total bases, 169361 mutations (9.96%), G=1000000, d=0.70, r=.100 - -Model: -1 1923695 -2 659051 -3 51375 -4 1018 - - -Observed Counts: -1 1920979 -2 658167 -3 52661 -4 1161 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out.eval deleted file mode 100644 index d9b067f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 659051 51375 1018 -obs: 1920979 658167 52661 1161 -diff: 2716 884 -1286 -143 -diffp: 0.14 0.13 -2.44 -12.32 -#sweep.k31//sim-d0.70-r.100-k31-g1000000-out sumkmer 2632968 sumdiff: 2171 score: 99.918 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out deleted file mode 100644 index 0c8dea2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.200 -Simulated 1700000 total bases, 339808 mutations (19.99%), G=1000000, d=0.70, r=.200 - -Model: -1 1998019 -2 698911 -3 1385 -4 0 - - -Observed Counts: -1 1998006 -2 699062 -3 1270 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out.eval deleted file mode 100644 index d012956..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998019 698911 1385 0 -obs: 1998006 699062 1270 0 -diff: 13 -151 115 0 -diffp: 0.00 -0.02 9.06 0.00 -#sweep.k31//sim-d0.70-r.200-k31-g1000000-out sumkmer 2698338 sumdiff: -23 score: 100.001 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out deleted file mode 100644 index 4556018..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.300 -Simulated 1700000 total bases, 510362 mutations (30.02%), G=1000000, d=0.70, r=.300 - -Model: -1 1999968 -2 699982 -3 22 -4 0 - - -Observed Counts: -1 1999944 -2 699953 -3 30 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out.eval deleted file mode 100644 index bbf0aec..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 699982 22 0 -obs: 1999944 699953 30 0 -diff: 24 29 -8 0 -diffp: 0.00 0.00 -26.67 0.00 -#sweep.k31//sim-d0.70-r.300-k31-g1000000-out sumkmer 2699927 sumdiff: 45 score: 99.998 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out deleted file mode 100644 index a38274e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=0.00 -Simulated 1700000 total bases, 0 mutations (0.00%), G=1000000, d=0.70, r=0.00 - -Model: -1 0 -2 300000 -3 0 -4 700000 - - -Observed Counts: -2 300030 -4 699970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out.eval deleted file mode 100644 index b020b06..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.70-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 300000 0 700000 -obs: 0 300030 0 699970 -diff: 0 -30 0 30 -diffp: 0.00 -0.01 0.00 0.00 -#sweep.k31//sim-d0.70-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out deleted file mode 100644 index 34a9fa3..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.001 -Simulated 1800000 total bases, 1808 mutations (0.10%), G=1000000, d=0.80, r=.001 - -Model: -1 61078 -2 194638 -3 47370 -4 751882 - - -Observed Counts: -1 61036 -2 195267 -3 48338 -4 750839 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out.eval deleted file mode 100644 index 37b2550..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 194638 47370 751882 -obs: 61036 195267 48338 750839 -diff: 42 -629 -968 1043 -diffp: 0.07 -0.32 -2.00 0.14 -#sweep.k31//sim-d0.80-r.001-k31-g1000000-out sumkmer 1055480 sumdiff: -512 score: 100.049 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out deleted file mode 100644 index 8f40931..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.010 -Simulated 1800000 total bases, 17987 mutations (1.00%), G=1000000, d=0.80, r=.010 - -Model: -1 535393 -2 203789 -3 313656 -4 429014 - - -Observed Counts: -1 534197 -2 203172 -3 315101 -4 428524 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out.eval deleted file mode 100644 index a26666f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 203789 313656 429014 -obs: 534197 203172 315101 428524 -diff: 1196 617 -1445 490 -diffp: 0.22 0.30 -0.46 0.11 -#sweep.k31//sim-d0.80-r.010-k31-g1000000-out sumkmer 1480994 sumdiff: 858 score: 99.942 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out deleted file mode 100644 index 3340e11..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.050 -Simulated 1800000 total bases, 89908 mutations (4.99%), G=1000000, d=0.80, r=.050 - -Model: -1 1592186 -2 547792 -3 259726 -4 33262 - - -Observed Counts: -1 1586529 -2 548725 -3 257615 -4 35779 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out.eval deleted file mode 100644 index 8f05f35..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592186 547792 259726 33262 -obs: 1586529 548725 257615 35779 -diff: 5657 -933 2111 -2517 -diffp: 0.36 -0.17 0.82 -7.03 -#sweep.k31//sim-d0.80-r.050-k31-g1000000-out sumkmer 2428648 sumdiff: 4318 score: 99.822 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out deleted file mode 100644 index cb875f0..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.100 -Simulated 1800000 total bases, 180696 mutations (10.04%), G=1000000, d=0.80, r=.100 - -Model: -1 1923695 -2 747751 -3 58714 -4 1164 - - -Observed Counts: -1 1924846 -2 749753 -3 56948 -4 1186 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out.eval deleted file mode 100644 index a30d5e9..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 747751 58714 1164 -obs: 1924846 749753 56948 1186 -diff: -1151 -2002 1766 -22 -diffp: -0.06 -0.27 3.10 -1.85 -#sweep.k31//sim-d0.80-r.100-k31-g1000000-out sumkmer 2732733 sumdiff: -1409 score: 100.052 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out deleted file mode 100644 index 43edc43..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.200 -Simulated 1800000 total bases, 360637 mutations (20.04%), G=1000000, d=0.80, r=.200 - -Model: -1 1998018 -2 798614 -3 1582 -4 0 - - -Observed Counts: -1 1998220 -2 798478 -3 1588 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out.eval deleted file mode 100644 index abe1d3c..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 798614 1582 0 -obs: 1998220 798478 1588 0 -diff: -202 136 -6 0 -diffp: -0.01 0.02 -0.38 0.00 -#sweep.k31//sim-d0.80-r.200-k31-g1000000-out sumkmer 2798286 sumdiff: -72 score: 100.003 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out deleted file mode 100644 index 2678c8a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.300 -Simulated 1800000 total bases, 540140 mutations (30.01%), G=1000000, d=0.80, r=.300 - -Model: -1 1999968 -2 799977 -3 25 -4 0 - - -Observed Counts: -1 1999981 -2 799960 -3 13 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out.eval deleted file mode 100644 index 71bac75..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 799977 25 0 -obs: 1999981 799960 13 0 -diff: -13 17 12 0 -diffp: -0.00 0.00 92.31 0.00 -#sweep.k31//sim-d0.80-r.300-k31-g1000000-out sumkmer 2799954 sumdiff: 16 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out deleted file mode 100644 index a662139..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=0.00 -Simulated 1800000 total bases, 0 mutations (0.00%), G=1000000, d=0.80, r=0.00 - -Model: -1 0 -2 199999 -3 0 -4 800000 - - -Observed Counts: -2 200030 -4 799970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out.eval deleted file mode 100644 index 6f21ac7..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.80-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 199999 0 800000 -obs: 0 200030 0 799970 -diff: 0 -31 0 30 -diffp: 0.00 -0.02 0.00 0.00 -#sweep.k31//sim-d0.80-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out deleted file mode 100644 index f213977..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.001, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.001 -Simulated 1900000 total bases, 1932 mutations (0.10%), G=1000000, d=0.90, r=.001 - -Model: -1 61078 -2 97785 -3 53292 -4 845868 - - -Observed Counts: -1 62051 -2 97953 -3 54237 -4 844818 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out.eval deleted file mode 100644 index 82a05c0..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 97785 53292 845868 -obs: 62051 97953 54237 844818 -diff: -973 -168 -945 1050 -diffp: -1.57 -0.17 -1.74 0.12 -#sweep.k31//sim-d0.90-r.001-k31-g1000000-out sumkmer 1059059 sumdiff: -1036 score: 100.098 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out deleted file mode 100644 index 9109964..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.010, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.010 -Simulated 1900000 total bases, 19005 mutations (1.00%), G=1000000, d=0.90, r=.010 - -Model: -1 535393 -2 137725 -3 352863 -4 482641 - - -Observed Counts: -1 531018 -2 140720 -3 352118 -4 482782 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out.eval deleted file mode 100644 index 9d22791..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535393 137725 352863 482641 -obs: 531018 140720 352118 482782 -diff: 4375 -2995 745 -141 -diffp: 0.82 -2.13 0.21 -0.03 -#sweep.k31//sim-d0.90-r.010-k31-g1000000-out sumkmer 1506638 sumdiff: 1984 score: 99.868 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out deleted file mode 100644 index f242dee..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.050, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.050 -Simulated 1900000 total bases, 95034 mutations (5.00%), G=1000000, d=0.90, r=.050 - -Model: -1 1592185 -2 590778 -3 292191 -4 37420 - - -Observed Counts: -1 1585131 -2 594046 -3 291263 -4 38232 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out.eval deleted file mode 100644 index e939d9b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 590778 292191 37420 -obs: 1585131 594046 291263 38232 -diff: 7054 -3268 928 -812 -diffp: 0.45 -0.55 0.32 -2.12 -#sweep.k31//sim-d0.90-r.050-k31-g1000000-out sumkmer 2508672 sumdiff: 3902 score: 99.844 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out deleted file mode 100644 index fb65b08..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.100, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.100 -Simulated 1900000 total bases, 189779 mutations (9.99%), G=1000000, d=0.90, r=.100 - -Model: -1 1923695 -2 836451 -3 66053 -4 1310 - - -Observed Counts: -1 1920773 -2 835582 -3 67685 -4 1237 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out.eval deleted file mode 100644 index c5cf8ea..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923695 836451 66053 1310 -obs: 1920773 835582 67685 1237 -diff: 2922 869 -1632 73 -diffp: 0.15 0.10 -2.41 5.90 -#sweep.k31//sim-d0.90-r.100-k31-g1000000-out sumkmer 2825277 sumdiff: 2232 score: 99.921 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out deleted file mode 100644 index fc073b8..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.200, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.200 -Simulated 1900000 total bases, 379985 mutations (20.00%), G=1000000, d=0.90, r=.200 - -Model: -1 1998018 -2 898317 -3 1780 -4 0 - - -Observed Counts: -1 1997955 -2 898188 -3 1867 -4 2 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out.eval deleted file mode 100644 index a50298d..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 898317 1780 0 -obs: 1997955 898188 1867 2 -diff: 63 129 -87 -2 -diffp: 0.00 0.01 -4.66 -100.00 -#sweep.k31//sim-d0.90-r.200-k31-g1000000-out sumkmer 2898012 sumdiff: 103 score: 99.996 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out deleted file mode 100644 index 1dd409f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.90, r=.300, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.300 -Simulated 1900000 total bases, 569912 mutations (30.00%), G=1000000, d=0.90, r=.300 - -Model: -1 1999968 -2 899973 -3 28 -4 0 - - -Observed Counts: -1 1999964 -2 899943 -3 30 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out.eval deleted file mode 100644 index e5975f4..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999968 899973 28 0 -obs: 1999964 899943 30 0 -diff: 4 30 -2 0 -diffp: 0.00 0.00 -6.67 0.00 -#sweep.k31//sim-d0.90-r.300-k31-g1000000-out sumkmer 2899937 sumdiff: 32 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out deleted file mode 100644 index 3cb240a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=0.00, k=31 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=0.00 -Simulated 1900000 total bases, 0 mutations (0.00%), G=1000000, d=0.90, r=0.00 - -Model: -1 0 -2 99999 -3 0 -4 900000 - - -Observed Counts: -2 100030 -4 899970 diff --git a/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out.eval deleted file mode 100644 index b2e7332..0000000 --- a/analysis/genomesim/sweep.k31/sim-d0.90-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 99999 0 900000 -obs: 0 100030 0 899970 -diff: 0 -31 0 30 -diffp: 0.00 -0.03 0.00 0.00 -#sweep.k31//sim-d0.90-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out deleted file mode 100644 index f8a1f5a..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.001, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.001 -Simulated 2000000 total bases, 2015 mutations (0.10%), G=1000000, d=1.00, r=.001 - -Model: -1 61078 -2 932 -3 59213 -4 939853 - - -Observed Counts: -1 61690 -2 848 -3 60054 -4 939098 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out.eval deleted file mode 100644 index 90bf319..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.001-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 61078 932 59213 939853 -obs: 61690 848 60054 939098 -diff: -612 84 -841 755 -diffp: -0.99 9.91 -1.40 0.08 -#sweep.k31//sim-d1.00-r.001-k31-g1000000-out sumkmer 1061690 sumdiff: -614 score: 100.058 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out deleted file mode 100644 index 763497f..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.010, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.010 -Simulated 2000000 total bases, 20148 mutations (1.01%), G=1000000, d=1.00, r=.010 - -Model: -1 535392 -2 71661 -3 392070 -4 536268 - - -Observed Counts: -1 538169 -2 74392 -3 395733 -4 531447 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out.eval deleted file mode 100644 index dbb9455..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.010-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 535392 71661 392070 536268 -obs: 538169 74392 395733 531447 -diff: -2777 -2731 -3663 4821 -diffp: -0.52 -3.67 -0.93 0.91 -#sweep.k31//sim-d1.00-r.010-k31-g1000000-out sumkmer 1539741 sumdiff: -4350 score: 100.283 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out deleted file mode 100644 index 22b5f4e..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.050, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.050 -Simulated 2000000 total bases, 100019 mutations (5.00%), G=1000000, d=1.00, r=.050 - -Model: -1 1592185 -2 633764 -3 324657 -4 41577 - - -Observed Counts: -1 1585512 -2 638646 -3 323796 -4 41437 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out.eval deleted file mode 100644 index e372a01..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.050-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1592185 633764 324657 41577 -obs: 1585512 638646 323796 41437 -diff: 6673 -4882 861 140 -diffp: 0.42 -0.76 0.27 0.34 -#sweep.k31//sim-d1.00-r.050-k31-g1000000-out sumkmer 2589391 sumdiff: 2792 score: 99.892 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out deleted file mode 100644 index 387e223..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.100, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.100 -Simulated 2000000 total bases, 199183 mutations (9.96%), G=1000000, d=1.00, r=.100 - -Model: -1 1923694 -2 925151 -3 73392 -4 1455 - - -Observed Counts: -1 1921241 -2 925001 -3 74215 -4 1513 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out.eval deleted file mode 100644 index 4291dcd..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.100-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1923694 925151 73392 1455 -obs: 1921241 925001 74215 1513 -diff: 2453 150 -823 -58 -diffp: 0.13 0.02 -1.11 -3.83 -#sweep.k31//sim-d1.00-r.100-k31-g1000000-out sumkmer 2921970 sumdiff: 1722 score: 99.941 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out deleted file mode 100644 index d1018ef..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=1.00, r=.200, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.200 -Simulated 2000000 total bases, 400272 mutations (20.01%), G=1000000, d=1.00, r=.200 - -Model: -1 1998018 -2 998020 -3 1978 -4 0 - - -Observed Counts: -1 1998069 -2 998042 -3 1929 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out.eval deleted file mode 100644 index 786dac2..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.200-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1998018 998020 1978 0 -obs: 1998069 998042 1929 0 -diff: -51 -22 49 0 -diffp: -0.00 -0.00 2.54 0.00 -#sweep.k31//sim-d1.00-r.200-k31-g1000000-out sumkmer 2998040 sumdiff: -24 score: 100.001 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out deleted file mode 100644 index b3999cf..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=1.00, r=.300, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.300 -Simulated 2000000 total bases, 599937 mutations (30.00%), G=1000000, d=1.00, r=.300 - -Model: -1 1999967 -2 999968 -3 31 -4 0 - - -Observed Counts: -1 1999952 -2 999922 -3 48 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out.eval deleted file mode 100644 index c4d1d7b..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r.300-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999967 999968 31 0 -obs: 1999952 999922 48 0 -diff: 15 46 -17 0 -diffp: 0.00 0.00 -35.42 0.00 -#sweep.k31//sim-d1.00-r.300-k31-g1000000-out sumkmer 2999922 sumdiff: 44 score: 99.999 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out b/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out deleted file mode 100644 index 5b6bbda..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=0.00, k=31 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=0.00 -Simulated 2000000 total bases, 0 mutations (0.00%), G=1000000, d=1.00, r=0.00 - -Model: -1 0 -2 0 -3 0 -4 1000000 - - -Observed Counts: -2 30 -4 999970 diff --git a/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out.eval b/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out.eval deleted file mode 100644 index 7d1ac10..0000000 --- a/analysis/genomesim/sweep.k31/sim-d1.00-r0.00-k31-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 0 0 1000000 -obs: 0 30 0 999970 -diff: 0 -30 0 30 -diffp: 0.00 -100.00 0.00 0.00 -#sweep.k31//sim-d1.00-r0.00-k31-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out deleted file mode 100644 index 7ec7812..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.001 -Simulated 1000000 total bases, 960 mutations (0.10%), G=1000000, d=0.00, r=.001 - -Model: -1 99491 -2 950254 -3 0 -4 0 - - -Observed Counts: -1 95872 -2 952014 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out.eval deleted file mode 100644 index cf40664..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99491 950254 0 0 -obs: 95872 952014 0 0 -diff: 3619 -1760 0 0 -diffp: 3.77 -0.18 0.00 0.00 -#sweep.k51//sim-d0.00-r.001-k51-g1000000-out sumkmer 1047886 sumdiff: 1859 score: 99.823 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out deleted file mode 100644 index 7222018..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.010 -Simulated 1000000 total bases, 10146 mutations (1.01%), G=1000000, d=0.00, r=.010 - -Model: -1 802087 -2 598956 -3 0 -4 0 - - -Observed Counts: -1 809160 -2 595370 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out.eval deleted file mode 100644 index 6a48665..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 598956 0 0 -obs: 809160 595370 0 0 -diff: -7073 3586 0 0 -diffp: -0.87 0.60 0.00 0.00 -#sweep.k51//sim-d0.00-r.010-k51-g1000000-out sumkmer 1404530 sumdiff: -3487 score: 100.248 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out deleted file mode 100644 index edd2668..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.050 -Simulated 1000000 total bases, 49838 mutations (4.98%), G=1000000, d=0.00, r=.050 - -Model: -1 1853804 -2 73097 -3 0 -4 0 - - -Observed Counts: -1 1850130 -2 74885 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out.eval deleted file mode 100644 index adc5add..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 73097 0 0 -obs: 1850130 74885 0 0 -diff: 3674 -1788 0 0 -diffp: 0.20 -2.39 0.00 0.00 -#sweep.k51//sim-d0.00-r.050-k51-g1000000-out sumkmer 1925015 sumdiff: 1886 score: 99.902 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out deleted file mode 100644 index af66159..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.100 -Simulated 1000000 total bases, 99876 mutations (9.99%), G=1000000, d=0.00, r=.100 - -Model: -1 1990723 -2 4638 -3 0 -4 0 - - -Observed Counts: -1 1990188 -2 4856 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out.eval deleted file mode 100644 index 2e3d5fa..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990723 4638 0 0 -obs: 1990188 4856 0 0 -diff: 535 -218 0 0 -diffp: 0.03 -4.49 0.00 0.00 -#sweep.k51//sim-d0.00-r.100-k51-g1000000-out sumkmer 1995044 sumdiff: 317 score: 99.984 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out deleted file mode 100644 index b8e22a9..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.00, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.200 -Simulated 1000000 total bases, 199739 mutations (19.97%), G=1000000, d=0.00, r=.200 - -Model: -1 1999977 -2 11 -3 0 -4 0 - - -Observed Counts: -1 1999898 -2 1 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out.eval deleted file mode 100644 index 59fe5f7..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999977 11 0 0 -obs: 1999898 1 0 0 -diff: 79 10 0 0 -diffp: 0.00 1000.00 0.00 0.00 -#sweep.k51//sim-d0.00-r.200-k51-g1000000-out sumkmer 1999899 sumdiff: 89 score: 99.996 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out deleted file mode 100644 index c92216a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=.300 -Simulated 1000000 total bases, 299245 mutations (29.92%), G=1000000, d=0.00, r=.300 - -Model: -1 1999999 -2 0 -3 0 -4 0 - - -Observed Counts: -1 1999900 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out.eval deleted file mode 100644 index 625cc1c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 0 0 0 -obs: 1999900 0 0 0 -diff: 99 0 0 0 -diffp: 0.00 0.00 0.00 0.00 -#sweep.k51//sim-d0.00-r.300-k51-g1000000-out sumkmer 1999900 sumdiff: 99 score: 99.995 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out deleted file mode 100644 index 84054b9..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out +++ /dev/null @@ -1,15 +0,0 @@ -Simulating G=1000000, d=0.00, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.00, newlen=1000000 - ... add heterozygosity r=0.00 -Simulated 1000000 total bases, 0 mutations (0.00%), G=1000000, d=0.00, r=0.00 - -Model: -1 0 -2 1000000 -3 0 -4 0 - - -Observed Counts: -2 999950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out.eval deleted file mode 100644 index e61e83b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.00-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 1000000 0 0 -obs: 0 999950 0 0 -diff: 0 50 0 0 -diffp: 0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.00-r0.00-k51-g1000000-out sumkmer 999950 sumdiff: 50 score: 99.995 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out deleted file mode 100644 index 4e3b70d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.001 -Simulated 1100000 total bases, 1120 mutations (0.10%), G=1000000, d=0.10, r=.001 - -Model: -1 99490 -2 855476 -3 9454 -4 90298 - - -Observed Counts: -1 102064 -2 853928 -3 9108 -4 90664 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out.eval deleted file mode 100644 index 38e027a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 855476 9454 90298 -obs: 102064 853928 9108 90664 -diff: -2574 1548 346 -366 -diffp: -2.52 0.18 3.80 -0.40 -#sweep.k51//sim-d0.10-r.001-k51-g1000000-out sumkmer 1055764 sumdiff: -1046 score: 100.099 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out deleted file mode 100644 index 916ea4f..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.010 -Simulated 1100000 total bases, 11039 mutations (1.00%), G=1000000, d=0.10, r=.010 - -Model: -1 802087 -2 555144 -3 48041 -4 35874 - - -Observed Counts: -1 807750 -2 552892 -3 49374 -4 34561 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out.eval deleted file mode 100644 index e9eff7c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 555144 48041 35874 -obs: 807750 552892 49374 34561 -diff: -5663 2252 -1333 1313 -diffp: -0.70 0.41 -2.70 3.80 -#sweep.k51//sim-d0.10-r.010-k51-g1000000-out sumkmer 1444577 sumdiff: -3431 score: 100.238 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out deleted file mode 100644 index ab84e94..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.10, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.050 -Simulated 1100000 total bases, 54573 mutations (4.96%), G=1000000, d=0.10, r=.050 - -Model: -1 1853803 -2 151702 -3 13550 -4 534 - - -Observed Counts: -1 1854381 -2 150587 -3 13911 -4 653 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out.eval deleted file mode 100644 index 70b7ed4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853803 151702 13550 534 -obs: 1854381 150587 13911 653 -diff: -578 1115 -361 -119 -diffp: -0.03 0.74 -2.60 -18.22 -#sweep.k51//sim-d0.10-r.050-k51-g1000000-out sumkmer 2019532 sumdiff: 57 score: 99.997 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out deleted file mode 100644 index 9633681..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.10, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.100 -Simulated 1100000 total bases, 110102 mutations (10.01%), G=1000000, d=0.10, r=.100 - -Model: -1 1990722 -2 103249 -3 923 -4 2 - - -Observed Counts: -1 1990640 -2 103127 -3 1002 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out.eval deleted file mode 100644 index e957ba8..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 103249 923 2 -obs: 1990640 103127 1002 0 -diff: 82 122 -79 2 -diffp: 0.00 0.12 -7.88 0.00 -#sweep.k51//sim-d0.10-r.100-k51-g1000000-out sumkmer 2094769 sumdiff: 127 score: 99.994 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out deleted file mode 100644 index 06d5ff8..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.200 -Simulated 1100000 total bases, 219833 mutations (19.98%), G=1000000, d=0.10, r=.200 - -Model: -1 1999976 -2 100007 -3 2 -4 0 - - -Observed Counts: -1 2000000 -2 99950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out.eval deleted file mode 100644 index 2256633..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 100007 2 0 -obs: 2000000 99950 0 0 -diff: -24 57 2 0 -diffp: -0.00 0.06 0.00 0.00 -#sweep.k51//sim-d0.10-r.200-k51-g1000000-out sumkmer 2099950 sumdiff: 35 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out deleted file mode 100644 index a8d1a86..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=.300 -Simulated 1100000 total bases, 330646 mutations (30.06%), G=1000000, d=0.10, r=.300 - -Model: -1 1999999 -2 100000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 99950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out.eval deleted file mode 100644 index acb688a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 100000 0 0 -obs: 2000000 99950 0 0 -diff: -1 50 0 0 -diffp: -0.00 0.05 0.00 0.00 -#sweep.k51//sim-d0.10-r.300-k51-g1000000-out sumkmer 2099950 sumdiff: 49 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out deleted file mode 100644 index 3e162f2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.10, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.10, newlen=1100000 - ... add heterozygosity r=0.00 -Simulated 1100000 total bases, 0 mutations (0.00%), G=1000000, d=0.10, r=0.00 - -Model: -1 0 -2 900000 -3 0 -4 100000 - - -Observed Counts: -2 900050 -4 99950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out.eval deleted file mode 100644 index c76938d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.10-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 900000 0 100000 -obs: 0 900050 0 99950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.05 -#sweep.k51//sim-d0.10-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out deleted file mode 100644 index 8643fb7..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.001 -Simulated 1200000 total bases, 1224 mutations (0.10%), G=1000000, d=0.20, r=.001 - -Model: -1 99490 -2 760698 -3 18908 -4 180596 - - -Observed Counts: -1 100126 -2 761325 -3 20380 -4 178996 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out.eval deleted file mode 100644 index 8878ca3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 760698 18908 180596 -obs: 100126 761325 20380 178996 -diff: -636 -627 -1472 1600 -diffp: -0.64 -0.08 -7.22 0.89 -#sweep.k51//sim-d0.20-r.001-k51-g1000000-out sumkmer 1060827 sumdiff: -1135 score: 100.107 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out deleted file mode 100644 index 4847d3b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.010 -Simulated 1200000 total bases, 11845 mutations (0.99%), G=1000000, d=0.20, r=.010 - -Model: -1 802087 -2 511332 -3 96083 -4 71749 - - -Observed Counts: -1 789799 -2 518221 -3 94489 -4 72548 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out.eval deleted file mode 100644 index 1cb5595..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 511332 96083 71749 -obs: 789799 518221 94489 72548 -diff: 12288 -6889 1594 -799 -diffp: 1.56 -1.33 1.69 -1.10 -#sweep.k51//sim-d0.20-r.010-k51-g1000000-out sumkmer 1475057 sumdiff: 6194 score: 99.580 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out deleted file mode 100644 index 0fa61de..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.050 -Simulated 1200000 total bases, 59524 mutations (4.96%), G=1000000, d=0.20, r=.050 - -Model: -1 1853803 -2 230307 -3 27101 -4 1068 - - -Observed Counts: -1 1848814 -2 231952 -3 27458 -4 1202 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out.eval deleted file mode 100644 index 9bbb910..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853803 230307 27101 1068 -obs: 1848814 231952 27458 1202 -diff: 4989 -1645 -357 -134 -diffp: 0.27 -0.71 -1.30 -11.15 -#sweep.k51//sim-d0.20-r.050-k51-g1000000-out sumkmer 2109426 sumdiff: 2853 score: 99.865 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out deleted file mode 100644 index aa17495..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.20, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.100 -Simulated 1200000 total bases, 120062 mutations (10.01%), G=1000000, d=0.20, r=.100 - -Model: -1 1990722 -2 201859 -3 1846 -4 4 - - -Observed Counts: -1 1990398 -2 201636 -3 2070 -4 5 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out.eval deleted file mode 100644 index 98097ab..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 201859 1846 4 -obs: 1990398 201636 2070 5 -diff: 324 223 -224 -1 -diffp: 0.02 0.11 -10.82 -20.00 -#sweep.k51//sim-d0.20-r.100-k51-g1000000-out sumkmer 2194109 sumdiff: 322 score: 99.985 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out deleted file mode 100644 index 2e8f4ea..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.200 -Simulated 1200000 total bases, 239590 mutations (19.97%), G=1000000, d=0.20, r=.200 - -Model: -1 1999976 -2 200004 -3 4 -4 0 - - -Observed Counts: -1 1999944 -2 199978 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out.eval deleted file mode 100644 index db7614d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 200004 4 0 -obs: 1999944 199978 0 0 -diff: 32 26 4 0 -diffp: 0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.20-r.200-k51-g1000000-out sumkmer 2199922 sumdiff: 62 score: 99.997 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out deleted file mode 100644 index dcefab4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=.300 -Simulated 1200000 total bases, 360146 mutations (30.01%), G=1000000, d=0.20, r=.300 - -Model: -1 1999999 -2 200000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 199950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out.eval deleted file mode 100644 index 27366f3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 200000 0 0 -obs: 2000000 199950 0 0 -diff: -1 50 0 0 -diffp: -0.00 0.03 0.00 0.00 -#sweep.k51//sim-d0.20-r.300-k51-g1000000-out sumkmer 2199950 sumdiff: 49 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out deleted file mode 100644 index a22e091..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.20, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.20, newlen=1200000 - ... add heterozygosity r=0.00 -Simulated 1200000 total bases, 0 mutations (0.00%), G=1000000, d=0.20, r=0.00 - -Model: -1 0 -2 800000 -3 0 -4 200000 - - -Observed Counts: -2 800050 -4 199950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out.eval deleted file mode 100644 index d298788..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.20-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 800000 0 200000 -obs: 0 800050 0 199950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.03 -#sweep.k51//sim-d0.20-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out deleted file mode 100644 index 90c8615..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.001 -Simulated 1300000 total bases, 1311 mutations (0.10%), G=1000000, d=0.30, r=.001 - -Model: -1 99490 -2 665920 -3 28362 -4 270895 - - -Observed Counts: -1 100959 -2 665213 -3 27733 -4 271329 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out.eval deleted file mode 100644 index 160659e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 665920 28362 270895 -obs: 100959 665213 27733 271329 -diff: -1469 707 629 -434 -diffp: -1.46 0.11 2.27 -0.16 -#sweep.k51//sim-d0.30-r.001-k51-g1000000-out sumkmer 1065234 sumdiff: -567 score: 100.053 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out deleted file mode 100644 index 138a42e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.010 -Simulated 1300000 total bases, 12926 mutations (0.99%), G=1000000, d=0.30, r=.010 - -Model: -1 802087 -2 467520 -3 144124 -4 107624 - - -Observed Counts: -1 796264 -2 470344 -3 144188 -4 107596 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out.eval deleted file mode 100644 index 8c32f6d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 467520 144124 107624 -obs: 796264 470344 144188 107596 -diff: 5823 -2824 -64 28 -diffp: 0.73 -0.60 -0.04 0.03 -#sweep.k51//sim-d0.30-r.010-k51-g1000000-out sumkmer 1518392 sumdiff: 2963 score: 99.805 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out deleted file mode 100644 index 1f5e0f5..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.050 -Simulated 1300000 total bases, 65269 mutations (5.02%), G=1000000, d=0.30, r=.050 - -Model: -1 1853803 -2 308912 -3 40652 -4 1602 - - -Observed Counts: -1 1853936 -2 308303 -3 41074 -4 1534 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out.eval deleted file mode 100644 index 93e3b93..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853803 308912 40652 1602 -obs: 1853936 308303 41074 1534 -diff: -133 609 -422 68 -diffp: -0.01 0.20 -1.03 4.43 -#sweep.k51//sim-d0.30-r.050-k51-g1000000-out sumkmer 2204847 sumdiff: 122 score: 99.994 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out deleted file mode 100644 index 17c5e21..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.30, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.100 -Simulated 1300000 total bases, 130445 mutations (10.03%), G=1000000, d=0.30, r=.100 - -Model: -1 1990723 -2 300470 -3 2770 -4 6 - - -Observed Counts: -1 1991428 -2 300391 -3 2558 -4 4 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out.eval deleted file mode 100644 index 559cef5..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990723 300470 2770 6 -obs: 1991428 300391 2558 4 -diff: -705 79 212 2 -diffp: -0.04 0.03 8.29 50.00 -#sweep.k51//sim-d0.30-r.100-k51-g1000000-out sumkmer 2294381 sumdiff: -412 score: 100.018 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out deleted file mode 100644 index 3dba958..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.30, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.200 -Simulated 1300000 total bases, 260472 mutations (20.04%), G=1000000, d=0.30, r=.200 - -Model: -1 1999976 -2 300001 -3 6 -4 0 - - -Observed Counts: -1 1999982 -2 299941 -3 12 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out.eval deleted file mode 100644 index 47e952a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 300001 6 0 -obs: 1999982 299941 12 0 -diff: -6 60 -6 0 -diffp: -0.00 0.02 -50.00 0.00 -#sweep.k51//sim-d0.30-r.200-k51-g1000000-out sumkmer 2299935 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out deleted file mode 100644 index 449ed7a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=.300 -Simulated 1300000 total bases, 390252 mutations (30.02%), G=1000000, d=0.30, r=.300 - -Model: -1 1999999 -2 300000 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 299950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out.eval deleted file mode 100644 index 2b8837e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 300000 0 0 -obs: 2000000 299950 0 0 -diff: -1 50 0 0 -diffp: -0.00 0.02 0.00 0.00 -#sweep.k51//sim-d0.30-r.300-k51-g1000000-out sumkmer 2299950 sumdiff: 49 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out deleted file mode 100644 index c777f7b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.30, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.30, newlen=1300000 - ... add heterozygosity r=0.00 -Simulated 1300000 total bases, 0 mutations (0.00%), G=1000000, d=0.30, r=0.00 - -Model: -1 0 -2 700000 -3 0 -4 300000 - - -Observed Counts: -2 700050 -4 299950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out.eval deleted file mode 100644 index df6899a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.30-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 700000 0 300000 -obs: 0 700050 0 299950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.02 -#sweep.k51//sim-d0.30-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out deleted file mode 100644 index 9d03532..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.001 -Simulated 1400000 total bases, 1397 mutations (0.10%), G=1000000, d=0.40, r=.001 - -Model: -1 99490 -2 571142 -3 37816 -4 361193 - - -Observed Counts: -1 100215 -2 570535 -3 36873 -4 361999 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out.eval deleted file mode 100644 index 1c863ca..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 571142 37816 361193 -obs: 100215 570535 36873 361999 -diff: -725 607 943 -806 -diffp: -0.72 0.11 2.56 -0.22 -#sweep.k51//sim-d0.40-r.001-k51-g1000000-out sumkmer 1069622 sumdiff: 19 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out deleted file mode 100644 index ffe3f8e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.010 -Simulated 1400000 total bases, 13943 mutations (1.00%), G=1000000, d=0.40, r=.010 - -Model: -1 802087 -2 423708 -3 192166 -4 143499 - - -Observed Counts: -1 797348 -2 421532 -3 196016 -4 142860 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out.eval deleted file mode 100644 index 5ce3e73..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 423708 192166 143499 -obs: 797348 421532 196016 142860 -diff: 4739 2176 -3850 639 -diffp: 0.59 0.52 -1.96 0.45 -#sweep.k51//sim-d0.40-r.010-k51-g1000000-out sumkmer 1557756 sumdiff: 3704 score: 99.762 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out deleted file mode 100644 index 3a0f78f..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.050 -Simulated 1400000 total bases, 69730 mutations (4.98%), G=1000000, d=0.40, r=.050 - -Model: -1 1853803 -2 387517 -3 54203 -4 2137 - - -Observed Counts: -1 1848352 -2 388589 -3 55418 -4 2029 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out.eval deleted file mode 100644 index d79e7b0..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853803 387517 54203 2137 -obs: 1848352 388589 55418 2029 -diff: 5451 -1072 -1215 108 -diffp: 0.29 -0.28 -2.19 5.32 -#sweep.k51//sim-d0.40-r.050-k51-g1000000-out sumkmer 2294388 sumdiff: 3272 score: 99.857 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out deleted file mode 100644 index ac85235..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.40, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.100 -Simulated 1400000 total bases, 140016 mutations (10.00%), G=1000000, d=0.40, r=.100 - -Model: -1 1990722 -2 399080 -3 3693 -4 8 - - -Observed Counts: -1 1990648 -2 398442 -3 4116 -4 5 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out.eval deleted file mode 100644 index 104d392..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 399080 3693 8 -obs: 1990648 398442 4116 5 -diff: 74 638 -423 3 -diffp: 0.00 0.16 -10.28 60.00 -#sweep.k51//sim-d0.40-r.100-k51-g1000000-out sumkmer 2393211 sumdiff: 292 score: 99.988 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out deleted file mode 100644 index 24985d5..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.40, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.200 -Simulated 1400000 total bases, 280211 mutations (20.02%), G=1000000, d=0.40, r=.200 - -Model: -1 1999977 -2 399997 -3 9 -4 0 - - -Observed Counts: -1 1999950 -2 399945 -3 20 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out.eval deleted file mode 100644 index 64559a7..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999977 399997 9 0 -obs: 1999950 399945 20 0 -diff: 27 52 -11 0 -diffp: 0.00 0.01 -55.00 0.00 -#sweep.k51//sim-d0.40-r.200-k51-g1000000-out sumkmer 2399915 sumdiff: 68 score: 99.997 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out deleted file mode 100644 index 99420f4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=.300 -Simulated 1400000 total bases, 419561 mutations (29.97%), G=1000000, d=0.40, r=.300 - -Model: -1 1999999 -2 399999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 399950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out.eval deleted file mode 100644 index d8856e0..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 399999 0 0 -obs: 2000000 399950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.40-r.300-k51-g1000000-out sumkmer 2399950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out deleted file mode 100644 index 0d798b2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.40, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.40, newlen=1400000 - ... add heterozygosity r=0.00 -Simulated 1400000 total bases, 0 mutations (0.00%), G=1000000, d=0.40, r=0.00 - -Model: -1 0 -2 600000 -3 0 -4 400000 - - -Observed Counts: -2 600050 -4 399950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out.eval deleted file mode 100644 index ced851e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.40-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 600000 0 400000 -obs: 0 600050 0 399950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.01 -#sweep.k51//sim-d0.40-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out deleted file mode 100644 index a3c16ae..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.001 -Simulated 1500000 total bases, 1592 mutations (0.11%), G=1000000, d=0.50, r=.001 - -Model: -1 99490 -2 476364 -3 47270 -4 451491 - - -Observed Counts: -1 105540 -2 475167 -3 49050 -4 449219 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out.eval deleted file mode 100644 index cbdc9a2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 476364 47270 451491 -obs: 105540 475167 49050 449219 -diff: -6050 1197 -1780 2272 -diffp: -5.73 0.25 -3.63 0.51 -#sweep.k51//sim-d0.50-r.001-k51-g1000000-out sumkmer 1078976 sumdiff: -4361 score: 100.404 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out deleted file mode 100644 index 83efe18..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.010 -Simulated 1500000 total bases, 14994 mutations (1.00%), G=1000000, d=0.50, r=.010 - -Model: -1 802087 -2 379896 -3 240207 -4 179374 - - -Observed Counts: -1 800491 -2 380161 -3 242633 -4 177797 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out.eval deleted file mode 100644 index 2e5c37f..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 379896 240207 179374 -obs: 800491 380161 242633 177797 -diff: 1596 -265 -2426 1577 -diffp: 0.20 -0.07 -1.00 0.89 -#sweep.k51//sim-d0.50-r.010-k51-g1000000-out sumkmer 1601082 sumdiff: 482 score: 99.970 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out deleted file mode 100644 index ad20c12..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.50, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.050 -Simulated 1500000 total bases, 74979 mutations (5.00%), G=1000000, d=0.50, r=.050 - -Model: -1 1853804 -2 466122 -3 67754 -4 2671 - - -Observed Counts: -1 1855054 -2 466135 -3 67040 -4 2864 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out.eval deleted file mode 100644 index 5ecc417..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 466122 67754 2671 -obs: 1855054 466135 67040 2864 -diff: -1250 -13 714 -193 -diffp: -0.07 -0.00 1.07 -6.74 -#sweep.k51//sim-d0.50-r.050-k51-g1000000-out sumkmer 2391093 sumdiff: -742 score: 100.031 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out deleted file mode 100644 index 983be57..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.50, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.100 -Simulated 1500000 total bases, 150500 mutations (10.03%), G=1000000, d=0.50, r=.100 - -Model: -1 1990722 -2 497691 -3 4616 -4 10 - - -Observed Counts: -1 1990713 -2 497770 -3 4549 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out.eval deleted file mode 100644 index 8e85b1f..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 497691 4616 10 -obs: 1990713 497770 4549 0 -diff: 9 -79 67 10 -diffp: 0.00 -0.02 1.47 0.00 -#sweep.k51//sim-d0.50-r.100-k51-g1000000-out sumkmer 2493032 sumdiff: 7 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out deleted file mode 100644 index 3c04525..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.50, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.200 -Simulated 1500000 total bases, 300112 mutations (20.01%), G=1000000, d=0.50, r=.200 - -Model: -1 1999976 -2 499994 -3 11 -4 0 - - -Observed Counts: -1 1999982 -2 499953 -3 4 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out.eval deleted file mode 100644 index 5b6b16a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 499994 11 0 -obs: 1999982 499953 4 0 -diff: -6 41 7 0 -diffp: -0.00 0.01 175.00 0.00 -#sweep.k51//sim-d0.50-r.200-k51-g1000000-out sumkmer 2499939 sumdiff: 42 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out deleted file mode 100644 index cf22a0e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=.300 -Simulated 1500000 total bases, 449389 mutations (29.96%), G=1000000, d=0.50, r=.300 - -Model: -1 1999999 -2 499999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 499950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out.eval deleted file mode 100644 index d82cf93..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 499999 0 0 -obs: 2000000 499950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.50-r.300-k51-g1000000-out sumkmer 2499950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out deleted file mode 100644 index 8900409..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.50, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.50, newlen=1500000 - ... add heterozygosity r=0.00 -Simulated 1500000 total bases, 0 mutations (0.00%), G=1000000, d=0.50, r=0.00 - -Model: -1 0 -2 500000 -3 0 -4 500000 - - -Observed Counts: -2 500050 -4 499950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out.eval deleted file mode 100644 index aa80316..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.50-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 500000 0 500000 -obs: 0 500050 0 499950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.01 -#sweep.k51//sim-d0.50-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out deleted file mode 100644 index 59be246..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.001 -Simulated 1600000 total bases, 1611 mutations (0.10%), G=1000000, d=0.60, r=.001 - -Model: -1 99491 -2 381586 -3 56725 -4 541790 - - -Observed Counts: -1 100588 -2 381543 -3 56414 -4 541746 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out.eval deleted file mode 100644 index 7b97d5a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99491 381586 56725 541790 -obs: 100588 381543 56414 541746 -diff: -1097 43 311 44 -diffp: -1.09 0.01 0.55 0.01 -#sweep.k51//sim-d0.60-r.001-k51-g1000000-out sumkmer 1080291 sumdiff: -699 score: 100.065 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out deleted file mode 100644 index a452b8c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.010 -Simulated 1600000 total bases, 15976 mutations (1.00%), G=1000000, d=0.60, r=.010 - -Model: -1 802087 -2 336084 -3 288249 -4 215248 - - -Observed Counts: -1 797135 -2 336574 -3 287215 -4 216993 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out.eval deleted file mode 100644 index 7f5deef..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 336084 288249 215248 -obs: 797135 336574 287215 216993 -diff: 4952 -490 1034 -1745 -diffp: 0.62 -0.15 0.36 -0.80 -#sweep.k51//sim-d0.60-r.010-k51-g1000000-out sumkmer 1637917 sumdiff: 3751 score: 99.771 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out deleted file mode 100644 index 20d4365..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.050 -Simulated 1600000 total bases, 79988 mutations (5.00%), G=1000000, d=0.60, r=.050 - -Model: -1 1853804 -2 544727 -3 81305 -4 3205 - - -Observed Counts: -1 1849447 -2 543415 -3 83077 -4 3598 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out.eval deleted file mode 100644 index fb04424..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 544727 81305 3205 -obs: 1849447 543415 83077 3598 -diff: 4357 1312 -1772 -393 -diffp: 0.24 0.24 -2.13 -10.92 -#sweep.k51//sim-d0.60-r.050-k51-g1000000-out sumkmer 2479537 sumdiff: 3504 score: 99.859 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out deleted file mode 100644 index 24e5763..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.60, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.100 -Simulated 1600000 total bases, 159394 mutations (9.96%), G=1000000, d=0.60, r=.100 - -Model: -1 1990722 -2 596302 -3 5540 -4 12 - - -Observed Counts: -1 1990208 -2 596042 -3 5864 -4 4 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out.eval deleted file mode 100644 index 44de657..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 596302 5540 12 -obs: 1990208 596042 5864 4 -diff: 514 260 -324 8 -diffp: 0.03 0.04 -5.53 200.00 -#sweep.k51//sim-d0.60-r.100-k51-g1000000-out sumkmer 2592118 sumdiff: 458 score: 99.982 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out deleted file mode 100644 index aca8a4d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.60, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.200 -Simulated 1600000 total bases, 319585 mutations (19.97%), G=1000000, d=0.60, r=.200 - -Model: -1 1999976 -2 599990 -3 13 -4 0 - - -Observed Counts: -1 1999979 -2 599929 -3 21 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out.eval deleted file mode 100644 index f381fef..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 599990 13 0 -obs: 1999979 599929 21 0 -diff: -3 61 -8 0 -diffp: -0.00 0.01 -38.10 0.00 -#sweep.k51//sim-d0.60-r.200-k51-g1000000-out sumkmer 2599929 sumdiff: 50 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out deleted file mode 100644 index 112f89a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=.300 -Simulated 1600000 total bases, 480083 mutations (30.01%), G=1000000, d=0.60, r=.300 - -Model: -1 1999999 -2 599999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 599950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out.eval deleted file mode 100644 index a06aa00..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 599999 0 0 -obs: 2000000 599950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.60-r.300-k51-g1000000-out sumkmer 2599950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out deleted file mode 100644 index 22b7e54..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.60, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.60, newlen=1600000 - ... add heterozygosity r=0.00 -Simulated 1600000 total bases, 0 mutations (0.00%), G=1000000, d=0.60, r=0.00 - -Model: -1 0 -2 400000 -3 0 -4 600000 - - -Observed Counts: -2 400050 -4 599950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out.eval deleted file mode 100644 index dc9791e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.60-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 400000 0 600000 -obs: 0 400050 0 599950 -diff: 0 -50 0 50 -diffp: 0.00 -0.01 0.00 0.01 -#sweep.k51//sim-d0.60-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out deleted file mode 100644 index ef177c6..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.001 -Simulated 1700000 total bases, 1684 mutations (0.10%), G=1000000, d=0.70, r=.001 - -Model: -1 99490 -2 286808 -3 66179 -4 632088 - - -Observed Counts: -1 98319 -2 288386 -3 64791 -4 632609 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out.eval deleted file mode 100644 index e873d15..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 286808 66179 632088 -obs: 98319 288386 64791 632609 -diff: 1171 -1578 1388 -521 -diffp: 1.19 -0.55 2.14 -0.08 -#sweep.k51//sim-d0.70-r.001-k51-g1000000-out sumkmer 1084105 sumdiff: 460 score: 99.958 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out deleted file mode 100644 index d0349e5..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.010 -Simulated 1700000 total bases, 16751 mutations (0.99%), G=1000000, d=0.70, r=.010 - -Model: -1 802087 -2 292272 -3 336290 -4 251123 - - -Observed Counts: -1 793073 -2 294694 -3 333357 -4 254342 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out.eval deleted file mode 100644 index 795b215..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 292272 336290 251123 -obs: 793073 294694 333357 254342 -diff: 9014 -2422 2933 -3219 -diffp: 1.14 -0.82 0.88 -1.27 -#sweep.k51//sim-d0.70-r.010-k51-g1000000-out sumkmer 1675466 sumdiff: 6306 score: 99.624 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out deleted file mode 100644 index 5d456d1..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.050 -Simulated 1700000 total bases, 85016 mutations (5.00%), G=1000000, d=0.70, r=.050 - -Model: -1 1853804 -2 623332 -3 94856 -4 3740 - - -Observed Counts: -1 1849300 -2 621721 -3 97798 -4 3441 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out.eval deleted file mode 100644 index f7c9ce3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 623332 94856 3740 -obs: 1849300 621721 97798 3441 -diff: 4504 1611 -2942 299 -diffp: 0.24 0.26 -3.01 8.69 -#sweep.k51//sim-d0.70-r.050-k51-g1000000-out sumkmer 2572260 sumdiff: 3472 score: 99.865 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out deleted file mode 100644 index 42e8b99..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.70, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.100 -Simulated 1700000 total bases, 169740 mutations (9.98%), G=1000000, d=0.70, r=.100 - -Model: -1 1990722 -2 694912 -3 6463 -4 15 - - -Observed Counts: -1 1990350 -2 694775 -3 6660 -4 5 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out.eval deleted file mode 100644 index b5bc9af..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 694912 6463 15 -obs: 1990350 694775 6660 5 -diff: 372 137 -197 10 -diffp: 0.02 0.02 -2.96 200.00 -#sweep.k51//sim-d0.70-r.100-k51-g1000000-out sumkmer 2691790 sumdiff: 322 score: 99.988 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out deleted file mode 100644 index d75b45d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.70, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.200 -Simulated 1700000 total bases, 339567 mutations (19.97%), G=1000000, d=0.70, r=.200 - -Model: -1 1999976 -2 699987 -3 15 -4 0 - - -Observed Counts: -1 1999983 -2 699933 -3 17 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out.eval deleted file mode 100644 index e29e032..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 699987 15 0 -obs: 1999983 699933 17 0 -diff: -7 54 -2 0 -diffp: -0.00 0.01 -11.76 0.00 -#sweep.k51//sim-d0.70-r.200-k51-g1000000-out sumkmer 2699933 sumdiff: 45 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out deleted file mode 100644 index 8afd321..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=.300 -Simulated 1700000 total bases, 510411 mutations (30.02%), G=1000000, d=0.70, r=.300 - -Model: -1 1999999 -2 699999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 699950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out.eval deleted file mode 100644 index f6e0ba3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 699999 0 0 -obs: 2000000 699950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.70-r.300-k51-g1000000-out sumkmer 2699950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out deleted file mode 100644 index 3bca7ca..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.70, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.70, newlen=1700000 - ... add heterozygosity r=0.00 -Simulated 1700000 total bases, 0 mutations (0.00%), G=1000000, d=0.70, r=0.00 - -Model: -1 0 -2 300000 -3 0 -4 700000 - - -Observed Counts: -2 300050 -4 699950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out.eval deleted file mode 100644 index ce949fd..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.70-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 300000 0 700000 -obs: 0 300050 0 699950 -diff: 0 -50 0 50 -diffp: 0.00 -0.02 0.00 0.01 -#sweep.k51//sim-d0.70-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out deleted file mode 100644 index 4a6b914..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.001 -Simulated 1800000 total bases, 1868 mutations (0.10%), G=1000000, d=0.80, r=.001 - -Model: -1 99490 -2 192030 -3 75633 -4 722386 - - -Observed Counts: -1 102809 -2 192369 -3 79295 -4 718617 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out.eval deleted file mode 100644 index efa7407..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 192030 75633 722386 -obs: 102809 192369 79295 718617 -diff: -3319 -339 -3662 3769 -diffp: -3.23 -0.18 -4.62 0.52 -#sweep.k51//sim-d0.80-r.001-k51-g1000000-out sumkmer 1093090 sumdiff: -3551 score: 100.325 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out deleted file mode 100644 index 5e9307a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.010 -Simulated 1800000 total bases, 17976 mutations (1.00%), G=1000000, d=0.80, r=.010 - -Model: -1 802087 -2 248460 -3 384332 -4 286998 - - -Observed Counts: -1 796236 -2 246510 -3 382340 -4 290906 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out.eval deleted file mode 100644 index 2f8ba6d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 248460 384332 286998 -obs: 796236 246510 382340 290906 -diff: 5851 1950 1992 -3908 -diffp: 0.73 0.79 0.52 -1.34 -#sweep.k51//sim-d0.80-r.010-k51-g1000000-out sumkmer 1715992 sumdiff: 5885 score: 99.657 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out deleted file mode 100644 index 3565bf3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.050 -Simulated 1800000 total bases, 89626 mutations (4.98%), G=1000000, d=0.80, r=.050 - -Model: -1 1853804 -2 701937 -3 108407 -4 4274 - - -Observed Counts: -1 1851435 -2 702699 -3 108521 -4 4376 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out.eval deleted file mode 100644 index da82246..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 701937 108407 4274 -obs: 1851435 702699 108521 4376 -diff: 2369 -762 -114 -102 -diffp: 0.13 -0.11 -0.11 -2.33 -#sweep.k51//sim-d0.80-r.050-k51-g1000000-out sumkmer 2667031 sumdiff: 1391 score: 99.948 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out deleted file mode 100644 index e93fc6b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.80, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.100 -Simulated 1800000 total bases, 179787 mutations (9.99%), G=1000000, d=0.80, r=.100 - -Model: -1 1990723 -2 793523 -3 7387 -4 17 - - -Observed Counts: -1 1990749 -2 793599 -3 7271 -4 35 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out.eval deleted file mode 100644 index 12861a4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990723 793523 7387 17 -obs: 1990749 793599 7271 35 -diff: -26 -76 116 -18 -diffp: -0.00 -0.01 1.60 -51.43 -#sweep.k51//sim-d0.80-r.100-k51-g1000000-out sumkmer 2791654 sumdiff: -4 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out deleted file mode 100644 index 46d96e5..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.80, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.200 -Simulated 1800000 total bases, 360983 mutations (20.05%), G=1000000, d=0.80, r=.200 - -Model: -1 1999976 -2 799984 -3 18 -4 0 - - -Observed Counts: -1 1999996 -2 799949 -3 2 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out.eval deleted file mode 100644 index 8396b67..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 799984 18 0 -obs: 1999996 799949 2 0 -diff: -20 35 16 0 -diffp: -0.00 0.00 800.00 0.00 -#sweep.k51//sim-d0.80-r.200-k51-g1000000-out sumkmer 2799947 sumdiff: 31 score: 99.999 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out deleted file mode 100644 index 8c38b97..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=.300 -Simulated 1800000 total bases, 541186 mutations (30.07%), G=1000000, d=0.80, r=.300 - -Model: -1 1999999 -2 799999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 799950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out.eval deleted file mode 100644 index 7742d65..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 799999 0 0 -obs: 2000000 799950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.80-r.300-k51-g1000000-out sumkmer 2799950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out deleted file mode 100644 index 8743dfb..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.80, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.80, newlen=1800000 - ... add heterozygosity r=0.00 -Simulated 1800000 total bases, 0 mutations (0.00%), G=1000000, d=0.80, r=0.00 - -Model: -1 0 -2 199999 -3 0 -4 800000 - - -Observed Counts: -2 200050 -4 799950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out.eval deleted file mode 100644 index 9913547..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.80-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 199999 0 800000 -obs: 0 200050 0 799950 -diff: 0 -51 0 50 -diffp: 0.00 -0.03 0.00 0.01 -#sweep.k51//sim-d0.80-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out deleted file mode 100644 index a86409e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.001, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.001 -Simulated 1900000 total bases, 1852 mutations (0.10%), G=1000000, d=0.90, r=.001 - -Model: -1 99490 -2 97252 -3 85087 -4 812685 - - -Observed Counts: -1 96302 -2 97809 -3 83076 -4 814688 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out.eval deleted file mode 100644 index 6fca8d9..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 97252 85087 812685 -obs: 96302 97809 83076 814688 -diff: 3188 -557 2011 -2003 -diffp: 3.31 -0.57 2.42 -0.25 -#sweep.k51//sim-d0.90-r.001-k51-g1000000-out sumkmer 1091875 sumdiff: 2639 score: 99.758 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out deleted file mode 100644 index 1bf989b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.010, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.010 -Simulated 1900000 total bases, 19193 mutations (1.01%), G=1000000, d=0.90, r=.010 - -Model: -1 802087 -2 204648 -3 432373 -4 322873 - - -Observed Counts: -1 805022 -2 210559 -3 432604 -4 318987 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out.eval deleted file mode 100644 index 8f1c73c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 204648 432373 322873 -obs: 805022 210559 432604 318987 -diff: -2935 -5911 -231 3886 -diffp: -0.36 -2.81 -0.05 1.22 -#sweep.k51//sim-d0.90-r.010-k51-g1000000-out sumkmer 1767172 sumdiff: -5191 score: 100.294 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out deleted file mode 100644 index 483c460..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.050, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.050 -Simulated 1900000 total bases, 95221 mutations (5.01%), G=1000000, d=0.90, r=.050 - -Model: -1 1853804 -2 780542 -3 121958 -4 4808 - - -Observed Counts: -1 1853758 -2 782477 -3 121064 -4 4499 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out.eval deleted file mode 100644 index 4c79fb9..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853804 780542 121958 4808 -obs: 1853758 782477 121064 4499 -diff: 46 -1935 894 309 -diffp: 0.00 -0.25 0.74 6.87 -#sweep.k51//sim-d0.90-r.050-k51-g1000000-out sumkmer 2761798 sumdiff: -686 score: 100.025 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out deleted file mode 100644 index 7c3e7f2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=0.90, r=.100, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.100 -Simulated 1900000 total bases, 189972 mutations (10.00%), G=1000000, d=0.90, r=.100 - -Model: -1 1990722 -2 892134 -3 8310 -4 19 - - -Observed Counts: -1 1990742 -2 892156 -3 8190 -4 69 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out.eval deleted file mode 100644 index c55ae34..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 892134 8310 19 -obs: 1990742 892156 8190 69 -diff: -20 -22 120 -50 -diffp: -0.00 -0.00 1.47 -72.46 -#sweep.k51//sim-d0.90-r.100-k51-g1000000-out sumkmer 2891157 sumdiff: 28 score: 99.999 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out deleted file mode 100644 index 829236c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=0.90, r=.200, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.200 -Simulated 1900000 total bases, 380801 mutations (20.04%), G=1000000, d=0.90, r=.200 - -Model: -1 1999976 -2 899980 -3 20 -4 0 - - -Observed Counts: -1 1999943 -2 899893 -3 57 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out.eval deleted file mode 100644 index ace9c8f..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 899980 20 0 -obs: 1999943 899893 57 0 -diff: 33 87 -37 0 -diffp: 0.00 0.01 -64.91 0.00 -#sweep.k51//sim-d0.90-r.200-k51-g1000000-out sumkmer 2899893 sumdiff: 83 score: 99.997 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out deleted file mode 100644 index cfac3b2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=.300, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=.300 -Simulated 1900000 total bases, 570493 mutations (30.03%), G=1000000, d=0.90, r=.300 - -Model: -1 1999999 -2 899999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 899950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out.eval deleted file mode 100644 index 6bf3674..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 899999 0 0 -obs: 2000000 899950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.01 0.00 0.00 -#sweep.k51//sim-d0.90-r.300-k51-g1000000-out sumkmer 2899950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out deleted file mode 100644 index 2f86dd3..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=0.90, r=0.00, k=51 - ... simulating progenitor - ... duplicated 0.90, newlen=1900000 - ... add heterozygosity r=0.00 -Simulated 1900000 total bases, 0 mutations (0.00%), G=1000000, d=0.90, r=0.00 - -Model: -1 0 -2 99999 -3 0 -4 900000 - - -Observed Counts: -2 100050 -4 899950 diff --git a/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out.eval deleted file mode 100644 index edc195a..0000000 --- a/analysis/genomesim/sweep.k51/sim-d0.90-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 99999 0 900000 -obs: 0 100050 0 899950 -diff: 0 -51 0 50 -diffp: 0.00 -0.05 0.00 0.01 -#sweep.k51//sim-d0.90-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: -1 score: 100.000 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out deleted file mode 100644 index c5603b6..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.001, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.001 -Simulated 2000000 total bases, 2017 mutations (0.10%), G=1000000, d=1.00, r=.001 - -Model: -1 99490 -2 2474 -3 94541 -4 902983 - - -Observed Counts: -1 100018 -2 2388 -3 95362 -4 902255 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out.eval deleted file mode 100644 index 25cc7ba..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.001-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 99490 2474 94541 902983 -obs: 100018 2388 95362 902255 -diff: -528 86 -821 728 -diffp: -0.53 3.60 -0.86 0.08 -#sweep.k51//sim-d1.00-r.001-k51-g1000000-out sumkmer 1100023 sumdiff: -535 score: 100.049 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out deleted file mode 100644 index 00ab9a4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.010, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.010 -Simulated 2000000 total bases, 20079 mutations (1.00%), G=1000000, d=1.00, r=.010 - -Model: -1 802087 -2 160836 -3 480415 -4 358748 - - -Observed Counts: -1 801297 -2 163165 -3 483251 -4 355630 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out.eval deleted file mode 100644 index a31df6e..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.010-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 802087 160836 480415 358748 -obs: 801297 163165 483251 355630 -diff: 790 -2329 -2836 3118 -diffp: 0.10 -1.43 -0.59 0.88 -#sweep.k51//sim-d1.00-r.010-k51-g1000000-out sumkmer 1803343 sumdiff: -1257 score: 100.070 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out deleted file mode 100644 index bdecdbf..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.050, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.050 -Simulated 2000000 total bases, 99752 mutations (4.99%), G=1000000, d=1.00, r=.050 - -Model: -1 1853803 -2 859147 -3 135508 -4 5343 - - -Observed Counts: -1 1846364 -2 854047 -3 141370 -4 5333 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out.eval deleted file mode 100644 index fdc30f4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.050-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1853803 859147 135508 5343 -obs: 1846364 854047 141370 5333 -diff: 7439 5100 -5862 10 -diffp: 0.40 0.60 -4.15 0.19 -#sweep.k51//sim-d1.00-r.050-k51-g1000000-out sumkmer 2847114 sumdiff: 6687 score: 99.765 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out deleted file mode 100644 index 039c18b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out +++ /dev/null @@ -1,18 +0,0 @@ -Simulating G=1000000, d=1.00, r=.100, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.100 -Simulated 2000000 total bases, 199509 mutations (9.98%), G=1000000, d=1.00, r=.100 - -Model: -1 1990722 -2 990744 -3 9233 -4 21 - - -Observed Counts: -1 1990450 -2 990467 -3 9476 -4 22 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out.eval deleted file mode 100644 index 1e8f59b..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.100-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1990722 990744 9233 21 -obs: 1990450 990467 9476 22 -diff: 272 277 -243 -1 -diffp: 0.01 0.03 -2.56 -4.55 -#sweep.k51//sim-d1.00-r.100-k51-g1000000-out sumkmer 2990415 sumdiff: 305 score: 99.990 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out deleted file mode 100644 index 04b8ba2..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out +++ /dev/null @@ -1,17 +0,0 @@ -Simulating G=1000000, d=1.00, r=.200, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.200 -Simulated 2000000 total bases, 399528 mutations (19.98%), G=1000000, d=1.00, r=.200 - -Model: -1 1999976 -2 999977 -3 22 -4 0 - - -Observed Counts: -1 1999997 -2 999947 -3 3 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out.eval deleted file mode 100644 index 0c1820c..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.200-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999976 999977 22 0 -obs: 1999997 999947 3 0 -diff: -21 30 19 0 -diffp: -0.00 0.00 633.33 0.00 -#sweep.k51//sim-d1.00-r.200-k51-g1000000-out sumkmer 2999947 sumdiff: 28 score: 99.999 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out deleted file mode 100644 index e1e0672..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=.300, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=.300 -Simulated 2000000 total bases, 600546 mutations (30.03%), G=1000000, d=1.00, r=.300 - -Model: -1 1999999 -2 999999 -3 0 -4 0 - - -Observed Counts: -1 2000000 -2 999950 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out.eval deleted file mode 100644 index 6ea19b4..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r.300-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 1999999 999999 0 0 -obs: 2000000 999950 0 0 -diff: -1 49 0 0 -diffp: -0.00 0.00 0.00 0.00 -#sweep.k51//sim-d1.00-r.300-k51-g1000000-out sumkmer 2999950 sumdiff: 48 score: 99.998 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out b/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out deleted file mode 100644 index 3283c7d..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out +++ /dev/null @@ -1,16 +0,0 @@ -Simulating G=1000000, d=1.00, r=0.00, k=51 - ... simulating progenitor - ... duplicated 1.00, newlen=2000000 - ... add heterozygosity r=0.00 -Simulated 2000000 total bases, 0 mutations (0.00%), G=1000000, d=1.00, r=0.00 - -Model: -1 0 -2 0 -3 0 -4 1000000 - - -Observed Counts: -2 50 -4 999950 diff --git a/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out.eval b/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out.eval deleted file mode 100644 index 171a056..0000000 --- a/analysis/genomesim/sweep.k51/sim-d1.00-r0.00-k51-g1000000-out.eval +++ /dev/null @@ -1,5 +0,0 @@ -model: 0 0 0 1000000 -obs: 0 50 0 999950 -diff: 0 -50 0 50 -diffp: 0.00 -100.00 0.00 0.01 -#sweep.k51//sim-d1.00-r0.00-k51-g1000000-out sumkmer 1000000 sumdiff: 0 score: 100.000 diff --git a/analysis/heterozygosity_commands.py b/analysis/heterozygosity_commands.py new file mode 100644 index 0000000..4afcb05 --- /dev/null +++ b/analysis/heterozygosity_commands.py @@ -0,0 +1,39 @@ +import itertools + +num_het = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +t = 0 #topology = 0 (full model) +genome_filename = "random_genome.fa" +k = 21 +coverage = 15 +read_length = 100 +br = 0 +err = 0.01 +model = "Partition" + +COMMANDS_file = open("HETEROZYGOSITY_COMMANDS", 'w') +for i in range(1,8): + for p in [2,3,4,5,6]: + COMMANDS_file.write("parallel -j 17 < HETEROZYGOSITY_COMMANDS"+str(i)+"_p"+str(p)+"\n") + +COMMANDS_file.close() + +for p in [2, 3, 4, 5, 6]: + files = [open("HETEROZYGOSITY_COMMANDS" + str(i) + "_p" + str(p),'w') for i in range(1, 8)] + lines = [] + for d in [0.1]: #10% repetitiveness + rs = [[0.005*x/(num_het[p]) for _ in range(num_het[p])] for x in range(51)] #heterozygosity from 0% to 25% in 0.5% increments, each het form has equal het + for r in rs: + lines.append("python parameteranalysis.py " + str(k) + " " + str(p) + " " + str(coverage) + " " + str(read_length) + " " + str(br) + " " + ' '.join(['%.6f' % x for x in r]) + " " + genome_filename + " " + str(err) + " " + model + " " + '%.3f' % d + " " + str(t) + "\n") + readfilenameprefix = genome_filename + "_k" + str(k) + "_p" + str(p) + "_cov" + str(coverage) + "_rl" + str(read_length) + "_br" + str(br) + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(float(t)) + "_" + model + "_reads" + lines.append("jellyfish count -C -m21 -s 1000000000 -t15 <(zcat " + readfilenameprefix + ".fa.gz) -o " + readfilenameprefix + ".jf" + "\n") + lines.append("jellyfish histo -t15 " + readfilenameprefix + ".jf > " + readfilenameprefix + ".histo" + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 0" + " -o HETEROZYGOSITY_OUTPUT_p" + str(p) + "_transform_exp0 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 1" + " -o HETEROZYGOSITY_OUTPUT_p" + str(p) + "_transform_exp1 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 2" + " -o HETEROZYGOSITY_OUTPUT_p" + str(p) + "_transform_exp2 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 3" + " -o HETEROZYGOSITY_OUTPUT_p" + str(p) + "_transform_exp3 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + for i in range(7): + files[i].write(lines[i]) + lines = [] + + for i in range(7): + files[i].close() diff --git a/analysis/heterozygosity_smudgeplot_commands.py b/analysis/heterozygosity_smudgeplot_commands.py new file mode 100644 index 0000000..26e0e13 --- /dev/null +++ b/analysis/heterozygosity_smudgeplot_commands.py @@ -0,0 +1,43 @@ +import itertools + +num_het = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +t = 0 #topology = 0 (full model) +genome_filename = "random_genome_010Mbp.fa" +k = 21 +coverage = 40 +read_length = 100 +br = 0 +err = 0.01 +model = "Partition" + +COMMANDS_file = open("HETEROZYGOSITY_smudgeplot_COMMANDS", 'w') +for i in range(1,7): + for p in [2,3,4,5,6]: + if i in [1, 5]: + COMMANDS_file.write("parallel -j 17 < HETEROZYGOSITY_smudgeplot_COMMANDS"+str(i)+"_p"+str(p)+"\n") + else: + COMMANDS_file.write("bash HETEROZYGOSITY_smudgeplot_COMMANDS"+str(i)+"_p"+str(p)+"\n") + +COMMANDS_file.close() + +p_to_rs = {2:[[0.005*x] for x in range(1,51)], 3:[[0.005*x+0.004, 0.001] for x in range(50)], 4:[[0, 0.005*x+0.003, 0.001, 0.001] for x in range(50)] + [[0.005*x+0.003, 0, 0.001, 0.001] for x in range(50)], 5:[[0.005*x+0.002, 0, 0.001, 0, 0.001, 0.001] for x in range(50)], 6:[[0.005*x+0.001, 0, 0, 0.001, 0, 0, 0.001, 0, 0.001, 0.001] for x in range(50)]} + +for p in [2, 3, 4, 5, 6]: + files = [open("HETEROZYGOSITY_smudgeplot_COMMANDS" + str(i) + "_p" + str(p),'w') for i in range(1, 7)] + lines = [] + for d in [0.1]: #10% repetitiveness + rs = p_to_rs[p] #heterozygosity from 0.5% to 25% in 0.5% increments + for r in rs: + lines.append("python parameteranalysis.py " + str(k) + " " + str(p) + " " + str(coverage) + " " + str(read_length) + " " + str(br) + " " + ' '.join(['%.6f' % x for x in r]) + " " + genome_filename + " " + str(err) + " " + model + " " + '%.3f' % d + " " + str(t) + "\n") + readfilenameprefix = genome_filename + "_k" + str(k) + "_p" + str(p) + "_cov" + str(coverage) + "_rl" + str(read_length) + "_br" + str(br) + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(float(t)) + "_" + model + "_reads" + lines.append("kmc -k" + str(k) + " -m256 -ci1 -cs10000 -fm " + readfilenameprefix + ".fa.gz " + readfilenameprefix + " tmp/\n") + lines.append("kmc_tools transform " + readfilenameprefix + " histogram " + readfilenameprefix + ".histo\n") + lines.append("kmc_tools transform " + readfilenameprefix + " -ci10 -cx300 reduce " + readfilenameprefix + "_L10_U300\n") + lines.append("smudge_pairs " + readfilenameprefix + "_L10_U300 " + readfilenameprefix + "_L10_U300_coverages.tsv\n") + lines.append("smudgeplot.py plot " + readfilenameprefix + "_L10_U300_coverages.tsv -o " + readfilenameprefix + "_L10_U300_coverages\n") + for i in range(6): + files[i].write(lines[i]) + lines = [] + + for i in range(6): + files[i].close() diff --git a/analysis/length_commands.py b/analysis/length_commands.py new file mode 100644 index 0000000..37527a6 --- /dev/null +++ b/analysis/length_commands.py @@ -0,0 +1,39 @@ +import itertools + +num_het = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +t = 0 #topology = 0 (full model) +k = 21 +coverage = 15 +read_length = 100 +br = 0 +err = 0.01 +model = "Partition" +d = 0.10 + +COMMANDS_file = open("LENGTH_COMMANDS", 'w') +for i in range(1,8): + for p in [1,2,3,4,5,6]: + COMMANDS_file.write("parallel -j 4 < LENGTH_COMMANDS"+str(i)+"_p"+str(p)+"\n") + +COMMANDS_file.close() + +for p in [1, 2, 3, 4, 5, 6]: + files = [open("LENGTH_COMMANDS" + str(i) + "_p" + str(p),'w') for i in range(1, 8)] + lines = [] + for genome_filename in ["random_genome_001Mbp.fa", "random_genome_010Mbp.fa", "random_genome_100Mbp.fa", "random_genome_001Gbp.fa"]: + rs = [[0.001/(num_het[p]) for _ in range(num_het[p])]] #heterozygosity 2.0%, equally divided among each het form + for r in rs: + lines.append("python parameteranalysis.py " + str(k) + " " + str(p) + " " + str(coverage) + " " + str(read_length) + " " + str(br) + " " + ' '.join(['%.6f' % x for x in r]) + " " + genome_filename + " " + str(err) + " " + model + " " + '%.3f' % d + " " + str(t) + "\n") + readfilenameprefix = genome_filename + "_k" + str(k) + "_p" + str(p) + "_cov" + str(coverage) + "_rl" + str(read_length) + "_br" + str(br) + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(float(t)) + "_" + model + "_reads" + lines.append("jellyfish count -C -m21 -s 1000000000 -t15 <(zcat " + readfilenameprefix + ".fa.gz) -o " + readfilenameprefix + ".jf" + "\n") + lines.append("jellyfish histo -t15 " + readfilenameprefix + ".jf > " + readfilenameprefix + ".histo" + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 0" + " -o LENGTH_OUTPUT_p" + str(p) + "_transform_exp0 -n " + genome_filename + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 1" + " -o LENGTH_OUTPUT_p" + str(p) + "_transform_exp1 -n " + genome_filename + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 2" + " -o LENGTH_OUTPUT_p" + str(p) + "_transform_exp2 -n " + genome_filename + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 3" + " -o LENGTH_OUTPUT_p" + str(p) + "_transform_exp3 -n " + genome_filename + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + for i in range(7): + files[i].write(lines[i]) + lines = [] + + for i in range(7): + files[i].close() diff --git a/analysis/make_random_genome.py b/analysis/make_random_genome.py new file mode 100644 index 0000000..95f2db2 --- /dev/null +++ b/analysis/make_random_genome.py @@ -0,0 +1,18 @@ +#python make_random_genome.py length output + +#requires Python 3.6 or higher +import random +import sys + +length = int(sys.argv[1]) +output = sys.argv[2] + +f = open(output, 'w') +num_lines_before_last = length//50 +num_chars_last_line = length - num_lines_before_last*50 + +for i in range(num_lines_before_last): + f.write("".join(random.choices("actg", k=50))+"\n") + +f.write("".join(random.choices("actg", k=num_chars_last_line))) +f.close() diff --git a/analysis/parameteranalysis.py b/analysis/parameteranalysis.py new file mode 100644 index 0000000..858299d --- /dev/null +++ b/analysis/parameteranalysis.py @@ -0,0 +1,93 @@ +#Given a reference sequence, introduce a given rate of heterozygosity and create Illumina reads based on the wanted coverage level, readlength, and read duplication level. + +#!/usr/bin/python +import os +import os.path +import gzip +import sys +#modify to your need: +#sys.path.append("/seq/schatz/fritz/kmers/simul/") +from chromosomeMutator import * +import math +import random +mutate = {"A": "CGT", "C": "GTA", "G": "TAC", "T": "ACG"} + +num_params = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +cl=1 #compression level +k=int(sys.argv[1]) +p=int(sys.argv[2]) +coverage = int(sys.argv[3]) +readlength= int(sys.argv[4]) +br = int(sys.argv[5]) +r = [float(sys.argv[i]) for i in range(6, 6+num_params[p])] +genomefile = sys.argv[6+num_params[p]] +error = float(sys.argv[7+num_params[p]]) +topology_model = sys.argv[8+num_params[p]] +d = float(sys.argv[9+num_params[p]]) +top = float(sys.argv[10+num_params[p]]) +limit=300 + +genomename = genomefile +fileprefix = genomename+"_k"+str(k)+"_p"+str(p)+"_cov"+str(coverage)+"_rl"+str(readlength)+"_br"+str(br)+"_het"+'_'.join(['%.6f' % x for x in r])+"_err"+'%.3f' % error +"_d"+ '%.3f' % d + "_top" + str(top) +illuminafile=fileprefix+"_" + topology_model + "_reads.fa.gz" +if os.path.isfile(illuminafile)!=True: + f = open(genomefile) + genomestring = "".join(f.readlines()[1:]) #assumes has name as first line, and only one sequence + #print(genomestrings[0]) + genomestring = genomestring.replace("\n","") + #genomestring = genomestring.replace("a","A") + genomestring = genomestring.upper() + f.close() + length = len(genomestring) + genomestring = genomestring + genomestring[:int(length*d) + 1] #append sequence to make it repetitive + length = len(genomestring) + print(length) + #for i in range(1,p): + # genomestrings[i]=chromosomeMutator(genomestrings[0],r) + genomestrings = chromosomeMutator(genomestring,r,p, topology_model, top) #genomestrings is a dictionary from i to i-th (homologous set of) chromosome(s) (i is 1-indexed) + illumina_reads=gzip.open(illuminafile, 'wb', compresslevel=cl) + x=1 + iterate = p*length * coverage / readlength #num_reads + print("Creating Illumina Reads...") + while(iterate>0): + start = random.randint(0,length-readlength) + end = start + readlength + selectset = random.randint(1,p) + seqstring=genomestrings[selectset][start:end] + #biasnum=numpy.random.poisson(br) + #biasnum=math.ceil(biasnum) + biasnum = 1 #added to get rid of bias + #Simulate error, each base in the sequence string has a possibility of error. + #For each base in the read, generate a number, if it's less than the error alter that base + read=seqstring + for i in range(0,int(biasnum)): + seqstring=read + if error!=0: + A="CGT" + C="GTA" + G="TAC" + T="ACG" + for j in range(readlength): + chance=random.random() + if chance <= error: + currentbp=seqstring[j] + num = random.randint(0,2) + if currentbp == "A": + newbp=A[num] + elif currentbp == "C": + newbp=C[num] + elif currentbp == "G": + newbp=G[num] + else: + newbp=T[num] + seqstring=seqstring[:j]+newbp+seqstring[j+1:] + ##if biasnum!=0: + ## for i in range(0,int(biasnum)): + illumina_reads.write((">"+str(x)+"_"+str(i)+"\n").encode()) #dedented 1 + illumina_reads.write(("%s\n" % seqstring).encode()) #dedented 1 + iterate-=biasnum + x+=1 + illumina_reads.close() +else: + print("Reads Already Exist") + diff --git a/analysis/real_data/.DS_Store b/analysis/real_data/.DS_Store deleted file mode 100644 index 9503fb4..0000000 Binary files a/analysis/real_data/.DS_Store and /dev/null differ diff --git a/analysis/real_data/._.DS_Store b/analysis/real_data/._.DS_Store deleted file mode 100644 index 746d21f..0000000 Binary files a/analysis/real_data/._.DS_Store and /dev/null differ diff --git a/analysis/real_data/ara_F1_100bp_21.hist b/analysis/real_data/ara_F1_100bp_21.hist deleted file mode 100644 index 54f8331..0000000 --- a/analysis/real_data/ara_F1_100bp_21.hist +++ /dev/null @@ -1,24742 +0,0 @@ -1 398558798 -2 20510187 -3 4448867 -4 2021116 -5 1095317 -6 684526 -7 488031 -8 403773 -9 396767 -10 453765 -11 579419 -12 769072 -13 1021830 -14 1333141 -15 1682372 -16 2043149 -17 2380557 -18 2682538 -19 2915377 -20 3060490 -21 3113837 -22 3076739 -23 2962785 -24 2783624 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r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.019e-02 3.878e-04 77.84 <2e-16 *** -r 1.038e-02 1.118e-05 927.93 <2e-16 *** -kmercov 2.215e+01 2.199e-03 10075.36 <2e-16 *** -bias 4.464e-01 1.270e-03 351.64 <2e-16 *** -length 1.064e+08 4.464e+04 2384.40 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5285 on 972 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 6.001e-07 - diff --git a/analysis/real_data/ara_F1_100bp_21.hist_results/plot.log.png b/analysis/real_data/ara_F1_100bp_21.hist_results/plot.log.png deleted file mode 100644 index 367fd8c..0000000 Binary files a/analysis/real_data/ara_F1_100bp_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/ara_F1_100bp_21.hist_results/plot.png b/analysis/real_data/ara_F1_100bp_21.hist_results/plot.png deleted file mode 100644 index 30292ae..0000000 Binary files a/analysis/real_data/ara_F1_100bp_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/ara_F1_100bp_21.hist_results/progress.txt b/analysis/real_data/ara_F1_100bp_21.hist_results/progress.txt deleted file mode 100644 index b51b9f9..0000000 --- a/analysis/real_data/ara_F1_100bp_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 106085864840.139 -round 1 trimming to 14 trying 4peak model... converged. score: 73884793319.6319 -round 2 trimming to 19 trying 4peak model... converged. score: 40956269750.1548 -round 3 trimming to 24 trying 4peak model... converged. score: 38377686321.8143 -done diff --git a/analysis/real_data/ara_F1_100bp_21.hist_results/summary.txt b/analysis/real_data/ara_F1_100bp_21.hist_results/summary.txt deleted file mode 100644 index f933aaf..0000000 --- a/analysis/real_data/ara_F1_100bp_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03547% 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-514473 1 -516732 1 -516769 1 -517897 1 -521053 1 -521529 1 -523037 1 -541291 1 -547000 1 -565310 1 -565466 1 -577583 1 -581379 1 -598225 1 -600139 1 -601177 1 -605676 1 -608386 1 -610384 1 -613154 1 -616398 1 -616774 1 -618082 1 -621162 1 -621693 1 -624929 1 -627300 1 -636335 1 -637144 1 -663780 1 -730833 1 -737802 1 -738025 1 -738828 1 -742502 1 -742775 1 -745763 1 -748008 1 -965147 1 -967487 1 -985751 1 -987948 1 -1000001 134 diff --git a/analysis/real_data/ara_F1_21.hist_results/model.txt b/analysis/real_data/ara_F1_21.hist_results/model.txt deleted file mode 100644 index bd81c80..0000000 --- a/analysis/real_data/ara_F1_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.019e-02 3.878e-04 77.84 <2e-16 *** -r 1.038e-02 1.118e-05 927.93 <2e-16 *** -kmercov 2.215e+01 2.199e-03 10075.36 <2e-16 *** -bias 4.464e-01 1.270e-03 351.64 <2e-16 *** -length 1.064e+08 4.464e+04 2384.40 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5285 on 972 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 6.001e-07 - diff --git a/analysis/real_data/ara_F1_21.hist_results/plot.log.png b/analysis/real_data/ara_F1_21.hist_results/plot.log.png deleted file mode 100644 index 367fd8c..0000000 Binary files a/analysis/real_data/ara_F1_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/ara_F1_21.hist_results/plot.png b/analysis/real_data/ara_F1_21.hist_results/plot.png deleted file mode 100644 index 30292ae..0000000 Binary files a/analysis/real_data/ara_F1_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/ara_F1_21.hist_results/progress.txt b/analysis/real_data/ara_F1_21.hist_results/progress.txt deleted file mode 100644 index b51b9f9..0000000 --- a/analysis/real_data/ara_F1_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 106085864840.139 -round 1 trimming to 14 trying 4peak model... converged. score: 73884793319.6319 -round 2 trimming to 19 trying 4peak model... converged. score: 40956269750.1548 -round 3 trimming to 24 trying 4peak model... converged. score: 38377686321.8143 -done diff --git a/analysis/real_data/ara_F1_21.hist_results/summary.txt b/analysis/real_data/ara_F1_21.hist_results/summary.txt deleted file mode 100644 index f933aaf..0000000 --- a/analysis/real_data/ara_F1_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03547% 1.03994% -Genome Haploid Length 119,207,549 bp 119,254,884 bp 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r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.708e-03 3.752e-04 23.21 <2e-16 *** -r 7.228e-03 8.798e-06 821.56 <2e-16 *** -kmercov 1.120e+01 1.630e-03 6872.35 <2e-16 *** -bias 4.656e-01 1.642e-03 283.52 <2e-16 *** -length 1.005e+09 3.578e+05 2810.01 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 55060 on 987 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.088e-06 - diff --git a/analysis/real_data/bird_21.hist_results/plot.log.png b/analysis/real_data/bird_21.hist_results/plot.log.png deleted file mode 100644 index 31485ed..0000000 Binary files a/analysis/real_data/bird_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/bird_21.hist_results/plot.png b/analysis/real_data/bird_21.hist_results/plot.png deleted file mode 100644 index 3f9e9dd..0000000 Binary files a/analysis/real_data/bird_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/bird_21.hist_results/progress.txt b/analysis/real_data/bird_21.hist_results/progress.txt deleted file mode 100644 index 397008e..0000000 --- a/analysis/real_data/bird_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 6799908136310.42 -round 1 trimming to 9 trying 4peak model... converged. score: 6216867175236.58 -round 2 trimming to 14 trying 4peak model... converged. score: 25423715865516 -round 3 trimming to 19 trying 4peak model... converged. score: 10113507973167.7 -done diff --git a/analysis/real_data/bird_21.hist_results/summary.txt b/analysis/real_data/bird_21.hist_results/summary.txt deleted file mode 100644 index a19b0e7..0000000 --- a/analysis/real_data/bird_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.721043% 0.724563% -Genome Haploid Length 1,056,718,631 bp 1,057,333,865 bp -Genome Repeat Length 60,163,623 bp 60,198,651 bp -Genome Unique Length 996,555,008 bp 997,135,214 bp -Model Fit 98.6372% 99.1397% -Read Error Rate 0.509729% 0.509729% diff --git a/analysis/real_data/dros2_21.hist b/analysis/real_data/dros2_21.hist deleted file mode 100644 index 8de34ff..0000000 --- a/analysis/real_data/dros2_21.hist +++ /dev/null @@ -1,13634 +0,0 @@ -1 170269064 -2 7620659 -3 1659672 -4 663084 -5 377831 -6 288243 -7 280982 -8 326989 -9 406136 -10 520379 -11 657587 -12 824742 -13 1003102 -14 1190481 -15 1376766 -16 1552347 -17 1708725 -18 1849661 -19 1963628 -20 2058716 -21 2143186 -22 2204059 -23 2270824 -24 2343094 -25 2418945 -26 2511276 -27 2618699 -28 2748144 -29 2896866 -30 3053961 -31 3222590 -32 3393958 -33 3568585 -34 3724159 -35 3860242 -36 3975453 -37 4060798 -38 4116372 -39 4131143 -40 4113578 -41 4060166 -42 3970844 -43 3858784 -44 3712131 -45 3546601 -46 3362443 -47 3153896 -48 2941640 -49 2718555 -50 2498222 -51 2282863 -52 2066302 -53 1861915 -54 1664871 -55 1480068 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a/analysis/real_data/dros2_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.849e-03 1.130e-03 8.72 <2e-16 *** -r 6.462e-03 2.301e-05 280.81 <2e-16 *** -kmercov 2.073e+01 8.471e-03 2447.04 <2e-16 *** -bias 1.525e+00 7.929e-03 192.37 <2e-16 *** -length 1.179e+08 1.326e+05 889.73 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 15190 on 989 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 4.034e-06 - diff --git a/analysis/real_data/dros2_21.hist_results/plot.log.png b/analysis/real_data/dros2_21.hist_results/plot.log.png deleted file mode 100644 index 0d835a3..0000000 Binary files a/analysis/real_data/dros2_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/dros2_21.hist_results/plot.png b/analysis/real_data/dros2_21.hist_results/plot.png deleted file mode 100644 index c831bdd..0000000 Binary files a/analysis/real_data/dros2_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/dros2_21.hist_results/progress.txt b/analysis/real_data/dros2_21.hist_results/progress.txt deleted file mode 100644 index 79fb36f..0000000 --- a/analysis/real_data/dros2_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 220468102876.825 -round 1 trimming to 12 trying 4peak model... converged. score: 221629466989.963 -round 2 trimming to 17 trying 4peak model... converged. score: 279772306077.669 -round 3 trimming to 22 trying 4peak model... converged. score: 541450077222.046 -done diff --git a/analysis/real_data/dros2_21.hist_results/summary.txt b/analysis/real_data/dros2_21.hist_results/summary.txt deleted file mode 100644 index b7c63e9..0000000 --- a/analysis/real_data/dros2_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.641599% 0.650804% -Genome Haploid Length 128,795,869 bp 129,006,575 bp -Genome Repeat Length 12,092,224 bp 12,112,007 bp -Genome Unique Length 116,703,645 bp 116,894,568 bp -Model Fit 96.9349% 97.9933% -Read Error Rate 0.17281% 0.17281% diff --git a/analysis/real_data/oyster_21.hist b/analysis/real_data/oyster_21.hist deleted file mode 100644 index 43ac339..0000000 --- a/analysis/real_data/oyster_21.hist +++ /dev/null @@ -1,33529 +0,0 @@ -1 478540078 -2 23921201 -3 6365954 -4 3156751 -5 2085082 -6 1654908 -7 1518068 -8 1549324 -9 1725968 -10 2030500 -11 2476284 -12 3079211 -13 3835373 -14 4750112 -15 5798263 -16 6955781 -17 8171959 -18 9379318 -19 10545437 -20 11588709 -21 12451066 -22 13107104 -23 13492909 -24 13626699 -25 13515255 -26 13192192 -27 12675458 -28 12033090 -29 11295132 -30 10544610 -31 9802856 -32 9098959 -33 8516296 -34 8019246 -35 7638933 -36 7371139 -37 7221099 -38 7168324 -39 7205357 -40 7309797 -41 7472527 -42 7667490 -43 7879500 -44 8082026 -45 8278794 -46 8455387 -47 8580246 -48 8646638 -49 8669217 -50 8629419 -51 8534446 -52 8384376 -53 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(1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.943e-02 1.276e-03 70.1 <2e-16 *** -r 1.938e-02 3.426e-05 565.7 <2e-16 *** -kmercov 2.578e+01 1.291e-02 1996.0 <2e-16 *** -bias 1.130e+00 5.703e-03 198.2 <2e-16 *** -length 3.598e+08 3.948e+05 911.3 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 46880 on 974 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.683e-06 - diff --git a/analysis/real_data/oyster_21.hist_results/plot.log.png b/analysis/real_data/oyster_21.hist_results/plot.log.png deleted file mode 100644 index 7a8476c..0000000 Binary files a/analysis/real_data/oyster_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/oyster_21.hist_results/plot.png b/analysis/real_data/oyster_21.hist_results/plot.png deleted file mode 100644 index 58c3d5f..0000000 Binary files a/analysis/real_data/oyster_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/oyster_21.hist_results/progress.txt b/analysis/real_data/oyster_21.hist_results/progress.txt deleted file mode 100644 index 17b15ff..0000000 --- a/analysis/real_data/oyster_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 4195080502441.76 -round 1 trimming to 12 trying 4peak model... converged. score: 3378251117758.5 -round 2 trimming to 17 trying 4peak model... converged. score: 2427855591887.56 -round 3 trimming to 22 trying 4peak model... converged. score: 1903803879516.66 -done diff --git a/analysis/real_data/oyster_21.hist_results/summary.txt b/analysis/real_data/oyster_21.hist_results/summary.txt deleted file mode 100644 index 8271d30..0000000 --- a/analysis/real_data/oyster_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.9311% 1.94481% -Genome Haploid Length 470,107,886 bp 471,050,947 bp -Genome Repeat Length 139,151,672 bp 139,430,818 bp -Genome Unique Length 330,956,213 bp 331,620,129 bp -Model Fit 94.0678% 97.8381% -Read Error Rate 0.149148% 0.149148% diff --git a/analysis/real_data/pear_21.hist b/analysis/real_data/pear_21.hist deleted file mode 100644 index a611c08..0000000 --- a/analysis/real_data/pear_21.hist +++ /dev/null @@ -1,87248 +0,0 @@ -1 2545857104 -2 369706150 -3 144610986 -4 67097906 -5 34144351 -6 19078587 -7 11641650 -8 7720193 -9 5478537 -10 4125696 -11 3265399 -12 2706946 -13 2320787 -14 2048729 -15 1863453 -16 1726155 -17 1624966 -18 1557516 -19 1522649 -20 1519635 -21 1558082 -22 1632858 -23 1746874 -24 1910023 -25 2117883 -26 2369338 -27 2661510 -28 2991599 -29 3348900 -30 3738456 -31 4133664 -32 4535259 -33 4942147 -34 5319616 -35 5662682 -36 5970766 -37 6224778 -38 6417768 -39 6551414 -40 6611765 -41 6606216 -42 6534253 -43 6404367 -44 6208191 -45 5973779 -46 5694590 -47 5379170 -48 5051717 -49 4717895 -50 4385741 -51 4062125 -52 3756754 -53 3474759 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a/analysis/real_data/pear_21.hist_results/model.txt b/analysis/real_data/pear_21.hist_results/model.txt deleted file mode 100644 index 4f1726f..0000000 --- a/analysis/real_data/pear_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.253e-01 3.274e-03 68.82 <2e-16 *** -r 1.664e-02 8.860e-05 187.79 <2e-16 *** -kmercov 4.255e+01 4.386e-02 970.10 <2e-16 *** -bias 1.555e+00 1.890e-02 82.28 <2e-16 *** -length 2.816e+08 1.005e+06 280.27 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 92110 on 966 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 9.011e-07 - diff --git a/analysis/real_data/pear_21.hist_results/plot.log.png b/analysis/real_data/pear_21.hist_results/plot.log.png deleted file mode 100644 index dbb0640..0000000 Binary files a/analysis/real_data/pear_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/pear_21.hist_results/plot.png b/analysis/real_data/pear_21.hist_results/plot.png deleted file mode 100644 index caa81c4..0000000 Binary files a/analysis/real_data/pear_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/pear_21.hist_results/progress.txt b/analysis/real_data/pear_21.hist_results/progress.txt deleted file mode 100644 index cbaaf2d..0000000 --- a/analysis/real_data/pear_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 9515880555236.97 -round 1 trimming to 20 trying 4peak model... converged. score: 8911896793635.29 -round 2 trimming to 25 trying 4peak model... converged. score: 8278010660966.41 -round 3 trimming to 30 trying 4peak model... converged. score: 8012064749163.44 -done diff --git a/analysis/real_data/pear_21.hist_results/summary.txt b/analysis/real_data/pear_21.hist_results/summary.txt deleted file mode 100644 index 01926fd..0000000 --- a/analysis/real_data/pear_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.64606% 1.68149% -Genome Haploid Length 519,913,764 bp 522,061,956 bp -Genome Repeat Length 296,629,676 bp 297,855,298 bp -Genome Unique Length 223,284,088 bp 224,206,658 bp -Model Fit 84.2203% 95.5895% -Read Error Rate 0.506105% 0.506105% diff --git a/analysis/real_data/seabass_21.hist b/analysis/real_data/seabass_21.hist deleted file mode 100644 index f8a5cb7..0000000 --- a/analysis/real_data/seabass_21.hist +++ /dev/null @@ -1,9925 +0,0 @@ -1 1980777694 -2 54271234 -3 9250071 -4 3552172 -5 1904040 -6 1214141 -7 869422 -8 686833 -9 583994 -10 533218 -11 514414 -12 520606 -13 549048 -14 593510 -15 650022 -16 721995 -17 811999 -18 911899 -19 1024101 -20 1160553 -21 1305448 -22 1468485 -23 1646043 -24 1836705 -25 2038416 -26 2243590 -27 2460548 -28 2678977 -29 2889861 -30 3107234 -31 3311750 -32 3515285 -33 3696668 -34 3862728 -35 4019715 -36 4161380 -37 4293114 -38 4412700 -39 4524801 -40 4640958 -41 4752710 -42 4865250 -43 4998396 -44 5140966 -45 5295045 -46 5471035 -47 5665163 -48 5880543 -49 6121595 -50 6381203 -51 6663097 -52 6978344 -53 7301723 -54 7647583 -55 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-9956 3 -9957 1 -9958 4 -9959 6 -9960 1 -9961 1 -9962 3 -9963 2 -9964 3 -9965 3 -9966 6 -9967 2 -9968 2 -9969 3 -9971 4 -9972 2 -9973 4 -9974 1 -9975 5 -9977 5 -9979 3 -9980 2 -9981 3 -9982 3 -9983 4 -9984 4 -9985 4 -9986 3 -9987 3 -9988 5 -9989 6 -9990 1 -9991 5 -9992 3 -9993 1 -9994 1 -9995 2 -9996 5 -9998 3 -9999 2 -10000 4 -10001 32878 diff --git a/analysis/real_data/seabass_21.hist_results/model.txt b/analysis/real_data/seabass_21.hist_results/model.txt deleted file mode 100644 index 82f80d3..0000000 --- a/analysis/real_data/seabass_21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.781e-04 1.764e-03 0.441 0.659 -r 4.728e-03 3.223e-05 146.683 <2e-16 *** -kmercov 3.669e+01 1.907e-02 1924.124 <2e-16 *** -bias 2.554e+00 1.574e-02 162.301 <2e-16 *** -length 5.367e+08 1.067e+06 503.180 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 92470 on 980 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 4.203e-06 - diff --git a/analysis/real_data/seabass_21.hist_results/plot.log.png b/analysis/real_data/seabass_21.hist_results/plot.log.png deleted file mode 100644 index 778b1de..0000000 Binary files a/analysis/real_data/seabass_21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/real_data/seabass_21.hist_results/plot.png b/analysis/real_data/seabass_21.hist_results/plot.png deleted file mode 100644 index ad764aa..0000000 Binary files a/analysis/real_data/seabass_21.hist_results/plot.png and /dev/null differ diff --git a/analysis/real_data/seabass_21.hist_results/progress.txt b/analysis/real_data/seabass_21.hist_results/progress.txt deleted file mode 100644 index 500298c..0000000 --- a/analysis/real_data/seabass_21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 8351798984874.69 -round 1 trimming to 16 trying 4peak model... converged. score: 8348606967840.26 -round 2 trimming to 21 trying 4peak model... converged. score: 8349015336998.65 -round 3 trimming to 26 trying 4peak model... converged. score: 8459463190066.2 -done diff --git a/analysis/real_data/seabass_21.hist_results/summary.txt b/analysis/real_data/seabass_21.hist_results/summary.txt deleted file mode 100644 index 4f15d1d..0000000 --- a/analysis/real_data/seabass_21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.466308% 0.4792% -Genome Haploid Length 551,149,870 bp 552,296,830 bp -Genome Repeat Length 15,411,354 bp 15,443,425 bp -Genome Unique Length 535,738,516 bp 536,853,405 bp -Model Fit 94.6804% 95.2101% -Read Error Rate 0.248369% 0.248369% diff --git a/analysis/repetitiveness_commands.py b/analysis/repetitiveness_commands.py new file mode 100644 index 0000000..5817f95 --- /dev/null +++ b/analysis/repetitiveness_commands.py @@ -0,0 +1,39 @@ +import itertools + +num_het = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +t = 0 #topology = 0 (full model) +genome_filename = "random_genome.fa" +k = 21 +coverage = 15 +read_length = 100 +br = 0 +err = 0.01 +model = "Partition" + +COMMANDS_file = open("REPETITIVENESS_COMMANDS", 'w') +for i in range(1,8): + for p in [1,2,3,4,5,6]: + COMMANDS_file.write("parallel -j 17 < REPETITIVENESS_COMMANDS"+str(i)+"_p"+str(p)+"\n") + +COMMANDS_file.close() + +for p in [1, 2, 3, 4, 5, 6]: + files = [open("REPETITIVENESS_COMMANDS" + str(i) + "_p" + str(p),'w') for i in range(1, 8)] + lines = [] + for d in [0.01*x for x in range(51)]: #repetitiveness from 0% to 50% in 1.0% increments + rs = [[0.02/(num_het[p]) for _ in range(num_het[p])]] #heterozygosity 2.0%, equally divided among each het form + for r in rs: + lines.append("python parameteranalysis.py " + str(k) + " " + str(p) + " " + str(coverage) + " " + str(read_length) + " " + str(br) + " " + ' '.join(['%.6f' % x for x in r]) + " " + genome_filename + " " + str(err) + " " + model + " " + '%.3f' % d + " " + str(t) + "\n") + readfilenameprefix = genome_filename + "_k" + str(k) + "_p" + str(p) + "_cov" + str(coverage) + "_rl" + str(read_length) + "_br" + str(br) + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(float(t)) + "_" + model + "_reads" + lines.append("jellyfish count -C -m21 -s 1000000000 -t15 <(zcat " + readfilenameprefix + ".fa.gz) -o " + readfilenameprefix + ".jf" + "\n") + lines.append("jellyfish histo -t15 " + readfilenameprefix + ".jf > " + readfilenameprefix + ".histo" + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 0" + " -o REPETITIVENESS_OUTPUT_p" + str(p) + "_transform_exp0 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 1" + " -o REPETITIVENESS_OUTPUT_p" + str(p) + "_transform_exp1 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 2" + " -o REPETITIVENESS_OUTPUT_p" + str(p) + "_transform_exp2 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + lines.append("genomescope.R -i " + readfilenameprefix + ".histo -k" + str(k) + " -p" + str(p) + " -l10 -t 0 --transform_exp 3" + " -o REPETITIVENESS_OUTPUT_p" + str(p) + "_transform_exp3 -n " + "het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(t) + " --testing --true_params=" + '%.3f' % d + "," + ",".join(['%.6f' % x for x in r]) + "," + str(t) + "\n") + for i in range(7): + files[i].write(lines[i]) + lines = [] + + for i in range(7): + files[i].close() diff --git a/analysis/repetitiveness_smudgeplot_commands.py b/analysis/repetitiveness_smudgeplot_commands.py new file mode 100644 index 0000000..fa229f5 --- /dev/null +++ b/analysis/repetitiveness_smudgeplot_commands.py @@ -0,0 +1,43 @@ +import itertools + +num_het = {1:0, 2:1, 3:2, 4:4, 5:6, 6:10} #full model +t = 0 #topology = 0 (full model) +genome_filename = "random_genome_010Mbp.fa" +k = 21 +coverage = 40 +read_length = 100 +br = 0 +err = 0.01 +model = "Partition" + +COMMANDS_file = open("REPETITIVENESS_smudgeplot_COMMANDS", 'w') +for i in range(1,7): + for p in [2,3,4,5,6]: + if i in [1, 5]: + COMMANDS_file.write("parallel -j 17 < REPETITIVENESS_smudgeplot_COMMANDS"+str(i)+"_p"+str(p)+"\n") + else: + COMMANDS_file.write("bash REPETITIVENESS_smudgeplot_COMMANDS"+str(i)+"_p"+str(p)+"\n") + +COMMANDS_file.close() + +p_to_rs = {1:[[]], 2:[[0.02]], 3:[[0.019, 0.001]], 4:[[0, 0.018, 0.001, 0.001], [0.018, 0, 0.001, 0.001]], 5:[[0.017, 0, 0.001, 0, 0.001, 0.001]], 6:[[0.016, 0, 0, 0.001, 0, 0, 0.001, 0, 0.001, 0.001]]} + +for p in [2, 3, 4, 5, 6]: + files = [open("REPETITIVENESS_smudgeplot_COMMANDS" + str(i) + "_p" + str(p),'w') for i in range(1, 7)] + lines = [] + for d in [0.01*x for x in range(51)]: #repetitiveness from 0% to 50% in 1.0% increments + rs = p_to_rs[p] #heterozygosity 2.0% + for r in rs: + lines.append("python parameteranalysis.py " + str(k) + " " + str(p) + " " + str(coverage) + " " + str(read_length) + " " + str(br) + " " + ' '.join(['%.6f' % x for x in r]) + " " + genome_filename + " " + str(err) + " " + model + " " + '%.3f' % d + " " + str(t) + "\n") + readfilenameprefix = genome_filename + "_k" + str(k) + "_p" + str(p) + "_cov" + str(coverage) + "_rl" + str(read_length) + "_br" + str(br) + "_het" + '_'.join(['%.6f' % x for x in r]) + "_err" + '%.3f' % err + "_d" + '%.3f' % d + "_top" + str(float(t)) + "_" + model + "_reads" + lines.append("kmc -k" + str(k) + " -m256 -ci1 -cs10000 -fm " + readfilenameprefix + ".fa.gz " + readfilenameprefix + " tmp/\n") + lines.append("kmc_tools transform " + readfilenameprefix + " histogram " + readfilenameprefix + ".histo\n") + lines.append("kmc_tools transform " + readfilenameprefix + " -ci10 -cx300 reduce " + readfilenameprefix + "_L10_U300\n") + lines.append("smudge_pairs " + readfilenameprefix + "_L10_U300 " + readfilenameprefix + "_L10_U300_coverages.tsv\n") + lines.append("smudgeplot.py plot " + readfilenameprefix + "_L10_U300_coverages.tsv -o " + readfilenameprefix + "_L10_U300_coverages\n") + for i in range(6): + files[i].write(lines[i]) + lines = [] + + for i in range(6): + files[i].close() diff --git a/analysis/scripts/chromosomeMutator.py b/analysis/scripts/chromosomeMutator.py deleted file mode 100644 index 9ff973c..0000000 --- a/analysis/scripts/chromosomeMutator.py +++ /dev/null @@ -1,23 +0,0 @@ -def chromosomeMutator(chromosome,heterozygosity): - import random - A="CGT" - C="AGT" - G="ACT" - T="ACG" - mutlist=list(chromosome) - for i in range(0,len(chromosome)-1): - chance=random.random() - if chance <= heterozygosity: - currentbp=mutlist[i] - num = random.randint(0,2) - if currentbp == "A": - newbp=A[num] - elif currentbp == "C": - newbp=C[num] - elif currentbp == "G": - newbp=G[num] - else: - newbp=T[num] - mutlist[i]=newbp - mutatedchromosome="".join(mutlist) - return mutatedchromosome diff --git a/analysis/scripts/comp_dup_rate.sh b/analysis/scripts/comp_dup_rate.sh deleted file mode 100644 index 4a0ea33..0000000 --- a/analysis/scripts/comp_dup_rate.sh +++ /dev/null @@ -1,3 +0,0 @@ -prefix=${reads/.fq/} -file=$prefix'.bwa-mem.mapped.sort.bam' -/home/schatz/fsedlaze/programs/picard-tools MarkDuplicates I=$file M=$file'.picard.dups' O=$file'.tmp' diff --git a/analysis/scripts/comp_seq_error.sh b/analysis/scripts/comp_seq_error.sh deleted file mode 100644 index deb49ab..0000000 --- a/analysis/scripts/comp_seq_error.sh +++ /dev/null @@ -1 +0,0 @@ -/sonas-hs/schatz/hpc/home/fsedlaze/programs/samtools view $reads |cut -f12 | sed 's/NM:i://g' | awk '{print $1/=100}' | awk '{ sum += $1; n++ } END { if (n > 0) print sum / n; }' > $reads'.seqerr' diff --git a/analysis/scripts/parameteranalysis.py b/analysis/scripts/parameteranalysis.py deleted file mode 100644 index 0e5be3e..0000000 --- a/analysis/scripts/parameteranalysis.py +++ /dev/null @@ -1,88 +0,0 @@ -#Given a reference sequence, introduce a given rate of heterozygosity and create Illumina reads based on the wanted coverage level, readlength, and read duplication level. - -#!/usr/bin/python -import os -import os.path -import gzip -import sys -#modify to your need: -sys.path.append("/seq/schatz/fritz/kmers/simul/") -from chromosomeMutator import * -import math -import numpy -import random -#Command Line Parameters -# parameteranalysis.py k coverage readlength br genomefile -cl=1 #compression level -k=int(sys.argv[1]) -coverage = int(sys.argv[2]) -readlength= int(sys.argv[3]) -br = int(sys.argv[4]) -r = float(sys.argv[5]) -genomefile = sys.argv[6] -error = float(sys.argv[7]) -limit=300 -#q = genomefile.rfinqd("/") -#genomename = genomefile[q+1:] -#q = genomename.rfind(".") -#genomename = genomename[:q] -genomename = genomefile -fileprefix = genomename+"_het"+str(r)+"_br"+str(br)+"_rl"+str(readlength)+"_cov"+str(coverage)+"_err"+str(error) -illuminafile=fileprefix+"_reads.fa.gz" -if os.path.isfile(illuminafile)!=True: - f = open(genomefile) - genomestring = "".join(f.readlines()[1:]) - genomestring = genomestring.replace("\n","") - genomestring = genomestring.replace("a","A") - genomestring = genomestring.upper() - f.close() - length = len(genomestring) - mutatedstring=chromosomeMutator(genomestring,r) - illumina_reads=gzip.open(illuminafile, 'wb', compresslevel=cl) - x=1 - iterate = length * coverage / readlength - print "Creating Illumina Reads..." - while(iterate>0): - start = random.randint(1,length-readlength) - end = start + readlength - selectset = random.random() - if(selectset<.5): - seqstring=genomestring[start:end] - if(selectset>=.5): - seqstring=mutatedstring[start:end] - biasnum=numpy.random.poisson(br) - biasnum=math.ceil(biasnum) - #Simulate error, each base in the sequence string has a possibility of error. - #For each base in the read, generate a number, if it's less than the error alter that base - read=seqstring - for i in range(0,int(biasnum)): - seqstring=read - if error!=0: - A="CGT" - C="AGT" - G="ACT" - T="ACG" - for i in range(0,readlength): - chance=random.random() - if chance <= error: - currentbp=seqstring[i] - num = random.randint(0,2) - if currentbp == "A": - newbp=A[num] - elif currentbp == "C": - newbp=C[num] - elif currentbp == "G": - newbp=G[num] - else: - newbp=T[num] - seqstring=seqstring[:i]+newbp+seqstring[i+1:] - ##if biasnum!=0: - ## for i in range(0,int(biasnum)): - illumina_reads.write(">"+str(x)+"_"+str(i)+"\n") - illumina_reads.write("%s\n" % seqstring) - iterate-=biasnum - x=x+1 - illumina_reads.close() -else: - print "Reads Already Exist" - diff --git a/analysis/scripts/run_jelly.py b/analysis/scripts/run_jelly.py deleted file mode 100644 index e735f67..0000000 --- a/analysis/scripts/run_jelly.py +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/python -import os -import os.path -import sys -illuminafile = sys.argv[1] -k=int(sys.argv[2]) -limit=1000000 - -histfilename = illuminafile+sys.argv[2]+".hist" -outputname = illuminafile+sys.argv[2]+"_output" -mergename = illuminafile+sys.argv[2]+"_merge" - -os.system("jellyfish count -m %s -o %s -c 3 -C -s 10000000000 -t 15 %s" %(k, outputname,illuminafile)) - #More than one output file, merge them -if os.path.isfile(outputname+"_1"): - print "More than one output file detected, merging with jellyfish..." - os.system("jellyfish merge -o %s %s_*"%(mergename,outputname)) - print "Creating merged histogram file with jellyfish..." - os.system("jellyfish histo -h %s -o %s %s"%(limit,histfilename,mergename)) - #Otherwise, make the histogram with only the first output file -else: - print "Only one output file detected, creating histogram file with jellyfish..." - os.system("jellyfish histo -h %s -o %s %s"%(limit,histfilename,outputname)) - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 95c3866..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8971 +0,0 @@ -1 187639710 -2 3760877 -3 255303 -4 65610 -5 23954 -6 10310 -7 4689 -8 2192 -9 1364 -10 840 -11 701 -12 799 -13 1055 -14 1217 -15 2023 -16 3168 -17 4744 -18 7144 -19 10470 -20 14511 -21 20484 -22 27983 -23 37217 -24 47382 -25 59744 -26 72256 -27 87225 -28 103034 -29 118799 -30 134255 -31 150218 -32 165281 -33 177839 -34 189402 -35 200474 -36 206442 -37 213064 -38 215040 -39 216056 -40 216988 -41 213056 -42 211374 -43 209815 -44 209806 -45 211434 -46 216582 -47 226519 -48 239842 -49 258747 -50 287435 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(1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.759e-02 2.930e-04 94.16 <2e-16 *** -r 1.061e-03 5.016e-06 211.56 <2e-16 *** -kmercov 3.924e+01 2.332e-03 16829.06 <2e-16 *** -bias 9.899e-01 1.441e-03 686.93 <2e-16 *** -length 1.075e+08 4.546e+04 2365.11 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3966 on 970 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 7.461e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e1affea..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index c4925c7..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 76c22ef..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 15257785004.1294 -round 1 trimming to 16 trying 4peak model... converged. score: 15257784447.9139 -round 2 trimming to 21 trying 4peak model... converged. score: 15257777387.4694 -round 3 trimming to 26 trying 4peak model... converged. score: 15257765972.6136 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3d9509d..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.105118% 0.107125% -Genome Haploid Length 116,086,859 bp 116,114,454 bp -Genome Repeat Length 11,550,231 bp 11,552,977 bp -Genome Unique Length 104,536,628 bp 104,561,478 bp -Model Fit 98.0589% 99.2028% -Read Error Rate 0.101823% 0.101823% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 773ecb7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7915 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.756e-02 2.668e-04 103.3 <2e-16 *** -r 1.083e-03 4.789e-06 226.2 <2e-16 *** -kmercov 3.248e+01 1.859e-03 17475.1 <2e-16 *** -bias 8.218e-01 1.211e-03 678.6 <2e-16 *** -length 1.075e+08 4.113e+04 2614.9 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3873 on 971 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 3.815e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 61c4612..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index aa63f2b..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2eaf001..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 14614871808.4824 -round 1 trimming to 20 trying 4peak model... converged. score: 14575274570.5748 -round 2 trimming to 25 trying 4peak model... converged. score: 14568081438.1697 -round 3 trimming to 30 trying 4peak model... converged. score: 14730920534.5295 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cd894cc..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.107371% 0.109287% -Genome Haploid Length 116,703,666 bp 116,730,383 bp -Genome Repeat Length 12,128,473 bp 12,131,250 bp -Genome Unique Length 104,575,193 bp 104,599,133 bp -Model Fit 98.1221% 99.3133% -Read Error Rate 1.00686% 1.00686% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index ee4c95b..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6854 +0,0 @@ -1 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d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.780e-02 2.467e-04 112.7 <2e-16 *** -r 1.166e-03 4.524e-06 257.8 <2e-16 *** -kmercov 2.627e+01 1.492e-03 17602.2 <2e-16 *** -bias 6.667e-01 1.039e-03 641.7 <2e-16 *** -length 1.077e+08 3.759e+04 2866.0 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3865 on 976 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 2.471e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3c316d4..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0a02cc7..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3cae8d0..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 15334957938.2411 -round 1 trimming to 20 trying 4peak model... converged. score: 14371171775.1794 -round 2 trimming to 25 trying 4peak model... converged. score: 14407332570.3312 -round 3 trimming to 30 trying 4peak model... converged. score: 20941323632.2846 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3314b31..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.115738% 0.117548% -Genome Haploid Length 117,588,319 bp 117,615,044 bp -Genome Repeat Length 12,851,699 bp 12,854,620 bp -Genome Unique Length 104,736,620 bp 104,760,424 bp -Model Fit 98.2261% 99.4682% -Read Error Rate 1.99749% 1.99749% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 5cceaf7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8983 +0,0 @@ -1 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-353948 1 -356964 1 -1000001 1 diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 72cc407..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.647e-02 4.583e-04 57.76 <2e-16 *** -r 1.151e-03 8.277e-06 139.05 <2e-16 *** -kmercov 3.936e+01 4.580e-03 8593.27 <2e-16 *** -bias 1.972e+00 3.516e-03 560.94 <2e-16 *** -length 1.074e+08 6.810e+04 1577.74 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5594 on 977 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.377e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 91d939e..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6ee03ac..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fd6a9e5..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... round 0 trimming to 400 trying 4peak model... converged. score: 30569299419.2492 -round 1 trimming to 14 trying 4peak model... round 1 trimming to 405 trying 4peak model... converged. score: 30569296696.0636 -round 2 trimming to 19 trying 4peak model... round 2 trimming to 410 trying 4peak model... converged. score: 30569286398.0161 -round 3 trimming to 24 trying 4peak model... round 3 trimming to 415 trying 4peak model... converged. score: 30570073259.9434 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 815401b..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.113439% 0.11675% -Genome Haploid Length 115,738,941 bp 115,792,828 bp -Genome Repeat Length 11,156,894 bp 11,162,088 bp -Genome Unique Length 104,582,047 bp 104,630,739 bp -Model Fit 97.4046% 98.5162% -Read Error Rate 0.101777% 0.101777% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.638e-02 4.082e-04 64.62 <2e-16 *** -r 1.174e-03 7.583e-06 154.77 <2e-16 *** -kmercov 3.257e+01 3.514e-03 9268.60 <2e-16 *** -bias 1.635e+00 2.816e-03 580.68 <2e-16 *** -length 1.075e+08 6.002e+04 1790.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5371 on 976 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.296e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5fe97db..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index ee52835..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4c992d1..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 28189797785.9357 -round 1 trimming to 20 trying 4peak model... converged. score: 28128693216.6616 -round 2 trimming to 25 trying 4peak model... converged. score: 28177158619.214 -round 3 trimming to 30 trying 4peak model... converged. score: 30697253009.3685 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 31132e8..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.11584% 0.118873% -Genome Haploid Length 116,385,188 bp 116,435,427 bp -Genome Repeat Length 11,762,919 bp 11,767,996 bp -Genome Unique Length 104,622,270 bp 104,667,431 bp -Model Fit 97.5741% 98.7446% -Read Error Rate 1.00621% 1.00621% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index e1db704..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6854 +0,0 @@ -1 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d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.663e-02 3.594e-04 74.1 <2e-16 *** -r 1.286e-03 7.356e-06 174.8 <2e-16 *** -kmercov 2.634e+01 2.641e-03 9974.1 <2e-16 *** -bias 1.323e+00 2.245e-03 589.4 <2e-16 *** -length 1.077e+08 5.197e+04 2071.7 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5123 on 976 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 8.503e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index c7ebeb7..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2678e21..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3fa8641..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 26352608805.9506 -round 1 trimming to 20 trying 4peak model... converged. score: 25613689938.0613 -round 2 trimming to 25 trying 4peak model... converged. score: 27008907000.7723 -round 3 trimming to 30 trying 4peak model... converged. score: 63863907112.6039 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index aa0a224..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.127094% 0.130036% -Genome Haploid Length 117,278,932 bp 117,325,975 bp -Genome Repeat Length 12,488,966 bp 12,493,975 bp -Genome Unique Length 104,789,966 bp 104,831,999 bp -Model Fit 97.7504% 98.9714% -Read Error Rate 1.99595% 1.99595% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index d5d9e83..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8970 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index e4fef44..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.425e-02 6.342e-04 38.23 <2e-16 *** -r 1.293e-03 1.227e-05 105.35 <2e-16 *** -kmercov 3.951e+01 7.453e-03 5301.22 <2e-16 *** -bias 2.948e+00 6.808e-03 432.99 <2e-16 *** -length 1.072e+08 8.846e+04 1211.46 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7037 on 982 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 7.259e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 23e3b7e..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0983797..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4daada2..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 48621120478.5439 -round 1 trimming to 14 trying 4peak model... converged. score: 48621104290.4832 -round 2 trimming to 19 trying 4peak model... converged. score: 48621114604.1833 -round 3 trimming to 24 trying 4peak model... converged. score: 48642409162.5849 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5c8afb9..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.126848% 0.131758% -Genome Haploid Length 115,259,939 bp 115,346,940 bp -Genome Repeat Length 10,729,127 bp 10,737,226 bp -Genome Unique Length 104,530,811 bp 104,609,714 bp -Model Fit 96.8291% 97.9263% -Read Error Rate 0.101886% 0.101886% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 2fde456..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7916 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.426e-02 5.608e-04 43.26 <2e-16 *** -r 1.324e-03 1.131e-05 117.04 <2e-16 *** -kmercov 3.270e+01 5.619e-03 5819.41 <2e-16 *** -bias 2.434e+00 5.319e-03 457.59 <2e-16 *** -length 1.072e+08 7.716e+04 1389.39 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6711 on 976 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.913e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d7ca323..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index c3e1573..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 10a5f9a..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 44009027257.7891 -round 1 trimming to 20 trying 4peak model... converged. score: 43962970714.3326 -round 2 trimming to 25 trying 4peak model... converged. score: 44488710495.7962 -round 3 trimming to 30 trying 4peak model... converged. score: 54775103337.2864 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 42432bb..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.13015% 0.134675% -Genome Haploid Length 115,917,193 bp 115,996,896 bp -Genome Repeat Length 11,349,885 bp 11,357,690 bp -Genome Unique Length 104,567,307 bp 104,639,207 bp -Model Fit 97.0854% 98.2446% -Read Error Rate 1.00594% 1.00594% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index d4805b8..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6858 +0,0 @@ -1 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+0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.497e-02 4.530e-04 55.13 <2e-16 *** -r 1.478e-03 1.038e-05 142.45 <2e-16 *** -kmercov 2.645e+01 3.839e-03 6890.02 <2e-16 *** -bias 1.956e+00 3.837e-03 509.73 <2e-16 *** -length 1.074e+08 6.099e+04 1760.95 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5867 on 976 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.35e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8211821..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index fb0e7ad..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index aa8568c..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 34085358570.3242 -round 1 trimming to 20 trying 4peak model... converged. score: 33741780240.08 -round 2 trimming to 25 trying 4peak model... converged. score: 40518221519.5189 -round 3 trimming to 30 trying 4peak model... converged. score: 131941316912.948 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a054c08..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.145734% 0.149885% -Genome Haploid Length 116,822,226 bp 116,890,067 bp -Genome Repeat Length 12,136,208 bp 12,143,255 bp -Genome Unique Length 104,686,019 bp 104,746,812 bp -Model Fit 97.4719% 98.6827% -Read Error Rate 1.99442% 1.99442% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 1e0252c..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8478 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.793e-02 3.592e-04 77.77 <2e-16 *** -r 1.035e-02 6.473e-06 1599.46 <2e-16 *** -kmercov 3.926e+01 2.815e-03 13947.23 <2e-16 *** -bias 9.887e-01 1.367e-03 723.50 <2e-16 *** -length 1.081e+08 4.169e+04 2592.50 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3944 on 972 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 7.573e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index fcf478b..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2e5a5f8..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ab21e4a..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 15078462151.3596 -round 1 trimming to 14 trying 4peak model... converged. score: 15078349701.8591 -round 2 trimming to 19 trying 4peak model... converged. score: 15072781954.7639 -round 3 trimming to 24 trying 4peak model... converged. score: 15048063540.0435 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 343846e..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03402% 1.03661% -Genome Haploid Length 116,450,685 bp 116,484,087 bp -Genome Repeat Length 11,278,922 bp 11,282,158 bp -Genome Unique Length 105,171,762 bp 105,201,929 bp -Model Fit 98.3542% 99.2492% -Read Error Rate 0.101816% 0.101816% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 7ce2f09..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7400 +0,0 @@ -1 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+ (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.745e-02 5.294e-04 51.84 <2e-16 *** -r 1.031e-02 9.667e-06 1066.49 <2e-16 *** -kmercov 3.251e+01 3.764e-03 8637.64 <2e-16 *** -bias 8.343e-01 1.920e-03 434.58 <2e-16 *** -length 1.083e+08 6.100e+04 1775.11 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6271 on 974 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.755e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bf48055..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b2e6e72..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 69460cb..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 38739468759.8193 -round 1 trimming to 17 trying 4peak model... converged. score: 38609557263.9034 -round 2 trimming to 22 trying 4peak model... converged. score: 38603617199.336 -round 3 trimming to 27 trying 4peak model... converged. score: 40801156842.6977 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b7ff3bc..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02905% 1.03291% -Genome Haploid Length 117,094,350 bp 117,148,587 bp -Genome Repeat Length 11,694,109 bp 11,699,526 bp -Genome Unique Length 105,400,241 bp 105,449,062 bp -Model Fit 97.9439% 98.8698% -Read Error Rate 1.00001% 1.00001% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 8f4dee2..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6449 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index df6d9cf..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.759e-02 5.969e-04 46.23 <2e-16 *** -r 1.035e-02 1.107e-05 934.34 <2e-16 *** -kmercov 2.628e+01 3.827e-03 6866.46 <2e-16 *** -bias 6.893e-01 2.040e-03 337.95 <2e-16 *** -length 1.087e+08 6.759e+04 1608.13 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7677 on 980 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 7.065e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b733567..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1039e25..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6bfa1d4..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 60202423115.9488 -round 1 trimming to 16 trying 4peak model... converged. score: 57581870100.1376 -round 2 trimming to 21 trying 4peak model... converged. score: 59345023791.4143 -round 3 trimming to 26 trying 4peak model... converged. score: 93301601181.977 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2b3d1fd..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03237% 1.0368% -Genome Haploid Length 118,049,097 bp 118,117,886 bp -Genome Repeat Length 12,262,492 bp 12,269,638 bp -Genome Unique Length 105,786,605 bp 105,848,248 bp -Model Fit 97.8302% 98.7887% -Read Error Rate 1.98494% 1.98494% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 2306366..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8416 +0,0 @@ -1 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-98577 1 -129263 1 -129881 1 -130921 1 -316118 1 -323106 1 -323774 1 -1000001 1 diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9e0847d..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.455e-02 7.299e-04 33.63 <2e-16 *** -r 1.045e-02 1.386e-05 753.93 <2e-16 *** -kmercov 3.944e+01 8.058e-03 4894.39 <2e-16 *** -bias 1.996e+00 4.643e-03 429.91 <2e-16 *** -length 1.079e+08 7.910e+04 1364.08 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7267 on 974 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 9.601e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7f502ef..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index eb92018..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7a7afce..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 51422266035.8214 -round 1 trimming to 12 trying 4peak model... converged. score: 51418121783.4503 -round 2 trimming to 17 trying 4peak model... converged. score: 51337011693.1348 -round 3 trimming to 22 trying 4peak model... converged. score: 51169730165.9855 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5fe3a40..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04249% 1.04804% -Genome Haploid Length 115,860,570 bp 115,955,297 bp -Genome Repeat Length 10,550,951 bp 10,559,578 bp -Genome Unique Length 105,309,619 bp 105,395,719 bp -Model Fit 97.4392% 98.3202% -Read Error Rate 0.103073% 0.103073% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index b0f4c39..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7404 +0,0 @@ -1 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(1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.435e-02 7.940e-04 30.66 <2e-16 *** -r 1.041e-02 1.536e-05 677.49 <2e-16 *** -kmercov 3.263e+01 7.758e-03 4206.42 <2e-16 *** -bias 1.673e+00 4.753e-03 351.95 <2e-16 *** -length 1.082e+08 8.537e+04 1266.85 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8529 on 975 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.035e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0b7c1ba..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index c79316e..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5dfa348..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 72075034942.0885 -round 1 trimming to 16 trying 4peak model... converged. score: 71249494389.0045 -round 2 trimming to 21 trying 4peak model... converged. score: 71182429161.8675 -round 3 trimming to 26 trying 4peak model... converged. score: 74494159701.8398 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 71377e7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03747% 1.04362% -Genome Haploid Length 116,590,801 bp 116,701,723 bp -Genome Repeat Length 11,016,966 bp 11,027,447 bp -Genome Unique Length 105,573,835 bp 105,674,276 bp -Model Fit 97.3456% 98.2578% -Read Error Rate 1.00082% 1.00082% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index a0785b7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6444 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 03dc0fc..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.456e-02 7.736e-04 31.75 <2e-16 *** -r 1.047e-02 1.533e-05 682.71 <2e-16 *** -kmercov 2.637e+01 6.627e-03 3979.75 <2e-16 *** -bias 1.374e+00 4.294e-03 320.06 <2e-16 *** -length 1.086e+08 8.147e+04 1332.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8989 on 980 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.304e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4dd0bed..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c152ce0..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ce385cb..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 85343009668.9916 -round 1 trimming to 16 trying 4peak model... converged. score: 79193962543.3335 -round 2 trimming to 21 trying 4peak model... converged. score: 82309414254.3946 -round 3 trimming to 26 trying 4peak model... converged. score: 131664039437.5 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 50fa2de..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04351% 1.04964% -Genome Haploid Length 117,601,332 bp 117,719,591 bp -Genome Repeat Length 11,626,161 bp 11,637,852 bp -Genome Unique Length 105,975,171 bp 106,081,739 bp -Model Fit 97.3965% 98.3472% -Read Error Rate 1.98516% 1.98516% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 7697170..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,8452 +0,0 @@ -1 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(1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.092e-02 1.021e-03 20.48 <2e-16 *** -r 1.058e-02 2.074e-05 510.24 <2e-16 *** -kmercov 3.963e+01 1.435e-02 2761.45 <2e-16 *** -bias 3.016e+00 9.960e-03 302.78 <2e-16 *** -length 1.076e+08 1.020e+05 1054.86 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9117 on 975 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.48e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2f88ec3..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0c38361..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d576c97..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 81720960259.8458 -round 1 trimming to 11 trying 4peak model... converged. score: 81671964991.882 -round 2 trimming to 16 trying 4peak model... converged. score: 81282403387.8603 -round 3 trimming to 21 trying 4peak model... converged. score: 80984651273.8365 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d1555ad..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05403% 1.06233% -Genome Haploid Length 115,270,606 bp 115,437,698 bp -Genome Repeat Length 9,886,402 bp 9,900,733 bp -Genome Unique Length 105,384,204 bp 105,536,965 bp -Model Fit 96.9207% 97.7947% -Read Error Rate 0.103784% 0.103784% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 7380ea8..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7451 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.071e-02 1.062e-03 19.51 <2e-16 *** -r 1.053e-02 2.198e-05 479.17 <2e-16 *** -kmercov 3.277e+01 1.293e-02 2535.11 <2e-16 *** -bias 2.518e+00 9.591e-03 262.59 <2e-16 *** -length 1.079e+08 1.050e+05 1027.62 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10190 on 976 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.506e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d094c8d..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index e4d37cb..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5418ed0..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 105559349460.55 -round 1 trimming to 15 trying 4peak model... converged. score: 102187315628.938 -round 2 trimming to 20 trying 4peak model... converged. score: 102003214403.853 -round 3 trimming to 25 trying 4peak model... converged. score: 106983770810.256 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c85f4dc..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.0488% 1.05759% -Genome Haploid Length 116,044,297 bp 116,227,541 bp -Genome Repeat Length 10,342,902 bp 10,359,235 bp -Genome Unique Length 105,701,395 bp 105,868,306 bp -Model Fit 96.8672% 97.7865% -Read Error Rate 1.00142% 1.00142% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 968f835..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6428 +0,0 @@ -1 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b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index e8dc98e..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.158e-02 9.456e-04 22.82 <2e-16 *** -r 1.056e-02 2.012e-05 524.63 <2e-16 *** -kmercov 2.646e+01 9.861e-03 2683.34 <2e-16 *** -bias 2.058e+00 7.720e-03 266.57 <2e-16 *** -length 1.084e+08 9.151e+04 1184.86 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9783 on 981 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.519e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6b86e8d..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6eb6ed9..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4622cf6..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 112797808640.349 -round 1 trimming to 15 trying 4peak model... converged. score: 93787392466.6628 -round 2 trimming to 20 trying 4peak model... converged. score: 96370411190.903 -round 3 trimming to 25 trying 4peak model... converged. score: 144687218343.71 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e0ddd3a..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05155% 1.05959% -Genome Haploid Length 117,185,961 bp 117,360,778 bp -Genome Repeat Length 11,081,445 bp 11,097,976 bp -Genome Unique Length 106,104,516 bp 106,262,801 bp -Model Fit 97.1231% 98.0878% -Read Error Rate 1.98474% 1.98474% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 2560138..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,7956 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index a7997f7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.779e-02 4.504e-04 61.7 <2e-16 *** -r 2.057e-02 1.061e-05 1939.8 <2e-16 *** -kmercov 3.932e+01 3.207e-03 12260.5 <2e-16 *** -bias 9.891e-01 1.327e-03 745.2 <2e-16 *** -length 1.086e+08 4.036e+04 2691.6 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4387 on 972 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 7.565e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ade9941..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index f309c71..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a7a5b26..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 17856743271.2604 -round 1 trimming to 14 trying 4peak model... converged. score: 17855337859.1641 -round 2 trimming to 19 trying 4peak model... converged. score: 17771147488.2306 -round 3 trimming to 24 trying 4peak model... converged. score: 17217007295.0648 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 17d5df5..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.0551% 2.05934% -Genome Haploid Length 116,641,166 bp 116,679,227 bp -Genome Repeat Length 10,670,151 bp 10,673,633 bp -Genome Unique Length 105,971,015 bp 106,005,594 bp -Model Fit 98.4397% 99.1675% -Read Error Rate 0.103072% 0.103072% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index ab8bdfa..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7065 +0,0 @@ -1 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(d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.588e-02 6.701e-04 38.62 <2e-16 *** -r 2.058e-02 1.592e-05 1293.18 <2e-16 *** -kmercov 3.260e+01 4.400e-03 7409.96 <2e-16 *** -bias 8.361e-01 1.896e-03 441.10 <2e-16 *** -length 1.088e+08 5.925e+04 1835.55 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7014 on 975 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.42e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9f0faf2..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2a0c42b..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a186518..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 48426895208.1167 -round 1 trimming to 16 trying 4peak model... converged. score: 48133222436.5282 -round 2 trimming to 21 trying 4peak model... converged. score: 47964153822.392 -round 3 trimming to 26 trying 4peak model... converged. score: 50198007302.9146 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 76eb403..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.05524% 2.06161% -Genome Haploid Length 117,110,642 bp 117,173,877 bp -Genome Repeat Length 10,849,066 bp 10,854,924 bp -Genome Unique Length 106,261,576 bp 106,318,953 bp -Model Fit 97.8897% 98.6271% -Read Error Rate 0.996297% 0.996297% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 3f0030a..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6054 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.403e-02 9.148e-04 26.27 <2e-16 *** -r 2.061e-02 2.206e-05 934.21 <2e-16 *** -kmercov 2.639e+01 5.522e-03 4778.49 <2e-16 *** -bias 6.973e-01 2.413e-03 288.98 <2e-16 *** -length 1.092e+08 7.894e+04 1382.99 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10360 on 981 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.961e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 08a5b63..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 74f0d6b..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4b77404..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 109522385590.439 -round 1 trimming to 15 trying 4peak model... converged. score: 104636042098.375 -round 2 trimming to 20 trying 4peak model... converged. score: 108873947735.053 -round 3 trimming to 25 trying 4peak model... converged. score: 206914323340.625 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e91b309..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.05642% 2.06525% -Genome Haploid Length 117,892,285 bp 117,991,012 bp -Genome Repeat Length 11,060,501 bp 11,069,764 bp -Genome Unique Length 106,831,784 bp 106,921,249 bp -Model Fit 97.3841% 98.1392% -Read Error Rate 1.97896% 1.97896% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index b3f0801..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,7951 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index b11bd28..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.087e-02 8.246e-04 25.3 <2e-16 *** -r 2.088e-02 2.064e-05 1011.4 <2e-16 *** -kmercov 3.961e+01 8.896e-03 4452.6 <2e-16 *** -bias 2.017e+00 4.142e-03 486.9 <2e-16 *** -length 1.082e+08 6.756e+04 1601.4 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7186 on 974 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 4.54e-07 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2c14481..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e219637..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2b0626f..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 50680971199.0136 -round 1 trimming to 12 trying 4peak model... converged. score: 50639723727.625 -round 2 trimming to 17 trying 4peak model... converged. score: 49699907924.2543 -round 3 trimming to 22 trying 4peak model... converged. score: 46798206054.812 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cde89fa..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08389% 2.09215% -Genome Haploid Length 115,673,446 bp 115,777,409 bp -Genome Repeat Length 9,500,644 bp 9,509,182 bp -Genome Unique Length 106,172,803 bp 106,268,227 bp -Model Fit 97.726% 98.4539% -Read Error Rate 0.105806% 0.105806% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 93bc31f..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,7032 +0,0 @@ -1 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-244651 1 -953492 1 diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0a2fbed..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.877e-02 1.009e-03 18.6 <2e-16 *** -r 2.091e-02 2.577e-05 811.3 <2e-16 *** -kmercov 3.285e+01 9.814e-03 3347.0 <2e-16 *** -bias 1.682e+00 4.813e-03 349.4 <2e-16 *** -length 1.083e+08 8.181e+04 1324.0 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9445 on 976 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.763e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3963088..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8fd399e..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0852543..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 92682013703.233 -round 1 trimming to 15 trying 4peak model... converged. score: 89071242384.2633 -round 2 trimming to 20 trying 4peak model... converged. score: 86975269348.2142 -round 3 trimming to 25 trying 4peak model... converged. score: 89507222836.9908 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cbb4084..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08582% 2.09613% -Genome Haploid Length 116,123,233 bp 116,262,094 bp -Genome Repeat Length 9,649,085 bp 9,660,624 bp -Genome Unique Length 106,474,147 bp 106,601,470 bp -Model Fit 97.2687% 98.0234% -Read Error Rate 0.999303% 0.999303% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 769b9aa..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,6076 +0,0 @@ -1 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b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index f9b0b4c..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.734e-02 1.109e-03 15.64 <2e-16 *** -r 2.091e-02 2.931e-05 713.23 <2e-16 *** -kmercov 2.657e+01 9.685e-03 2743.62 <2e-16 *** -bias 1.391e+00 4.887e-03 284.56 <2e-16 *** -length 1.088e+08 8.789e+04 1238.40 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11200 on 981 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.251e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a7a5a5e..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index bdd7fb4..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 43ad65e..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 141383616431.43 -round 1 trimming to 15 trying 4peak model... converged. score: 122126940912.164 -round 2 trimming to 20 trying 4peak model... converged. score: 128312281722.157 -round 3 trimming to 25 trying 4peak model... converged. score: 246250346948.529 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c40cc12..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08471% 2.09643% -Genome Haploid Length 117,002,212 bp 117,172,918 bp -Genome Repeat Length 9,886,682 bp 9,901,106 bp -Genome Unique Length 107,115,531 bp 107,271,812 bp -Model Fit 97.1207% 97.8906% -Read Error Rate 1.9803% 1.9803% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 70e356b..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,7922 +0,0 @@ -1 188266478 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b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d08fc85..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.225e-02 1.188e-03 10.31 <2e-16 *** -r 2.131e-02 3.336e-05 638.70 <2e-16 *** -kmercov 4.000e+01 1.774e-02 2254.78 <2e-16 *** -bias 3.071e+00 9.410e-03 326.41 <2e-16 *** -length 1.077e+08 8.846e+04 1217.11 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9120 on 975 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.291e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1b62c95..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 79fc48d..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 38018b4..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 88321284326.0507 -round 1 trimming to 11 trying 4peak model... converged. score: 87902550726.2751 -round 2 trimming to 16 trying 4peak model... converged. score: 84003646089.9882 -round 3 trimming to 21 trying 4peak model... converged. score: 78092442180.5913 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d1f6fc7..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12432% 2.13767% -Genome Haploid Length 114,446,252 bp 114,649,461 bp -Genome Repeat Length 8,018,145 bp 8,032,382 bp -Genome Unique Length 106,428,107 bp 106,617,079 bp -Model Fit 97.153% 97.8903% -Read Error Rate 0.107554% 0.107554% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index c6a1bf9..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,6973 +0,0 @@ -1 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a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.029e-02 1.310e-03 7.852 1.08e-14 *** -r 2.130e-02 3.784e-05 562.803 < 2e-16 *** -kmercov 3.315e+01 1.733e-02 1913.484 < 2e-16 *** -bias 2.555e+00 9.742e-03 262.284 < 2e-16 *** -length 1.079e+08 9.697e+04 1112.313 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10780 on 977 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.074e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b561159..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3df5cbb..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 01a7ae6..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 131341228410.079 -round 1 trimming to 14 trying 4peak model... converged. score: 118195259315.25 -round 2 trimming to 19 trying 4peak model... converged. score: 113537894088.858 -round 3 trimming to 24 trying 4peak model... converged. score: 118121871524.305 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3cbb608..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12199% 2.13712% -Genome Haploid Length 114,953,989 bp 115,194,544 bp -Genome Repeat Length 8,164,098 bp 8,181,182 bp -Genome Unique Length 106,789,891 bp 107,013,361 bp -Model Fit 96.9262% 97.6602% -Read Error Rate 1.00094% 1.00094% diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 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-37659 1 -41017 1 -42460 1 -67922 1 -79221 1 -80148 1 -81341 1 -200652 1 -204481 1 -207013 1 -787854 1 diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index b0bfd14..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.889e-03 1.430e-03 6.216 7.55e-10 *** -r 2.125e-02 4.332e-05 490.467 < 2e-16 *** -kmercov 2.680e+01 1.669e-02 1605.506 < 2e-16 *** -bias 2.118e+00 9.541e-03 222.025 < 2e-16 *** -length 1.085e+08 1.028e+05 1055.155 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12570 on 982 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.936e-06 - diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e5e1e51..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4d016fe..0000000 Binary files a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e2deaf2..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 213766579914.976 -round 1 trimming to 14 trying 4peak model... converged. score: 151703144901.401 -round 2 trimming to 19 trying 4peak model... converged. score: 156109022628.063 -round 3 trimming to 24 trying 4peak model... converged. score: 269961989077.679 -done diff --git a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4cdf0f6..0000000 --- a/analysis/simulation_results_100x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.11627% 2.1336% -Genome Haploid Length 115,925,449 bp 116,214,629 bp -Genome Repeat Length 8,420,436 bp 8,441,441 bp -Genome Unique Length 107,505,014 bp 107,773,188 bp -Model Fit 96.8245% 97.6335% -Read Error Rate 1.98143% 1.98143% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 43ee6ec..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.448e-02 2.594e-04 55.83 <2e-16 *** -r 1.095e-03 4.361e-06 251.01 <2e-16 *** -kmercov 3.924e+01 2.008e-03 19541.01 <2e-16 *** -bias 9.867e-01 1.240e-03 795.83 <2e-16 *** -length 1.172e+08 4.318e+04 2715.01 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3776 on 972 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 6.357e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cc8ff42..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7418bd3..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bea8c53..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 14 trying 4peak model... converged. score: 13856490814.7376 -round 1 trimming to 19 trying 4peak model... converged. score: 13856488404.1529 -round 2 trimming to 24 trying 4peak model... converged. score: 13856485072.1112 -round 3 trimming to 29 trying 4peak model... converged. score: 13858368791.9812 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a173402..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.108589% 0.110333% -Genome Haploid Length 125,851,762 bp 125,877,526 bp -Genome Repeat Length 10,336,945 bp 10,339,061 bp -Genome Unique Length 115,514,817 bp 115,538,465 bp -Model Fit 98.1625% 99.2676% -Read Error Rate 0.107492% 0.107492% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 89624d5..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,11002 +0,0 @@ -1 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index c88ade8..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.443e-02 2.260e-04 63.83 <2e-16 *** -r 1.203e-03 4.764e-06 252.44 <2e-16 *** -kmercov 3.247e+01 1.531e-03 21207.34 <2e-16 *** -bias 8.163e-01 1.001e-03 815.86 <2e-16 *** -length 1.175e+08 3.759e+04 3125.80 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3530 on 966 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 3.47e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 49c9519..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index acf0b4e..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1d8a5d1..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 16746057684.3514 -round 1 trimming to 20 trying 4peak model... converged. score: 14924908914.2721 -round 2 trimming to 25 trying 4peak model... converged. score: 12602147144.2357 -round 3 trimming to 30 trying 4peak model... converged. score: 12028836120.9358 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2523f6d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.119315% 0.12122% -Genome Haploid Length 127,263,987 bp 127,287,993 bp -Genome Repeat Length 11,458,199 bp 11,460,361 bp -Genome Unique Length 115,805,788 bp 115,827,633 bp -Model Fit 98.2248% 99.4269% -Read Error Rate 1.04564% 1.04564% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 20b1cab..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,9329 +0,0 @@ -1 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index f225cbc..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.484e-02 2.312e-04 64.21 <2e-16 *** -r 1.359e-03 5.344e-06 254.30 <2e-16 *** -kmercov 2.623e+01 1.370e-03 19143.06 <2e-16 *** -bias 6.794e-01 9.705e-04 700.07 <2e-16 *** -length 1.188e+08 3.823e+04 3106.62 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3914 on 971 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 3.473e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 20a5af0..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index b88d0ac..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index de18263..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 44259419336.8653 -round 1 trimming to 20 trying 4peak model... converged. score: 16602316244.6345 -round 2 trimming to 25 trying 4peak model... converged. score: 14894039986.4563 -round 3 trimming to 30 trying 4peak model... converged. score: 23353860314.238 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e198d1a..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.134825% 0.136963% -Genome Haploid Length 130,058,448 bp 130,085,627 bp -Genome Repeat Length 13,079,565 bp 13,082,298 bp -Genome Unique Length 116,978,883 bp 117,003,328 bp -Model Fit 98.1695% 99.4479% -Read Error Rate 2.03176% 2.03176% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index c3c510d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,12818 +0,0 @@ -1 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-313443 1 -347205 1 -359066 1 -437147 1 -543599 1 diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d010686..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.314e-02 4.958e-04 26.51 <2e-16 *** -r 1.192e-03 8.838e-06 134.83 <2e-16 *** -kmercov 3.937e+01 4.825e-03 8158.52 <2e-16 *** -bias 1.975e+00 3.711e-03 532.27 <2e-16 *** -length 1.172e+08 7.908e+04 1481.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6505 on 975 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.567e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9bfa139..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8889d4b..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fdadcb0..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 41260465527.6374 -round 1 trimming to 16 trying 4peak model... converged. score: 41260454356.4526 -round 2 trimming to 21 trying 4peak model... converged. score: 41260452441.5663 -round 3 trimming to 26 trying 4peak model... converged. score: 41270072289.5965 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4dbefcb..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.117394% 0.120929% -Genome Haploid Length 125,425,017 bp 125,486,526 bp -Genome Repeat Length 9,811,270 bp 9,816,081 bp -Genome Unique Length 115,613,747 bp 115,670,444 bp -Model Fit 97.2766% 98.3587% -Read Error Rate 0.107532% 0.107532% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 32b5ee3..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,10979 +0,0 @@ -1 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index cd93832..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.334e-02 3.727e-04 35.78 <2e-16 *** -r 1.379e-03 7.272e-06 189.62 <2e-16 *** -kmercov 3.258e+01 3.123e-03 10430.08 <2e-16 *** -bias 1.622e+00 2.498e-03 649.21 <2e-16 *** -length 1.175e+08 5.871e+04 2000.56 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5271 on 971 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 5.131e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0feea48..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0fdc052..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 217b81b..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 30328844176.4339 -round 1 trimming to 20 trying 4peak model... converged. score: 27792933954.8884 -round 2 trimming to 25 trying 4peak model... converged. score: 26734188561.4121 -round 3 trimming to 30 trying 4peak model... converged. score: 26782776952.8505 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6581f18..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.136439% 0.139348% -Genome Haploid Length 126,942,144 bp 126,990,837 bp -Genome Repeat Length 11,070,266 bp 11,074,513 bp -Genome Unique Length 115,871,878 bp 115,916,324 bp -Model Fit 97.6858% 98.8669% -Read Error Rate 1.04217% 1.04217% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 147eb84..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,9337 +0,0 @@ -1 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index d759fb6..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.383e-02 3.306e-04 41.84 <2e-16 *** -r 1.555e-03 8.977e-06 173.21 <2e-16 *** -kmercov 2.630e+01 2.399e-03 10965.64 <2e-16 *** -bias 1.330e+00 2.114e-03 629.36 <2e-16 *** -length 1.187e+08 5.156e+04 2302.22 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5089 on 971 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 8.724e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b0aaafe..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index bc99df3..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 19df8bf..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 58444768917.8056 -round 1 trimming to 20 trying 4peak model... converged. score: 26279270777.6561 -round 2 trimming to 25 trying 4peak model... converged. score: 25646703638.1962 -round 3 trimming to 30 trying 4peak model... converged. score: 54333965468.5144 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 944fc6d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.153685% 0.157276% -Genome Haploid Length 129,761,396 bp 129,808,739 bp -Genome Repeat Length 12,712,501 bp 12,717,139 bp -Genome Unique Length 117,048,895 bp 117,091,599 bp -Model Fit 97.7714% 99.0378% -Read Error Rate 2.02809% 2.02809% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index ab3c5ff..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,12867 +0,0 @@ -1 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a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.075e-02 6.129e-04 17.55 <2e-16 *** -r 1.321e-03 1.170e-05 112.92 <2e-16 *** -kmercov 3.950e+01 7.001e-03 5642.88 <2e-16 *** -bias 2.949e+00 6.421e-03 459.26 <2e-16 *** -length 1.169e+08 9.179e+04 1273.15 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7315 on 981 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.208e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 82c6510..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index b942a03..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 728c019..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 52489342537.3633 -round 1 trimming to 15 trying 4peak model... converged. score: 52489306563.1697 -round 2 trimming to 20 trying 4peak model... converged. score: 52489580378.5395 -round 3 trimming to 25 trying 4peak model... converged. score: 52556295934.2294 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3078f4b..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.129791% 0.134471% -Genome Haploid Length 124,951,302 bp 125,039,906 bp -Genome Repeat Length 9,382,012 bp 9,388,665 bp -Genome Unique Length 115,569,290 bp 115,651,241 bp -Model Fit 96.9078% 97.9884% -Read Error Rate 0.107519% 0.107519% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 3faeb69..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,11062 +0,0 @@ -1 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* d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.155e-02 4.393e-04 26.28 <2e-16 *** -r 1.600e-03 9.585e-06 166.96 <2e-16 *** -kmercov 3.271e+01 4.294e-03 7617.69 <2e-16 *** -bias 2.400e+00 4.073e-03 589.24 <2e-16 *** -length 1.171e+08 6.467e+04 1811.23 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5654 on 971 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.75e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index afab5c6..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b9dbcf5..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 16b6878..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 33581949352.5045 -round 1 trimming to 20 trying 4peak model... converged. score: 31278010748.3932 -round 2 trimming to 25 trying 4peak model... converged. score: 31044340834.4114 -round 3 trimming to 30 trying 4peak model... converged. score: 32170821217.8589 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 02b238d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.158115% 0.161949% -Genome Haploid Length 126,473,793 bp 126,540,221 bp -Genome Repeat Length 10,719,785 bp 10,725,416 bp -Genome Unique Length 115,754,008 bp 115,814,806 bp -Model Fit 97.4891% 98.6654% -Read Error Rate 1.0394% 1.0394% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index f072ac2..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,9389 +0,0 @@ -1 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-161185 1 -162623 1 -164523 1 -164545 1 -165561 1 -166664 1 -167857 1 -205489 1 -210599 1 -233821 1 -241625 1 -299170 1 -364585 1 diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 815e193..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.211e-02 4.306e-04 28.13 <2e-16 *** -r 1.797e-03 9.692e-06 185.39 <2e-16 *** -kmercov 2.641e+01 3.569e-03 7399.69 <2e-16 *** -bias 1.959e+00 3.567e-03 549.39 <2e-16 *** -length 1.184e+08 6.228e+04 1901.81 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6025 on 976 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.52e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 95215e7..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 20ff633..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fdc87b1..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 66968524155.9432 -round 1 trimming to 20 trying 4peak model... converged. score: 33585443500.1599 -round 2 trimming to 25 trying 4peak model... converged. score: 34014577858.0829 -round 3 trimming to 30 trying 4peak model... converged. score: 89493508290.7409 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9e98149..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.177741% 0.181617% -Genome Haploid Length 129,307,721 bp 129,377,639 bp -Genome Repeat Length 12,335,171 bp 12,341,841 bp -Genome Unique Length 116,972,550 bp 117,035,798 bp -Model Fit 97.5365% 98.7987% -Read Error Rate 2.02474% 2.02474% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index e9bf2cc..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,11938 +0,0 @@ -1 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a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 52b5c1e..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.412e-02 4.022e-04 35.1 <2e-16 *** -r 1.061e-02 7.206e-06 1473.0 <2e-16 *** -kmercov 3.928e+01 3.072e-03 12787.6 <2e-16 *** -bias 9.882e-01 1.503e-03 657.6 <2e-16 *** -length 1.185e+08 5.021e+04 2360.8 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4765 on 970 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.482e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 32004b2..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 84cd68c..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7fdf343..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 22075087201.9574 -round 1 trimming to 16 trying 4peak model... converged. score: 22073938530.6722 -round 2 trimming to 21 trying 4peak model... converged. score: 22049099889.3021 -round 3 trimming to 26 trying 4peak model... converged. score: 22014960964.4129 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 062dd72..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05998% 1.06286% -Genome Haploid Length 127,041,321 bp 127,081,066 bp -Genome Repeat Length 10,125,448 bp 10,128,615 bp -Genome Unique Length 116,915,873 bp 116,952,451 bp -Model Fit 98.1995% 99.0983% -Read Error Rate 0.106411% 0.106411% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 7d04271..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,10373 +0,0 @@ -1 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+0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.353e-02 5.591e-04 24.2 <2e-16 *** -r 1.058e-02 1.023e-05 1034.3 <2e-16 *** -kmercov 3.249e+01 3.922e-03 8284.3 <2e-16 *** -bias 8.529e-01 2.017e-03 422.8 <2e-16 *** -length 1.192e+08 6.959e+04 1713.4 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7160 on 972 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.01e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 35fc53d..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0e36f00..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 07d8629..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 14 trying 4peak model... converged. score: 52471812233.0205 -round 1 trimming to 19 trying 4peak model... converged. score: 50301311067.0135 -round 2 trimming to 24 trying 4peak model... converged. score: 50070989750.0967 -round 3 trimming to 29 trying 4peak model... converged. score: 55620840192.8054 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 532d3cc..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05611% 1.0602% -Genome Haploid Length 128,702,100 bp 128,764,258 bp -Genome Repeat Length 11,049,310 bp 11,054,646 bp -Genome Unique Length 117,652,791 bp 117,709,612 bp -Model Fit 97.7867% 98.7567% -Read Error Rate 1.02664% 1.02664% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 67146ef..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,8756 +0,0 @@ -1 2615750499 -2 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index d67eeb8..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.377e-02 6.709e-04 20.53 <2e-16 *** -r 1.062e-02 1.245e-05 852.93 <2e-16 *** -kmercov 2.625e+01 4.281e-03 6130.95 <2e-16 *** -bias 7.256e-01 2.328e-03 311.75 <2e-16 *** -length 1.206e+08 8.245e+04 1462.43 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9375 on 978 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.042e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ed9b43f..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 97df703..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index dbcc068..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 13 trying 4peak model... converged. score: 121080883873.166 -round 1 trimming to 18 trying 4peak model... converged. score: 85053734145.5339 -round 2 trimming to 23 trying 4peak model... converged. score: 90210085981.1702 -round 3 trimming to 28 trying 4peak model... converged. score: 198219370293.155 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 11ed8e7..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05941% 1.06439% -Genome Haploid Length 131,440,278 bp 131,526,061 bp -Genome Repeat Length 12,500,243 bp 12,508,401 bp -Genome Unique Length 118,940,035 bp 119,017,660 bp -Model Fit 97.4722% 98.5149% -Read Error Rate 2.00452% 2.00452% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index fdfb053..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,12051 +0,0 @@ -1 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a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index fbb0558..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.050e-02 7.712e-04 13.61 <2e-16 *** -r 1.074e-02 1.456e-05 737.40 <2e-16 *** -kmercov 3.945e+01 8.312e-03 4746.80 <2e-16 *** -bias 2.000e+00 4.829e-03 414.17 <2e-16 *** -length 1.183e+08 8.971e+04 1318.80 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8277 on 972 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 7.323e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 48dbad2..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2e891f2..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a4f4552..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 66898087234.273 -round 1 trimming to 14 trying 4peak model... converged. score: 66875115469.4185 -round 2 trimming to 19 trying 4peak model... converged. score: 66695084053.8414 -round 3 trimming to 24 trying 4peak model... converged. score: 66582524612.3433 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 993a388..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.07096% 1.07679% -Genome Haploid Length 126,378,612 bp 126,485,153 bp -Genome Repeat Length 9,307,777 bp 9,315,624 bp -Genome Unique Length 117,070,835 bp 117,169,529 bp -Model Fit 97.3553% 98.247% -Read Error Rate 0.107393% 0.107393% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index a3f5407..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,10329 +0,0 @@ -1 1550927249 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1 -168755 1 -168865 1 -181753 1 -182132 1 -182420 1 -183622 1 -186005 1 -186659 1 -188381 1 -189046 1 -189992 1 -233100 1 -238420 1 -265915 1 -275105 1 -335544 1 -406877 1 diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 26cae17..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.055e-02 7.629e-04 13.83 <2e-16 *** -r 1.066e-02 1.477e-05 722.22 <2e-16 *** -kmercov 3.259e+01 7.319e-03 4453.02 <2e-16 *** -bias 1.686e+00 4.513e-03 373.56 <2e-16 *** -length 1.191e+08 8.858e+04 1344.74 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8871 on 973 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 7.202e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index afe1c17..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a46997b..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fa172e2..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 13 trying 4peak model... converged. score: 83635965380.8309 -round 1 trimming to 18 trying 4peak model... converged. score: 77136836742.3886 -round 2 trimming to 23 trying 4peak model... converged. score: 76788547114.2053 -round 3 trimming to 28 trying 4peak model... converged. score: 82595204788.4874 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5a9fd55..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.06353% 1.06944% -Genome Haploid Length 128,256,063 bp 128,371,323 bp -Genome Repeat Length 10,394,918 bp 10,404,260 bp -Genome Unique Length 117,861,145 bp 117,967,063 bp -Model Fit 97.2826% 98.2545% -Read Error Rate 1.02675% 1.02675% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 24534b0..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,8775 +0,0 @@ -1 2608582703 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a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index f95de06..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.086e-02 8.070e-04 13.45 <2e-16 *** -r 1.075e-02 1.599e-05 672.20 <2e-16 *** -kmercov 2.632e+01 6.840e-03 3847.71 <2e-16 *** -bias 1.413e+00 4.508e-03 313.36 <2e-16 *** -length 1.206e+08 9.203e+04 1310.05 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10190 on 979 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 5.6e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 250da00..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index f1a2568..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 80ec626..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 190263688063.448 -round 1 trimming to 17 trying 4peak model... converged. score: 95995734701.4807 -round 2 trimming to 22 trying 4peak model... converged. score: 98398034387.8865 -round 3 trimming to 27 trying 4peak model... converged. score: 184831996503.632 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index efc8bc7..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.07143% 1.07782% -Genome Haploid Length 131,115,064 bp 131,251,439 bp -Genome Repeat Length 11,871,311 bp 11,883,659 bp -Genome Unique Length 119,243,752 bp 119,367,780 bp -Model Fit 97.1615% 98.2163% -Read Error Rate 2.00291% 2.00291% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index d0d20e5..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,12070 +0,0 @@ -1 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(2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.751e-03 1.044e-03 6.466 1.59e-10 *** -r 1.087e-02 2.106e-05 515.950 < 2e-16 *** -kmercov 3.963e+01 1.430e-02 2770.843 < 2e-16 *** -bias 3.015e+00 1.004e-02 300.363 < 2e-16 *** -length 1.180e+08 1.120e+05 1053.809 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10050 on 973 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.727e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2f86685..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 21c3243..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1eca28d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 99145048292.2823 -round 1 trimming to 13 trying 4peak model... converged. score: 98971569876.9904 -round 2 trimming to 18 trying 4peak model... converged. score: 98429933767.6046 -round 3 trimming to 23 trying 4peak model... converged. score: 98324347835.0653 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ef66898..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08238% 1.09081% -Genome Haploid Length 125,790,726 bp 125,972,449 bp -Genome Repeat Length 8,599,599 bp 8,612,022 bp -Genome Unique Length 117,191,127 bp 117,360,427 bp -Model Fit 96.9004% 97.7952% -Read Error Rate 0.10795% 0.10795% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 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05e7343..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.940e-03 9.478e-04 7.322 5.09e-13 *** -r 1.080e-02 1.951e-05 553.589 < 2e-16 *** -kmercov 3.272e+01 1.129e-02 2898.134 < 2e-16 *** -bias 2.541e+00 8.319e-03 305.418 < 2e-16 *** -length 1.190e+08 1.005e+05 1183.465 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9841 on 978 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 9.115e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 935451a..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3f271f5..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f79390d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 13 trying 4peak model... converged. score: 102702361806.002 -round 1 trimming to 18 trying 4peak model... converged. score: 93117070695.9063 -round 2 trimming to 23 trying 4peak model... converged. score: 93251308585.3669 -round 3 trimming to 28 trying 4peak model... converged. score: 104740803983.895 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6fe5860..0000000 --- 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7ce8575..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.125e-03 8.756e-04 9.28 <2e-16 *** -r 1.088e-02 1.868e-05 582.29 <2e-16 *** -kmercov 2.640e+01 9.017e-03 2927.59 <2e-16 *** -bias 2.099e+00 7.234e-03 290.16 <2e-16 *** -length 1.204e+08 9.178e+04 1311.96 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9819 on 979 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 8.008e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3d76ba0..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 93fa760..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e1affbb..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 207439873117.565 -round 1 trimming to 17 trying 4peak model... converged. score: 91294708078.1673 -round 2 trimming to 22 trying 4peak model... converged. score: 94359949536.9919 -round 3 trimming to 27 trying 4peak model... converged. score: 191325949096.137 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6404df7..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08426% 1.09173% -Genome Haploid Length 130,717,153 bp 130,895,875 bp -Genome Repeat Length 11,320,216 bp 11,335,693 bp -Genome Unique Length 119,396,937 bp 119,560,182 bp -Model Fit 97.0979% 98.1769% -Read Error Rate 2.00209% 2.00209% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index d9a9a22..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,11198 +0,0 @@ -1 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+++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.392e-02 4.532e-04 30.7 <2e-16 *** -r 2.100e-02 1.062e-05 1977.7 <2e-16 *** -kmercov 3.933e+01 3.163e-03 12433.5 <2e-16 *** -bias 9.922e-01 1.323e-03 749.9 <2e-16 *** -length 1.197e+08 4.380e+04 2733.5 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4806 on 971 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 7.062e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 77d2e49..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 14dd26f..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 30a33d6..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 22483176248.9328 -round 1 trimming to 15 trying 4peak model... converged. score: 22479156277.0426 -round 2 trimming to 20 trying 4peak model... converged. score: 22316657902.7043 -round 3 trimming to 25 trying 4peak model... converged. score: 21725857482.1422 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c482d1f..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.09809% 2.10234% -Genome Haploid Length 128,013,975 bp 128,055,166 bp -Genome Repeat Length 9,745,131 bp 9,748,266 bp -Genome Unique Length 118,268,845 bp 118,306,899 bp -Model Fit 98.3698% 99.1256% -Read Error Rate 0.106404% 0.106404% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index fe0fab5..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,9631 +0,0 @@ -1 1590283259 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-155730 1 -163619 1 -164296 1 -164540 1 -164933 1 -167193 1 -167808 1 -169171 1 -170433 1 -171427 1 -209029 1 -213748 1 -245016 1 -253894 1 -304252 1 -378514 1 diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index b0acde7..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.068e-02 8.735e-04 12.22 <2e-16 *** -r 2.090e-02 2.065e-05 1012.28 <2e-16 *** -kmercov 3.261e+01 5.777e-03 5644.16 <2e-16 *** -bias 8.614e-01 2.548e-03 338.10 <2e-16 *** -length 1.203e+08 8.416e+04 1429.89 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9968 on 973 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 5.873e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e8b58ad..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7a9dfcb..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2e2440c..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 13 trying 4peak model... converged. score: 100524382380.611 -round 1 trimming to 18 trying 4peak model... converged. score: 97537559048.9963 -round 2 trimming to 23 trying 4peak model... converged. score: 97121633094.8519 -round 3 trimming to 28 trying 4peak model... converged. score: 117389996362.743 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e32b95e..0000000 --- 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a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6ac0cc4..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.669e-03 1.125e-03 7.706 3.19e-14 *** -r 2.096e-02 2.705e-05 774.721 < 2e-16 *** -kmercov 2.639e+01 6.878e-03 3837.313 < 2e-16 *** -bias 7.423e-01 3.119e-03 238.025 < 2e-16 *** -length 1.215e+08 1.058e+05 1148.698 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13910 on 979 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.551e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b91314f..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0ab1398..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index dc14b70..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 242569010305.073 -round 1 trimming to 17 trying 4peak model... converged. score: 189299828282.92 -round 2 trimming to 22 trying 4peak model... converged. score: 215894321957.219 -round 3 trimming to 27 trying 4peak model... converged. score: 531126340901.406 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 316a446..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.09041% 2.10123% -Genome Haploid Length 131,738,898 bp 131,876,294 bp -Genome Repeat Length 11,215,926 bp 11,227,624 bp -Genome Unique Length 120,522,972 bp 120,648,670 bp -Model Fit 96.851% 97.7177% -Read Error Rate 1.99107% 1.99107% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 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r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.937e-03 8.738e-04 6.795 1.89e-11 *** -r 2.133e-02 2.176e-05 980.497 < 2e-16 *** -kmercov 3.964e+01 9.202e-03 4307.739 < 2e-16 *** -bias 2.015e+00 4.331e-03 465.295 < 2e-16 *** -length 1.192e+08 7.713e+04 1545.795 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8284 on 973 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 6.277e-07 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index fd6c6e4..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 79492b6..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2a4470e..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 69226046898.0757 -round 1 trimming to 13 trying 4peak model... converged. score: 69105473119.323 -round 2 trimming to 18 trying 4peak model... converged. score: 67365977530.3831 -round 3 trimming to 23 trying 4peak model... converged. score: 63812002969.0988 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2a02ccc..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12895% 2.13765% -Genome Haploid Length 126,859,115 bp 126,976,967 bp -Genome Repeat Length 8,299,854 bp 8,307,564 bp -Genome Unique Length 118,559,262 bp 118,669,402 bp -Model Fit 97.5735% 98.3403% -Read Error Rate 0.109551% 0.109551% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 628eb52..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.983e-03 1.133e-03 2.632 0.00862 ** -r 2.127e-02 2.887e-05 736.886 < 2e-16 *** -kmercov 3.285e+01 1.115e-02 2947.532 < 2e-16 *** -bias 1.720e+00 5.588e-03 307.855 < 2e-16 *** -length 1.199e+08 1.002e+05 1196.978 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11540 on 974 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 5.72e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0fceeaa..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index c6382ac..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6628f84..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 147742534303.013 -round 1 trimming to 17 trying 4peak model... converged. score: 132228603734.005 -round 2 trimming to 22 trying 4peak model... converged. score: 129713539424.765 -round 3 trimming to 27 trying 4peak model... converged. score: 147644196494.633 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 363c7a2..0000000 --- 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b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 582a721..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.845e-03 1.267e-03 1.456 0.146 -r 2.128e-02 3.363e-05 632.844 <2e-16 *** -kmercov 2.656e+01 1.119e-02 2373.621 <2e-16 *** -bias 1.453e+00 5.833e-03 249.026 <2e-16 *** -length 1.213e+08 1.092e+05 1110.592 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13940 on 980 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.638e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 96ebf22..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6d12f94..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e2c5122..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 275136054491.906 -round 1 trimming to 16 trying 4peak model... converged. score: 185419677925.57 -round 2 trimming to 21 trying 4peak model... converged. score: 195411496701.001 -round 3 trimming to 26 trying 4peak model... converged. score: 404000308530.423 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6cf74e1..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12136% 2.13481% -Genome Haploid Length 130,879,553 bp 131,100,296 bp -Genome Repeat Length 9,912,756 bp 9,929,475 bp -Genome Unique Length 120,966,797 bp 121,170,821 bp -Model Fit 96.775% 97.6749% -Read Error Rate 1.99112% 1.99112% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 56609ed..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,11303 +0,0 @@ -1 209310865 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(1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.448e-03 1.257e-03 -2.742 0.00621 ** -r 2.178e-02 3.513e-05 620.042 < 2e-16 *** -kmercov 4.004e+01 1.831e-02 2186.709 < 2e-16 *** -bias 3.069e+00 9.857e-03 311.360 < 2e-16 *** -length 1.186e+08 1.009e+05 1175.206 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10500 on 974 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.112e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3c7c139..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index bcd9628..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 39e41ff..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 118795552832.676 -round 1 trimming to 12 trying 4peak model... converged. score: 117792183124.964 -round 2 trimming to 17 trying 4peak model... converged. score: 111615005296.302 -round 3 trimming to 22 trying 4peak model... converged. score: 105391617186.961 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9172b85..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.17094% 2.18499% -Genome Haploid Length 125,472,332 bp 125,702,061 bp -Genome Repeat Length 6,614,941 bp 6,627,053 bp -Genome Unique Length 118,857,391 bp 119,075,008 bp -Model Fit 96.996% 97.7551% -Read Error Rate 0.111359% 0.111359% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 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05c136a..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.418e-03 1.403e-03 -3.861 0.00012 *** -r 2.169e-02 4.059e-05 534.387 < 2e-16 *** -kmercov 3.314e+01 1.874e-02 1768.597 < 2e-16 *** -bias 2.608e+00 1.090e-02 239.143 < 2e-16 *** -length 1.194e+08 1.138e+05 1049.823 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12530 on 975 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 4.099e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 57f3d1b..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index ffa525a..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0781c8c..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 198127965044.382 -round 1 trimming to 16 trying 4peak model... converged. score: 156752234167.568 -round 2 trimming to 21 trying 4peak model... converged. score: 153027564373.605 -round 3 trimming to 26 trying 4peak model... converged. score: 176307917514.365 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1dce8e3..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.16081% 2.17704% -Genome Haploid Length 127,169,937 bp 127,457,881 bp -Genome Repeat Length 7,299,315 bp 7,315,842 bp -Genome Unique Length 119,870,623 bp 120,142,039 bp -Model Fit 96.7236% 97.5383% -Read Error Rate 1.01954% 1.01954% diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 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dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.441e-03 1.530e-03 -4.209 2.8e-05 *** -r 2.168e-02 4.689e-05 462.337 < 2e-16 *** -kmercov 2.677e+01 1.812e-02 1477.492 < 2e-16 *** -bias 2.194e+00 1.107e-02 198.129 < 2e-16 *** -length 1.210e+08 1.212e+05 998.308 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 14590 on 980 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 6.045e-06 - diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dfd935b..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index f5b129c..0000000 Binary files a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f74539d..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 430486462030.257 -round 1 trimming to 16 trying 4peak model... converged. score: 207228186556.589 -round 2 trimming to 21 trying 4peak model... converged. score: 231693751060.643 -round 3 trimming to 26 trying 4peak model... converged. score: 468935987746.336 -done diff --git a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 940ef25..0000000 --- a/analysis/simulation_results_100x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.15831% 2.17706% -Genome Haploid Length 129,786,884 bp 130,138,731 bp -Genome Repeat Length 8,324,017 bp 8,346,583 bp -Genome Unique Length 121,462,867 bp 121,792,147 bp -Model Fit 96.5965% 97.5277% -Read Error Rate 1.99022% 1.99022% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist 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-1497 1 -1523 1 -1539 2 -1550 1 -1570 1 -1588 1 -1617 1 -1625 1 -1636 1 -1705 1 -1841 1 -1854 1 -2005 1 -2008 1 -2016 1 -2032 1 -2173 1 -2203 1 -2223 1 -2240 1 -2395 1 -2817 1 -2832 1 -2900 1 -2911 1 -2915 1 -2967 1 -2982 1 -3033 1 -3418 1 -3473 1 -3500 1 -3553 1 -3554 1 -3560 1 -3564 1 -3572 1 -3580 1 -3584 1 -3590 1 -3597 1 -3627 1 -3650 1 -3688 1 -3709 1 -3738 1 -3794 1 -3836 1 -3981 1 -4239 1 -4266 1 -4273 1 -4454 1 -4532 1 -5199 1 -5331 1 -5422 1 -5587 1 -5736 1 -5932 1 -6140 1 -6146 1 -6300 1 diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3b311ae..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.971e-03 3.363e-04 8.833 <2e-16 *** -r 1.033e-03 5.588e-06 184.938 <2e-16 *** -kmercov 3.925e+01 2.549e-03 15396.479 <2e-16 *** -bias 9.939e-01 1.580e-03 628.989 <2e-16 *** -length 4.523e+06 2.136e+03 2117.505 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 186.9 on 908 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 9.981e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1224100..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8e0b01f..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fde5cc7..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... round 0 trimming to 635 trying 4peak model... round 0 trimming to 638 trying 4peak model... round 0 trimming to 641 trying 4peak model... round 0 trimming to 643 trying 4peak model... round 0 trimming to 658 trying 4peak model... round 0 trimming to 661 trying 4peak model... round 0 trimming to 662 trying 4peak model... round 0 trimming to 665 trying 4peak model... round 0 trimming to 672 trying 4peak model... round 0 trimming to 676 trying 4peak model... round 0 trimming to 693 trying 4peak model... round 0 trimming to 698 trying 4peak model... round 0 trimming to 752 trying 4peak model... round 0 trimming to 798 trying 4peak model... round 0 trimming to 807 trying 4peak model... round 0 trimming to 837 trying 4peak model... round 0 trimming to 855 trying 4peak model... round 0 trimming to 857 trying 4peak model... round 0 trimming to 860 trying 4peak model... round 0 trimming to 867 trying 4peak model... round 0 trimming to 870 trying 4peak model... round 0 trimming to 873 trying 4peak model... round 0 trimming to 874 trying 4peak model... round 0 trimming to 877 trying 4peak model... round 0 trimming to 878 trying 4peak model... round 0 trimming to 887 trying 4peak model... round 0 trimming to 890 trying 4peak model... round 0 trimming to 891 trying 4peak model... round 0 trimming to 894 trying 4peak model... round 0 trimming to 895 trying 4peak model... round 0 trimming to 896 trying 4peak model... round 0 trimming to 900 trying 4peak model... round 0 trimming to 901 trying 4peak model... round 0 trimming to 902 trying 4peak model... round 0 trimming to 903 trying 4peak model... round 0 trimming to 910 trying 4peak model... round 0 trimming to 912 trying 4peak model... round 0 trimming to 913 trying 4peak model... round 0 trimming to 916 trying 4peak model... round 0 trimming to 933 trying 4peak model... round 0 trimming to 936 trying 4peak model... round 0 trimming to 940 trying 4peak model... round 0 trimming to 944 trying 4peak model... round 0 trimming to 966 trying 4peak model... round 0 trimming to 972 trying 4peak model... round 0 trimming to 973 trying 4peak model... round 0 trimming to 975 trying 4peak model... round 0 trimming to 978 trying 4peak model... round 0 trimming to 997 trying 4peak model... round 0 trimming to 999 trying 4peak model... round 0 trimming to 1015 trying 4peak model... round 0 trimming to 1016 trying 4peak model... round 0 trimming to 1018 trying 4peak model... round 0 trimming to 1094 trying 4peak model... round 0 trimming to 1103 trying 4peak model... round 0 trimming to 1123 trying 4peak model... round 0 trimming to 1125 trying 4peak model... round 0 trimming to 1127 trying 4peak model... round 0 trimming to 1135 trying 4peak model... round 0 trimming to 1137 trying 4peak model... round 0 trimming to 1184 trying 4peak model... round 0 trimming to 1192 trying 4peak model... round 0 trimming to 1199 trying 4peak model... converged. score: 31712098.2666421 -round 1 trimming to 12 trying 4peak model... round 1 trimming to 640 trying 4peak model... round 1 trimming to 643 trying 4peak model... round 1 trimming to 646 trying 4peak model... round 1 trimming to 648 trying 4peak model... round 1 trimming to 663 trying 4peak model... round 1 trimming to 666 trying 4peak model... round 1 trimming to 667 trying 4peak model... round 1 trimming to 670 trying 4peak model... round 1 trimming to 677 trying 4peak model... round 1 trimming to 681 trying 4peak model... round 1 trimming to 698 trying 4peak model... round 1 trimming to 703 trying 4peak model... round 1 trimming to 757 trying 4peak model... round 1 trimming to 803 trying 4peak model... round 1 trimming to 812 trying 4peak model... round 1 trimming to 842 trying 4peak model... round 1 trimming to 860 trying 4peak model... round 1 trimming to 862 trying 4peak model... round 1 trimming to 865 trying 4peak model... round 1 trimming to 872 trying 4peak model... round 1 trimming to 875 trying 4peak model... round 1 trimming to 878 trying 4peak model... round 1 trimming to 879 trying 4peak model... round 1 trimming to 882 trying 4peak model... round 1 trimming to 883 trying 4peak model... round 1 trimming to 892 trying 4peak model... round 1 trimming to 895 trying 4peak model... round 1 trimming to 896 trying 4peak model... round 1 trimming to 899 trying 4peak model... round 1 trimming to 900 trying 4peak model... round 1 trimming to 901 trying 4peak model... round 1 trimming to 905 trying 4peak model... round 1 trimming to 906 trying 4peak model... round 1 trimming to 907 trying 4peak model... round 1 trimming to 908 trying 4peak model... round 1 trimming to 915 trying 4peak model... round 1 trimming to 917 trying 4peak model... round 1 trimming to 918 trying 4peak model... round 1 trimming to 921 trying 4peak model... round 1 trimming to 938 trying 4peak model... round 1 trimming to 941 trying 4peak model... round 1 trimming to 945 trying 4peak model... round 1 trimming to 949 trying 4peak model... round 1 trimming to 971 trying 4peak model... round 1 trimming to 977 trying 4peak model... round 1 trimming to 978 trying 4peak model... round 1 trimming to 980 trying 4peak model... round 1 trimming to 983 trying 4peak model... round 1 trimming to 1002 trying 4peak model... round 1 trimming to 1004 trying 4peak model... round 1 trimming to 1020 trying 4peak model... round 1 trimming to 1021 trying 4peak model... round 1 trimming to 1023 trying 4peak model... round 1 trimming to 1099 trying 4peak model... round 1 trimming to 1108 trying 4peak model... round 1 trimming to 1128 trying 4peak model... round 1 trimming to 1130 trying 4peak model... round 1 trimming to 1132 trying 4peak model... round 1 trimming to 1140 trying 4peak model... round 1 trimming to 1142 trying 4peak model... round 1 trimming to 1189 trying 4peak model... round 1 trimming to 1197 trying 4peak model... round 1 trimming to 1204 trying 4peak model... converged. score: 31712098.2666258 -round 2 trimming to 17 trying 4peak model... round 2 trimming to 645 trying 4peak model... round 2 trimming to 648 trying 4peak model... round 2 trimming to 651 trying 4peak model... round 2 trimming to 653 trying 4peak model... round 2 trimming to 668 trying 4peak model... round 2 trimming to 671 trying 4peak model... round 2 trimming to 672 trying 4peak model... round 2 trimming to 675 trying 4peak model... round 2 trimming to 682 trying 4peak model... round 2 trimming to 686 trying 4peak model... round 2 trimming to 703 trying 4peak model... round 2 trimming to 708 trying 4peak model... round 2 trimming to 762 trying 4peak model... round 2 trimming to 808 trying 4peak model... round 2 trimming to 817 trying 4peak model... round 2 trimming to 847 trying 4peak model... round 2 trimming to 865 trying 4peak model... round 2 trimming to 867 trying 4peak model... round 2 trimming to 870 trying 4peak model... round 2 trimming to 877 trying 4peak model... round 2 trimming to 880 trying 4peak model... round 2 trimming to 883 trying 4peak model... round 2 trimming to 884 trying 4peak model... round 2 trimming to 887 trying 4peak model... round 2 trimming to 888 trying 4peak model... round 2 trimming to 897 trying 4peak model... round 2 trimming to 900 trying 4peak model... round 2 trimming to 901 trying 4peak model... round 2 trimming to 904 trying 4peak model... round 2 trimming to 905 trying 4peak model... round 2 trimming to 906 trying 4peak model... round 2 trimming to 910 trying 4peak model... round 2 trimming to 911 trying 4peak model... round 2 trimming to 912 trying 4peak model... round 2 trimming to 913 trying 4peak model... round 2 trimming to 920 trying 4peak model... round 2 trimming to 922 trying 4peak model... round 2 trimming to 923 trying 4peak model... round 2 trimming to 926 trying 4peak model... round 2 trimming to 943 trying 4peak model... round 2 trimming to 946 trying 4peak model... round 2 trimming to 950 trying 4peak model... round 2 trimming to 954 trying 4peak model... round 2 trimming to 976 trying 4peak model... round 2 trimming to 982 trying 4peak model... round 2 trimming to 983 trying 4peak model... round 2 trimming to 985 trying 4peak model... round 2 trimming to 988 trying 4peak model... round 2 trimming to 1007 trying 4peak model... round 2 trimming to 1009 trying 4peak model... round 2 trimming to 1025 trying 4peak model... round 2 trimming to 1026 trying 4peak model... round 2 trimming to 1028 trying 4peak model... round 2 trimming to 1104 trying 4peak model... round 2 trimming to 1113 trying 4peak model... round 2 trimming to 1133 trying 4peak model... round 2 trimming to 1135 trying 4peak model... round 2 trimming to 1137 trying 4peak model... round 2 trimming to 1145 trying 4peak model... round 2 trimming to 1147 trying 4peak model... round 2 trimming to 1194 trying 4peak model... round 2 trimming to 1202 trying 4peak model... round 2 trimming to 1209 trying 4peak model... converged. score: 31712098.2724293 -round 3 trimming to 22 trying 4peak model... round 3 trimming to 650 trying 4peak model... round 3 trimming to 653 trying 4peak model... round 3 trimming to 656 trying 4peak model... round 3 trimming to 658 trying 4peak model... round 3 trimming to 673 trying 4peak model... round 3 trimming to 676 trying 4peak model... round 3 trimming to 677 trying 4peak model... round 3 trimming to 680 trying 4peak model... round 3 trimming to 687 trying 4peak model... round 3 trimming to 691 trying 4peak model... round 3 trimming to 708 trying 4peak model... round 3 trimming to 713 trying 4peak model... round 3 trimming to 767 trying 4peak model... round 3 trimming to 813 trying 4peak model... round 3 trimming to 822 trying 4peak model... round 3 trimming to 852 trying 4peak model... round 3 trimming to 870 trying 4peak model... round 3 trimming to 872 trying 4peak model... round 3 trimming to 875 trying 4peak model... round 3 trimming to 882 trying 4peak model... round 3 trimming to 885 trying 4peak model... round 3 trimming to 888 trying 4peak model... round 3 trimming to 889 trying 4peak model... round 3 trimming to 892 trying 4peak model... round 3 trimming to 893 trying 4peak model... round 3 trimming to 902 trying 4peak model... round 3 trimming to 905 trying 4peak model... round 3 trimming to 906 trying 4peak model... round 3 trimming to 909 trying 4peak model... round 3 trimming to 910 trying 4peak model... round 3 trimming to 911 trying 4peak model... round 3 trimming to 915 trying 4peak model... round 3 trimming to 916 trying 4peak model... round 3 trimming to 917 trying 4peak model... round 3 trimming to 918 trying 4peak model... round 3 trimming to 925 trying 4peak model... round 3 trimming to 927 trying 4peak model... round 3 trimming to 928 trying 4peak model... round 3 trimming to 931 trying 4peak model... round 3 trimming to 948 trying 4peak model... round 3 trimming to 951 trying 4peak model... round 3 trimming to 955 trying 4peak model... round 3 trimming to 959 trying 4peak model... round 3 trimming to 981 trying 4peak model... round 3 trimming to 987 trying 4peak model... round 3 trimming to 988 trying 4peak model... round 3 trimming to 990 trying 4peak model... round 3 trimming to 993 trying 4peak model... round 3 trimming to 1012 trying 4peak model... round 3 trimming to 1014 trying 4peak model... round 3 trimming to 1030 trying 4peak model... round 3 trimming to 1031 trying 4peak model... round 3 trimming to 1033 trying 4peak model... round 3 trimming to 1109 trying 4peak model... round 3 trimming to 1118 trying 4peak model... round 3 trimming to 1138 trying 4peak model... round 3 trimming to 1140 trying 4peak model... round 3 trimming to 1142 trying 4peak model... round 3 trimming to 1150 trying 4peak model... round 3 trimming to 1152 trying 4peak model... round 3 trimming to 1199 trying 4peak model... round 3 trimming to 1207 trying 4peak model... round 3 trimming to 1214 trying 4peak model... converged. score: 31712098.4740641 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1d7345c..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.10222% 0.104455% -Genome Haploid Length 4,613,538 bp 4,614,737 bp -Genome Repeat Length 104,742 bp 104,769 bp -Genome Unique Length 4,508,797 bp 4,509,968 bp -Model Fit 98.605% 98.9719% -Read Error Rate 0.100512% 0.100512% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 6cb1e21..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1087 +0,0 @@ -1 57221218 -2 5693340 -3 509257 -4 67849 -5 22485 -6 10240 -7 4855 -8 2219 -9 1092 -10 577 -11 328 -12 332 -13 328 -14 389 -15 528 -16 864 -17 1248 -18 1602 -19 2008 -20 2663 -21 3305 -22 4069 -23 5066 -24 5804 -25 6625 -26 7265 -27 8069 -28 9065 -29 9275 -30 9909 -31 10198 -32 10502 -33 10702 -34 10732 -35 10912 -36 11055 -37 11457 -38 12294 -39 13070 -40 14897 -41 16630 -42 19920 -43 23350 -44 27643 -45 32494 -46 38153 -47 44449 -48 52025 -49 59790 -50 69639 -51 78180 -52 87640 -53 97104 -54 106288 -55 115883 -56 124757 -57 133678 -58 141417 -59 147977 -60 154317 -61 157670 -62 161856 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- d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.962e-03 3.493e-04 8.48 <2e-16 *** -r 1.026e-03 5.902e-06 173.80 <2e-16 *** -kmercov 3.244e+01 2.308e-03 14054.19 <2e-16 *** -bias 8.141e-01 1.506e-03 540.64 <2e-16 *** -length 4.523e+06 2.206e+03 2050.74 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 208.7 on 769 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 2.047e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2963e5d..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 63e934a..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 71f12c1..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... round 0 trimming to 13 trying 4peak model... converged. score: 33517131.0497512 -round 1 trimming to 16 trying 4peak model... round 1 trimming to 18 trying 4peak model... converged. score: 33517046.4749048 -round 2 trimming to 21 trying 4peak model... round 2 trimming to 23 trying 4peak model... converged. score: 33517014.8470792 -round 3 trimming to 26 trying 4peak model... round 3 trimming to 28 trying 4peak model... converged. score: 33590678.3755926 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 272caca..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.101394% 0.103755% -Genome Haploid Length 4,616,896 bp 4,618,210 bp -Genome Repeat Length 107,694 bp 107,725 bp -Genome Unique Length 4,509,201 bp 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r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.876e-03 2.358e-04 12.19 <2e-16 *** -r 1.052e-03 4.072e-06 258.23 <2e-16 *** -kmercov 2.621e+01 1.350e-03 19414.88 <2e-16 *** -bias 6.589e-01 9.433e-04 698.50 <2e-16 *** -length 4.523e+06 1.473e+03 3071.39 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 152 on 850 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 5.922e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0c7c929..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6f03ad8..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f4aac65..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 19646992.376465 -round 1 trimming to 17 trying 4peak model... converged. score: 19644522.2423064 -round 2 trimming to 22 trying 4peak model... converged. score: 19712271.2479273 -round 3 trimming to 27 trying 4peak model... converged. score: 24031978.9667598 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d68af32..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.104341% 0.105969% -Genome Haploid Length 4,638,344 bp 4,639,300 bp -Genome Repeat Length 129,041 bp 129,067 bp -Genome Unique Length 4,509,303 bp 4,510,232 bp -Model Fit 98.9146% 99.3071% -Read Error Rate 2.0006% 2.0006% diff --git 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.057e-03 6.081e-04 1.739 0.0824 . -r 1.100e-03 1.072e-05 102.681 <2e-16 *** -kmercov 3.937e+01 5.781e-03 6809.524 <2e-16 *** -bias 1.989e+00 4.478e-03 444.034 <2e-16 *** -length 4.523e+06 3.705e+03 1220.959 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 304.7 on 920 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.933e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 15887f5..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2e87adf..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 84cd5a7..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... round 0 trimming to 309 trying 4peak model... round 0 trimming to 382 trying 4peak model... round 0 trimming to 415 trying 4peak model... round 0 trimming to 431 trying 4peak model... round 0 trimming to 454 trying 4peak model... round 0 trimming to 469 trying 4peak model... round 0 trimming to 471 trying 4peak model... round 0 trimming to 599 trying 4peak model... round 0 trimming to 849 trying 4peak model... round 0 trimming to 857 trying 4peak model... converged. score: 85393337.8773222 -round 1 trimming to 11 trying 4peak model... round 1 trimming to 314 trying 4peak model... round 1 trimming to 387 trying 4peak model... round 1 trimming to 420 trying 4peak model... round 1 trimming to 436 trying 4peak model... round 1 trimming to 459 trying 4peak model... round 1 trimming to 474 trying 4peak model... round 1 trimming to 476 trying 4peak model... round 1 trimming to 604 trying 4peak model... round 1 trimming to 854 trying 4peak model... round 1 trimming to 862 trying 4peak model... converged. score: 85393337.8366025 -round 2 trimming to 16 trying 4peak model... round 2 trimming to 319 trying 4peak model... round 2 trimming to 392 trying 4peak model... round 2 trimming to 425 trying 4peak model... round 2 trimming to 441 trying 4peak model... round 2 trimming to 464 trying 4peak model... round 2 trimming to 479 trying 4peak model... round 2 trimming to 481 trying 4peak model... round 2 trimming to 609 trying 4peak model... round 2 trimming to 859 trying 4peak model... round 2 trimming to 867 trying 4peak model... converged. score: 85393337.89 -round 3 trimming to 21 trying 4peak model... round 3 trimming to 324 trying 4peak model... round 3 trimming to 397 trying 4peak model... round 3 trimming to 430 trying 4peak model... round 3 trimming to 446 trying 4peak model... round 3 trimming to 469 trying 4peak model... round 3 trimming to 484 trying 4peak model... round 3 trimming to 486 trying 4peak model... round 3 trimming to 614 trying 4peak model... round 3 trimming to 864 trying 4peak model... round 3 trimming to 872 trying 4peak model... converged. score: 85393352.2063164 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 0513a0e..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.107887% 0.112173% -Genome Haploid Length 4,598,739 bp 4,601,441 bp -Genome Repeat Length 81,469 bp 81,517 bp -Genome Unique Length 4,517,270 bp 4,519,924 bp -Model Fit 97.689% 98.0495% -Read Error Rate 0.100734% 0.100734% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist 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b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index db5a0fc..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.250e-03 4.735e-04 2.64 0.00845 ** -r 1.117e-03 8.517e-06 131.19 < 2e-16 *** -kmercov 3.253e+01 3.877e-03 8390.10 < 2e-16 *** -bias 1.651e+00 3.142e-03 525.59 < 2e-16 *** -length 4.518e+06 2.851e+03 1585.04 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 255.6 on 821 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.011e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e0ddab3..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0b22fd1..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 73bcff9..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 11 trying 4peak model... converged. score: 53627068.8088267 -round 1 trimming to 16 trying 4peak model... converged. score: 53626741.6489093 -round 2 trimming to 21 trying 4peak model... converged. score: 53632549.9174229 -round 3 trimming to 26 trying 4peak model... converged. score: 54467565.6498808 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 49364de..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.110025% 0.113432% -Genome Haploid Length 4,603,626 bp 4,605,821 bp -Genome Repeat Length 92,186 bp 92,230 bp -Genome Unique Length 4,511,440 bp 4,513,591 bp -Model Fit 98.1786% 98.5501% -Read Error Rate 1.00361% 1.00361% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 0077522..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,930 +0,0 @@ -1 95304322 -2 13026679 -3 1739331 -4 244180 -5 64125 -6 30983 -7 18726 -8 11406 -9 7431 -10 4678 -11 3289 -12 2866 -13 2785 -14 3286 -15 3801 -16 4686 -17 5716 -18 6814 -19 7690 -20 8884 -21 9590 -22 10613 -23 11471 -24 12618 -25 14012 -26 15388 -27 17229 -28 19225 -29 22075 -30 25356 -31 29465 -32 33694 -33 39166 -34 45259 -35 52161 -36 60242 -37 67902 -38 77400 -39 85900 -40 94805 -41 104677 -42 114692 -43 122963 -44 131658 -45 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0841d01..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.581e-03 3.700e-04 4.273 2.15e-05 *** -r 1.117e-03 6.826e-06 163.673 < 2e-16 *** -kmercov 2.627e+01 2.558e-03 10267.506 < 2e-16 *** -bias 1.311e+00 2.181e-03 600.921 < 2e-16 *** -length 4.517e+06 2.199e+03 2054.656 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 217.3 on 833 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 4.479e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5b0a2d5..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index fe11b1e..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f66d932..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 13 trying 4peak model... converged. score: 39200702.455713 -round 1 trimming to 18 trying 4peak model... converged. score: 39243278.5178553 -round 2 trimming to 23 trying 4peak model... converged. score: 42012380.4316568 -round 3 trimming to 28 trying 4peak model... converged. score: 87446965.2781178 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7862b59..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.11035% 0.11308% -Genome Haploid Length 4,626,810 bp 4,628,613 bp -Genome Repeat Length 117,539 bp 117,584 bp -Genome Unique Length 4,509,272 bp 4,511,029 bp -Model Fit 98.4851% 98.8775% -Read Error Rate 2.0012% 2.0012% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index d594cc4..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,1289 +0,0 @@ -1 7500431 -2 112923 -3 2165 -4 208 -5 79 -6 21 -7 59 -8 103 -9 107 -10 174 -11 201 -12 297 -13 398 -14 685 -15 729 -16 1069 -17 997 -18 1350 -19 1742 -20 1991 -21 2265 -22 2606 -23 3160 -24 3731 -25 4076 -26 4278 -27 5009 -28 5490 -29 5637 -30 6187 -31 6758 -32 7410 -33 7575 -34 8657 -35 9296 -36 9687 -37 10880 -38 11174 -39 12224 -40 13181 -41 14489 -42 16130 -43 17318 -44 18562 -45 20131 -46 22506 -47 24512 -48 26328 -49 29768 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5c9388b..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.508e-03 6.890e-04 -2.188 0.0289 * -r 1.286e-03 1.304e-05 98.569 <2e-16 *** -kmercov 3.949e+01 7.699e-03 5129.967 <2e-16 *** -bias 2.984e+00 7.137e-03 418.036 <2e-16 *** -length 4.506e+06 3.924e+03 1148.164 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 312.7 on 904 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.573e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 896ac39..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2104d9b..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2d95b38..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... round 0 trimming to 326 trying 4peak model... round 0 trimming to 336 trying 4peak model... round 0 trimming to 343 trying 4peak model... round 0 trimming to 393 trying 4peak model... round 0 trimming to 398 trying 4peak model... round 0 trimming to 411 trying 4peak model... round 0 trimming to 432 trying 4peak model... round 0 trimming to 436 trying 4peak model... round 0 trimming to 445 trying 4peak model... round 0 trimming to 469 trying 4peak model... round 0 trimming to 590 trying 4peak model... round 0 trimming to 606 trying 4peak model... round 0 trimming to 607 trying 4peak model... converged. score: 88397737.8914415 -round 1 trimming to 11 trying 4peak model... round 1 trimming to 331 trying 4peak model... round 1 trimming to 341 trying 4peak model... round 1 trimming to 348 trying 4peak model... round 1 trimming to 398 trying 4peak model... round 1 trimming to 403 trying 4peak model... round 1 trimming to 416 trying 4peak model... round 1 trimming to 437 trying 4peak model... round 1 trimming to 441 trying 4peak model... round 1 trimming to 450 trying 4peak model... round 1 trimming to 474 trying 4peak model... round 1 trimming to 595 trying 4peak model... round 1 trimming to 611 trying 4peak model... round 1 trimming to 612 trying 4peak model... converged. score: 88397735.8103691 -round 2 trimming to 16 trying 4peak model... round 2 trimming to 336 trying 4peak model... round 2 trimming to 346 trying 4peak model... round 2 trimming to 353 trying 4peak model... round 2 trimming to 403 trying 4peak model... round 2 trimming to 408 trying 4peak model... round 2 trimming to 421 trying 4peak model... round 2 trimming to 442 trying 4peak model... round 2 trimming to 446 trying 4peak model... round 2 trimming to 455 trying 4peak model... round 2 trimming to 479 trying 4peak model... round 2 trimming to 600 trying 4peak model... round 2 trimming to 616 trying 4peak model... round 2 trimming to 617 trying 4peak model... converged. score: 88397729.446936 -round 3 trimming to 21 trying 4peak model... round 3 trimming to 341 trying 4peak model... round 3 trimming to 351 trying 4peak model... round 3 trimming to 358 trying 4peak model... round 3 trimming to 408 trying 4peak model... round 3 trimming to 413 trying 4peak model... round 3 trimming to 426 trying 4peak model... round 3 trimming to 447 trying 4peak model... round 3 trimming to 451 trying 4peak model... round 3 trimming to 460 trying 4peak model... round 3 trimming to 484 trying 4peak model... round 3 trimming to 605 trying 4peak model... round 3 trimming to 621 trying 4peak model... round 3 trimming to 622 trying 4peak model... converged. score: 88401341.4241275 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1d598da..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.125943% 0.13116% -Genome Haploid Length 4,582,807 bp 4,586,382 bp -Genome Repeat Length 72,077 bp 72,133 bp -Genome Unique Length 4,510,731 bp 4,514,249 bp -Model Fit 97.4728% 97.859% -Read Error Rate 0.10085% 0.10085% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 72fc41c..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1168 +0,0 @@ -1 56955503 -2 5761779 -3 533414 -4 71771 -5 22387 -6 10351 -7 4911 -8 2397 -9 1339 -10 885 -11 918 -12 1062 -13 1246 -14 1499 -15 1861 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-2986 1 -3002 1 -3012 2 -3017 1 -3021 1 -3025 1 -3044 1 -3058 1 -3069 2 -3088 1 -3099 1 -3116 1 -3137 1 -3194 1 -3236 1 -3315 1 -3503 1 -3601 1 -3609 1 -3706 1 -3824 1 -3916 1 -4435 1 -4537 1 -4637 1 -4778 1 -4928 1 -5088 1 -5220 1 -5261 1 -5388 1 diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 732f568..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.793e-04 6.286e-04 -1.081 0.28 -r 1.245e-03 1.214e-05 102.504 <2e-16 *** -kmercov 3.263e+01 5.959e-03 5476.026 <2e-16 *** -bias 2.443e+00 5.711e-03 427.761 <2e-16 *** -length 4.507e+06 3.548e+03 1270.302 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 309.3 on 826 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.764e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 024f321..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 55049c1..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f0e8680..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 79023782.7292416 -round 1 trimming to 15 trying 4peak model... converged. score: 79023561.2202185 -round 2 trimming to 20 trying 4peak model... converged. score: 79099258.0715 -round 3 trimming to 25 trying 4peak model... converged. score: 82602088.6347458 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index bf17309..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.122047% 0.126905% -Genome Haploid Length 4,589,324 bp 4,592,678 bp -Genome Repeat Length 81,318 bp 81,377 bp -Genome Unique Length 4,508,006 bp 4,511,300 bp -Model Fit 97.7704% 98.1584% -Read Error Rate 1.00251% 1.00251% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 1707482..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,984 +0,0 @@ -1 95059967 -2 13050703 -3 1764236 -4 247945 -5 63105 -6 30865 -7 18655 -8 11847 -9 7636 -10 5426 -11 4176 -12 3793 -13 3868 -14 4520 -15 5205 -16 5990 -17 6831 -18 7902 -19 8617 -20 10072 -21 11482 -22 13171 -23 14560 -24 16291 -25 17750 -26 20487 -27 22905 -28 26133 -29 30026 -30 34494 -31 38788 -32 44217 -33 49717 -34 56256 -35 62901 -36 69712 -37 77075 -38 83481 -39 90590 -40 98457 -41 105673 -42 112589 -43 118698 -44 124088 -45 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* d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.011e-04 5.124e-04 -0.978 0.328 -r 1.279e-03 1.016e-05 125.917 <2e-16 *** -kmercov 2.637e+01 4.070e-03 6478.570 <2e-16 *** -bias 1.963e+00 4.083e-03 480.645 <2e-16 *** -length 4.506e+06 2.837e+03 1588.430 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 273.3 on 862 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.958e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5c98824..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6fd807a..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b9f3256..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 12 trying 4peak model... converged. score: 63498887.0815628 -round 1 trimming to 17 trying 4peak model... converged. score: 63548985.9241306 -round 2 trimming to 22 trying 4peak model... converged. score: 70073291.5044975 -round 3 trimming to 27 trying 4peak model... converged. score: 131459973.631138 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f50ceb8..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.125881% 0.129945% -Genome Haploid Length 4,610,047 bp 4,612,894 bp -Genome Repeat Length 103,098 bp 103,161 bp -Genome Unique Length 4,506,950 bp 4,509,733 bp -Model Fit 98.095% 98.5072% -Read Error Rate 1.99926% 1.99926% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 851dad6..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,1322 +0,0 @@ -1 7496634 -2 100382 -3 1581 -4 144 -5 31 -6 3 -7 2 -9 9 -10 23 -11 33 -12 95 -13 220 -14 392 -15 700 -16 1101 -17 1791 -18 2580 -19 3935 -20 5598 -21 7723 -22 10438 -23 13843 -24 17724 -25 22075 -26 27685 -27 32358 -28 38567 -29 44607 -30 50394 -31 56622 -32 62337 -33 67335 -34 71320 -35 73830 -36 76951 -37 78984 -38 79278 -39 79402 -40 78389 -41 75636 -42 72029 -43 68121 -44 64704 -45 61174 -46 56961 -47 51948 -48 48125 -49 44573 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1 -3513 1 -3556 1 -3597 1 -3600 1 -3722 1 -3837 1 -3930 1 -4843 1 -4947 1 -4962 1 -5030 1 -5288 1 -5320 1 -5492 1 -5674 1 -5730 1 diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0c56a45..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.083e-03 4.306e-04 4.839 1.54e-06 *** -r 1.014e-02 7.513e-06 1350.036 < 2e-16 *** -kmercov 3.926e+01 3.209e-03 12234.587 < 2e-16 *** -bias 9.861e-01 1.564e-03 630.606 < 2e-16 *** -length 4.526e+06 2.048e+03 2209.886 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 194.4 on 895 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 2.3e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f570082..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index da32843..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5aa2732..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... round 0 trimming to 592 trying 4peak model... round 0 trimming to 596 trying 4peak model... round 0 trimming to 615 trying 4peak model... round 0 trimming to 619 trying 4peak model... round 0 trimming to 620 trying 4peak model... round 0 trimming to 621 trying 4peak model... round 0 trimming to 622 trying 4peak model... round 0 trimming to 629 trying 4peak model... round 0 trimming to 648 trying 4peak model... round 0 trimming to 651 trying 4peak model... round 0 trimming to 764 trying 4peak model... round 0 trimming to 768 trying 4peak model... round 0 trimming to 774 trying 4peak model... round 0 trimming to 792 trying 4peak model... round 0 trimming to 818 trying 4peak model... round 0 trimming to 821 trying 4peak model... round 0 trimming to 824 trying 4peak model... round 0 trimming to 826 trying 4peak model... round 0 trimming to 828 trying 4peak model... round 0 trimming to 841 trying 4peak model... round 0 trimming to 843 trying 4peak model... round 0 trimming to 847 trying 4peak model... round 0 trimming to 848 trying 4peak model... round 0 trimming to 851 trying 4peak model... round 0 trimming to 853 trying 4peak model... round 0 trimming to 858 trying 4peak model... round 0 trimming to 860 trying 4peak model... round 0 trimming to 863 trying 4peak model... round 0 trimming to 864 trying 4peak model... round 0 trimming to 867 trying 4peak model... round 0 trimming to 868 trying 4peak model... round 0 trimming to 869 trying 4peak model... round 0 trimming to 873 trying 4peak model... round 0 trimming to 875 trying 4peak model... round 0 trimming to 876 trying 4peak model... round 0 trimming to 881 trying 4peak model... round 0 trimming to 889 trying 4peak model... round 0 trimming to 890 trying 4peak model... round 0 trimming to 905 trying 4peak model... round 0 trimming to 907 trying 4peak model... round 0 trimming to 915 trying 4peak model... round 0 trimming to 917 trying 4peak model... round 0 trimming to 919 trying 4peak model... round 0 trimming to 922 trying 4peak model... round 0 trimming to 925 trying 4peak model... round 0 trimming to 926 trying 4peak model... round 0 trimming to 929 trying 4peak model... round 0 trimming to 933 trying 4peak model... round 0 trimming to 934 trying 4peak model... round 0 trimming to 937 trying 4peak model... round 0 trimming to 938 trying 4peak model... round 0 trimming to 941 trying 4peak model... round 0 trimming to 944 trying 4peak model... round 0 trimming to 945 trying 4peak model... round 0 trimming to 953 trying 4peak model... round 0 trimming to 954 trying 4peak model... round 0 trimming to 957 trying 4peak model... round 0 trimming to 959 trying 4peak model... round 0 trimming to 960 trying 4peak model... round 0 trimming to 962 trying 4peak model... round 0 trimming to 963 trying 4peak model... round 0 trimming to 964 trying 4peak model... round 0 trimming to 973 trying 4peak model... round 0 trimming to 974 trying 4peak model... round 0 trimming to 976 trying 4peak model... round 0 trimming to 979 trying 4peak model... round 0 trimming to 986 trying 4peak model... round 0 trimming to 987 trying 4peak model... round 0 trimming to 988 trying 4peak model... round 0 trimming to 1014 trying 4peak model... round 0 trimming to 1015 trying 4peak model... round 0 trimming to 1017 trying 4peak model... round 0 trimming to 1018 trying 4peak model... round 0 trimming to 1025 trying 4peak model... round 0 trimming to 1047 trying 4peak model... round 0 trimming to 1067 trying 4peak model... round 0 trimming to 1077 trying 4peak model... round 0 trimming to 1081 trying 4peak model... round 0 trimming to 1085 trying 4peak model... round 0 trimming to 1089 trying 4peak model... round 0 trimming to 1090 trying 4peak model... round 0 trimming to 1099 trying 4peak model... round 0 trimming to 1100 trying 4peak model... round 0 trimming to 1106 trying 4peak model... round 0 trimming to 1129 trying 4peak model... round 0 trimming to 1152 trying 4peak model... round 0 trimming to 1156 trying 4peak model... round 0 trimming to 1159 trying 4peak model... round 0 trimming to 1160 trying 4peak model... round 0 trimming to 1163 trying 4peak model... round 0 trimming to 1164 trying 4peak model... round 0 trimming to 1167 trying 4peak model... round 0 trimming to 1168 trying 4peak model... round 0 trimming to 1172 trying 4peak model... round 0 trimming to 1174 trying 4peak model... round 0 trimming to 1175 trying 4peak model... round 0 trimming to 1176 trying 4peak model... round 0 trimming to 1177 trying 4peak model... round 0 trimming to 1178 trying 4peak model... round 0 trimming to 1180 trying 4peak model... round 0 trimming to 1183 trying 4peak model... round 0 trimming to 1190 trying 4peak model... round 0 trimming to 1195 trying 4peak model... round 0 trimming to 1196 trying 4peak model... round 0 trimming to 1197 trying 4peak model... round 0 trimming to 1204 trying 4peak model... round 0 trimming to 1205 trying 4peak model... round 0 trimming to 1206 trying 4peak model... round 0 trimming to 1207 trying 4peak model... round 0 trimming to 1212 trying 4peak model... round 0 trimming to 1213 trying 4peak model... round 0 trimming to 1217 trying 4peak model... round 0 trimming to 1224 trying 4peak model... round 0 trimming to 1235 trying 4peak model... round 0 trimming to 1236 trying 4peak model... round 0 trimming to 1241 trying 4peak model... round 0 trimming to 1242 trying 4peak model... round 0 trimming to 1244 trying 4peak model... round 0 trimming to 1246 trying 4peak model... round 0 trimming to 1249 trying 4peak model... converged. score: 33812097.2142693 -round 1 trimming to 12 trying 4peak model... round 1 trimming to 597 trying 4peak model... round 1 trimming to 601 trying 4peak model... round 1 trimming to 620 trying 4peak model... round 1 trimming to 624 trying 4peak model... round 1 trimming to 625 trying 4peak model... round 1 trimming to 626 trying 4peak model... round 1 trimming to 627 trying 4peak model... round 1 trimming to 634 trying 4peak model... round 1 trimming to 653 trying 4peak model... round 1 trimming to 656 trying 4peak model... round 1 trimming to 769 trying 4peak model... round 1 trimming to 773 trying 4peak model... round 1 trimming to 779 trying 4peak model... round 1 trimming to 797 trying 4peak model... round 1 trimming to 823 trying 4peak model... round 1 trimming to 826 trying 4peak model... round 1 trimming to 829 trying 4peak model... round 1 trimming to 831 trying 4peak model... round 1 trimming to 833 trying 4peak model... round 1 trimming to 846 trying 4peak model... round 1 trimming to 848 trying 4peak model... round 1 trimming to 852 trying 4peak model... round 1 trimming to 853 trying 4peak model... round 1 trimming to 856 trying 4peak model... round 1 trimming to 858 trying 4peak model... round 1 trimming to 863 trying 4peak model... round 1 trimming to 865 trying 4peak model... round 1 trimming to 868 trying 4peak model... round 1 trimming to 869 trying 4peak model... round 1 trimming to 872 trying 4peak model... round 1 trimming to 873 trying 4peak model... round 1 trimming to 874 trying 4peak model... round 1 trimming to 878 trying 4peak model... round 1 trimming to 880 trying 4peak model... round 1 trimming to 881 trying 4peak model... round 1 trimming to 886 trying 4peak model... round 1 trimming to 894 trying 4peak model... round 1 trimming to 895 trying 4peak model... round 1 trimming to 910 trying 4peak model... round 1 trimming to 912 trying 4peak model... round 1 trimming to 920 trying 4peak model... round 1 trimming to 922 trying 4peak model... round 1 trimming to 924 trying 4peak model... round 1 trimming to 927 trying 4peak model... round 1 trimming to 930 trying 4peak model... round 1 trimming to 931 trying 4peak model... round 1 trimming to 934 trying 4peak model... round 1 trimming to 938 trying 4peak model... round 1 trimming to 939 trying 4peak model... round 1 trimming to 942 trying 4peak model... round 1 trimming to 943 trying 4peak model... round 1 trimming to 946 trying 4peak model... round 1 trimming to 949 trying 4peak model... round 1 trimming to 950 trying 4peak model... round 1 trimming to 958 trying 4peak model... round 1 trimming to 959 trying 4peak model... round 1 trimming to 962 trying 4peak model... round 1 trimming to 964 trying 4peak model... round 1 trimming to 965 trying 4peak model... round 1 trimming to 967 trying 4peak model... round 1 trimming to 968 trying 4peak model... round 1 trimming to 969 trying 4peak model... round 1 trimming to 978 trying 4peak model... round 1 trimming to 979 trying 4peak model... round 1 trimming to 981 trying 4peak model... round 1 trimming to 984 trying 4peak model... round 1 trimming to 991 trying 4peak model... round 1 trimming to 992 trying 4peak model... round 1 trimming to 993 trying 4peak model... round 1 trimming to 1019 trying 4peak model... round 1 trimming to 1020 trying 4peak model... round 1 trimming to 1022 trying 4peak model... round 1 trimming to 1023 trying 4peak model... round 1 trimming to 1030 trying 4peak model... round 1 trimming to 1052 trying 4peak model... round 1 trimming to 1072 trying 4peak model... round 1 trimming to 1082 trying 4peak model... round 1 trimming to 1086 trying 4peak model... round 1 trimming to 1090 trying 4peak model... round 1 trimming to 1094 trying 4peak model... round 1 trimming to 1095 trying 4peak model... round 1 trimming to 1104 trying 4peak model... round 1 trimming to 1105 trying 4peak model... round 1 trimming to 1111 trying 4peak model... round 1 trimming to 1134 trying 4peak model... round 1 trimming to 1157 trying 4peak model... round 1 trimming to 1161 trying 4peak model... round 1 trimming to 1164 trying 4peak model... round 1 trimming to 1165 trying 4peak model... round 1 trimming to 1168 trying 4peak model... round 1 trimming to 1169 trying 4peak model... round 1 trimming to 1172 trying 4peak model... round 1 trimming to 1173 trying 4peak model... round 1 trimming to 1177 trying 4peak model... round 1 trimming to 1179 trying 4peak model... round 1 trimming to 1180 trying 4peak model... round 1 trimming to 1181 trying 4peak model... round 1 trimming to 1182 trying 4peak model... round 1 trimming to 1183 trying 4peak model... round 1 trimming to 1185 trying 4peak model... round 1 trimming to 1188 trying 4peak model... round 1 trimming to 1195 trying 4peak model... round 1 trimming to 1200 trying 4peak model... round 1 trimming to 1201 trying 4peak model... round 1 trimming to 1202 trying 4peak model... round 1 trimming to 1209 trying 4peak model... round 1 trimming to 1210 trying 4peak model... round 1 trimming to 1211 trying 4peak model... round 1 trimming to 1212 trying 4peak model... round 1 trimming to 1217 trying 4peak model... round 1 trimming to 1218 trying 4peak model... round 1 trimming to 1222 trying 4peak model... round 1 trimming to 1229 trying 4peak model... round 1 trimming to 1240 trying 4peak model... round 1 trimming to 1241 trying 4peak model... round 1 trimming to 1246 trying 4peak model... round 1 trimming to 1247 trying 4peak model... round 1 trimming to 1249 trying 4peak model... round 1 trimming to 1251 trying 4peak model... round 1 trimming to 1254 trying 4peak model... converged. score: 33812097.2142531 -round 2 trimming to 17 trying 4peak model... round 2 trimming to 602 trying 4peak model... round 2 trimming to 606 trying 4peak model... round 2 trimming to 625 trying 4peak model... round 2 trimming to 629 trying 4peak model... round 2 trimming to 630 trying 4peak model... round 2 trimming to 631 trying 4peak model... round 2 trimming to 632 trying 4peak model... round 2 trimming to 639 trying 4peak model... round 2 trimming to 658 trying 4peak model... round 2 trimming to 661 trying 4peak model... round 2 trimming to 774 trying 4peak model... round 2 trimming to 778 trying 4peak model... round 2 trimming to 784 trying 4peak model... round 2 trimming to 802 trying 4peak model... round 2 trimming to 828 trying 4peak model... round 2 trimming to 831 trying 4peak model... round 2 trimming to 834 trying 4peak model... round 2 trimming to 836 trying 4peak model... round 2 trimming to 838 trying 4peak model... round 2 trimming to 851 trying 4peak model... round 2 trimming to 853 trying 4peak model... round 2 trimming to 857 trying 4peak model... round 2 trimming to 858 trying 4peak model... round 2 trimming to 861 trying 4peak model... round 2 trimming to 863 trying 4peak model... round 2 trimming to 868 trying 4peak model... round 2 trimming to 870 trying 4peak model... round 2 trimming to 873 trying 4peak model... round 2 trimming to 874 trying 4peak model... round 2 trimming to 877 trying 4peak model... round 2 trimming to 878 trying 4peak model... round 2 trimming to 879 trying 4peak model... round 2 trimming to 883 trying 4peak model... round 2 trimming to 885 trying 4peak model... round 2 trimming to 886 trying 4peak model... round 2 trimming to 891 trying 4peak model... round 2 trimming to 899 trying 4peak model... round 2 trimming to 900 trying 4peak model... round 2 trimming to 915 trying 4peak model... round 2 trimming to 917 trying 4peak model... round 2 trimming to 925 trying 4peak model... round 2 trimming to 927 trying 4peak model... round 2 trimming to 929 trying 4peak model... round 2 trimming to 932 trying 4peak model... round 2 trimming to 935 trying 4peak model... round 2 trimming to 936 trying 4peak model... round 2 trimming to 939 trying 4peak model... round 2 trimming to 943 trying 4peak model... round 2 trimming to 944 trying 4peak model... round 2 trimming to 947 trying 4peak model... round 2 trimming to 948 trying 4peak model... round 2 trimming to 951 trying 4peak model... round 2 trimming to 954 trying 4peak model... round 2 trimming to 955 trying 4peak model... round 2 trimming to 963 trying 4peak model... round 2 trimming to 964 trying 4peak model... round 2 trimming to 967 trying 4peak model... round 2 trimming to 969 trying 4peak model... round 2 trimming to 970 trying 4peak model... round 2 trimming to 972 trying 4peak model... round 2 trimming to 973 trying 4peak model... round 2 trimming to 974 trying 4peak model... round 2 trimming to 983 trying 4peak model... round 2 trimming to 984 trying 4peak model... round 2 trimming to 986 trying 4peak model... round 2 trimming to 989 trying 4peak model... round 2 trimming to 996 trying 4peak model... round 2 trimming to 997 trying 4peak model... round 2 trimming to 998 trying 4peak model... round 2 trimming to 1024 trying 4peak model... round 2 trimming to 1025 trying 4peak model... round 2 trimming to 1027 trying 4peak model... round 2 trimming to 1028 trying 4peak model... round 2 trimming to 1035 trying 4peak model... round 2 trimming to 1057 trying 4peak model... round 2 trimming to 1077 trying 4peak model... round 2 trimming to 1087 trying 4peak model... round 2 trimming to 1091 trying 4peak model... round 2 trimming to 1095 trying 4peak model... round 2 trimming to 1099 trying 4peak model... round 2 trimming to 1100 trying 4peak model... round 2 trimming to 1109 trying 4peak model... round 2 trimming to 1110 trying 4peak model... round 2 trimming to 1116 trying 4peak model... round 2 trimming to 1139 trying 4peak model... round 2 trimming to 1162 trying 4peak model... round 2 trimming to 1166 trying 4peak model... round 2 trimming to 1169 trying 4peak model... round 2 trimming to 1170 trying 4peak model... round 2 trimming to 1173 trying 4peak model... round 2 trimming to 1174 trying 4peak model... round 2 trimming to 1177 trying 4peak model... round 2 trimming to 1178 trying 4peak model... round 2 trimming to 1182 trying 4peak model... round 2 trimming to 1184 trying 4peak model... round 2 trimming to 1185 trying 4peak model... round 2 trimming to 1186 trying 4peak model... round 2 trimming to 1187 trying 4peak model... round 2 trimming to 1188 trying 4peak model... round 2 trimming to 1190 trying 4peak model... round 2 trimming to 1193 trying 4peak model... round 2 trimming to 1200 trying 4peak model... round 2 trimming to 1205 trying 4peak model... round 2 trimming to 1206 trying 4peak model... round 2 trimming to 1207 trying 4peak model... round 2 trimming to 1214 trying 4peak model... round 2 trimming to 1215 trying 4peak model... round 2 trimming to 1216 trying 4peak model... round 2 trimming to 1217 trying 4peak model... round 2 trimming to 1222 trying 4peak model... round 2 trimming to 1223 trying 4peak model... round 2 trimming to 1227 trying 4peak model... round 2 trimming to 1234 trying 4peak model... round 2 trimming to 1245 trying 4peak model... round 2 trimming to 1246 trying 4peak model... round 2 trimming to 1251 trying 4peak model... round 2 trimming to 1252 trying 4peak model... round 2 trimming to 1254 trying 4peak model... round 2 trimming to 1256 trying 4peak model... round 2 trimming to 1259 trying 4peak model... converged. score: 33812253.3863139 -round 3 trimming to 22 trying 4peak model... round 3 trimming to 607 trying 4peak model... round 3 trimming to 611 trying 4peak model... round 3 trimming to 630 trying 4peak model... round 3 trimming to 634 trying 4peak model... round 3 trimming to 635 trying 4peak model... round 3 trimming to 636 trying 4peak model... round 3 trimming to 637 trying 4peak model... round 3 trimming to 644 trying 4peak model... round 3 trimming to 663 trying 4peak model... round 3 trimming to 666 trying 4peak model... round 3 trimming to 779 trying 4peak model... round 3 trimming to 783 trying 4peak model... round 3 trimming to 789 trying 4peak model... round 3 trimming to 807 trying 4peak model... round 3 trimming to 833 trying 4peak model... round 3 trimming to 836 trying 4peak model... round 3 trimming to 839 trying 4peak model... round 3 trimming to 841 trying 4peak model... round 3 trimming to 843 trying 4peak model... round 3 trimming to 856 trying 4peak model... round 3 trimming to 858 trying 4peak model... round 3 trimming to 862 trying 4peak model... round 3 trimming to 863 trying 4peak model... round 3 trimming to 866 trying 4peak model... round 3 trimming to 868 trying 4peak model... round 3 trimming to 873 trying 4peak model... round 3 trimming to 875 trying 4peak model... round 3 trimming to 878 trying 4peak model... round 3 trimming to 879 trying 4peak model... round 3 trimming to 882 trying 4peak model... round 3 trimming to 883 trying 4peak model... round 3 trimming to 884 trying 4peak model... round 3 trimming to 888 trying 4peak model... round 3 trimming to 890 trying 4peak model... round 3 trimming to 891 trying 4peak model... round 3 trimming to 896 trying 4peak model... round 3 trimming to 904 trying 4peak model... round 3 trimming to 905 trying 4peak model... round 3 trimming to 920 trying 4peak model... round 3 trimming to 922 trying 4peak model... round 3 trimming to 930 trying 4peak model... round 3 trimming to 932 trying 4peak model... round 3 trimming to 934 trying 4peak model... round 3 trimming to 937 trying 4peak model... round 3 trimming to 940 trying 4peak model... round 3 trimming to 941 trying 4peak model... round 3 trimming to 944 trying 4peak model... round 3 trimming to 948 trying 4peak model... round 3 trimming to 949 trying 4peak model... round 3 trimming to 952 trying 4peak model... round 3 trimming to 953 trying 4peak model... round 3 trimming to 956 trying 4peak model... round 3 trimming to 959 trying 4peak model... round 3 trimming to 960 trying 4peak model... round 3 trimming to 968 trying 4peak model... round 3 trimming to 969 trying 4peak model... round 3 trimming to 972 trying 4peak model... round 3 trimming to 974 trying 4peak model... round 3 trimming to 975 trying 4peak model... round 3 trimming to 977 trying 4peak model... round 3 trimming to 978 trying 4peak model... round 3 trimming to 979 trying 4peak model... round 3 trimming to 988 trying 4peak model... round 3 trimming to 989 trying 4peak model... round 3 trimming to 991 trying 4peak model... round 3 trimming to 994 trying 4peak model... round 3 trimming to 1001 trying 4peak model... round 3 trimming to 1002 trying 4peak model... round 3 trimming to 1003 trying 4peak model... round 3 trimming to 1029 trying 4peak model... round 3 trimming to 1030 trying 4peak model... round 3 trimming to 1032 trying 4peak model... round 3 trimming to 1033 trying 4peak model... round 3 trimming to 1040 trying 4peak model... round 3 trimming to 1062 trying 4peak model... round 3 trimming to 1082 trying 4peak model... round 3 trimming to 1092 trying 4peak model... round 3 trimming to 1096 trying 4peak model... round 3 trimming to 1100 trying 4peak model... round 3 trimming to 1104 trying 4peak model... round 3 trimming to 1105 trying 4peak model... round 3 trimming to 1114 trying 4peak model... round 3 trimming to 1115 trying 4peak model... round 3 trimming to 1121 trying 4peak model... round 3 trimming to 1144 trying 4peak model... round 3 trimming to 1167 trying 4peak model... round 3 trimming to 1171 trying 4peak model... round 3 trimming to 1174 trying 4peak model... round 3 trimming to 1175 trying 4peak model... round 3 trimming to 1178 trying 4peak model... round 3 trimming to 1179 trying 4peak model... round 3 trimming to 1182 trying 4peak model... round 3 trimming to 1183 trying 4peak model... round 3 trimming to 1187 trying 4peak model... round 3 trimming to 1189 trying 4peak model... round 3 trimming to 1190 trying 4peak model... round 3 trimming to 1191 trying 4peak model... round 3 trimming to 1192 trying 4peak model... round 3 trimming to 1193 trying 4peak model... round 3 trimming to 1195 trying 4peak model... round 3 trimming to 1198 trying 4peak model... round 3 trimming to 1205 trying 4peak model... round 3 trimming to 1210 trying 4peak model... round 3 trimming to 1211 trying 4peak model... round 3 trimming to 1212 trying 4peak model... round 3 trimming to 1219 trying 4peak model... round 3 trimming to 1220 trying 4peak model... round 3 trimming to 1221 trying 4peak model... round 3 trimming to 1222 trying 4peak model... round 3 trimming to 1227 trying 4peak model... round 3 trimming to 1228 trying 4peak model... round 3 trimming to 1232 trying 4peak model... round 3 trimming to 1239 trying 4peak model... round 3 trimming to 1250 trying 4peak model... round 3 trimming to 1251 trying 4peak model... round 3 trimming to 1256 trying 4peak model... round 3 trimming to 1257 trying 4peak model... round 3 trimming to 1259 trying 4peak model... round 3 trimming to 1261 trying 4peak model... round 3 trimming to 1264 trying 4peak model... converged. score: 33834077.9716026 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b9283f3..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.01273% 1.01573% -Genome Haploid Length 4,614,716 bp 4,616,225 bp -Genome Repeat Length 98,369 bp 98,401 bp -Genome Unique Length 4,516,347 bp 4,517,824 bp -Model Fit 98.7399% 99.0231% -Read Error Rate 0.100327% 0.100327% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 1e61793..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1088 +0,0 @@ -1 58133229 -2 5293320 -3 443893 -4 57367 -5 17458 -6 7197 -7 3490 -8 1553 -9 896 -10 691 -11 753 -12 1108 -13 1836 -14 2954 -15 4742 -16 6841 -17 9746 -18 13718 -19 18783 -20 24519 -21 31114 -22 38043 -23 45700 -24 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-243 39 -244 41 -245 42 -246 35 -247 21 -248 33 -249 34 -250 36 -251 21 -252 35 -253 34 -254 24 -255 27 -256 34 -257 24 -258 37 -259 37 -260 39 -261 43 -262 25 -263 36 -264 32 -265 31 -266 29 -267 39 -268 32 -269 42 -270 41 -271 30 -272 30 -273 41 -274 35 -275 28 -276 19 -277 31 -278 35 -279 23 -280 22 -281 33 -282 39 -283 34 -284 32 -285 26 -286 24 -287 48 -288 34 -289 39 -290 24 -291 38 -292 34 -293 43 -294 30 -295 38 -296 29 -297 35 -298 30 -299 34 -300 27 -301 25 -302 39 -303 43 -304 18 -305 31 -306 26 -307 31 -308 26 -309 30 -310 28 -311 26 -312 25 -313 30 -314 16 -315 21 -316 31 -317 32 -318 18 -319 21 -320 36 -321 16 -322 22 -323 26 -324 25 -325 20 -326 22 -327 29 -328 24 -329 23 -330 29 -331 31 -332 24 -333 36 -334 32 -335 20 -336 41 -337 23 -338 28 -339 29 -340 23 -341 32 -342 27 -343 28 -344 29 -345 29 -346 31 -347 37 -348 36 -349 32 -350 38 -351 37 -352 34 -353 31 -354 33 -355 36 -356 40 -357 37 -358 40 -359 27 -360 37 -361 33 -362 35 -363 48 -364 49 -365 33 -366 35 -367 38 -368 31 -369 36 -370 39 -371 49 -372 44 -373 27 -374 39 -375 46 -376 35 -377 49 -378 30 -379 34 -380 42 -381 38 -382 53 -383 32 -384 38 -385 47 -386 42 -387 45 -388 55 -389 44 -390 46 -391 41 -392 42 -393 51 -394 50 -395 39 -396 47 -397 45 -398 53 -399 49 -400 46 -401 41 -402 36 -403 53 -404 51 -405 35 -406 30 -407 43 -408 41 -409 34 -410 41 -411 40 -412 33 -413 33 -414 39 -415 38 -416 38 -417 35 -418 40 -419 37 -420 41 -421 38 -422 25 -423 33 -424 35 -425 43 -426 39 -427 37 -428 32 -429 34 -430 44 -431 21 -432 35 -433 43 -434 38 -435 38 -436 42 -437 37 -438 47 -439 43 -440 44 -441 37 -442 35 -443 26 -444 32 -445 29 -446 26 -447 34 -448 26 -449 26 -450 23 -451 24 -452 28 -453 24 -454 21 -455 21 -456 26 -457 14 -458 21 -459 9 -460 14 -461 15 -462 13 -463 14 -464 19 -465 14 -466 16 -467 16 -468 16 -469 18 -470 14 -471 16 -472 14 -473 17 -474 13 -475 13 -476 24 -477 12 -478 9 -479 11 -480 5 -481 14 -482 17 -483 16 -484 7 -485 9 -486 9 -487 10 -488 13 -489 8 -490 11 -491 10 -492 9 -493 5 -494 7 -495 7 -496 10 -497 10 -498 5 -499 6 -500 11 -501 8 -502 6 -503 6 -504 3 -505 4 -506 8 -507 4 -508 4 -509 7 -510 6 -511 4 -512 1 -513 2 -514 4 -515 1 -517 4 -518 2 -519 8 -520 3 -521 7 -522 7 -523 3 -524 4 -525 3 -526 10 -527 4 -528 4 -529 2 -530 6 -531 6 -532 6 -533 8 -534 7 -535 6 -536 9 -537 4 -538 7 -539 9 -540 9 -541 8 -542 6 -543 7 -544 7 -545 10 -546 5 -547 11 -548 8 -549 6 -550 6 -551 7 -552 7 -553 14 -554 3 -555 7 -556 6 -557 4 -558 5 -559 5 -560 6 -561 7 -562 3 -563 4 -564 10 -565 4 -566 7 -567 10 -568 14 -569 9 -570 5 -571 11 -572 11 -573 10 -574 10 -575 13 -576 9 -577 19 -578 10 -579 8 -580 12 -581 14 -582 8 -583 10 -584 12 -585 14 -586 6 -587 11 -588 11 -589 7 -590 19 -591 7 -592 12 -593 16 -594 7 -595 12 -596 6 -597 12 -598 11 -599 5 -600 17 -601 14 -602 5 -603 8 -604 11 -605 11 -606 9 -607 16 -608 12 -609 13 -610 9 -611 4 -612 5 -613 9 -614 11 -615 9 -616 5 -617 5 -618 2 -619 11 -620 6 -621 8 -622 7 -623 12 -624 9 -625 12 -626 4 -627 11 -628 8 -629 9 -630 4 -631 5 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.705e-03 5.775e-04 2.952 0.00324 ** -r 1.008e-02 1.018e-05 990.503 < 2e-16 *** -kmercov 3.248e+01 3.861e-03 8410.692 < 2e-16 *** -bias 8.150e-01 1.976e-03 412.479 < 2e-16 *** -length 4.528e+06 2.726e+03 1661.312 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 281.5 on 859 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.392e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index c716ad9..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b285c32..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eb3cb7e..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 68110379.0621099 -round 1 trimming to 15 trying 4peak model... converged. score: 68103618.3291623 -round 2 trimming to 20 trying 4peak model... converged. score: 68088595.9632031 -round 3 trimming to 25 trying 4peak model... converged. score: 68874896.9488635 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b1ea155..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.00589% 1.00996% -Genome Haploid Length 4,623,372 bp 4,625,572 bp -Genome Repeat Length 103,819 bp 103,868 bp -Genome Unique Length 4,519,554 bp 4,521,704 bp -Model Fit 98.474% 98.7756% -Read Error Rate 0.998839% 0.998839% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 3fd3aeb..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,933 +0,0 @@ -1 97839556 -2 12105577 -3 1504199 -4 204922 -5 52878 -6 25444 -7 14546 -8 8891 -9 6050 -10 5269 -11 5859 -12 7796 -13 11450 -14 16594 -15 23421 -16 32344 -17 42461 -18 53136 -19 63851 -20 74840 -21 84456 -22 93799 -23 100902 -24 105870 -25 107610 -26 107960 -27 106176 -28 101937 -29 96947 -30 91003 -31 85459 -32 79343 -33 74212 -34 70670 -35 68001 -36 67536 -37 68418 -38 71491 -39 76525 -40 83121 -41 90436 -42 98872 -43 109317 -44 116960 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7ba6c66..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.062e-04 7.038e-04 1.288 0.198 -r 1.026e-02 1.267e-05 810.370 <2e-16 *** -kmercov 2.623e+01 4.243e-03 6182.644 <2e-16 *** -bias 6.742e-01 2.273e-03 296.558 <2e-16 *** -length 4.538e+06 3.247e+03 1397.398 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 370.9 on 855 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.247e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f4fa31b..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 13f9e30..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 99f906d..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 118684445.831787 -round 1 trimming to 15 trying 4peak model... converged. score: 118673871.037925 -round 2 trimming to 20 trying 4peak model... converged. score: 123026712.122237 -round 3 trimming to 25 trying 4peak model... converged. score: 173366716.535801 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e6de157..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02395% 1.02902% -Genome Haploid Length 4,640,312 bp 4,643,315 bp -Genome Repeat Length 108,011 bp 108,081 bp -Genome Unique Length 4,532,301 bp 4,535,235 bp -Model Fit 98.2377% 98.5445% -Read Error Rate 1.99381% 1.99381% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index 6fb666e..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,1290 +0,0 @@ -1 7476619 -2 103017 -3 2063 -4 122 -5 71 -6 60 -7 77 -8 184 -9 217 -10 404 -11 681 -12 1141 -13 1804 -14 2389 -15 3471 -16 4416 -17 5980 -18 8229 -19 10587 -20 12795 -21 15994 -22 18427 -23 22878 -24 26227 -25 30162 -26 34219 -27 38438 -28 42649 -29 46265 -30 50406 -31 53940 -32 57541 -33 59723 -34 62581 -35 63352 -36 65139 -37 66868 -38 66986 -39 66475 -40 66105 -41 65476 -42 62866 -43 61416 -44 60508 -45 57496 -46 56449 -47 55749 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index e280524..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.839e-03 8.596e-04 -3.303 0.000996 *** -r 1.032e-02 1.586e-05 650.571 < 2e-16 *** -kmercov 3.945e+01 9.013e-03 4376.865 < 2e-16 *** -bias 2.016e+00 5.285e-03 381.508 < 2e-16 *** -length 4.516e+06 3.803e+03 1187.587 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 350.3 on 867 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.776e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bf7f8b7..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0570c76..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3ced423..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 105044781.16619 -round 1 trimming to 11 trying 4peak model... converged. score: 105042447.444187 -round 2 trimming to 16 trying 4peak model... converged. score: 104931099.189548 -round 3 trimming to 21 trying 4peak model... converged. score: 104537794.809934 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a5faca3..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02834% 1.03468% -Genome Haploid Length 4,588,162 bp 4,592,357 bp -Genome Repeat Length 62,081 bp 62,138 bp -Genome Unique Length 4,526,081 bp 4,530,219 bp -Model Fit 97.7488% 98.0496% -Read Error Rate 0.10264% 0.10264% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 3d714ef..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1109 +0,0 @@ -1 58055773 -2 5324079 -3 459617 -4 59905 -5 18600 -6 8177 -7 3963 -8 1991 -9 1756 -10 2115 -11 2841 -12 4134 -13 6011 -14 8039 -15 11214 -16 14072 -17 18261 -18 22811 -19 27579 -20 33121 -21 39150 -22 44577 -23 49707 -24 55327 -25 60072 -26 64546 -27 68275 -28 71778 -29 74059 -30 75735 -31 76734 -32 77671 -33 77466 -34 75684 -35 74193 -36 73041 -37 70547 -38 68644 -39 67427 -40 65413 -41 64483 -42 64030 -43 63598 -44 63812 -45 64659 -46 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.924e-03 9.266e-04 -3.155 0.00166 ** -r 1.011e-02 1.731e-05 584.167 < 2e-16 *** -kmercov 3.258e+01 8.539e-03 3815.078 < 2e-16 *** -bias 1.685e+00 5.327e-03 316.332 < 2e-16 *** -length 4.526e+06 4.077e+03 1109.936 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 408.9 on 837 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.304e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0692d98..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 88b2b58..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 826b662..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 140048308.550206 -round 1 trimming to 14 trying 4peak model... converged. score: 139974323.605439 -round 2 trimming to 19 trying 4peak model... converged. score: 139944343.753252 -round 3 trimming to 24 trying 4peak model... converged. score: 141663734.727109 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2b0dd9e..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.00801% 1.01493% -Genome Haploid Length 4,604,150 bp 4,608,980 bp -Genome Repeat Length 68,232 bp 68,304 bp -Genome Unique Length 4,535,918 bp 4,540,676 bp -Model Fit 97.7517% 98.0633% -Read Error Rate 1.00057% 1.00057% diff --git 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mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.896e-03 8.246e-04 -2.299 0.0218 * -r 1.025e-02 1.579e-05 649.023 <2e-16 *** -kmercov 2.634e+01 6.589e-03 3997.583 <2e-16 *** -bias 1.349e+00 4.275e-03 315.557 <2e-16 *** -length 4.525e+06 3.549e+03 1275.212 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 394 on 868 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.261e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d36fe26..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index da2d5ca..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ae7aba8..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 135571698.800604 -round 1 trimming to 14 trying 4peak model... converged. score: 134751448.317367 -round 2 trimming to 19 trying 4peak model... converged. score: 137115033.909692 -round 3 trimming to 24 trying 4peak model... converged. score: 173254986.277817 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d774ef6..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02176% 1.02808% -Genome Haploid Length 4,618,762 bp 4,623,386 bp -Genome Repeat Length 87,343 bp 87,431 bp -Genome Unique Length 4,531,419 bp 4,535,956 bp -Model Fit 98.0178% 98.3336% -Read Error Rate 1.99552% 1.99552% diff --git 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.623e-03 1.079e-03 -5.21 2.34e-07 *** -r 1.033e-02 2.126e-05 486.06 < 2e-16 *** -kmercov 3.959e+01 1.428e-02 2773.07 < 2e-16 *** -bias 3.026e+00 1.013e-02 298.74 < 2e-16 *** -length 4.507e+06 4.427e+03 1018.05 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 396.7 on 910 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.326e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d342e14..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 45ceb05..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 929f69a..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 143446318.305982 -round 1 trimming to 10 trying 4peak model... converged. score: 143411199.379017 -round 2 trimming to 15 trying 4peak model... converged. score: 142966390.584464 -round 3 trimming to 20 trying 4peak model... converged. score: 142447079.763213 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a24c1f3..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02906% 1.03756% -Genome Haploid Length 4,571,251 bp 4,577,849 bp -Genome Repeat Length 43,298 bp 43,360 bp -Genome Unique Length 4,527,953 bp 4,534,489 bp -Model Fit 97.4956% 97.8122% -Read Error Rate 0.102875% 0.102875% diff --git 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2054d19..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.240e-03 1.083e-03 -4.836 1.55e-06 *** -r 1.034e-02 2.171e-05 476.488 < 2e-16 *** -kmercov 3.272e+01 1.231e-02 2657.179 < 2e-16 *** -bias 2.490e+00 9.184e-03 271.137 < 2e-16 *** -length 4.510e+06 4.390e+03 1027.391 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 429.1 on 904 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.359e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d15e5a7..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a6963df..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9f28975..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 167408450.283269 -round 1 trimming to 13 trying 4peak model... converged. score: 166704575.186706 -round 2 trimming to 18 trying 4peak model... converged. score: 166478442.307341 -round 3 trimming to 23 trying 4peak model... converged. score: 169654621.57389 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 077eda0..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03005% 1.03873% -Genome Haploid Length 4,583,788 bp 4,590,694 bp -Genome Repeat Length 54,572 bp 54,654 bp -Genome Unique Length 4,529,216 bp 4,536,040 bp -Model Fit 97.6503% 97.9842% -Read Error Rate 1.00131% 1.00131% diff --git 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length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.712e-03 1.017e-03 -5.616 2.61e-08 *** -r 1.026e-02 2.084e-05 492.241 < 2e-16 *** -kmercov 2.642e+01 9.790e-03 2698.815 < 2e-16 *** -bias 2.010e+00 7.718e-03 260.390 < 2e-16 *** -length 4.515e+06 4.045e+03 1116.176 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 435.6 on 901 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.37e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index c111253..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 64f2110..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 193b6dc..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 173752652.382992 -round 1 trimming to 14 trying 4peak model... converged. score: 170967299.935324 -round 2 trimming to 19 trying 4peak model... converged. score: 177402901.731195 -round 3 trimming to 24 trying 4peak model... converged. score: 242386358.547827 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 611a0c8..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02188% 1.03022% -Genome Haploid Length 4,601,611 bp 4,608,436 bp -Genome Repeat Length 64,845 bp 64,941 bp -Genome Unique Length 4,536,766 bp 4,543,495 bp -Model Fit 97.6385% 97.9925% -Read Error Rate 1.99725% 1.99725% diff --git 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8bd2438..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.351e-04 5.221e-04 1.217 0.224 -r 2.025e-02 1.183e-05 1711.396 <2e-16 *** -kmercov 3.930e+01 3.598e-03 10921.207 <2e-16 *** -bias 9.878e-01 1.479e-03 667.679 <2e-16 *** -length 4.531e+06 1.911e+03 2371.115 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 209.3 on 878 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 8.372e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ed80193..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index fbaa8a5..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9617cf1..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... round 0 trimming to 317 trying 4peak model... round 0 trimming to 520 trying 4peak model... round 0 trimming to 554 trying 4peak model... round 0 trimming to 562 trying 4peak model... round 0 trimming to 574 trying 4peak model... round 0 trimming to 609 trying 4peak model... round 0 trimming to 624 trying 4peak model... round 0 trimming to 628 trying 4peak model... round 0 trimming to 629 trying 4peak model... round 0 trimming to 663 trying 4peak model... round 0 trimming to 676 trying 4peak model... round 0 trimming to 684 trying 4peak model... round 0 trimming to 687 trying 4peak model... round 0 trimming to 691 trying 4peak model... round 0 trimming to 694 trying 4peak model... round 0 trimming to 736 trying 4peak model... round 0 trimming to 750 trying 4peak model... round 0 trimming to 756 trying 4peak model... round 0 trimming to 1014 trying 4peak model... round 0 trimming to 1054 trying 4peak model... round 0 trimming to 1057 trying 4peak model... round 0 trimming to 1096 trying 4peak model... round 0 trimming to 1140 trying 4peak model... converged. score: 33611535.4685853 -round 1 trimming to 11 trying 4peak model... round 1 trimming to 322 trying 4peak model... round 1 trimming to 525 trying 4peak model... round 1 trimming to 559 trying 4peak model... round 1 trimming to 567 trying 4peak model... round 1 trimming to 579 trying 4peak model... round 1 trimming to 614 trying 4peak model... round 1 trimming to 629 trying 4peak model... round 1 trimming to 633 trying 4peak model... round 1 trimming to 634 trying 4peak model... round 1 trimming to 668 trying 4peak model... round 1 trimming to 681 trying 4peak model... round 1 trimming to 689 trying 4peak model... round 1 trimming to 692 trying 4peak model... round 1 trimming to 696 trying 4peak model... round 1 trimming to 699 trying 4peak model... round 1 trimming to 741 trying 4peak model... round 1 trimming to 755 trying 4peak model... round 1 trimming to 761 trying 4peak model... round 1 trimming to 1019 trying 4peak model... round 1 trimming to 1059 trying 4peak model... round 1 trimming to 1062 trying 4peak model... round 1 trimming to 1101 trying 4peak model... round 1 trimming to 1145 trying 4peak model... converged. score: 33611417.0685268 -round 2 trimming to 16 trying 4peak model... round 2 trimming to 327 trying 4peak model... round 2 trimming to 530 trying 4peak model... round 2 trimming to 564 trying 4peak model... round 2 trimming to 572 trying 4peak model... round 2 trimming to 584 trying 4peak model... round 2 trimming to 619 trying 4peak model... round 2 trimming to 634 trying 4peak model... round 2 trimming to 638 trying 4peak model... round 2 trimming to 639 trying 4peak model... round 2 trimming to 673 trying 4peak model... round 2 trimming to 686 trying 4peak model... round 2 trimming to 694 trying 4peak model... round 2 trimming to 697 trying 4peak model... round 2 trimming to 701 trying 4peak model... round 2 trimming to 704 trying 4peak model... round 2 trimming to 746 trying 4peak model... round 2 trimming to 760 trying 4peak model... round 2 trimming to 766 trying 4peak model... round 2 trimming to 1024 trying 4peak model... round 2 trimming to 1064 trying 4peak model... round 2 trimming to 1067 trying 4peak model... round 2 trimming to 1106 trying 4peak model... round 2 trimming to 1150 trying 4peak model... converged. score: 33591809.6914118 -round 3 trimming to 21 trying 4peak model... round 3 trimming to 332 trying 4peak model... round 3 trimming to 535 trying 4peak model... round 3 trimming to 569 trying 4peak model... round 3 trimming to 577 trying 4peak model... round 3 trimming to 589 trying 4peak model... round 3 trimming to 624 trying 4peak model... round 3 trimming to 639 trying 4peak model... round 3 trimming to 643 trying 4peak model... round 3 trimming to 644 trying 4peak model... round 3 trimming to 678 trying 4peak model... round 3 trimming to 691 trying 4peak model... round 3 trimming to 699 trying 4peak model... round 3 trimming to 702 trying 4peak model... round 3 trimming to 706 trying 4peak model... round 3 trimming to 709 trying 4peak model... round 3 trimming to 751 trying 4peak model... round 3 trimming to 765 trying 4peak model... round 3 trimming to 771 trying 4peak model... round 3 trimming to 1029 trying 4peak model... round 3 trimming to 1069 trying 4peak model... round 3 trimming to 1072 trying 4peak model... round 3 trimming to 1111 trying 4peak model... round 3 trimming to 1155 trying 4peak model... converged. score: 33261813.2707723 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 06a105d..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.02274% 2.02748% -Genome Haploid Length 4,609,163 bp 4,610,851 bp -Genome Repeat Length 81,620 bp 81,650 bp -Genome Unique Length 4,527,543 bp 4,529,202 bp -Model Fit 98.9135% 99.1497% -Read Error Rate 0.102618% 0.102618% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 03b4bdc..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1085 +0,0 @@ -1 59037889 -2 4909002 -3 396708 -4 49522 -5 14323 -6 5833 -7 2580 -8 1194 -9 736 -10 733 -11 1225 -12 1969 -13 3501 -14 5448 -15 8264 -16 12615 -17 18165 -18 25007 -19 33740 -20 44099 -21 56588 -22 70229 -23 84798 -24 99106 -25 113783 -26 126656 -27 139926 -28 149386 -29 157604 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dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.669e-03 6.255e-04 -2.668 0.00776 ** -r 2.028e-02 1.431e-05 1417.737 < 2e-16 *** -kmercov 3.253e+01 3.965e-03 8205.865 < 2e-16 *** -bias 8.356e-01 1.710e-03 488.599 < 2e-16 *** -length 4.536e+06 2.257e+03 2009.645 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 269.5 on 906 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.102e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 88d6eca..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a8a8015..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 664f4e7..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 65912995.1016125 -round 1 trimming to 15 trying 4peak model... converged. score: 65881196.2453919 -round 2 trimming to 20 trying 4peak model... converged. score: 65840952.9654896 -round 3 trimming to 25 trying 4peak model... converged. score: 67792032.4329947 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8fd5f32..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.02525% 2.03098% -Genome Haploid Length 4,622,146 bp 4,624,400 bp -Genome Repeat Length 80,526 bp 80,566 bp -Genome Unique Length 4,541,620 bp 4,543,834 bp -Model Fit 98.5403% 98.7874% -Read Error Rate 0.996787% 0.996787% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist deleted file mode 100644 index 66d257a..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist +++ /dev/null @@ -1,933 +0,0 @@ -1 99906077 -2 11358825 -3 1344166 -4 178677 -5 46012 -6 21322 -7 11658 -8 7564 -9 5891 -10 6379 -11 8771 -12 13621 -13 20549 -14 30812 -15 43617 -16 58279 -17 75604 -18 94904 -19 114281 -20 133977 -21 153497 -22 169920 -23 181872 -24 188806 -25 193993 -26 192578 -27 188850 -28 180605 -29 168827 -30 155575 -31 142760 -32 128662 -33 116418 -34 105143 -35 95026 -36 87599 -37 81945 -38 79630 -39 79012 -40 80582 -41 83646 -42 88665 -43 93228 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index ce706d4..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.709e-03 8.412e-04 -3.221 0.00133 ** -r 2.026e-02 1.949e-05 1039.653 < 2e-16 *** -kmercov 2.631e+01 4.828e-03 5449.513 < 2e-16 *** -bias 6.672e-01 2.105e-03 316.932 < 2e-16 *** -length 4.539e+06 2.970e+03 1528.435 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 392.9 on 857 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.028e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1af17d8..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c176ba9..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9fae538..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 132426525.543797 -round 1 trimming to 14 trying 4peak model... converged. score: 132257109.488402 -round 2 trimming to 19 trying 4peak model... converged. score: 135830970.636786 -round 3 trimming to 24 trying 4peak model... converged. score: 235916621.698321 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 18d76e6..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.02194% 2.02974% -Genome Haploid Length 4,628,925 bp 4,632,324 bp -Genome Repeat Length 80,309 bp 80,368 bp -Genome Unique Length 4,548,615 bp 4,551,955 bp -Model Fit 98.1355% 98.3926% -Read Error Rate 1.99148% 1.99148% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist deleted file mode 100644 index ad104b1..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist +++ /dev/null @@ -1,1333 +0,0 @@ -1 7499409 -2 93191 -3 1731 -4 102 -5 15 -6 86 -7 125 -8 330 -9 451 -10 712 -11 1360 -12 2073 -13 3022 -14 4736 -15 6293 -16 8094 -17 10818 -18 14484 -19 18740 -20 22922 -21 27336 -22 34193 -23 40271 -24 46579 -25 53649 -26 61948 -27 69177 -28 77459 -29 84100 -30 91076 -31 97709 -32 103235 -33 107788 -34 111539 -35 115018 -36 117504 -37 118396 -38 118417 -39 118555 -40 116309 -41 113457 -42 111406 -43 107151 -44 102824 -45 98797 -46 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r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -9.324e-03 9.650e-04 -9.662 <2e-16 *** -r 2.055e-02 2.321e-05 885.337 <2e-16 *** -kmercov 3.964e+01 1.010e-02 3925.603 <2e-16 *** -bias 2.041e+00 4.695e-03 434.703 <2e-16 *** -length 4.514e+06 3.215e+03 1404.178 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 344.6 on 915 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.788e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f83d5f4..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 5063b2d..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 77725f5..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... round 0 trimming to 516 trying 4peak model... round 0 trimming to 525 trying 4peak model... round 0 trimming to 542 trying 4peak model... round 0 trimming to 546 trying 4peak model... round 0 trimming to 564 trying 4peak model... round 0 trimming to 681 trying 4peak model... converged. score: 102479025.692132 -round 1 trimming to 10 trying 4peak model... round 1 trimming to 521 trying 4peak model... round 1 trimming to 530 trying 4peak model... round 1 trimming to 547 trying 4peak model... round 1 trimming to 551 trying 4peak model... round 1 trimming to 569 trying 4peak model... round 1 trimming to 686 trying 4peak model... converged. score: 102470617.394168 -round 2 trimming to 15 trying 4peak model... round 2 trimming to 526 trying 4peak model... round 2 trimming to 535 trying 4peak model... round 2 trimming to 552 trying 4peak model... round 2 trimming to 556 trying 4peak model... round 2 trimming to 574 trying 4peak model... round 2 trimming to 691 trying 4peak model... converged. score: 101867849.353114 -round 3 trimming to 20 trying 4peak model... round 3 trimming to 531 trying 4peak model... round 3 trimming to 540 trying 4peak model... round 3 trimming to 557 trying 4peak model... round 3 trimming to 561 trying 4peak model... round 3 trimming to 579 trying 4peak model... round 3 trimming to 696 trying 4peak model... converged. score: 98387060.9899378 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c420ea7..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.05021% 2.0595% -Genome Haploid Length 4,566,859 bp 4,571,515 bp -Genome Repeat Length 17,971 bp 17,989 bp -Genome Unique Length 4,548,888 bp 4,553,525 bp -Model Fit 97.9859% 98.2434% -Read Error Rate 0.105076% 0.105076% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index 1f422f0..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1136 +0,0 @@ -1 58929632 -2 4944750 -3 401827 -4 49285 -5 14917 -6 6132 -7 3184 -8 2308 -9 2507 -10 3424 -11 4854 -12 7530 -13 10612 -14 14373 -15 19310 -16 25634 -17 32717 -18 42440 -19 50708 -20 60496 -21 70397 -22 81743 -23 91205 -24 102511 -25 112146 -26 120328 -27 126255 -28 132357 -29 136622 -30 139869 -31 140683 -32 141000 -33 138287 -34 136187 -35 131648 -36 126535 -37 121697 -38 115632 -39 109390 -40 103455 -41 97532 -42 91779 -43 87068 -44 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.008e-02 1.096e-03 -9.194 <2e-16 *** -r 2.079e-02 2.700e-05 769.928 <2e-16 *** -kmercov 3.280e+01 1.048e-02 3129.632 <2e-16 *** -bias 1.655e+00 5.234e-03 316.198 <2e-16 *** -length 4.517e+06 3.682e+03 1226.750 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 422.1 on 949 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.208e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 80da0e6..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9308aa3..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1784267..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 174516265.860245 -round 1 trimming to 13 trying 4peak model... converged. score: 173593148.754286 -round 2 trimming to 18 trying 4peak model... converged. score: 171074416.402189 -round 3 trimming to 23 trying 4peak model... converged. score: 170740940.224912 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8fc3a6c..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.07346% 2.08426% -Genome Haploid Length 4,580,915 bp 4,586,773 bp -Genome Repeat Length 27,500 bp 27,535 bp -Genome Unique Length 4,553,415 bp 4,559,238 bp -Model Fit 97.664% 97.9379% -Read Error Rate 0.999175% 0.999175% diff --git 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mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -7.852e-03 1.023e-03 -7.674 4.47e-14 *** -r 2.050e-02 2.583e-05 793.738 < 2e-16 *** -kmercov 2.647e+01 8.424e-03 3141.776 < 2e-16 *** -bias 1.344e+00 4.144e-03 324.200 < 2e-16 *** -length 4.524e+06 3.313e+03 1365.547 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 427.6 on 868 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 9.946e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d35877b..0000000 Binary files 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a19698b..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 161980042.164766 -round 1 trimming to 13 trying 4peak model... converged. score: 157763323.417895 -round 2 trimming to 18 trying 4peak model... converged. score: 158182798.548573 -round 3 trimming to 23 trying 4peak model... converged. score: 232144627.485592 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b0e8fd9..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.04476% 2.05509% -Genome Haploid Length 4,598,130 bp 4,603,988 bp -Genome Repeat Length 45,620 bp 45,678 bp -Genome Unique Length 4,552,510 bp 4,558,310 bp -Model Fit 97.9357% 98.2102% -Read Error Rate 1.9932% 1.9932% diff --git 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(2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.487e-02 1.377e-03 -10.8 <2e-16 *** -r 2.093e-02 3.691e-05 567.1 <2e-16 *** -kmercov 3.992e+01 1.958e-02 2038.6 <2e-16 *** -bias 3.037e+00 1.022e-02 297.2 <2e-16 *** -length 4.493e+06 4.186e+03 1073.4 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 436.6 on 912 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 6.949e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bcaed17..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 32d1bbe..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c212219..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 173116787.956154 -round 1 trimming to 9 trying 4peak model... converged. score: 172905694.271078 -round 2 trimming to 14 trying 4peak model... converged. score: 168321811.068733 -round 3 trimming to 19 trying 4peak model... converged. score: 153279683.040921 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7987ae0..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08556% 2.10032% -Genome Haploid Length 4,529,454 bp 4,538,350 bp -Genome Repeat Length -17,488 bp -17,522 bp -Genome Unique Length 4,546,942 bp 4,555,872 bp -Model Fit 97.5242% 97.8036% -Read Error Rate 0.108202% 0.108202% diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist deleted file mode 100644 index f2ffb13..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1138 +0,0 @@ -1 58791771 -2 5003575 -3 414024 -4 52656 -5 15717 -6 7560 -7 5549 -8 5043 -9 6425 -10 8637 -11 11974 -12 15354 -13 19470 -14 25232 -15 30821 -16 37533 -17 44762 -18 51943 -19 60845 -20 68133 -21 76190 -22 84898 -23 91149 -24 99232 -25 105963 -26 111319 -27 115771 -28 119372 -29 122466 -30 125161 -31 124962 -32 125096 -33 123770 -34 122214 -35 119447 -36 116517 -37 113376 -38 110013 -39 106938 -40 103457 -41 99586 -42 96822 -43 93188 -44 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.882e-02 1.380e-03 -13.64 <2e-16 *** -r 2.100e-02 3.806e-05 551.80 <2e-16 *** -kmercov 3.310e+01 1.734e-02 1909.27 <2e-16 *** -bias 2.546e+00 9.719e-03 261.94 <2e-16 *** -length 4.495e+06 4.131e+03 1088.12 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 465.7 on 915 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 9.158e-07 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a1cfda0..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1e33a48..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1586582..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 214079796.700863 -round 1 trimming to 13 trying 4peak model... converged. score: 205899604.902921 -round 2 trimming to 18 trying 4peak model... converged. score: 197507485.493919 -round 3 trimming to 23 trying 4peak model... converged. score: 200011101.977157 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ce8c951..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.09241% 2.10763% -Genome Haploid Length 4,533,387 bp 4,542,895 bp -Genome Repeat Length -30,723 bp -30,787 bp -Genome Unique Length 4,564,110 bp 4,573,682 bp -Model Fit 97.3432% 97.6316% -Read Error Rate 1.00256% 1.00256% diff --git 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a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 014ff16..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.897e-02 1.520e-03 -12.48 <2e-16 *** -r 2.089e-02 4.347e-05 480.47 <2e-16 *** -kmercov 2.672e+01 1.660e-02 1609.95 <2e-16 *** -bias 2.061e+00 9.323e-03 221.06 <2e-16 *** -length 4.507e+06 4.442e+03 1014.61 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 552.1 on 861 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.52e-06 - diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6e96ba6..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index a3debfc..0000000 Binary files a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 12a7973..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 278366270.997899 -round 1 trimming to 13 trying 4peak model... converged. score: 258592989.819845 -round 2 trimming to 18 trying 4peak model... converged. score: 265283026.398874 -round 3 trimming to 23 trying 4peak model... converged. score: 431837373.181273 -done diff --git a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 20eaf58..0000000 --- a/analysis/simulation_results_100x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov100_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08004% 2.09743% -Genome Haploid Length 4,549,406 bp 4,560,723 bp -Genome Repeat Length -26,020 bp -26,085 bp -Genome Unique Length 4,575,426 bp 4,586,808 bp -Model Fit 97.2914% 97.6147% -Read Error Rate 1.99536% 1.99536% diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index f5874f5..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,1796 +0,0 @@ -1 22169188 -2 4746701 -3 6880544 -4 8857360 -5 10301267 -6 10983391 -7 10947485 -8 10250677 -9 9182640 -10 7844144 -11 6449505 -12 5134631 -13 3980871 -14 3010940 -15 2227730 -16 1621746 -17 1166090 -18 849447 -19 610346 -20 447390 -21 327850 -22 244715 -23 186477 -24 146061 -25 116470 -26 95770 -27 80757 -28 69057 -29 59197 -30 52200 -31 45824 -32 41464 -33 37191 -34 33305 -35 30342 -36 27815 -37 25299 -38 23016 -39 21899 -40 20352 -41 18606 -42 17314 -43 16213 -44 14999 -45 14198 -46 13485 -47 12704 -48 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a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist 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unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist 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a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9a74081..0000000 Binary files a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.485e-01 1.926e-02 23.29 <2e-16 *** -r 3.998e-02 1.189e-03 33.64 <2e-16 *** -kmercov 3.004e+01 2.295e-01 130.92 <2e-16 *** -bias 2.048e+00 6.714e-02 30.50 <2e-16 *** -length 7.816e+05 9.035e+03 86.50 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 533.6 on 966 degrees of freedom - -Number of iterations to convergence: 19 -Achieved convergence tolerance: 7.516e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 38ff860..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e098b7e..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 299f427..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 354662475.246053 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8daf165..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.76054% 4.23599% -Genome Haploid Length 2,192,000 bp 2,260,013 bp -Genome Repeat Length 1,653,098 bp 1,704,390 bp -Genome Unique Length 538,902 bp 555,623 bp -Model Fit 75.2903% 90.3219% -Read Error Rate 9.50398% 9.50398% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index e6da2bd..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2075 +0,0 @@ -1 197306751 -2 12597223 -3 11768685 -4 13417183 -5 14141785 -6 13742395 -7 12422765 -8 10573423 -9 8532943 -10 6570967 -11 4857361 -12 3471719 -13 2426101 -14 1650840 -15 1105278 -16 734935 -17 488377 -18 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index ea89a90..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.058e-01 1.240e-02 32.72 <2e-16 *** -r 3.457e-02 6.826e-04 50.65 <2e-16 *** -kmercov 2.991e+01 2.448e-01 122.15 <2e-16 *** -bias 2.186e+00 6.747e-02 32.39 <2e-16 *** -length 6.959e+05 5.778e+03 120.44 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 417.7 on 965 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 8.025e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6679d2d..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4e26f2b..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 36f00db..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 563033358.808977 -round 3 trimming to 30 trying 4peak model... converged. score: 199937175.202605 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cc4a127..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.32083% 3.59388% -Genome Haploid Length 1,792,145 bp 1,851,809 bp -Genome Repeat Length 1,309,515 bp 1,353,112 bp -Genome Unique Length 482,629 bp 498,697 bp -Model Fit 77.2537% 91.5682% -Read Error Rate 10.401% 10.401% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 3b95c46..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1800 +0,0 @@ -1 351693937 -2 22087690 -3 16797712 -4 17034526 -5 16021937 -6 13801857 -7 11056821 -8 8294432 -9 5923874 -10 4029971 -11 2652772 -12 1698074 -13 1068900 -14 669068 -15 422198 -16 274515 -17 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.979e-01 1.321e-02 30.13 <2e-16 *** -r 3.584e-02 7.476e-04 47.93 <2e-16 *** -kmercov 3.064e+01 2.621e-01 116.88 <2e-16 *** -bias 2.617e+00 8.405e-02 31.14 <2e-16 *** -length 5.811e+05 4.798e+03 121.11 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 311.6 on 938 degrees of freedom - -Number of iterations to convergence: 19 -Achieved convergence tolerance: 4.27e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 206eec4..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index a054a83..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index dcf6f88..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 249325804.312005 -round 3 trimming to 30 trying 4peak model... converged. score: 91046900.1465727 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9c7e08f..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.43402% 3.73307% -Genome Haploid Length 1,348,543 bp 1,395,498 bp -Genome Repeat Length 939,390 bp 972,098 bp -Genome Unique Length 409,153 bp 423,400 bp -Model Fit 80.5805% 93.2857% -Read Error Rate 11.5028% 11.5028% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 34e202c..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2383 +0,0 @@ -1 26740652 -2 6940592 -3 8382518 -4 9450717 -5 10017440 -6 10160786 -7 9842350 -8 9214456 -9 8355787 -10 7348262 -11 6329456 -12 5316732 -13 4376052 -14 3548445 -15 2817655 -16 2212952 -17 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b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0ba10a9..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.200e-01 1.488e-02 28.22 <2e-16 *** -r 3.786e-02 8.881e-04 42.63 <2e-16 *** -kmercov 2.952e+01 2.306e-01 128.05 <2e-16 *** -bias 2.012e+00 6.153e-02 32.70 <2e-16 *** -length 7.085e+05 6.478e+03 109.37 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 444.1 on 966 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 4.196e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 548f215..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 47d8400..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8a2a575..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 252307983.972974 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c77a802..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.60849% 3.96372% -Genome Haploid Length 1,847,989 bp 1,906,633 bp -Genome Repeat Length 1,353,048 bp 1,395,985 bp -Genome Unique Length 494,941 bp 510,648 bp -Model Fit 76.8116% 90.7376% -Read Error Rate 10.3271% 10.3271% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 668fe57..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1810 +0,0 @@ -1 352421084 -2 23063484 -3 15573360 -4 14756070 -5 13492279 -6 11743709 -7 9744820 -8 7757294 -9 5950304 -10 4429367 -11 3216881 -12 2283210 -13 1593495 -14 1093067 -15 745646 -16 508735 -17 347560 -18 243765 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.086e-01 1.510e-02 27.06 <2e-16 *** -r 3.857e-02 9.163e-04 42.10 <2e-16 *** -kmercov 2.413e+01 1.942e-01 124.27 <2e-16 *** -bias 1.451e+00 4.935e-02 29.40 <2e-16 *** -length 7.190e+05 6.592e+03 109.07 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 496.3 on 941 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 3.186e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a50228f..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 94eabcf..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3cb2f34..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 710758719.381787 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e7107a8..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.67414% 4.04066% -Genome Haploid Length 1,865,151 bp 1,926,167 bp -Genome Repeat Length 1,355,262 bp 1,399,598 bp -Genome Unique Length 509,889 bp 526,569 bp -Model Fit 76.2596% 89.5367% -Read Error Rate 11.1452% 11.1452% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 26e48be..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2375 +0,0 @@ -1 26290538 -2 6929151 -3 8327338 -4 8898432 -5 8971518 -6 8789440 -7 8435402 -8 7930277 -9 7253947 -10 6527275 -11 5755280 -12 5001532 -13 4279713 -14 3611232 -15 3000360 -16 2480204 -17 2021751 -18 1628645 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b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8980a20..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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-21580 1 -21707 1 -21862 1 -21879 1 -21901 1 -21956 1 -22190 1 -22221 1 -22419 1 -27578 1 -28335 1 -30961 1 -32128 1 -38247 1 -48872 1 diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index a66da2d..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.350e-01 1.747e-02 24.90 <2e-16 *** -r 3.897e-02 1.061e-03 36.71 <2e-16 *** -kmercov 3.005e+01 2.390e-01 125.72 <2e-16 *** -bias 2.144e+00 7.013e-02 30.57 <2e-16 *** -length 7.410e+05 7.723e+03 95.95 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 482.4 on 966 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 6.453e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dbb5ea9..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index c00e9ff..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6b561fb..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 294815847.208168 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7495c91..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.68438% 4.10893% -Genome Haploid Length 2,013,795 bp 2,078,904 bp -Genome Repeat Length 1,500,044 bp 1,548,543 bp -Genome Unique Length 513,751 bp 530,361 bp -Model Fit 76.2494% 90.7343% -Read Error Rate 9.87651% 9.87651% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index e7374e8..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1959 +0,0 @@ -1 203732955 -2 18228318 -3 16689209 -4 16801952 -5 15959064 -6 14315829 -7 12204770 -8 9946221 -9 7769013 -10 5855861 -11 4269954 -12 3022917 -13 2088063 -14 1417908 -15 950725 -16 628182 -17 421087 -18 284580 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0be0e64..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.976e-01 1.326e-02 29.98 <2e-16 *** -r 3.606e-02 7.542e-04 47.82 <2e-16 *** -kmercov 3.057e+01 2.554e-01 119.66 <2e-16 *** -bias 2.479e+00 7.854e-02 31.56 <2e-16 *** -length 6.460e+05 5.416e+03 119.29 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 362.3 on 960 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 5.548e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 29c207b..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 20d88b5..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1b1eade..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 932399894.03805 -round 3 trimming to 30 trying 4peak model... converged. score: 126022661.946585 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c9f7caa..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.45561% 3.75727% -Genome Haploid Length 1,582,145 bp 1,635,931 bp -Genome Repeat Length 1,126,362 bp 1,164,653 bp -Genome Unique Length 455,783 bp 471,277 bp -Model Fit 78.89% 92.5801% -Read Error Rate 10.8361% 10.8361% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index f9d1c92..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1701 +0,0 @@ -1 360660538 -2 27654995 -3 21013816 -4 19285747 -5 16625629 -6 13486949 -7 10313336 -8 7520828 -9 5254302 -10 3535797 -11 2309388 -12 1468842 -13 923952 -14 579413 -15 370356 -16 243253 -17 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mode 100644 index 69ff1f2..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.006e-01 1.426e-02 28.09 <2e-16 *** -r 3.635e-02 8.134e-04 44.69 <2e-16 *** -kmercov 2.484e+01 2.257e-01 110.08 <2e-16 *** -bias 1.860e+00 6.723e-02 27.67 <2e-16 *** -length 6.540e+05 5.754e+03 113.65 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 413.4 on 944 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 7.112e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 56b121e..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index a3f143e..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index facce0f..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 212542155.220081 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8d494d5..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.47227% 3.79764% -Genome Haploid Length 1,593,643 bp 1,652,624 bp -Genome Repeat Length 1,133,452 bp 1,175,401 bp -Genome Unique Length 460,192 bp 477,223 bp -Model Fit 78.6365% 91.7162% -Read Error Rate 11.6813% 11.6813% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 0753a4d..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2251 +0,0 @@ -1 30083101 -2 11099983 -3 12221879 -4 12487278 -5 12228900 -6 11605413 -7 10656343 -8 9535393 -9 8309593 -10 7107480 -11 5962611 -12 4897743 -13 3972591 -14 3181352 -15 2516730 -16 1950652 -17 1502078 -18 1147293 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b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index bb19c46..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1976 +0,0 @@ -1 203768074 -2 18203962 -3 15341887 -4 14689692 -5 13646840 -6 12205911 -7 10582469 -8 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mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.029e-01 1.419e-02 28.39 <2e-16 *** -r 3.730e-02 8.297e-04 44.95 <2e-16 *** -kmercov 2.969e+01 2.492e-01 119.17 <2e-16 *** -bias 2.201e+00 6.824e-02 32.26 <2e-16 *** -length 6.664e+05 5.842e+03 114.07 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 395.6 on 957 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 8.263e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9bd93bc..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index d44cf87..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8f03ab1..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 197247271.45577 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 22215bc..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.56405% 3.89593% -Genome Haploid Length 1,655,938 bp 1,712,470 bp -Genome Repeat Length 1,184,762 bp 1,225,208 bp -Genome Unique Length 471,176 bp 487,261 bp -Model Fit 77.6345% 90.9058% -Read Error Rate 10.7646% 10.7646% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 7be7a0d..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1702 +0,0 @@ -1 359807364 -2 27103430 -3 18798090 -4 16667585 -5 14375836 -6 11910417 -7 9500304 -8 7336711 -9 5502059 -10 4022210 -11 2878185 -12 2026642 -13 1403150 -14 955970 -15 651228 -16 444779 -17 304541 -18 213469 -19 153127 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.050e-01 1.523e-02 26.59 <2e-16 *** -r 3.832e-02 9.116e-04 42.03 <2e-16 *** -kmercov 2.407e+01 2.102e-01 114.48 <2e-16 *** -bias 1.600e+00 5.521e-02 28.98 <2e-16 *** -length 6.807e+05 6.169e+03 110.33 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 444.7 on 946 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 7.584e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ad0741b..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index ac9c33c..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f19dcc3..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 566642250.626284 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a4f1937..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.64954% 4.01418% -Genome Haploid Length 1,687,092 bp 1,747,086 bp -Genome Repeat Length 1,204,145 bp 1,246,965 bp -Genome Unique Length 482,947 bp 500,121 bp -Model Fit 77.4903% 90.183% -Read Error Rate 11.5763% 11.5763% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index e3ae9b9..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2239 +0,0 @@ -1 27966306 -2 9748040 -3 11371792 -4 11478768 -5 10877251 -6 10133433 -7 9283348 -8 8428291 -9 7491923 -10 6536280 -11 5611041 -12 4764247 -13 4004186 -14 3338285 -15 2752737 -16 2238225 -17 1814337 -18 1455118 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index ce8b7ab..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.230e-01 1.978e-02 21.39 <2e-16 *** -r 4.341e-02 1.341e-03 32.38 <2e-16 *** -kmercov 2.798e+01 2.088e-01 134.01 <2e-16 *** -bias 1.600e+00 4.733e-02 33.81 <2e-16 *** -length 7.207e+05 8.224e+03 87.63 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 485.3 on 960 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 6.863e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b2ab9c3..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index c062a9b..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 93666ff..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 1692187992.87227 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b539f08..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 4.07273% 4.60896% -Genome Haploid Length 1,862,351 bp 1,918,782 bp -Genome Repeat Length 1,342,206 bp 1,382,876 bp -Genome Unique Length 520,145 bp 535,906 bp -Model Fit 73.7496% 85.3513% -Read Error Rate 10.5249% 10.5249% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index ff42f8e..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1685 +0,0 @@ -1 356440532 -2 25953329 -3 17147871 -4 14891018 -5 12808012 -6 10784621 -7 8846417 -8 7068565 -9 5530958 -10 4245946 -11 3204431 -12 2376602 -13 1752301 -14 1273754 -15 916989 -16 657925 -17 473838 -18 339304 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,24 +0,0 @@ - -Formula: y ~ ((2 * (1 - d) * (1 - (1 - r)^k)) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + ((d * (1 - (1 - r)^k)^2) + (1 - - 2 * d) * ((1 - r)^k)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.869e-01 5.922e-03 48.44 <2e-16 *** -r 3.913e-02 7.090e-04 55.19 <2e-16 *** -kmercov 3.015e+01 1.890e-01 159.49 <2e-16 *** -bias 2.471e+00 5.799e-02 42.61 <2e-16 *** -length 7.838e+05 6.784e+03 115.55 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 227 on 1650 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 7.311e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0735264..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index d8183b0..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 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size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.214e-01 1.537e-02 27.42 <2e-16 *** -r 3.792e-02 9.144e-04 41.47 <2e-16 *** -kmercov 2.992e+01 2.397e-01 124.79 <2e-16 *** -bias 2.185e+00 6.869e-02 31.81 <2e-16 *** -length 7.044e+05 6.529e+03 107.89 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 429.7 on 965 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 7.825e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8661e4d..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index d24528d..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0aa83d2..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 237613398.45165 -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 24facda..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.60886% 3.97463% -Genome Haploid Length 1,837,539 bp 1,897,397 bp -Genome Repeat Length 1,346,145 bp 1,389,996 bp -Genome Unique Length 491,394 bp 507,401 bp -Model Fit 77.2508% 91.3706% -Read Error Rate 10.2929% 10.2929% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index fbe8302..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1842 +0,0 @@ -1 209852715 -2 23424444 -3 21261765 -4 19933706 -5 17649154 -6 14832221 -7 12011845 -8 9355818 -9 7081698 -10 5199751 -11 3715263 -12 2599350 -13 1786719 -14 1204255 -15 807173 -16 539231 -17 361525 -18 245397 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index d488904..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.162e-01 1.521e-02 27.37 <2e-16 *** -r 3.857e-02 9.230e-04 41.78 <2e-16 *** -kmercov 2.421e+01 1.894e-01 127.80 <2e-16 *** -bias 1.453e+00 4.907e-02 29.61 <2e-16 *** -length 7.339e+05 6.755e+03 108.65 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 504.3 on 949 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 5.23e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 55677fe..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index cce495e..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 37234cd..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 707073839.960493 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index edc6f44..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.67231% 4.04153% -Genome Haploid Length 1,925,700 bp 1,986,930 bp -Genome Repeat Length 1,408,811 bp 1,453,606 bp -Genome Unique Length 516,889 bp 533,324 bp -Model Fit 76.1513% 89.506% -Read Error Rate 10.9973% 10.9973% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 115a32a..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1612 +0,0 @@ -1 369241644 -2 32847147 -3 24923590 -4 21286162 -5 17176731 -6 13174158 -7 9669920 -8 6830501 -9 4650115 -10 3076676 -11 1983096 -12 1257170 -13 787889 -14 494894 -15 318316 -16 211568 -17 145734 -18 106973 -19 82680 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist 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b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e99cbbc..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 312c1a9..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 400115a..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1593 +0,0 @@ -1 366631670 -2 30895128 -3 21850104 -4 18492175 -5 15192581 -6 12050409 -7 9274227 -8 6940858 -9 5058850 -10 3630200 -11 2551119 -12 1767791 -13 1218359 -14 831393 -15 562012 -16 385510 -17 265872 -18 185076 -19 134158 -20 100704 -21 77874 -22 62540 -23 52005 -24 44537 -25 39195 -26 34981 -27 31097 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100644 index 76dcd51..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.021e-01 1.466e-02 27.43 <2e-16 *** -r 3.833e-02 8.770e-04 43.70 <2e-16 *** -kmercov 2.395e+01 2.049e-01 116.90 <2e-16 *** -bias 1.582e+00 5.280e-02 29.97 <2e-16 *** -length 6.385e+05 5.586e+03 114.29 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 404.1 on 930 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 5.55e-06 - diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index aa99424..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8513a00..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d47be30..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 429576225.858599 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e464ace..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.6572% 4.00802% -Genome Haploid Length 1,533,870 bp 1,587,271 bp -Genome Repeat Length 1,079,430 bp 1,117,009 bp -Genome Unique Length 454,441 bp 470,262 bp -Model Fit 78.2197% 90.3954% -Read Error Rate 12.0003% 12.0003% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index fb229c6..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2129 +0,0 @@ -1 29656602 -2 12293683 -3 14169058 -4 13781585 -5 12631034 -6 11345638 -7 10098606 -8 8875208 -9 7665043 -10 6538915 -11 5501167 -12 4577217 -13 3780627 -14 3092947 -15 2504154 -16 2021000 -17 1611390 -18 1278113 -19 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist 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a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 78d8d6e..0000000 Binary files a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index ea7cf9c..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,224 +0,0 @@ -1 879991 -2 200220 -3 301104 -4 381803 -5 444611 -6 473014 -7 468459 -8 434154 -9 388215 -10 327657 -11 269860 -12 215608 -13 164179 -14 123187 -15 86673 -16 60381 -17 42182 -18 28967 -19 19602 -20 12468 -21 8620 -22 5536 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a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.720e-01 1.294e-02 13.29 <2e-16 *** -r 2.484e-02 7.856e-04 31.62 <2e-16 *** -kmercov 2.399e+01 1.870e-01 128.30 <2e-16 *** -bias 1.152e+00 9.754e-02 11.81 <2e-16 *** -length 1.388e+04 1.717e+02 80.81 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 15.43 on 189 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 7.774e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4f3f83f..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 244c3f4..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 44dcb5d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 15212809.4385881 -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d3f05e6..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.32695% 2.6412% -Genome Haploid Length 21,628 bp 22,313 bp -Genome Repeat Length 9,917 bp 10,231 bp -Genome Unique Length 11,711 bp 12,082 bp -Model Fit 59.8153% 62.4382% -Read Error Rate 15.6067% 15.6067% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index 625cf3d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,194 +0,0 @@ -1 7079508 -2 399788 -3 429293 -4 512941 -5 543981 -6 531774 -7 481885 -8 410649 -9 327457 -10 250649 -11 185981 -12 132129 -13 91158 -14 59401 -15 37265 -16 23754 -17 14638 -18 9143 -19 6050 -20 3714 -21 2459 -22 1476 -23 1087 -24 842 -25 695 -26 526 -27 522 -28 480 -29 466 -30 376 -31 363 -32 308 -33 309 -34 305 -35 297 -36 261 -37 249 -38 288 -39 372 -40 289 -41 347 -42 343 -43 318 -44 334 -45 296 -46 270 -47 239 -48 256 -49 214 -50 204 -51 192 -52 149 -53 183 -54 134 -55 128 -56 120 -57 84 -58 87 -59 73 -60 70 -61 69 -62 47 -63 39 -64 44 -65 43 -66 38 -67 46 -68 31 -69 43 -70 49 -71 37 -72 39 -73 26 -74 40 -75 27 -76 35 -77 25 -78 29 -79 30 -80 24 -81 45 -82 18 -83 29 -84 40 -85 21 -86 25 -87 31 -88 22 -89 27 -90 27 -91 32 -92 38 -93 38 -94 37 -95 40 -96 31 -97 42 -98 35 -99 29 -100 48 -101 43 -102 44 -103 35 -104 28 -105 28 -106 30 -107 28 -108 26 -109 28 -110 27 -111 27 -112 42 -113 44 -114 51 -115 40 -116 37 -117 29 -118 28 -119 21 -120 20 -121 19 -122 13 -123 22 -124 17 -125 15 -126 11 -127 20 -128 11 -129 8 -130 15 -131 5 -132 8 -133 3 -134 8 -135 4 -136 1 -138 1 -140 1 -143 1 -144 2 -152 1 -155 1 -156 1 -158 1 -159 2 -160 2 -163 1 -166 1 -168 1 -191 1 -194 1 -195 1 -196 1 -198 1 -199 1 -224 1 -227 1 -245 1 -248 1 -249 1 -255 2 -260 1 -262 1 -284 1 -308 1 -314 1 -315 1 -317 1 -318 1 -320 1 -321 1 -323 2 -325 1 -326 1 -327 2 -328 1 -330 1 -336 1 -349 2 -354 1 -361 1 -363 1 -366 1 -372 1 -384 1 -415 1 -436 1 -447 1 -463 1 -466 1 -483 1 -498 1 -499 1 -513 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 845ee72..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.420e-01 1.452e-02 9.781 <2e-16 *** -r 2.976e-02 6.494e-04 45.827 <2e-16 *** -kmercov 2.150e+01 1.616e-01 133.095 <2e-16 *** -bias 6.584e-01 5.212e-02 12.633 <2e-16 *** -length 1.326e+04 1.739e+02 76.243 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 18.22 on 164 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 3.964e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 24e6cd0..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index abb734a..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7459f20..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... converged. score: 3201007.41660604 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6d910a4..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.84611% 3.10587% -Genome Haploid Length 18,303 bp 18,861 bp -Genome Repeat Length 6,683 bp 6,887 bp -Genome Unique Length 11,620 bp 11,974 bp -Model Fit 74.3269% 77.2042% -Read Error Rate 16.7078% 16.7078% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 80ff4b6..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,165 +0,0 @@ -1 12652693 -2 689890 -3 602977 -4 646571 -5 611247 -6 528053 -7 424208 -8 317592 -9 225614 -10 148503 -11 96067 -12 59629 -13 36076 -14 21293 -15 12381 -16 7365 -17 4280 -18 2475 -19 1614 -20 1238 -21 854 -22 719 -23 565 -24 522 -25 517 -26 492 -27 409 -28 419 -29 438 -30 385 -31 371 -32 375 -33 419 -34 365 -35 317 -36 312 -37 288 -38 242 -39 222 -40 221 -41 177 -42 153 -43 125 -44 102 -45 120 -46 124 -47 103 -48 82 -49 90 -50 97 -51 73 -52 92 -53 95 -54 100 -55 90 -56 85 -57 73 -58 79 -59 58 -60 88 -61 73 -62 45 -63 42 -64 32 -65 36 -66 27 -67 40 -68 33 -69 30 -70 27 -71 48 -72 31 -73 24 -74 36 -75 23 -76 33 -77 46 -78 38 -79 27 -80 32 -81 47 -82 32 -83 44 -84 41 -85 46 -86 54 -87 39 -88 50 -89 41 -90 45 -91 30 -92 46 -93 33 -94 39 -95 30 -96 32 -97 22 -98 14 -99 15 -100 17 -101 13 -102 10 -103 12 -104 8 -105 4 -106 3 -107 4 -108 7 -109 5 -110 3 -111 1 -113 2 -114 4 -115 2 -116 1 -118 2 -119 3 -120 3 -121 3 -123 1 -124 2 -136 1 -142 1 -149 1 -151 1 -156 1 -164 1 -165 1 -169 1 -170 1 -172 1 -176 1 -177 1 -197 1 -214 1 -217 1 -225 1 -235 1 -236 1 -247 1 -251 1 -252 1 -255 1 -256 2 -259 3 -262 2 -264 1 -271 1 -272 1 -274 1 -276 1 -283 1 -288 1 -289 1 -303 1 -304 1 -345 1 -370 1 -379 1 -384 1 -395 1 -403 1 -412 1 -416 1 -432 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index fbe91c3..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.442e-01 2.454e-02 9.95 < 2e-16 *** -r 4.965e-02 2.553e-03 19.45 < 2e-16 *** -kmercov 1.563e+01 1.712e-01 91.28 < 2e-16 *** -bias 1.620e-01 3.640e-02 4.45 1.74e-05 *** -length 1.643e+04 3.253e+02 50.52 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 23.77 on 140 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 8.079e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b9bb476..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 152dbbd..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0476c09..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... converged. score: 142657588.536654 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ba06897..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 4.45427% 5.47559% -Genome Haploid Length 28,246 bp 29,511 bp -Genome Repeat Length 14,397 bp 15,042 bp -Genome Unique Length 13,849 bp 14,469 bp -Model Fit 48.1749% 49.3279% -Read Error Rate 16.2278% 16.2278% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index d70bf77..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,214 +0,0 @@ -1 947933 -2 265739 -3 322570 -4 368990 -5 395582 -6 392249 -7 379383 -8 352646 -9 317241 -10 281944 -11 242625 -12 207388 -13 167396 -14 135691 -15 108936 -16 84410 -17 64582 -18 47467 -19 36033 -20 26934 -21 19560 -22 14894 -23 10570 -24 8248 -25 5623 -26 3722 -27 2856 -28 2025 -29 1460 -30 1001 -31 916 -32 675 -33 551 -34 417 -35 337 -36 367 -37 368 -38 305 -39 298 -40 339 -41 296 -42 278 -43 317 -44 316 -45 258 -46 296 -47 232 -48 290 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-334 1 -342 2 -343 1 -346 1 -347 1 -348 1 -349 1 -358 1 -364 2 -375 1 -380 1 -384 1 -391 1 -420 1 -426 1 -430 1 -436 2 -442 1 -447 2 -449 1 -452 1 -469 1 -474 1 -484 2 -498 2 -511 1 -521 1 -533 1 -540 1 -541 1 -562 1 -582 1 -583 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2a49d99..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index a1e6c93..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index 6e89c75..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,212 +0,0 @@ -1 7128812 -2 451696 -3 434277 -4 459568 -5 457200 -6 438129 -7 395924 -8 348045 -9 294325 -10 239217 -11 191326 -12 148379 -13 112567 -14 82193 -15 59632 -16 42783 -17 29945 -18 20293 -19 14411 -20 9581 -21 6652 -22 4621 -23 3232 -24 2260 -25 1326 -26 975 -27 838 -28 640 -29 546 -30 498 -31 437 -32 355 -33 374 -34 345 -35 343 -36 367 -37 351 -38 322 -39 296 -40 298 -41 292 -42 260 -43 234 -44 292 -45 238 -46 219 -47 222 -48 242 -49 188 -50 209 -51 168 -52 190 -53 192 -54 162 -55 152 -56 140 -57 112 -58 107 -59 135 -60 128 -61 108 -62 105 -63 128 -64 106 -65 103 -66 103 -67 64 -68 60 -69 67 -70 49 -71 67 -72 41 -73 51 -74 25 -75 41 -76 35 -77 35 -78 21 -79 21 -80 13 -81 10 -82 6 -83 5 -84 8 -85 7 -86 10 -87 16 -88 11 -89 14 -90 17 -91 17 -92 23 -93 15 -94 25 -95 23 -96 16 -97 17 -98 14 -99 12 -100 13 -101 19 -102 36 -103 25 -104 26 -105 29 -106 22 -107 21 -108 25 -109 29 -110 16 -111 27 -112 30 -113 22 -114 28 -115 29 -116 37 -117 32 -118 31 -119 36 -120 18 -121 24 -122 22 -123 19 -124 23 -125 21 -126 26 -127 20 -128 20 -129 24 -130 21 -131 20 -132 21 -133 16 -134 24 -135 22 -136 21 -137 10 -138 19 -139 16 -140 9 -141 11 -142 9 -143 9 -144 9 -145 5 -146 5 -147 4 -148 5 -149 8 -150 6 -151 4 -152 4 -153 6 -154 5 -155 5 -156 2 -157 1 -158 9 -159 1 -160 3 -161 3 -162 4 -163 2 -164 3 -166 1 -175 1 -177 1 -178 1 -181 2 -190 1 -195 1 -197 1 -206 1 -223 1 -229 1 -232 1 -240 1 -248 1 -250 1 -253 1 -259 1 -263 1 -266 1 -285 1 -287 1 -293 2 -295 1 -296 1 -298 1 -300 1 -301 1 -303 1 -307 1 -315 2 -316 1 -318 1 -319 1 -320 1 -322 1 -326 1 -328 1 -331 1 -332 1 -338 1 -459 1 -462 1 -465 1 -474 1 -496 2 -512 1 -514 1 -517 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index c7d05af..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.121e-01 2.800e-02 4.005 9.13e-05 *** -r 3.299e-02 1.182e-03 27.911 < 2e-16 *** -kmercov 2.366e+01 6.626e-01 35.711 < 2e-16 *** -bias 2.485e+00 3.778e-01 6.578 5.20e-10 *** -length 1.274e+04 3.235e+02 39.373 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 14.7 on 177 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 8.133e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a10d83e..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 89ca2a1..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 73db875..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 26798885.9001595 -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 66103d6..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.06271% 3.53552% -Genome Haploid Length 18,640 bp 20,852 bp -Genome Repeat Length 7,586 bp 8,487 bp -Genome Unique Length 11,054 bp 12,365 bp -Model Fit 52.1621% 53.7219% -Read Error Rate 16.1032% 16.1032% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index fa25a17..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,180 +0,0 @@ -1 12721008 -2 729772 -3 551821 -4 551244 -5 512766 -6 450312 -7 372104 -8 292213 -9 225248 -10 166124 -11 119713 -12 84674 -13 57402 -14 38313 -15 25071 -16 16463 -17 10876 -18 6736 -19 4371 -20 2868 -21 1900 -22 1413 -23 955 -24 699 -25 579 -26 475 -27 448 -28 372 -29 392 -30 333 -31 332 -32 285 -33 281 -34 275 -35 273 -36 253 -37 279 -38 274 -39 251 -40 259 -41 241 -42 218 -43 212 -44 160 -45 168 -46 152 -47 99 -48 117 -49 133 -50 131 -51 109 -52 109 -53 106 -54 84 -55 61 -56 91 -57 66 -58 68 -59 46 -60 55 -61 42 -62 36 -63 28 -64 25 -65 33 -66 33 -67 34 -68 32 -69 37 -70 32 -71 20 -72 39 -73 33 -74 30 -75 24 -76 37 -77 36 -78 39 -79 31 -80 28 -81 38 -82 24 -83 24 -84 34 -85 31 -86 33 -87 27 -88 23 -89 22 -90 24 -91 30 -92 31 -93 19 -94 23 -95 14 -96 29 -97 34 -98 22 -99 28 -100 20 -101 18 -102 10 -103 15 -104 16 -105 17 -106 17 -107 20 -108 12 -109 4 -110 11 -111 6 -112 6 -113 9 -114 9 -115 10 -116 4 -117 5 -118 8 -119 6 -120 5 -121 3 -122 6 -123 5 -124 3 -125 4 -126 7 -127 5 -128 5 -129 4 -130 4 -131 2 -132 3 -135 2 -136 1 -138 1 -139 1 -140 1 -141 5 -143 1 -155 2 -159 1 -170 1 -173 1 -174 1 -175 1 -178 1 -208 1 -211 1 -213 1 -217 2 -218 1 -219 1 -225 1 -226 1 -242 1 -247 1 -248 1 -249 1 -271 3 -276 1 -277 1 -278 1 -279 2 -280 1 -283 2 -285 1 -291 1 -293 1 -298 1 -306 1 -308 1 -313 1 -326 1 -329 1 -356 1 -372 1 -377 1 -378 1 -403 2 -413 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 390150c..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index e60f088..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index e1ebb8d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,239 +0,0 @@ -1 935955 -2 265355 -3 319766 -4 340837 -5 344522 -6 345720 -7 331753 -8 309088 -9 283878 -10 252395 -11 224983 -12 191813 -13 164803 -14 135298 -15 113219 -16 94204 -17 74714 -18 60317 -19 48833 -20 37821 -21 29065 -22 21883 -23 17087 -24 13701 -25 10152 -26 7685 -27 6051 -28 5018 -29 3478 -30 2504 -31 1832 -32 1603 -33 1048 -34 979 -35 704 -36 581 -37 519 -38 449 -39 467 -40 461 -41 325 -42 281 -43 316 -44 327 -45 251 -46 246 -47 177 -48 204 -49 205 -50 208 -51 183 -52 223 -53 240 -54 203 -55 194 -56 126 -57 150 -58 182 -59 128 -60 110 -61 133 -62 154 -63 183 -64 134 -65 123 -66 105 -67 149 -68 153 -69 134 -70 147 -71 100 -72 75 -73 97 -74 102 -75 79 -76 110 -77 97 -78 85 -79 100 -80 57 -81 51 -82 68 -83 51 -84 40 -85 52 -86 34 -87 39 -88 19 -89 32 -90 16 -91 14 -92 17 -93 15 -94 24 -95 20 -96 15 -97 26 -98 25 -99 16 -100 16 -101 14 -102 12 -103 17 -104 16 -105 7 -106 4 -107 9 -108 7 -109 17 -110 20 -111 15 -112 20 -113 9 -114 14 -115 17 -116 21 -117 25 -118 12 -119 21 -120 20 -121 13 -122 6 -123 10 -124 10 -125 11 -126 16 -127 7 -128 9 -129 25 -130 4 -131 14 -132 16 -133 18 -134 12 -135 25 -136 22 -137 14 -138 21 -139 19 -140 19 -141 31 -142 28 -143 23 -144 26 -145 24 -146 26 -147 20 -148 18 -149 24 -150 26 -151 11 -152 16 -153 23 -154 26 -155 19 -156 19 -157 24 -158 15 -159 19 -160 18 -161 19 -162 7 -163 16 -164 9 -165 11 -166 10 -167 10 -168 7 -169 7 -170 3 -171 4 -172 4 -173 4 -174 2 -175 9 -176 8 -177 9 -178 3 -179 5 -180 4 -181 5 -182 4 -183 2 -184 5 -185 2 -186 1 -187 1 -188 3 -189 2 -190 7 -192 1 -194 2 -196 1 -197 2 -199 1 -205 1 -236 2 -240 1 -243 1 -248 1 -251 1 -255 1 -259 1 -267 1 -282 1 -288 1 -325 2 -332 1 -345 1 -347 1 -348 1 -362 1 -363 1 -368 2 -369 1 -370 1 -371 1 -375 1 -378 1 -383 1 -387 1 -390 1 -391 1 -395 1 -414 1 -437 1 -439 1 -443 1 -459 1 -461 1 -480 1 -540 1 -546 1 -554 2 -562 1 -576 1 -585 1 -605 1 -612 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5189f2f..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.091e-02 8.634e-03 3.580 0.000423 *** -r 1.614e-02 1.603e-02 1.007 0.314968 -kmercov 5.720e+00 4.847e-01 11.802 < 2e-16 *** -bias 1.091e+00 2.342e-01 4.658 5.53e-06 *** -length 2.752e+06 1.113e+05 24.739 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 149.8 on 219 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 8.918e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f4eab36..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 56236fa..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7bac0eb..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 24427951885.6712 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index bc7e005..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -1.59128% 4.81975% -Genome Haploid Length 2,650,843 bp 3,732,611 bp -Genome Repeat Length 363,959 bp 512,485 bp -Genome Unique Length 2,286,885 bp 3,220,126 bp -Model Fit 87.6736% 87.5202% -Read Error Rate 0.226011% 0.226011% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index 88d26b6..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,220 +0,0 @@ -1 7083872 -2 455240 -3 406105 -4 412864 -5 403429 -6 381270 -7 346141 -8 307084 -9 264278 -10 223971 -11 185117 -12 151619 -13 121163 -14 94682 -15 73750 -16 56863 -17 42305 -18 31922 -19 24415 -20 17752 -21 12715 -22 9250 -23 7038 -24 4872 -25 3532 -26 2599 -27 1825 -28 1398 -29 1045 -30 747 -31 601 -32 420 -33 435 -34 390 -35 373 -36 309 -37 370 -38 318 -39 331 -40 280 -41 267 -42 277 -43 242 -44 281 -45 277 -46 230 -47 227 -48 190 -49 192 -50 210 -51 202 -52 146 -53 192 -54 143 -55 122 -56 148 -57 151 -58 140 -59 144 -60 138 -61 129 -62 134 -63 123 -64 133 -65 120 -66 100 -67 81 -68 80 -69 76 -70 85 -71 61 -72 57 -73 64 -74 48 -75 32 -76 36 -77 40 -78 20 -79 23 -80 35 -81 29 -82 19 -83 32 -84 36 -85 36 -86 19 -87 22 -88 12 -89 14 -90 13 -91 26 -92 15 -93 8 -94 10 -95 12 -96 14 -97 15 -98 13 -99 17 -100 20 -101 17 -102 17 -103 12 -104 10 -105 15 -106 14 -107 16 -108 26 -109 23 -110 26 -111 19 -112 17 -113 19 -114 21 -115 30 -116 19 -117 28 -118 20 -119 18 -120 15 -121 12 -122 21 -123 9 -124 13 -125 9 -126 19 -127 6 -128 13 -129 15 -130 8 -131 12 -132 16 -133 10 -134 17 -135 3 -136 7 -137 7 -138 10 -139 8 -140 4 -141 6 -142 5 -143 5 -144 3 -145 6 -146 4 -147 3 -148 7 -149 6 -150 6 -151 10 -152 7 -153 14 -154 6 -155 3 -156 10 -157 9 -158 2 -159 3 -160 3 -161 1 -162 4 -163 6 -164 4 -165 2 -166 4 -167 8 -168 1 -169 4 -170 2 -171 2 -172 1 -173 1 -174 1 -176 1 -178 1 -179 2 -184 2 -198 1 -201 1 -205 1 -218 2 -219 1 -220 1 -221 1 -237 2 -248 1 -251 1 -257 1 -260 2 -268 1 -278 1 -283 1 -284 1 -287 1 -304 2 -306 1 -307 1 -308 1 -312 1 -313 2 -317 2 -320 2 -340 1 -343 1 -358 1 -387 1 -394 1 -396 1 -404 1 -409 1 -417 1 -418 2 -420 1 -421 1 -436 1 -443 1 -448 1 -458 1 -462 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 91e0a92..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8b76dc0..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 0a9108c..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,176 +0,0 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a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index a099198..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 0ca7a3a..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,214 +0,0 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b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9b6485d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.024e-01 1.454e-02 13.920 < 2e-16 *** -r 2.967e-02 1.464e-03 20.267 < 2e-16 *** -kmercov 2.221e+01 2.270e-01 97.831 < 2e-16 *** -bias 1.111e+00 1.308e-01 8.495 7.46e-15 *** -length 1.424e+04 2.444e+02 58.274 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 14.45 on 179 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 5.186e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f05e474..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index a97c766..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index feed689..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 49821877.7534599 -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 243e4a0..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.67375% 3.25924% -Genome Haploid Length 24,348 bp 25,364 bp -Genome Repeat Length 12,597 bp 13,123 bp -Genome Unique Length 11,750 bp 12,241 bp -Model Fit 49.211% 50.7121% -Read Error Rate 15.4216% 15.4216% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index e8d5656..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,191 +0,0 @@ -1 7277035 -2 614082 -3 615193 -4 639134 -5 606999 -6 545850 -7 464057 -8 375628 -9 294641 -10 220041 -11 160294 -12 112218 -13 76441 -14 50717 -15 32621 -16 20994 -17 13097 -18 8473 -19 5188 -20 3492 -21 2079 -22 1298 -23 899 -24 695 -25 559 -26 474 -27 414 -28 459 -29 436 -30 461 -31 475 -32 418 -33 393 -34 317 -35 291 -36 307 -37 251 -38 268 -39 279 -40 228 -41 224 -42 217 -43 187 -44 213 -45 217 -46 199 -47 156 -48 171 -49 166 -50 141 -51 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-399 1 -406 1 -421 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ef008be..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index fb41917..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index 3e30523..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,173 +0,0 @@ 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-140 1 -141 1 -143 1 -144 1 -154 1 -181 1 -186 1 -202 2 -204 1 -205 1 -207 2 -209 1 -210 2 -211 1 -213 1 -218 1 -222 1 -224 1 -226 1 -227 1 -228 1 -230 1 -232 1 -235 1 -240 1 -241 1 -242 1 -247 1 -250 1 -277 1 -283 1 -284 1 -290 2 -311 1 -337 1 -345 1 -358 1 -360 1 -363 1 -366 1 -377 1 -384 1 -405 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8beb6c8..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.019e-01 5.190e-02 7.742 1.41e-12 *** -r 5.341e-02 4.955e-03 10.779 < 2e-16 *** -kmercov 1.512e+01 1.195e-01 126.573 < 2e-16 *** -bias 1.169e-01 3.537e-02 3.304 0.0012 ** -length 1.425e+04 4.357e+02 32.704 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 20.09 on 148 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 7.268e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7f2624e..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index e437e6a..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 50a8efd..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... converged. score: 358087542.924753 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 48d51ad..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 4.34983% 6.33174% -Genome Haploid Length 31,273 bp 32,277 bp -Genome Repeat Length 20,244 bp 20,894 bp -Genome Unique Length 11,029 bp 11,383 bp -Model Fit 36.5412% 37.144% -Read Error Rate 15.9764% 15.9764% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 4382c5d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,211 +0,0 @@ -1 1067032 -2 416315 -3 460503 -4 474747 -5 467036 -6 442152 -7 407305 -8 368241 -9 320578 -10 271214 -11 227644 -12 186059 -13 151545 -14 119617 -15 95033 -16 72118 -17 54860 -18 39617 -19 29805 -20 22306 -21 16687 -22 11959 -23 8956 -24 6184 -25 4487 -26 2698 -27 2450 -28 1646 -29 1221 -30 858 -31 795 -32 604 -33 533 -34 438 -35 390 -36 289 -37 325 -38 277 -39 254 -40 309 -41 239 -42 288 -43 260 -44 260 -45 316 -46 222 -47 273 -48 266 -49 244 -50 217 -51 213 -52 221 -53 169 -54 156 -55 154 -56 168 -57 169 -58 115 -59 147 -60 164 -61 168 -62 118 -63 119 -64 115 -65 99 -66 98 -67 96 -68 92 -69 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-502 1 -510 1 -517 1 -540 1 -543 1 -547 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4aa5a7c..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 54726a1..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index 1651cf8..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,194 +0,0 @@ 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6 -126 4 -127 7 -128 4 -129 2 -130 7 -131 5 -132 6 -133 3 -134 4 -135 5 -136 3 -137 6 -139 2 -140 1 -141 3 -143 2 -147 1 -148 2 -152 1 -153 1 -155 1 -156 1 -157 1 -165 1 -173 2 -174 1 -186 1 -187 1 -189 1 -191 1 -235 1 -243 1 -258 1 -260 1 -261 1 -265 1 -269 1 -271 1 -272 2 -273 1 -274 1 -276 1 -277 1 -279 1 -281 1 -283 1 -287 1 -293 1 -294 2 -298 1 -301 1 -304 1 -311 1 -320 1 -324 1 -333 1 -349 1 -357 2 -358 1 -369 2 -387 1 -405 1 -414 1 -430 1 -439 1 -458 1 -459 1 -465 1 -474 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e66c26b..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8e40eab..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index e29532d..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,157 +0,0 @@ -1 12892326 -2 885904 -3 677740 -4 616296 -5 537493 -6 449814 -7 356115 -8 275270 -9 204449 -10 148077 -11 105963 -12 73765 -13 50163 -14 34218 -15 22353 -16 14568 -17 8941 -18 5808 -19 3698 -20 2635 -21 1592 -22 1193 -23 871 -24 753 -25 578 -26 464 -27 465 -28 394 -29 370 -30 379 -31 389 -32 329 -33 315 -34 282 -35 283 -36 279 -37 253 -38 241 -39 217 -40 230 -41 191 -42 207 -43 155 -44 120 -45 115 -46 109 -47 102 -48 105 -49 114 -50 90 -51 93 -52 88 -53 72 -54 70 -55 60 -56 60 -57 48 -58 51 -59 42 -60 33 -61 34 -62 38 -63 38 -64 37 -65 33 -66 32 -67 35 -68 35 -69 31 -70 35 -71 35 -72 26 -73 36 -74 33 -75 44 -76 46 -77 28 -78 45 -79 40 -80 42 -81 33 -82 33 -83 36 -84 27 -85 30 -86 26 -87 22 -88 25 -89 32 -90 29 -91 25 -92 22 -93 21 -94 32 -95 31 -96 25 -97 28 -98 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a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 213dd3f..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov10_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist deleted file mode 100644 index 415ca80..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist +++ /dev/null @@ -1,238 +0,0 @@ -1 984677 -2 364741 -3 433400 -4 434671 -5 415186 -6 387239 -7 350881 -8 318149 -9 286252 -10 254215 -11 211673 -12 180056 -13 152421 -14 123728 -15 105844 -16 81691 -17 65329 -18 51738 -19 43131 -20 32601 -21 26364 -22 20839 -23 15588 -24 11866 -25 9443 -26 6721 -27 5116 -28 3915 -29 3075 -30 2158 -31 1897 -32 1351 -33 1136 -34 852 -35 674 -36 630 -37 623 -38 471 -39 395 -40 340 -41 371 -42 308 -43 297 -44 282 -45 256 -46 249 -47 276 -48 218 -49 199 -50 223 -51 232 -52 243 -53 217 -54 178 -55 162 -56 212 -57 126 -58 133 -59 154 -60 165 -61 121 -62 129 -63 73 -64 107 -65 117 -66 86 -67 94 -68 88 -69 51 -70 66 -71 72 -72 79 -73 56 -74 35 -75 32 -76 24 -77 35 -78 38 -79 22 -80 35 -81 33 -82 37 -83 26 -84 37 -85 17 -86 17 -87 17 -88 12 -89 8 -90 11 -91 21 -92 17 -93 25 -94 30 -95 33 -96 19 -97 22 -98 15 -99 18 -100 30 -101 19 -102 13 -103 31 -104 34 -105 16 -106 24 -107 12 -108 12 -109 25 -110 27 -111 19 -112 11 -113 25 -114 17 -115 18 -116 17 -117 21 -118 27 -119 29 -120 19 -121 16 -122 16 -123 19 -124 15 -125 20 -126 14 -127 17 -128 13 -129 14 -130 16 -131 12 -132 17 -133 19 -134 15 -135 29 -136 15 -137 17 -138 31 -139 12 -140 18 -141 14 -142 19 -143 19 -144 17 -145 19 -146 22 -147 22 -148 21 -149 14 -150 19 -151 10 -152 15 -153 12 -154 19 -155 9 -156 16 -157 20 -158 11 -159 10 -160 12 -161 6 -162 6 -163 6 -164 6 -165 9 -166 9 -167 11 -168 10 -169 7 -170 3 -171 4 -172 3 -173 1 -174 3 -175 1 -176 2 -180 1 -181 1 -182 2 -183 5 -184 2 -185 2 -186 3 -187 2 -189 3 -190 3 -191 4 -192 3 -195 3 -196 4 -197 4 -198 2 -199 7 -200 1 -204 1 -205 1 -206 1 -209 3 -211 1 -214 1 -223 1 -225 2 -233 1 -248 1 -273 1 -279 1 -280 1 -281 1 -295 1 -297 1 -302 1 -303 1 -304 1 -308 2 -310 1 -314 3 -317 2 -318 2 -327 1 -333 2 -353 1 -393 1 -394 1 -398 1 -410 1 -415 1 -435 1 -454 1 -459 2 -472 1 -485 1 -487 1 -491 1 -493 1 -497 1 -502 1 -503 1 -509 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 28431a8..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.048e-02 5.667e-03 10.671 < 2e-16 *** -r 8.230e-02 2.133e-03 38.585 < 2e-16 *** -kmercov 7.773e+00 4.163e-02 186.709 < 2e-16 *** -bias 1.694e-01 2.797e-02 6.055 6.07e-09 *** -length 2.946e+06 8.172e+04 36.053 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 137 on 218 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 6.081e-06 - diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cf2aa34..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index f7f84c9..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 96f0f92..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 416022054747.183 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9fae5f8..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 7.80378% 8.65702% -Genome Haploid Length 2,201,237 bp 2,248,906 bp -Genome Repeat Length -660,371 bp -674,672 bp -Genome Unique Length 2,861,608 bp 2,923,578 bp -Model Fit 45.2925% 45.3779% -Read Error Rate 0.342641% 0.342641% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist deleted file mode 100644 index 2024dd9..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist +++ /dev/null @@ -1,189 +0,0 @@ -1 7199113 -2 569662 -3 516277 -4 495598 -5 453136 -6 410624 -7 360337 -8 308593 -9 258359 -10 212375 -11 170690 -12 138591 -13 108557 -14 83683 -15 64246 -16 49180 -17 37232 -18 27723 -19 20318 -20 14984 -21 11341 -22 8223 -23 5954 -24 4319 -25 3258 -26 2386 -27 1819 -28 1296 -29 1015 -30 798 -31 673 -32 518 -33 460 -34 438 -35 382 -36 329 -37 286 -38 292 -39 299 -40 273 -41 257 -42 244 -43 240 -44 207 -45 202 -46 196 -47 184 -48 178 -49 160 -50 157 -51 152 -52 145 -53 97 -54 121 -55 105 -56 122 -57 110 -58 98 -59 78 -60 79 -61 82 -62 97 -63 78 -64 49 -65 58 -66 67 -67 48 -68 45 -69 52 -70 56 -71 36 -72 53 -73 48 -74 54 -75 47 -76 46 -77 46 -78 51 -79 49 -80 38 -81 44 -82 36 -83 43 -84 47 -85 44 -86 27 -87 28 -88 30 -89 32 -90 25 -91 33 -92 36 -93 30 -94 31 -95 32 -96 29 -97 32 -98 37 -99 32 -100 33 -101 30 -102 31 -103 36 -104 29 -105 33 -106 22 -107 34 -108 25 -109 25 -110 19 -111 18 -112 13 -113 14 -114 13 -115 11 -116 7 -117 10 -118 16 -119 9 -120 6 -121 11 -122 7 -123 4 -124 8 -125 8 -126 7 -127 5 -128 3 -129 4 -130 6 -131 6 -132 4 -133 10 -134 1 -135 5 -136 4 -137 2 -138 3 -139 4 -140 1 -141 2 -145 1 -146 1 -147 2 -159 2 -181 1 -189 2 -192 1 -193 1 -196 1 -197 1 -203 1 -207 1 -215 1 -217 1 -218 1 -250 1 -252 1 -260 1 -270 1 -272 1 -276 1 -277 1 -279 1 -281 1 -283 1 -287 1 -289 1 -292 1 -299 2 -300 1 -302 1 -304 1 -305 1 -306 1 -308 1 -314 1 -316 1 -318 1 -320 1 -383 1 -402 1 -408 1 -421 1 -447 1 -449 1 -467 1 -470 1 -474 1 diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9a05c3e..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a4eb8c8..0000000 Binary files a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist b/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist deleted file mode 100644 index ac4687f..0000000 --- a/analysis/simulation_results_10x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov10_err0.02_reads.fa21.hist +++ /dev/null @@ -1,172 +0,0 @@ -1 13088557 -2 1037625 -3 785814 -4 681390 -5 567143 -6 450773 -7 347484 -8 258143 -9 187904 -10 132488 -11 92588 -12 62315 -13 40960 -14 27475 -15 17793 -16 11677 -17 7710 -18 4947 -19 3035 -20 2078 -21 1451 -22 1115 -23 822 -24 635 -25 586 -26 464 -27 399 -28 359 -29 338 -30 317 -31 343 -32 298 -33 301 -34 286 -35 250 -36 228 -37 185 -38 181 -39 191 -40 162 -41 161 -42 151 -43 97 -44 90 -45 85 -46 71 -47 74 -48 68 -49 80 -50 71 -51 64 -52 54 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.735e-02 5.903e-04 46.34 <2e-16 *** -r 2.118e-03 1.867e-05 113.40 <2e-16 *** -kmercov 6.025e+00 1.675e-03 3596.42 <2e-16 *** -bias 9.059e-01 3.775e-03 239.99 <2e-16 *** -length 1.055e+08 4.544e+04 2322.26 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6047 on 994 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 9.763e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 961963d..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7b5552e..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 49711df..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 33595995297.2838 -round 1 trimming to 7 trying 4peak model... converged. score: 244997845977.733 -round 2 trimming to 12 trying 4peak model... converged. score: 34597395268678.5 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 09285b3..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.208039% 0.215509% -Genome Haploid Length 115,990,846 bp 116,119,924 bp -Genome Repeat Length 13,403,210 bp 13,418,125 bp -Genome Unique Length 102,587,636 bp 102,701,799 bp -Model Fit 98.4812% 99.5531% -Read Error Rate 0.0989323% 0.0989323% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 784bde6..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2070 +0,0 @@ -1 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 68be038..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.591e-02 7.004e-04 51.27 <2e-16 *** -r 3.165e-03 2.890e-05 109.52 <2e-16 *** -kmercov 5.029e+00 1.860e-03 2704.09 <2e-16 *** -bias 6.592e-01 4.378e-03 150.55 <2e-16 *** -length 1.044e+08 5.927e+04 1761.39 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6720 on 993 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 5.939e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 718f05a..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index bb40def..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b8def76..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 35884525857.3914 -round 1 trimming to 8 trying 4peak model... converged. score: 1178462354691.48 -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a66d5e3..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.310736% 0.322296% -Genome Haploid Length 115,507,670 bp 115,678,660 bp -Genome Repeat Length 14,922,331 bp 14,944,421 bp -Genome Unique Length 100,585,338 bp 100,734,238 bp -Model Fit 98.5649% 99.5991% -Read Error Rate 0.979896% 0.979896% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 1c622db..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1834 +0,0 @@ -1 457746400 -2 18171287 -3 7292499 -4 8901146 -5 10684916 -6 11753588 -7 11930052 -8 11264490 -9 10005922 -10 8415867 -11 6759025 -12 5207539 -13 3878849 -14 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mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.791e-02 1.096e-03 25.47 <2e-16 *** -r 4.999e-03 4.577e-05 109.22 <2e-16 *** -kmercov 6.403e+00 3.278e-03 1953.03 <2e-16 *** -bias 1.569e+00 1.012e-02 155.07 <2e-16 *** -length 9.967e+07 8.811e+04 1131.18 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5726 on 994 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 8.735e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 899d7fa..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index b478ed9..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index aa73ebd..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 21307246081.9973 -round 1 trimming to 7 trying 4peak model... converged. score: 90740586032.5402 -round 2 trimming to 12 trying 4peak model... converged. score: 13842997659689.7 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2510097..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.490711% 0.509018% -Genome Haploid Length 109,077,320 bp 109,300,950 bp -Genome Repeat Length 12,263,082 bp 12,288,224 bp -Genome Unique Length 96,814,238 bp 97,012,727 bp -Model Fit 98.7025% 99.6512% -Read Error Rate 0.0992758% 0.0992758% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 467c73a..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2083 +0,0 @@ -1 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist 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b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d7bf776..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.115e-02 1.080e-03 38.08 <2e-16 *** -r 9.379e-03 1.007e-04 93.10 <2e-16 *** -kmercov 6.954e+00 7.455e-03 932.74 <2e-16 *** -bias 1.913e+00 1.518e-02 126.02 <2e-16 *** -length 9.109e+07 1.496e+05 608.72 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2965 on 988 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 6.338e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 678b9bd..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1820f41..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 73c3977..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 26303730771.9816 -round 1 trimming to 7 trying 4peak model... converged. score: 12347253923.3951 -round 2 trimming to 12 trying 4peak model... unconverged -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1f4a869..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.917763% 0.958061% -Genome Haploid Length 100,295,364 bp 100,726,398 bp -Genome Repeat Length 13,018,669 bp 13,074,619 bp -Genome Unique Length 87,276,695 bp 87,651,780 bp -Model Fit 98.8814% 99.7565% -Read Error Rate 0.101094% 0.101094% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 26af3b7..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2077 +0,0 @@ -1 257299319 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3cd0ac5..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.453e-02 3.328e-03 22.39 <2e-16 *** -r 3.046e-02 2.432e-03 12.53 <2e-16 *** -kmercov 6.796e+00 9.912e-02 68.56 <2e-16 *** -bias 7.904e-01 7.052e-02 11.21 <2e-16 *** -length 8.268e+07 3.422e+05 241.63 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2724 on 981 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 6.864e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 96c4d2f..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 42cace8..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d228ee3..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 40302651723425 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 591d0cf..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.55977% 3.53244% -Genome Haploid Length 83,055,698 bp 88,047,086 bp -Genome Repeat Length 7,340,518 bp 7,781,660 bp -Genome Unique Length 75,715,181 bp 80,265,426 bp -Model Fit 82.2565% 82.7329% -Read Error Rate 0.983595% 0.983595% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index f5222f2..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,1846 +0,0 @@ -1 456923695 -2 21838222 -3 8715446 -4 8804392 -5 9181156 -6 9252315 -7 8964629 -8 8409061 -9 7649425 -10 6765179 -11 5831574 -12 4934408 -13 4088105 -14 3333055 -15 2674633 -16 2129350 -17 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-5706 1 -5716 1 -5739 1 -5748 1 -5753 1 -5765 1 -5769 1 -5787 1 -5794 1 -5831 1 -5870 1 -5893 1 -5939 1 -5952 1 -5979 1 -6081 1 -6106 1 -6210 1 -6409 1 -6511 1 -6539 1 -6548 1 -6647 1 -6705 1 -6717 1 -7022 1 -7898 1 -8009 1 -8656 1 -8738 1 -14900 1 -18917 1 -18983 1 -19101 1 -47788 1 -48839 1 -50289 1 -191400 1 diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index b882188..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.555e-02 7.202e-04 49.35 <2e-16 *** -r 1.148e-02 6.104e-05 188.07 <2e-16 *** -kmercov 6.022e+00 4.240e-03 1420.48 <2e-16 *** -bias 8.418e-01 7.248e-03 116.15 <2e-16 *** -length 1.057e+08 1.004e+05 1052.96 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4461 on 989 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 7.092e-07 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 816984f..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 70e2d32..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1ab10b8..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 42634267914.4992 -round 1 trimming to 7 trying 4peak model... converged. score: 37101642684.9973 -round 2 trimming to 12 trying 4peak model... converged. score: 12159133851008.2 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b503d7d..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.13586% 1.16028% -Genome Haploid Length 115,935,069 bp 116,261,996 bp -Genome Repeat Length 13,925,567 bp 13,964,835 bp -Genome Unique Length 102,009,503 bp 102,297,160 bp -Model Fit 98.7159% 99.579% -Read Error Rate 0.102583% 0.102583% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 49010ea..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1968 +0,0 @@ -1 260160645 -2 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist 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b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 71f6759..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2194 +0,0 @@ -1 32301883 -2 5459209 -3 6700507 -4 7280498 -5 7561184 -6 7689059 -7 7739525 -8 7613567 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2555508..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.209e-02 1.799e-03 40.08 <2e-16 *** -r 3.013e-02 6.696e-04 45.00 <2e-16 *** -kmercov 7.786e+00 4.711e-02 165.27 <2e-16 *** -bias 1.146e+00 4.203e-02 27.26 <2e-16 *** -length 8.206e+07 4.066e+05 201.81 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2412 on 981 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 7.401e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 798f43b..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8883cf2..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e885178..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 5943823418040.65 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d08bca7..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.87926% 3.14711% -Genome Haploid Length 88,070,917 bp 90,228,651 bp -Genome Repeat Length 11,524,671 bp 11,807,025 bp -Genome Unique Length 76,546,246 bp 78,421,626 bp -Model Fit 92.8377% 93.4354% -Read Error Rate 0.138355% 0.138355% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index d5e11e1..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1947 +0,0 @@ -1 260057838 -2 13211011 -3 8897711 -4 9145028 -5 9258519 -6 9185438 -7 8910963 -8 8420134 -9 7814736 -10 7145792 -11 6406206 -12 5659740 -13 4943074 -14 4256048 -15 3624225 -16 3039890 -17 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.173e-02 2.793e-03 25.69 <2e-16 *** -r 3.298e-02 1.826e-03 18.06 <2e-16 *** -kmercov 6.901e+00 8.995e-02 76.72 <2e-16 *** -bias 8.844e-01 6.610e-02 13.38 <2e-16 *** -length 9.305e+07 5.657e+05 164.48 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2734 on 981 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 1.823e-06 - diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 41d8b53..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7527469..0000000 Binary files a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4f9ee4f..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 8383918629298.89 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a5aac6b..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.93299% 3.66346% -Genome Haploid Length 97,995,445 bp 103,241,839 bp -Genome Repeat Length 12,150,426 bp 12,800,925 bp -Genome Unique Length 85,845,019 bp 90,440,914 bp -Model Fit 93.2685% 93.807% -Read Error Rate 0.142604% 0.142604% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 9d21b27..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,1852 +0,0 @@ -1 264249727 -2 15638777 -3 12189675 -4 12606494 -5 12532934 -6 12034979 -7 11204240 -8 10182184 -9 9040454 -10 7892887 -11 6777662 -12 5728138 -13 4760833 -14 3915980 -15 3182970 -16 2558770 -17 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt 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a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist 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* length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.526e-02 7.186e-04 21.24 <2e-16 *** -r 2.339e-03 2.299e-05 101.73 <2e-16 *** -kmercov 6.033e+00 2.005e-03 3008.72 <2e-16 *** -bias 8.809e-01 4.520e-03 194.88 <2e-16 *** -length 1.148e+08 6.020e+04 1906.43 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8108 on 994 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.151e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6db3f90..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index bf8162a..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3a7e48c..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 35343912255.3967 -round 1 trimming to 7 trying 4peak model... converged. score: 168493169826.48 -round 2 trimming to 12 trying 4peak model... converged. score: 25515036634509.2 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 35fa59e..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.229326% 0.238524% -Genome Haploid Length 130,828,890 bp 131,002,938 bp -Genome Repeat Length 17,883,983 bp 17,907,775 bp -Genome Unique Length 112,944,907 bp 113,095,163 bp -Model Fit 98.3643% 99.5982% -Read Error Rate 0.0998832% 0.0998832% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 9febeb6..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2749 +0,0 @@ -1 283920570 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b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2b89ea5..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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1 -6204 1 -6249 1 -6488 1 -6528 1 -6647 1 -6980 1 -7066 1 -7144 1 -7261 1 -7286 1 -7327 1 -7609 1 -8057 1 -8133 1 -8272 1 -8275 1 -8838 1 -9900 1 -9910 1 -9927 1 -9946 1 -9952 1 -10058 1 -10110 1 -10921 1 -10988 1 -15953 1 -16114 1 -16494 1 -22354 1 -22595 1 -22656 1 -24062 1 -24098 1 -24173 1 -24367 1 -24585 1 -24712 1 -24960 1 -25113 1 -25161 1 -30792 1 -31487 1 -35632 1 -36958 1 -44006 1 -52007 1 diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 05e7288..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.431e-01 2.013e-02 22.02 <2e-16 *** -r 4.073e-02 1.259e-03 32.35 <2e-16 *** -kmercov 3.023e+01 2.362e-01 127.94 <2e-16 *** -bias 2.181e+00 7.210e-02 30.25 <2e-16 *** -length 8.061e+05 9.549e+03 84.42 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 530.9 on 966 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 9.807e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f8ce326..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index f8a4194..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 17ee1dd..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 354584959.067786 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4eaca0e..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 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kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.219e-02 1.607e-03 7.585 7.62e-14 *** -r 5.260e-03 6.928e-05 75.918 < 2e-16 *** -kmercov 6.417e+00 4.828e-03 1329.207 < 2e-16 *** -bias 1.578e+00 1.481e-02 106.531 < 2e-16 *** -length 1.084e+08 1.419e+05 763.935 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9221 on 994 degrees of freedom - -Number of iterations to convergence: 19 -Achieved convergence tolerance: 9.599e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 75ae2b2..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index bdebd0d..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9a413b2..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 33928632517.0528 -round 1 trimming to 7 trying 4peak model... converged. score: 124829973741.149 -round 2 trimming to 12 trying 4peak model... converged. score: 14389880039480.7 -round 3 trimming to 17 trying 4peak model... converged. score: 173607653419756 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 62b8a07..0000000 --- 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index fb10a94..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.189e-02 1.140e-03 19.20 <2e-16 *** -r 9.355e-03 1.118e-04 83.68 <2e-16 *** -kmercov 6.942e+00 8.025e-03 864.94 <2e-16 *** -bias 1.984e+00 1.612e-02 123.08 <2e-16 *** -length 9.976e+07 1.752e+05 569.34 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3409 on 989 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 6.518e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3c802ef..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 77e8c37..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9178d75..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... unconverged -round 1 trimming to 7 trying 4peak model... converged. score: 20205516278.5627 -round 2 trimming to 12 trying 4peak model... converged. score: 2899696439753.11 -round 3 trimming to 17 trying 4peak model... converged. score: 41016291848638 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 070c50b..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.91315% 0.957869% -Genome Haploid Length 113,461,648 bp 113,987,580 bp -Genome Repeat Length 16,039,637 bp 16,113,985 bp -Genome Unique Length 97,422,012 bp 97,873,595 bp -Model Fit 98.5635% 99.6863% -Read Error Rate 0.101398% 0.101398% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index ebf8a8c..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2752 +0,0 @@ -1 284600305 -2 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b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a66b521..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git 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b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d9cb333..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.305e-03 1.056e-03 -2.182 0.0293 * -r 9.941e-03 6.822e-05 145.728 <2e-16 *** -kmercov 5.920e+00 5.200e-03 1138.338 <2e-16 *** -bias 1.141e+00 8.846e-03 128.975 <2e-16 *** -length 1.201e+08 1.427e+05 841.142 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8611 on 994 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 9.799e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dca943f..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index a577676..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7145480..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 53159969017.0924 -round 1 trimming to 7 trying 4peak model... converged. score: 63071644609.0586 -round 2 trimming to 12 trying 4peak model... converged. score: 15538146816952.8 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index dce13eb..0000000 --- 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ba78217..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 348357b..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist 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-21702 2 -21776 1 -21818 1 -21945 1 -22013 1 -22059 1 -22104 1 -22264 1 -22385 1 -22757 1 -27862 1 -28429 1 -32277 1 -33528 1 -41316 1 -49517 1 diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index e53e920..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.247e-01 1.666e-02 25.49 <2e-16 *** -r 3.920e-02 1.018e-03 38.50 <2e-16 *** -kmercov 3.003e+01 2.345e-01 128.07 <2e-16 *** -bias 2.143e+00 6.761e-02 31.69 <2e-16 *** -length 7.697e+05 7.631e+03 100.86 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 483.3 on 966 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 3.499e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 649a143..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index da7c71f..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b4ecea8..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 291635495.577708 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a9f275d..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5b3bcb1..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.715e-02 1.791e-03 26.33 <2e-16 *** -r 3.030e-02 1.218e-03 24.89 <2e-16 *** -kmercov 7.221e+00 5.638e-02 128.07 <2e-16 *** -bias 8.488e-01 4.142e-02 20.49 <2e-16 *** -length 1.020e+08 2.705e+05 377.17 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3162 on 981 degrees of freedom - -Number of iterations to convergence: 12 -Achieved convergence tolerance: 6.84e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5571162..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index d950669..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bb47cf3..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 36008163322057.5 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 410e8c3..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.78622% 3.27322% -Genome Haploid Length 107,748,008 bp 111,166,794 bp -Genome Repeat Length 10,940,231 bp 11,287,359 bp -Genome Unique Length 96,807,777 bp 99,879,435 bp -Model Fit 86.5239% 87.2655% -Read Error Rate 0.112811% 0.112811% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 2110dfe..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2633 +0,0 @@ -1 289498741 -2 15751285 -3 10457888 -4 10848010 -5 11221999 -6 11281033 -7 11017647 -8 10473324 -9 9696774 -10 8760642 -11 7740874 -12 6709644 -13 5694105 -14 4763323 -15 3910548 -16 3162104 -17 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist 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-33295 1 -40840 1 -51607 1 diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index a4c9131..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.280e-01 1.926e-02 22.22 <2e-16 *** -r 4.173e-02 1.244e-03 33.54 <2e-16 *** -kmercov 2.904e+01 2.254e-01 128.81 <2e-16 *** -bias 1.842e+00 5.719e-02 32.21 <2e-16 *** -length 8.010e+05 9.027e+03 88.73 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 541.1 on 966 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 7.817e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0db2ca1..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8344bb6..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 45b1461..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 742178049.946477 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index fc449fe..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.92441% 4.42214% -Genome Haploid Length 2,190,645 bp 2,259,746 bp -Genome Repeat Length 1,621,405 bp 1,672,549 bp -Genome Unique Length 569,240 bp 587,196 bp -Model Fit 74.7606% 88.5384% -Read Error Rate 11.3993% 11.3993% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index a178290..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2953 +0,0 @@ -1 36527978 -2 6177116 -3 7455715 -4 8140512 -5 8412782 -6 8560793 -7 8572817 -8 8421086 -9 8156052 -10 7705734 -11 7231541 -12 6696854 -13 6102437 -14 5522037 -15 4909240 -16 4350751 -17 3816587 -18 3303093 -19 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b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index f403293..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.059e-02 2.253e-03 22.46 <2e-16 *** -r 2.685e-02 1.146e-03 23.44 <2e-16 *** -kmercov 7.521e+00 7.795e-02 96.48 <2e-16 *** -bias 1.364e+00 6.062e-02 22.50 <2e-16 *** -length 9.226e+07 7.987e+05 115.52 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2874 on 981 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 4.549e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 22b8c2b..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 992a2bd..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 854aead..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 2629397842460.42 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 95dfe67..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.45617% 2.91439% -Genome Haploid Length 102,619,813 bp 106,964,176 bp -Genome Repeat Length 15,936,742 bp 16,611,417 bp -Genome Unique Length 86,683,071 bp 90,352,760 bp -Model Fit 95.1748% 96.0896% -Read Error Rate 0.128214% 0.128214% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 9010bf8..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2646 +0,0 @@ -1 288659076 -2 16277875 -3 10550740 -4 10427815 -5 10410808 -6 10250950 -7 9889502 -8 9349316 -9 8634366 -10 7872264 -11 7039238 -12 6213006 -13 5398598 -14 4634327 -15 3925851 -16 3284484 -17 2726861 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--git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index d80b82f..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.701e-02 3.721e-03 18.008 <2e-16 *** -r 3.773e-02 2.548e-03 14.811 <2e-16 *** -kmercov 6.761e+00 1.096e-01 61.675 <2e-16 *** -bias 7.318e-01 8.233e-02 8.889 <2e-16 *** -length 8.881e+07 4.227e+05 210.104 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2990 on 981 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 5.025e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ceab312..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3335a19..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 34e51e0..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 26698314992382.4 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2a3bcbd..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.26376% 4.28283% -Genome Haploid Length 94,131,454 bp 100,441,106 bp -Genome Repeat Length 12,101,852 bp 12,913,042 bp -Genome Unique Length 82,029,602 bp 87,528,064 bp -Model Fit 87.1134% 87.8875% -Read Error Rate 1.01734% 1.01734% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 3da73f5..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2254 +0,0 @@ -1 512126029 -2 29264762 -3 14477450 -4 13273855 -5 12645660 -6 11845571 -7 10846054 -8 9669175 -9 8435251 -10 7218300 -11 6043746 -12 4980830 -13 4049327 -14 3233263 -15 2551610 -16 1988368 -17 1533335 -18 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b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3febf71..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b1909ca..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 42492967092852.5 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 69b9f68..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 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1 -7263 1 -7296 1 -7475 1 -7778 1 -8059 1 -8080 1 -8087 1 -8143 1 -8204 1 -8215 1 -8222 1 -8845 1 -8926 1 -13063 1 -13146 1 -13474 1 -19375 1 -19572 1 -19609 1 -20393 1 -20487 1 -20546 1 -20601 1 -20875 1 -20892 1 -21100 1 -21158 1 -21471 1 -25994 1 -26518 1 -29857 1 -30889 1 -37053 1 -43932 1 diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 315d796..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.267e-01 1.727e-02 24.71 <2e-16 *** -r 3.935e-02 1.056e-03 37.25 <2e-16 *** -kmercov 3.014e+01 2.434e-01 123.83 <2e-16 *** -bias 2.297e+00 7.404e-02 31.02 <2e-16 *** -length 7.176e+05 7.206e+03 99.59 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 433.1 on 966 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 4.843e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 310b8ee..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3c6cb7d..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ad6b203..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 235902637.702301 -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 123aca8..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.72405% 4.14662% -Genome Haploid Length 1,863,211 bp 1,924,383 bp -Genome Repeat Length 1,360,543 bp 1,405,212 bp -Genome Unique Length 502,668 bp 519,171 bp -Model Fit 77.7406% 91.5673% -Read Error Rate 11.9223% 11.9223% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 5989f5c..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2786 +0,0 @@ -1 39002782 -2 9040768 -3 10487537 -4 11387449 -5 11810493 -6 11809760 -7 11465880 -8 10887624 -9 10100183 -10 9210777 -11 8308094 -12 7383560 -13 6484501 -14 5634142 -15 4832626 -16 4104997 -17 3452550 -18 2874718 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1 -10522 1 -10887 1 -12293 1 -12384 1 -12432 1 -12451 1 -12477 1 -12622 1 -12629 1 -13318 1 -13675 1 -19791 1 -20219 1 -20351 1 -27707 1 -27875 1 -28004 1 -30374 1 -30460 1 -30569 1 -30742 1 -30847 1 -30874 1 -31178 1 -31339 1 -31627 1 -38876 1 -39672 1 -44009 1 -46163 1 -55437 1 -68711 1 diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index ef72c00..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.788e-02 2.240e-03 25.85 <2e-16 *** -r 3.760e-02 1.258e-03 29.89 <2e-16 *** -kmercov 7.148e+00 5.946e-02 120.22 <2e-16 *** -bias 7.528e-01 4.821e-02 15.61 <2e-16 *** -length 1.007e+08 2.853e+05 352.87 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3021 on 981 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 9.02e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8ea24fb..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 81da52f..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c380199..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 21367600324926.5 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ccb94d0..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.50796% 4.01106% -Genome Haploid Length 108,106,070 bp 111,763,973 bp -Genome Repeat Length 13,047,224 bp 13,488,693 bp -Genome Unique Length 95,058,846 bp 98,275,280 bp -Model Fit 89.2573% 90.0486% -Read Error Rate 0.156361% 0.156361% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index a29a1a6..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2461 +0,0 @@ -1 294118826 -2 18814448 -3 14133387 -4 14261099 -5 14070334 -6 13445310 -7 12479976 -8 11303211 -9 9999383 -10 8699426 -11 7449255 -12 6271135 -13 5211385 -14 4270410 -15 3455351 -16 2760210 -17 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 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@@ - -Formula: y ~ ((2 * (1 - d) * (1 - (1 - r)^k)) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + ((d * (1 - (1 - r)^k)^2) + (1 - - 2 * d) * ((1 - r)^k)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.940e-01 6.497e-03 45.25 <2e-16 *** -r 4.196e-02 8.447e-04 49.68 <2e-16 *** -kmercov 2.910e+01 1.625e-01 179.03 <2e-16 *** -bias 1.980e+00 4.203e-02 47.12 <2e-16 *** -length 1.074e+06 8.829e+03 121.59 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 331.7 on 2112 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 9.419e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index befa122..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index ed82a08..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 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r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.469e-02 2.414e-03 26.80 <2e-16 *** -r 3.700e-02 7.034e-04 52.61 <2e-16 *** -kmercov 7.645e+00 5.585e-02 136.88 <2e-16 *** -bias 1.106e+00 5.445e-02 20.32 <2e-16 *** -length 8.989e+07 6.250e+05 143.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2708 on 981 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 6.736e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index eb3b30c..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 413d369..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 422890d..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 3630141467489.68 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7c1350a..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.55949% 3.84084% -Genome Haploid Length 100,497,142 bp 103,477,450 bp -Genome Repeat Length 15,920,962 bp 16,393,109 bp -Genome Unique Length 84,576,180 bp 87,084,342 bp -Model Fit 94.3748% 95.2763% -Read Error Rate 0.193467% 0.193467% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 1d740c6..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2465 +0,0 @@ -1 292703932 -2 18737175 -3 13583294 -4 13198021 -5 12726789 -6 12068309 -7 11213918 -8 10227046 -9 9135287 -10 8069723 -11 7022657 -12 6026282 -13 5115420 -14 4308042 -15 3589349 -16 2961977 -17 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- (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.339e-02 5.412e-03 13.56 < 2e-16 *** -r 3.964e-02 3.866e-03 10.26 < 2e-16 *** -kmercov 6.474e+00 1.713e-01 37.81 < 2e-16 *** -bias 7.572e-01 1.250e-01 6.06 1.94e-09 *** -length 8.871e+07 8.865e+05 100.07 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2920 on 981 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 2.129e-06 - diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ce7fc30..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 89d627e..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7f2150a..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 7711528216852.16 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ac88cbe..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.19106% 4.73728% -Genome Haploid Length 95,634,013 bp 106,317,658 bp -Genome Repeat Length 15,538,954 bp 17,274,870 bp -Genome Unique Length 80,095,060 bp 89,042,788 bp -Model Fit 92.5798% 93.4577% -Read Error Rate 1.07079% 1.07079% diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 2a77587..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2141 +0,0 @@ -1 519344169 -2 31778779 -3 17654745 -4 15913740 -5 14593876 -6 13133156 -7 11549096 -8 9961148 -9 8421060 -10 7001075 -11 5730770 -12 4620593 -13 3681382 -14 2896844 -15 2257931 -16 1745022 -17 1339491 -18 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a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9b15640..0000000 Binary files a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index f692ad8..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,305 +0,0 @@ -1 1173083 -2 48886 -3 80656 -4 127364 -5 180277 -6 241055 -7 290362 -8 333259 -9 366289 -10 379446 -11 376358 -12 354162 -13 327997 -14 293244 -15 253049 -16 212109 -17 174844 -18 139487 -19 108680 -20 82266 -21 62588 -22 46063 -23 33707 -24 23511 -25 16725 -26 12052 -27 8068 -28 5556 -29 4270 -30 2825 -31 2171 -32 1532 -33 1142 -34 1096 -35 771 -36 654 -37 595 -38 626 -39 459 -40 448 -41 431 -42 409 -43 407 -44 346 -45 330 -46 373 -47 363 -48 331 -49 296 -50 297 -51 223 -52 198 -53 224 -54 213 -55 228 -56 181 -57 214 -58 147 -59 162 -60 134 -61 119 -62 149 -63 135 -64 140 -65 129 -66 124 -67 145 -68 188 -69 190 -70 160 -71 180 -72 132 -73 151 -74 152 -75 157 -76 159 -77 152 -78 168 -79 155 -80 180 -81 144 -82 164 -83 143 -84 141 -85 123 -86 122 -87 133 -88 100 -89 103 -90 111 -91 105 -92 87 -93 92 -94 77 -95 77 -96 84 -97 71 -98 53 -99 59 -100 62 -101 75 -102 71 -103 78 -104 59 -105 51 -106 46 -107 49 -108 69 -109 52 -110 56 -111 62 -112 59 -113 37 -114 47 -115 43 -116 67 -117 34 -118 29 -119 34 -120 28 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1 -255 2 -257 1 -262 1 -279 2 -282 1 -286 1 -288 1 -299 1 -308 1 -319 1 -321 1 -355 1 -358 1 -359 1 -360 2 -363 1 -434 1 -440 1 -446 1 -447 1 -454 1 -455 1 -477 1 -486 1 -495 1 -497 1 -501 1 -505 1 -514 1 -517 2 -518 1 -521 1 -522 1 -524 1 -525 1 -528 1 -529 1 -533 1 -541 1 -551 2 -572 1 -616 1 -640 1 -651 1 -654 1 -677 2 -771 1 -797 1 -817 1 -836 1 -869 1 -908 1 -912 1 -937 1 -950 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 53176e1..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.795e-03 1.022e-03 -3.713 0.000244 *** -r 1.906e-03 3.197e-05 59.599 < 2e-16 *** -kmercov 6.016e+00 2.747e-03 2189.752 < 2e-16 *** -bias 9.528e-01 6.287e-03 151.551 < 2e-16 *** -length 4.442e+06 3.203e+03 1387.008 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 437 on 298 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.281e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4b027c4..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 096943f..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 27ca9ba..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 52481868.9037642 -round 1 trimming to 7 trying 4peak model... converged. score: 62963186.7414185 -round 2 trimming to 12 trying 4peak model... converged. score: 1988725102.07721 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a99714d..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.184171% 0.196961% -Genome Haploid Length 4,533,968 bp 4,542,258 bp -Genome Repeat Length 78,758 bp 78,902 bp -Genome Unique Length 4,455,210 bp 4,463,356 bp -Model Fit 98.9603% 99.4022% -Read Error Rate 0.0999237% 0.0999237% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 71ba052..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,272 +0,0 @@ -1 10262092 -2 265673 -3 151932 -4 221608 -5 297174 -6 362954 -7 413581 -8 437430 -9 439276 -10 409018 -11 367466 -12 318413 -13 265324 -14 213493 -15 166764 -16 126701 -17 94007 -18 67423 -19 45490 -20 31473 -21 20624 -22 13644 -23 8969 -24 5939 -25 4103 -26 2779 -27 2064 -28 1414 -29 1127 -30 827 -31 659 -32 513 -33 459 -34 451 -35 424 -36 362 -37 359 -38 297 -39 271 -40 258 -41 229 -42 276 -43 241 -44 225 -45 188 -46 184 -47 166 -48 192 -49 229 -50 209 -51 235 -52 233 -53 208 -54 211 -55 230 -56 188 -57 173 -58 177 -59 219 -60 221 -61 224 -62 243 -63 206 -64 217 -65 222 -66 199 -67 196 -68 170 -69 179 -70 160 -71 175 -72 118 -73 137 -74 141 -75 118 -76 87 -77 103 -78 97 -79 74 -80 87 -81 69 -82 67 -83 51 -84 45 -85 68 -86 54 -87 62 -88 45 -89 59 -90 55 -91 67 -92 41 -93 41 -94 51 -95 65 -96 49 -97 56 -98 70 -99 65 -100 74 -101 72 -102 62 -103 83 -104 60 -105 45 -106 48 -107 36 -108 41 -109 21 -110 22 -111 33 -112 26 -113 22 -114 22 -115 20 -116 14 -117 11 -118 11 -119 8 -120 3 -121 8 -122 7 -123 6 -124 9 -125 6 -126 12 -127 7 -128 10 -129 8 -130 7 -131 8 -132 4 -133 8 -134 3 -135 3 -136 4 -137 4 -138 5 -139 9 -140 8 -141 8 -142 11 -143 11 -144 20 -145 17 -146 24 -147 25 -148 28 -149 29 -150 24 -151 25 -152 28 -153 24 -154 22 -155 19 -156 19 -157 27 -158 19 -159 24 -160 22 -161 31 -162 25 -163 15 -164 27 -165 18 -166 17 -167 15 -168 17 -169 27 -170 14 -171 14 -172 18 -173 14 -174 14 -175 16 -176 13 -177 11 -178 14 -179 22 -180 14 -181 14 -182 6 -183 11 -184 13 -185 15 -186 20 -187 11 -188 11 -189 10 -190 10 -191 18 -192 15 -193 17 -194 8 -195 12 -196 9 -197 7 -198 14 -199 14 -200 4 -201 8 -202 8 -203 10 -204 11 -205 4 -206 4 -207 2 -208 6 -209 2 -210 5 -211 1 -212 1 -213 3 -214 3 -215 1 -217 1 -219 1 -220 1 -222 1 -224 1 -225 1 -226 1 -227 2 -228 1 -230 1 -236 1 -239 1 -261 1 -262 3 -263 1 -286 1 -294 1 -301 1 -339 1 -345 1 -346 1 -356 1 -359 1 -378 1 -383 1 -392 1 -409 1 -411 1 -416 1 -427 1 -436 1 -443 1 -449 1 -451 1 -453 3 -454 1 -457 1 -459 2 -465 1 -467 1 -477 1 -478 1 -490 1 -495 1 -496 1 -510 1 -526 1 -536 1 -669 1 -684 1 -697 1 -715 1 -721 1 -751 1 -764 1 -766 1 -790 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9f73f42..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.831e-03 1.110e-03 -1.649 0.1 -r 2.142e-03 4.623e-05 46.334 <2e-16 *** -kmercov 4.988e+00 2.740e-03 1820.380 <2e-16 *** -bias 7.569e-01 6.693e-03 113.092 <2e-16 *** -length 4.436e+06 3.772e+03 1176.075 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 445.2 on 264 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 5.997e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a9c6f31..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4b45c33..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index cac84e9..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 48949016.8922081 -round 1 trimming to 8 trying 4peak model... converged. score: 322671798.833751 -round 2 trimming to 13 trying 4peak model... converged. score: 1846659619270.62 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 20c7c11..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.204943% 0.223434% -Genome Haploid Length 4,523,568 bp 4,533,518 bp -Genome Repeat Length 83,958 bp 84,142 bp -Genome Unique Length 4,439,610 bp 4,449,376 bp -Model Fit 99.0397% 99.4979% -Read Error Rate 0.997056% 0.997056% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 6e6e740..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,232 +0,0 @@ -1 18360774 -2 621847 -3 286067 -4 373089 -5 457178 -6 503682 -7 509841 -8 479082 -9 423124 -10 356682 -11 284425 -12 216483 -13 157540 -14 110755 -15 76123 -16 50354 -17 32825 -18 20907 -19 13257 -20 8165 -21 5076 -22 3113 -23 2127 -24 1563 -25 1058 -26 922 -27 805 -28 666 -29 602 -30 560 -31 470 -32 445 -33 385 -34 408 -35 408 -36 354 -37 322 -38 302 -39 245 -40 252 -41 281 -42 273 -43 231 -44 246 -45 243 -46 222 -47 237 -48 237 -49 221 -50 238 -51 206 -52 233 -53 212 -54 221 -55 229 -56 192 -57 186 -58 178 -59 183 -60 177 -61 157 -62 153 -63 100 -64 103 -65 85 -66 99 -67 105 -68 83 -69 85 -70 89 -71 83 -72 63 -73 70 -74 71 -75 71 -76 50 -77 61 -78 65 -79 49 -80 57 -81 63 -82 68 -83 51 -84 59 -85 47 -86 48 -87 47 -88 52 -89 47 -90 39 -91 47 -92 27 -93 52 -94 26 -95 32 -96 27 -97 10 -98 20 -99 26 -100 18 -101 19 -102 15 -103 20 -104 8 -105 17 -106 16 -107 18 -108 21 -109 17 -110 27 -111 25 -112 15 -113 32 -114 27 -115 41 -116 26 -117 34 -118 27 -119 29 -120 39 -121 28 -122 32 -123 29 -124 29 -125 43 -126 35 -127 44 -128 35 -129 33 -130 28 -131 25 -132 24 -133 15 -134 17 -135 16 -136 19 -137 16 -138 21 -139 16 -140 6 -141 10 -142 16 -143 12 -144 10 -145 8 -146 9 -147 7 -148 12 -149 17 -150 5 -151 8 -152 8 -153 6 -154 5 -155 4 -156 10 -157 6 -158 9 -159 5 -160 3 -161 7 -162 6 -163 2 -164 1 -165 5 -166 4 -167 3 -168 1 -169 3 -170 2 -172 2 -173 1 -175 1 -176 2 -178 1 -179 2 -180 4 -181 1 -182 1 -183 1 -184 1 -185 2 -186 1 -192 1 -197 1 -198 1 -204 1 -206 1 -210 1 -216 1 -224 1 -228 1 -229 1 -242 1 -252 1 -260 1 -266 1 -272 1 -273 1 -287 1 -296 1 -299 1 -303 1 -314 1 -316 1 -329 1 -356 2 -358 2 -361 1 -362 2 -363 1 -364 1 -365 1 -368 1 -374 1 -376 2 -394 1 -400 1 -405 1 -411 1 -428 1 -429 1 -437 1 -547 1 -552 1 -569 1 -589 1 -611 1 -626 1 -636 1 -657 1 -682 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index c568bd0..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.062e-01 1.486e-02 13.88 <2e-16 *** -r 3.241e-02 6.615e-04 49.00 <2e-16 *** -kmercov 2.596e+01 3.025e-01 85.80 <2e-16 *** -bias 1.485e+00 8.480e-02 17.51 <2e-16 *** -length 1.290e+04 1.772e+02 72.79 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13.05 on 197 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 7.595e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 00e2b5b..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6eebd37..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9da91ab..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 309940.025535989 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 926160e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.10882% 3.37341% -Genome Haploid Length 17,617 bp 18,458 bp -Genome Repeat Length 6,961 bp 7,293 bp -Genome Unique Length 10,656 bp 11,164 bp -Model Fit 83.4112% 86.3148% -Read Error Rate 17.6859% 17.6859% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index ae61e76..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,299 +0,0 @@ -1 1205478 -2 95131 -3 134997 -4 175607 -5 217165 -6 255428 -7 282747 -8 300170 -9 312772 -10 318536 -11 309393 -12 291055 -13 271416 -14 246263 -15 223238 -16 194641 -17 167621 -18 145376 -19 120134 -20 98578 -21 80084 -22 65688 -23 52738 -24 40811 -25 30720 -26 24474 -27 18586 -28 14479 -29 11029 -30 8062 -31 6322 -32 4894 -33 3728 -34 2716 -35 2093 -36 1417 -37 1268 -38 1085 -39 807 -40 692 -41 592 -42 522 -43 385 -44 324 -45 336 -46 294 -47 239 -48 225 -49 284 -50 233 -51 214 -52 236 -53 174 -54 161 -55 161 -56 188 -57 177 -58 186 -59 187 -60 144 -61 141 -62 163 -63 178 -64 170 -65 158 -66 194 -67 164 -68 167 -69 127 -70 164 -71 148 -72 161 -73 173 -74 148 -75 166 -76 159 -77 158 -78 173 -79 180 -80 150 -81 170 -82 145 -83 150 -84 156 -85 164 -86 141 -87 128 -88 126 -89 104 -90 111 -91 109 -92 93 -93 90 -94 75 -95 103 -96 79 -97 55 -98 69 -99 79 -100 59 -101 60 -102 76 -103 47 -104 51 -105 72 -106 49 -107 48 -108 41 -109 37 -110 34 -111 36 -112 35 -113 36 -114 40 -115 30 -116 34 -117 30 -118 36 -119 30 -120 36 -121 38 -122 36 -123 42 -124 38 -125 38 -126 38 -127 28 -128 28 -129 23 -130 33 -131 34 -132 29 -133 28 -134 22 -135 40 -136 28 -137 35 -138 29 -139 36 -140 49 -141 36 -142 29 -143 22 -144 23 -145 16 -146 19 -147 21 -148 19 -149 21 -150 14 -151 18 -152 11 -153 23 -154 14 -155 21 -156 30 -157 24 -158 13 -159 20 -160 18 -161 21 -162 18 -163 28 -164 20 -165 37 -166 32 -167 33 -168 33 -169 28 -170 36 -171 40 -172 28 -173 26 -174 27 -175 18 -176 29 -177 21 -178 25 -179 21 -180 23 -181 20 -182 22 -183 18 -184 24 -185 21 -186 14 -187 9 -188 14 -189 13 -190 13 -191 11 -192 13 -193 7 -194 14 -195 9 -196 12 -197 4 -198 9 -199 9 -200 16 -201 4 -202 17 -203 13 -204 16 -205 12 -206 15 -207 8 -208 14 -209 17 -210 19 -211 17 -212 10 -213 15 -214 8 -215 13 -216 6 -217 17 -218 6 -219 9 -220 12 -221 6 -222 3 -223 6 -224 6 -225 6 -226 2 -227 5 -228 4 -229 1 -231 3 -232 3 -233 1 -234 7 -235 4 -236 1 -237 1 -242 1 -244 3 -245 1 -246 1 -256 1 -259 1 -261 1 -281 1 -295 1 -296 1 -298 1 -309 1 -311 1 -318 1 -337 1 -355 1 -388 1 -393 1 -395 1 -400 1 -402 1 -403 1 -406 1 -461 1 -468 1 -469 1 -472 1 -479 1 -493 1 -503 1 -513 1 -527 1 -532 1 -541 1 -555 1 -558 1 -559 1 -561 1 -564 1 -567 1 -568 1 -574 2 -576 1 -577 1 -578 1 -589 1 -602 2 -607 1 -667 1 -692 1 -695 1 -701 1 -735 1 -743 1 -822 1 -837 1 -848 1 -887 1 -913 1 -923 1 -945 1 -959 1 -972 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8179c20..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -8.711e-03 2.030e-03 -4.292 2.41e-05 *** -r 4.627e-03 8.238e-05 56.162 < 2e-16 *** -kmercov 6.380e+00 5.780e-03 1103.798 < 2e-16 *** -bias 1.671e+00 1.790e-02 93.326 < 2e-16 *** -length 4.216e+06 6.442e+03 654.434 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 460.3 on 292 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.37e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 51702ca..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 42db13e..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b310828..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 59627203.0995971 -round 1 trimming to 7 trying 4peak model... converged. score: 66670663.9268915 -round 2 trimming to 12 trying 4peak model... converged. score: 15902289926.6391 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7f39f14..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.446191% 0.479143% -Genome Haploid Length 4,271,311 bp 4,286,817 bp -Genome Repeat Length 26,696 bp 26,793 bp -Genome Unique Length 4,244,614 bp 4,260,024 bp -Model Fit 98.8994% 99.3166% -Read Error Rate 0.0997885% 0.0997885% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index dcffb02..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,264 +0,0 @@ -1 10296022 -2 337480 -3 208279 -4 260925 -5 308972 -6 343099 -7 362631 -8 370179 -9 359361 -10 340066 -11 310091 -12 277480 -13 239587 -14 203273 -15 167445 -16 136737 -17 109976 -18 86304 -19 66477 -20 50857 -21 37298 -22 28208 -23 20895 -24 15447 -25 10840 -26 7963 -27 5583 -28 4179 -29 2912 -30 2224 -31 1799 -32 1366 -33 1004 -34 801 -35 742 -36 613 -37 478 -38 393 -39 408 -40 354 -41 280 -42 292 -43 247 -44 232 -45 243 -46 224 -47 199 -48 229 -49 189 -50 185 -51 200 -52 212 -53 203 -54 191 -55 189 -56 208 -57 149 -58 166 -59 164 -60 155 -61 196 -62 153 -63 161 -64 152 -65 167 -66 198 -67 202 -68 168 -69 170 -70 194 -71 198 -72 169 -73 189 -74 176 -75 173 -76 148 -77 156 -78 142 -79 167 -80 121 -81 124 -82 110 -83 100 -84 92 -85 87 -86 84 -87 63 -88 57 -89 54 -90 56 -91 49 -92 42 -93 32 -94 45 -95 47 -96 37 -97 19 -98 29 -99 32 -100 23 -101 26 -102 25 -103 20 -104 24 -105 25 -106 18 -107 21 -108 13 -109 16 -110 26 -111 17 -112 27 -113 16 -114 27 -115 26 -116 25 -117 23 -118 24 -119 24 -120 12 -121 30 -122 24 -123 31 -124 28 -125 9 -126 24 -127 12 -128 15 -129 6 -130 13 -131 10 -132 18 -133 14 -134 15 -135 20 -136 16 -137 22 -138 27 -139 31 -140 28 -141 21 -142 19 -143 25 -144 37 -145 20 -146 32 -147 24 -148 23 -149 26 -150 21 -151 24 -152 14 -153 14 -154 16 -155 27 -156 21 -157 22 -158 21 -159 24 -160 22 -161 21 -162 13 -163 17 -164 16 -165 22 -166 31 -167 24 -168 28 -169 18 -170 16 -171 17 -172 15 -173 17 -174 21 -175 19 -176 23 -177 18 -178 20 -179 25 -180 17 -181 19 -182 14 -183 8 -184 12 -185 13 -186 8 -187 7 -188 10 -189 15 -190 7 -191 9 -192 11 -193 11 -194 12 -195 12 -196 7 -197 9 -198 6 -199 4 -200 5 -201 5 -202 5 -203 2 -205 2 -206 1 -207 5 -208 1 -211 1 -212 1 -237 1 -238 1 -239 1 -243 1 -250 1 -252 1 -253 1 -255 1 -257 1 -261 1 -277 1 -295 1 -298 1 -299 1 -303 1 -317 1 -318 1 -321 1 -326 1 -335 1 -347 1 -349 1 -356 1 -361 1 -377 1 -398 1 -420 1 -443 1 -446 1 -454 2 -455 1 -473 1 -474 1 -477 1 -479 1 -480 1 -481 1 -483 1 -488 2 -494 1 -504 2 -506 1 -521 1 -527 1 -533 1 -536 1 -627 1 -669 1 -685 1 -717 1 -727 1 -752 1 -767 1 -780 1 -785 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 24decf1..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.820e-02 2.098e-03 8.675 5.93e-16 *** -r 2.189e-02 4.711e-03 4.646 5.53e-06 *** -kmercov 6.107e+00 1.223e-01 49.952 < 2e-16 *** -bias 7.197e-01 6.175e-02 11.655 < 2e-16 *** -length 3.779e+06 9.822e+04 38.470 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 103.1 on 244 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.403e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2c41dcd..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 5663aec..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1f84a1c..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 53536858117.1902 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 15dacf6..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.24667% 3.13109% -Genome Haploid Length 3,565,896 bp 3,863,350 bp -Genome Repeat Length -10,230 bp -11,083 bp -Genome Unique Length 3,576,126 bp 3,874,433 bp -Model Fit 86.6831% 86.8379% -Read Error Rate 0.984254% 0.984254% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 7ca475e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,229 +0,0 @@ -1 18348439 -2 723933 -3 331528 -4 382227 -5 425471 -6 441407 -7 432268 -8 401917 -9 360842 -10 312124 -11 263499 -12 211479 -13 167361 -14 129143 -15 97678 -16 72193 -17 52774 -18 37260 -19 25664 -20 17614 -21 11988 -22 8274 -23 5356 -24 3614 -25 2594 -26 1795 -27 1332 -28 970 -29 724 -30 600 -31 491 -32 447 -33 355 -34 330 -35 307 -36 285 -37 254 -38 232 -39 265 -40 261 -41 272 -42 225 -43 217 -44 221 -45 218 -46 225 -47 206 -48 213 -49 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a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4749ab3..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 05f24c3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,334 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7 -246 4 -247 6 -248 5 -249 3 -250 10 -251 5 -252 5 -253 2 -254 6 -255 3 -256 10 -257 6 -258 6 -259 6 -260 5 -261 9 -262 5 -263 2 -264 10 -265 7 -266 1 -267 4 -268 2 -269 3 -270 5 -271 3 -272 3 -273 4 -274 3 -275 4 -276 1 -277 2 -278 1 -279 1 -280 4 -281 1 -282 2 -284 3 -285 2 -286 1 -287 1 -300 1 -317 1 -323 1 -326 1 -327 1 -329 1 -351 1 -353 1 -376 1 -423 1 -427 1 -436 1 -437 1 -450 1 -459 1 -477 1 -482 1 -485 1 -512 1 -520 1 -522 1 -527 1 -528 1 -529 2 -531 1 -539 1 -542 2 -544 2 -545 1 -551 1 -552 1 -557 1 -567 1 -622 1 -650 1 -655 1 -659 1 -684 1 -689 1 -757 1 -775 1 -794 1 -832 1 -859 1 -904 1 -928 1 -933 1 -963 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8a93cff..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.025e-02 2.998e-03 -3.417 0.000714 *** -r 8.798e-03 3.203e-04 27.468 < 2e-16 *** -kmercov 6.950e+00 2.186e-02 317.900 < 2e-16 *** -bias 2.144e+00 4.311e-02 49.735 < 2e-16 *** -length 3.883e+06 1.809e+04 214.679 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 352.5 on 322 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 6.362e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 28ca625..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2c15dd9..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 307625f..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 61761984.0293338 -round 1 trimming to 7 trying 4peak model... converged. score: 56289459.5028937 -round 2 trimming to 12 trying 4peak model... unconverged -round 3 trimming to 17 trying 4peak model... converged. score: 275654193.807585 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 64923e7..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.81573% 0.943848% -Genome Haploid Length 3,902,973 bp 3,952,393 bp -Genome Repeat Length 5,981 bp 6,057 bp -Genome Unique Length 3,896,992 bp 3,946,337 bp -Model Fit 98.906% 99.2896% -Read Error Rate 0.100309% 0.100309% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 73b9ca6..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,268 +0,0 @@ -1 10292181 -2 383890 -3 235102 -4 268585 -5 300145 -6 316285 -7 324701 -8 326628 -9 316350 -10 296276 -11 275789 -12 249694 -13 219416 -14 192254 -15 163029 -16 138939 -17 116066 -18 95729 -19 78753 -20 62602 -21 50268 -22 39675 -23 30455 -24 23834 -25 18390 -26 13421 -27 10028 -28 7418 -29 5810 -30 4337 -31 3504 -32 2497 -33 1909 -34 1469 -35 1125 -36 914 -37 780 -38 635 -39 484 -40 455 -41 368 -42 305 -43 310 -44 235 -45 262 -46 248 -47 266 -48 236 -49 223 -50 240 -51 189 -52 180 -53 200 -54 184 -55 192 -56 159 -57 176 -58 189 -59 175 -60 173 -61 187 -62 191 -63 180 -64 210 -65 199 -66 189 -67 172 -68 182 -69 183 -70 160 -71 153 -72 179 -73 145 -74 142 -75 119 -76 86 -77 83 -78 102 -79 73 -80 110 -81 104 -82 90 -83 90 -84 78 -85 75 -86 71 -87 77 -88 65 -89 61 -90 61 -91 60 -92 44 -93 49 -94 37 -95 61 -96 50 -97 42 -98 32 -99 31 -100 26 -101 37 -102 33 -103 39 -104 39 -105 36 -106 36 -107 48 -108 27 -109 26 -110 40 -111 23 -112 40 -113 22 -114 32 -115 25 -116 22 -117 28 -118 27 -119 26 -120 27 -121 27 -122 22 -123 36 -124 29 -125 24 -126 31 -127 45 -128 25 -129 26 -130 21 -131 15 -132 19 -133 19 -134 19 -135 15 -136 12 -137 12 -138 11 -139 12 -140 13 -141 4 -142 2 -143 6 -144 9 -145 12 -146 11 -147 9 -148 12 -149 16 -150 13 -151 19 -152 13 -153 14 -154 21 -155 31 -156 24 -157 21 -158 21 -159 22 -160 21 -161 21 -162 18 -163 31 -164 29 -165 38 -166 34 -167 30 -168 28 -169 18 -170 30 -171 23 -172 30 -173 27 -174 26 -175 19 -176 23 -177 23 -178 12 -179 28 -180 19 -181 21 -182 16 -183 19 -184 11 -185 12 -186 10 -187 11 -188 17 -189 11 -190 14 -191 10 -192 10 -193 15 -194 8 -195 10 -196 6 -197 15 -198 17 -199 14 -200 7 -201 9 -202 10 -203 11 -204 4 -205 7 -206 6 -207 5 -208 5 -209 2 -210 3 -211 4 -212 1 -213 1 -214 1 -215 1 -216 1 -218 1 -221 3 -222 3 -223 1 -227 1 -233 1 -242 1 -250 1 -263 1 -280 2 -284 1 -287 1 -369 1 -383 1 -389 1 -390 1 -395 1 -397 1 -403 1 -404 1 -407 1 -409 1 -414 2 -417 1 -431 1 -444 1 -447 1 -449 1 -453 1 -454 1 -457 1 -464 1 -472 1 -473 1 -476 1 -480 1 -482 1 -491 1 -548 1 -555 1 -556 1 -589 1 -596 1 -610 1 -615 1 -618 2 -644 1 -662 1 -685 1 -700 1 -712 1 -727 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1ea27af..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.857e-02 1.864e-03 9.964 <2e-16 *** -r 2.985e-02 1.809e-03 16.500 <2e-16 *** -kmercov 6.886e+00 8.087e-02 85.151 <2e-16 *** -bias 9.184e-01 5.188e-02 17.701 <2e-16 *** -length 3.377e+06 1.338e+04 252.426 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 103 on 248 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 4.842e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7ef0b1c..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index df37f52..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 13e3774..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 38822936698.6775 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 30c27a8..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.62275% 3.34628% -Genome Haploid Length 3,202,172 bp 3,356,214 bp -Genome Repeat Length -50,118 bp -52,528 bp -Genome Unique Length 3,252,290 bp 3,408,743 bp -Model Fit 87.297% 87.4777% -Read Error Rate 1.0007% 1.0007% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index a5079ef..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,239 +0,0 @@ -1 18324219 -2 780873 -3 343318 -4 368096 -5 387418 -6 392167 -7 379202 -8 357318 -9 323871 -10 285723 -11 245218 -12 206674 -13 167596 -14 134463 -15 106965 -16 82756 -17 63733 -18 49115 -19 36905 -20 27149 -21 19710 -22 14587 -23 10255 -24 7501 -25 5512 -26 4095 -27 3045 -28 2175 -29 1611 -30 1248 -31 1002 -32 797 -33 629 -34 515 -35 451 -36 397 -37 397 -38 365 -39 315 -40 253 -41 257 -42 252 -43 274 -44 237 -45 211 -46 233 -47 211 -48 235 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a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6c64ff0..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index a429f02..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,302 +0,0 @@ -1 1248514 -2 167745 -3 236549 -4 291685 -5 338848 -6 375053 -7 392205 -8 401623 -9 398642 -10 384108 -11 363454 -12 335061 -13 298258 -14 261520 -15 222175 -16 182927 -17 149133 -18 117760 -19 91573 -20 70743 -21 51785 -22 38378 -23 27369 -24 19566 -25 13551 -26 9717 -27 6613 -28 4943 -29 3531 -30 2319 -31 1615 -32 1239 -33 1008 -34 799 -35 650 -36 538 -37 498 -38 458 -39 424 -40 395 -41 342 -42 309 -43 291 -44 299 -45 324 -46 307 -47 235 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a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 69f1cf6..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.329e-02 1.399e-03 -9.501 <2e-16 *** -r 1.028e-02 8.375e-05 122.713 <2e-16 *** -kmercov 5.992e+00 6.691e-03 895.627 <2e-16 *** -bias 1.038e+00 1.065e-02 97.387 <2e-16 *** -length 4.508e+06 6.555e+03 687.708 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 472.8 on 295 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 4.711e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 821b7cd..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3113708..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4b8bc23..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 56738106.5183965 -round 1 trimming to 7 trying 4peak model... converged. score: 74475370.3941796 -round 2 trimming to 12 trying 4peak model... converged. score: 15486627727.4355 -round 3 trimming to 17 trying 4peak model... converged. score: 7630987846624.32 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 553ccc3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.01098% 1.04448% -Genome Haploid Length 4,544,762 bp 4,565,105 bp -Genome Repeat Length -10,338 bp -10,385 bp -Genome Unique Length 4,555,100 bp 4,575,490 bp -Model Fit 98.9912% 99.4911% -Read Error Rate 0.100824% 0.100824% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 1f3654e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,243 +0,0 @@ -1 10377843 -2 415285 -3 338885 -4 403950 -5 448390 -6 474471 -7 473536 -8 456530 -9 427979 -10 384352 -11 337339 -12 283046 -13 230947 -14 182566 -15 141416 -16 106884 -17 77071 -18 55952 -19 38598 -20 26994 -21 17543 -22 11530 -23 7881 -24 5227 -25 3453 -26 2193 -27 1597 -28 1267 -29 1037 -30 773 -31 617 -32 540 -33 440 -34 401 -35 380 -36 381 -37 347 -38 336 -39 267 -40 269 -41 251 -42 235 -43 257 -44 211 -45 199 -46 216 -47 241 -48 244 -49 216 -50 203 -51 195 -52 179 -53 148 -54 187 -55 206 -56 176 -57 211 -58 222 -59 212 -60 182 -61 192 -62 183 -63 181 -64 201 -65 183 -66 147 -67 156 -68 143 -69 135 -70 119 -71 107 -72 110 -73 92 -74 95 -75 97 -76 85 -77 73 -78 86 -79 71 -80 65 -81 48 -82 58 -83 47 -84 61 -85 55 -86 46 -87 59 -88 46 -89 58 -90 66 -91 66 -92 81 -93 82 -94 48 -95 58 -96 66 -97 52 -98 46 -99 61 -100 55 -101 35 -102 56 -103 36 -104 52 -105 26 -106 40 -107 36 -108 31 -109 21 -110 18 -111 14 -112 20 -113 13 -114 16 -115 18 -116 20 -117 13 -118 14 -119 13 -120 11 -121 13 -122 13 -123 14 -124 12 -125 11 -126 10 -127 16 -128 15 -129 17 -130 24 -131 28 -132 21 -133 22 -134 23 -135 38 -136 30 -137 37 -138 29 -139 41 -140 28 -141 41 -142 32 -143 32 -144 28 -145 22 -146 33 -147 28 -148 29 -149 39 -150 19 -151 25 -152 25 -153 29 -154 19 -155 28 -156 14 -157 14 -158 13 -159 18 -160 17 -161 16 -162 16 -163 15 -164 16 -165 19 -166 5 -167 9 -168 15 -169 6 -170 8 -171 8 -172 7 -173 3 -174 3 -175 5 -176 3 -177 6 -178 3 -179 4 -180 3 -181 4 -182 4 -183 4 -184 1 -185 5 -186 2 -187 2 -189 1 -190 2 -191 2 -192 2 -193 1 -196 1 -202 1 -206 1 -216 1 -228 1 -240 1 -242 1 -251 1 -255 1 -259 1 -261 1 -268 1 -270 1 -331 1 -364 1 -365 1 -377 1 -378 1 -382 1 -384 1 -406 1 -407 1 -409 1 -416 1 -422 1 -428 3 -431 1 -432 2 -440 2 -441 1 -448 1 -459 1 -467 1 -468 1 -482 1 -490 2 -510 1 -525 1 -545 1 -555 1 -559 1 -561 1 -570 1 -610 1 -613 1 -616 1 -668 1 -682 1 -693 1 -708 1 -719 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index aa46f17..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.001e-01 1.966e-02 15.27 <2e-16 *** -r 3.503e-02 1.138e-03 30.77 <2e-16 *** -kmercov 2.736e+01 3.161e-01 86.55 <2e-16 *** -bias 1.099e+00 6.764e-02 16.25 <2e-16 *** -length 1.323e+04 2.141e+02 61.77 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 19.2 on 208 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 9.983e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 66c4d48..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6e4e011..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fb179a9..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 3315601.41878264 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f22f841..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.27492% 3.73026% -Genome Haploid Length 20,472 bp 21,441 bp -Genome Repeat Length 10,347 bp 10,836 bp -Genome Unique Length 10,125 bp 10,604 bp -Model Fit 71.9314% 75.4553% -Read Error Rate 16.8875% 16.8875% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 454177f..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,210 +0,0 @@ -1 18549680 -2 804346 -3 494903 -4 546340 -5 567915 -6 560445 -7 521038 -8 458956 -9 390239 -10 316242 -11 246533 -12 186447 -13 134257 -14 93799 -15 63519 -16 41498 -17 27115 -18 17712 -19 11024 -20 7003 -21 4474 -22 2867 -23 1895 -24 1398 -25 1097 -26 815 -27 596 -28 562 -29 509 -30 454 -31 386 -32 359 -33 353 -34 381 -35 300 -36 310 -37 323 -38 306 -39 277 -40 286 -41 277 -42 207 -43 238 -44 240 -45 228 -46 232 -47 210 -48 183 -49 192 -50 247 -51 239 -52 230 -53 213 -54 221 -55 171 -56 201 -57 174 -58 158 -59 169 -60 149 -61 131 -62 144 -63 100 -64 92 -65 109 -66 109 -67 74 -68 77 -69 75 -70 71 -71 58 -72 58 -73 46 -74 50 -75 41 -76 36 -77 28 -78 32 -79 26 -80 38 -81 23 -82 31 -83 34 -84 22 -85 26 -86 30 -87 45 -88 45 -89 42 -90 41 -91 34 -92 36 -93 31 -94 34 -95 29 -96 28 -97 26 -98 20 -99 15 -100 19 -101 27 -102 18 -103 22 -104 19 -105 26 -106 26 -107 26 -108 26 -109 23 -110 13 -111 26 -112 19 -113 21 -114 30 -115 29 -116 34 -117 31 -118 25 -119 29 -120 25 -121 27 -122 18 -123 29 -124 29 -125 24 -126 25 -127 23 -128 24 -129 26 -130 27 -131 22 -132 28 -133 23 -134 24 -135 29 -136 30 -137 21 -138 16 -139 12 -140 24 -141 17 -142 11 -143 10 -144 15 -145 19 -146 10 -147 6 -148 14 -149 12 -150 11 -151 12 -152 5 -153 6 -154 7 -155 5 -156 6 -157 3 -158 2 -160 2 -164 1 -167 1 -173 1 -178 1 -183 1 -188 1 -189 1 -203 1 -214 1 -218 1 -232 1 -277 2 -279 1 -284 1 -293 1 -300 1 -311 2 -332 1 -333 1 -341 1 -342 1 -344 1 -349 1 -351 1 -352 1 -353 1 -357 1 -360 1 -361 1 -364 1 -365 1 -366 1 -368 1 -369 1 -378 1 -385 1 -420 1 -422 1 -431 1 -449 1 -458 1 -466 1 -475 1 -488 1 -495 1 -502 1 -534 1 -549 1 -558 1 -584 1 -585 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d799fd3..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index fe12a9c..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 954e9c8..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,313 +0,0 @@ -1 1289948 -2 215155 -3 265337 -4 305488 -5 333918 -6 350764 -7 361256 -8 360973 -9 345821 -10 335650 -11 314394 -12 286119 -13 258758 -14 226832 -15 200991 -16 173299 -17 149712 -18 126814 -19 103766 -20 84825 -21 69993 -22 54482 -23 43671 -24 34037 -25 26910 -26 20627 -27 16116 -28 12002 -29 8918 -30 6932 -31 5309 -32 4008 -33 2579 -34 2283 -35 1732 -36 1268 -37 1002 -38 769 -39 700 -40 633 -41 474 -42 386 -43 334 -44 293 -45 326 -46 261 -47 249 -48 199 -49 241 -50 262 -51 214 -52 235 -53 202 -54 188 -55 191 -56 170 -57 174 -58 183 -59 220 -60 187 -61 178 -62 178 -63 175 -64 181 -65 172 -66 148 -67 148 -68 146 -69 169 -70 189 -71 183 -72 155 -73 152 -74 138 -75 150 -76 134 -77 129 -78 106 -79 118 -80 110 -81 76 -82 69 -83 72 -84 68 -85 91 -86 68 -87 71 -88 106 -89 92 -90 77 -91 79 -92 85 -93 100 -94 102 -95 72 -96 95 -97 60 -98 86 -99 80 -100 66 -101 72 -102 58 -103 47 -104 38 -105 35 -106 47 -107 48 -108 34 -109 32 -110 49 -111 50 -112 46 -113 38 -114 46 -115 37 -116 45 -117 28 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3 -249 3 -250 1 -251 3 -252 3 -253 1 -254 1 -255 1 -256 1 -257 1 -258 2 -260 1 -261 2 -262 1 -263 3 -264 2 -265 4 -266 1 -267 1 -268 1 -269 2 -270 2 -271 1 -272 1 -278 1 -287 1 -289 2 -291 1 -316 1 -371 1 -423 1 -427 1 -429 1 -439 1 -442 1 -454 1 -455 2 -456 1 -461 1 -466 1 -469 1 -473 1 -482 1 -506 2 -510 1 -513 1 -514 2 -526 2 -528 1 -529 1 -541 1 -544 1 -575 1 -615 1 -622 1 -632 2 -643 1 -672 1 -683 1 -689 1 -711 1 -777 1 -784 1 -800 1 -827 1 -836 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1855c3d..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.355e-02 2.159e-03 6.274 1.26e-09 *** -r 1.759e-02 2.922e-03 6.018 5.25e-09 *** -kmercov 6.795e+00 1.189e-01 57.144 < 2e-16 *** -bias 1.152e+00 6.989e-02 16.481 < 2e-16 *** -length 3.798e+06 2.077e+04 182.897 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 152.9 on 293 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 9.414e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index da2dbd1..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index f994341..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b924f09..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 1354794371.69549 -round 1 trimming to 20 trying 4peak model... converged. score: 1036110075941.91 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c8678cb..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.17416% 2.34294% -Genome Haploid Length 3,847,219 bp 4,126,286 bp -Genome Repeat Length 222,388 bp 238,519 bp -Genome Unique Length 3,624,831 bp 3,887,767 bp -Model Fit 97.0455% 97.3141% -Read Error Rate 0.142986% 0.142986% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 5fbaa18..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,256 +0,0 @@ -1 10402345 -2 471272 -3 359205 -4 399247 -5 420521 -6 425706 -7 414162 -8 395498 -9 369862 -10 336091 -11 295862 -12 256290 -13 218047 -14 179789 -15 147257 -16 119443 -17 94748 -18 73601 -19 56945 -20 42729 -21 31919 -22 23877 -23 17691 -24 12720 -25 9068 -26 6510 -27 4843 -28 3613 -29 2545 -30 1969 -31 1504 -32 1113 -33 916 -34 730 -35 567 -36 440 -37 487 -38 422 -39 349 -40 388 -41 303 -42 362 -43 326 -44 249 -45 248 -46 250 -47 246 -48 237 -49 244 -50 218 -51 211 -52 228 -53 253 -54 230 -55 250 -56 238 -57 230 -58 221 -59 207 -60 189 -61 185 -62 186 -63 190 -64 144 -65 151 -66 163 -67 145 -68 143 -69 139 -70 153 -71 139 -72 121 -73 101 -74 116 -75 90 -76 89 -77 88 -78 96 -79 82 -80 81 -81 85 -82 89 -83 87 -84 78 -85 55 -86 65 -87 37 -88 45 -89 49 -90 45 -91 37 -92 29 -93 27 -94 29 -95 26 -96 28 -97 28 -98 21 -99 23 -100 27 -101 33 -102 26 -103 21 -104 28 -105 36 -106 24 -107 23 -108 20 -109 13 -110 25 -111 14 -112 9 -113 23 -114 17 -115 13 -116 9 -117 20 -118 13 -119 21 -120 15 -121 9 -122 10 -123 10 -124 8 -125 6 -126 8 -127 14 -128 13 -129 14 -130 14 -131 22 -132 15 -133 14 -134 14 -135 16 -136 29 -137 20 -138 24 -139 30 -140 31 -141 30 -142 31 -143 39 -144 25 -145 33 -146 31 -147 25 -148 37 -149 35 -150 23 -151 24 -152 22 -153 15 -154 21 -155 21 -156 23 -157 26 -158 19 -159 28 -160 22 -161 18 -162 14 -163 18 -164 27 -165 25 -166 11 -167 12 -168 11 -169 12 -170 7 -171 13 -172 11 -173 8 -174 7 -175 7 -176 10 -177 7 -178 9 -179 3 -180 4 -181 6 -182 5 -183 5 -184 3 -185 2 -186 3 -187 5 -188 1 -189 4 -190 7 -191 6 -192 4 -193 1 -194 4 -195 1 -196 2 -198 4 -199 2 -200 3 -201 1 -202 5 -203 1 -204 2 -205 1 -206 3 -207 1 -209 1 -211 1 -214 2 -217 1 -248 2 -280 1 -288 1 -310 1 -339 1 -340 1 -343 1 -344 1 -361 1 -364 1 -365 1 -375 1 -377 1 -379 1 -381 1 -382 1 -388 1 -391 1 -398 1 -400 1 -407 1 -415 1 -445 1 -449 1 -452 1 -454 1 -456 1 -457 1 -461 1 -462 1 -463 1 -470 1 -481 1 -488 1 -505 1 -506 1 -515 1 -605 1 -614 1 -618 1 -655 1 -663 1 -690 1 -698 1 -715 1 -734 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index cbc5aec..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.852e-02 2.705e-03 6.847 6.47e-11 *** -r 2.093e-02 6.469e-03 3.236 0.00139 ** -kmercov 5.890e+00 1.678e-01 35.106 < 2e-16 *** -bias 7.821e-01 8.165e-02 9.579 < 2e-16 *** -length 3.545e+06 1.149e+05 30.859 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 97.53 on 236 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 2.669e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index aecf945..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index f99238b..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1f68e0e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 2937566461.71671 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 31b456a..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.799523% 3.3873% -Genome Haploid Length 3,579,438 bp 4,011,923 bp -Genome Repeat Length 279,489 bp 313,258 bp -Genome Unique Length 3,299,949 bp 3,698,665 bp -Model Fit 95.7316% 95.9851% -Read Error Rate 1.06028% 1.06028% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index cf90e75..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,229 +0,0 @@ -1 18558516 -2 859674 -3 492434 -4 508870 -5 513264 -6 491868 -7 454713 -8 405076 -9 348568 -10 292418 -11 239979 -12 190031 -13 145548 -14 111471 -15 82308 -16 60262 -17 43588 -18 30513 -19 21245 -20 14846 -21 10266 -22 7167 -23 4999 -24 3376 -25 2425 -26 1647 -27 1286 -28 899 -29 764 -30 583 -31 487 -32 407 -33 374 -34 371 -35 325 -36 289 -37 298 -38 279 -39 297 -40 301 -41 295 -42 307 -43 259 -44 237 -45 259 -46 223 -47 235 -48 222 -49 238 -50 200 -51 194 -52 226 -53 197 -54 188 -55 168 -56 172 -57 160 -58 135 -59 116 -60 126 -61 84 -62 77 -63 86 -64 101 -65 86 -66 100 -67 91 -68 71 -69 69 -70 81 -71 66 -72 77 -73 80 -74 61 -75 77 -76 49 -77 54 -78 56 -79 48 -80 31 -81 36 -82 37 -83 37 -84 31 -85 33 -86 32 -87 29 -88 11 -89 22 -90 10 -91 20 -92 19 -93 15 -94 22 -95 16 -96 16 -97 20 -98 25 -99 20 -100 22 -101 18 -102 27 -103 29 -104 28 -105 30 -106 37 -107 25 -108 27 -109 27 -110 28 -111 25 -112 27 -113 27 -114 34 -115 33 -116 30 -117 33 -118 24 -119 21 -120 22 -121 21 -122 27 -123 14 -124 14 -125 19 -126 15 -127 12 -128 8 -129 12 -130 13 -131 10 -132 13 -133 14 -134 13 -135 11 -136 11 -137 15 -138 11 -139 9 -140 8 -141 10 -142 12 -143 9 -144 8 -145 8 -146 5 -147 8 -148 8 -149 4 -150 3 -151 11 -152 8 -153 15 -154 9 -155 18 -156 10 -157 16 -158 13 -159 9 -160 6 -161 3 -162 7 -163 9 -164 10 -165 16 -166 8 -167 6 -168 8 -169 3 -170 7 -171 5 -172 1 -173 5 -174 7 -175 4 -176 4 -177 2 -178 1 -179 5 -180 1 -181 4 -183 1 -184 1 -187 1 -188 1 -191 1 -192 1 -206 1 -218 1 -260 1 -263 1 -269 1 -273 1 -274 1 -276 1 -283 1 -299 2 -300 1 -307 2 -309 2 -310 1 -314 1 -316 1 -319 1 -325 1 -327 1 -343 1 -349 1 -351 1 -353 1 -356 1 -359 1 -365 1 -376 1 -384 1 -386 1 -392 1 -409 1 -410 1 -411 1 -454 1 -462 1 -473 1 -484 1 -492 1 -499 1 -509 1 -516 1 -530 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9cbb15d..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.354e-01 1.623e-02 14.50 <2e-16 *** -r 4.069e-02 1.561e-03 26.06 <2e-16 *** -kmercov 2.291e+01 2.497e-01 91.76 <2e-16 *** -bias 9.691e-01 7.756e-02 12.49 <2e-16 *** -length 1.416e+04 2.462e+02 57.53 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12.72 on 194 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 6.441e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d0db0ea..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 5222ffc..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b72085b..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 63563768.4366049 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4b9260f..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.75667% 4.38114% -Genome Haploid Length 25,063 bp 26,180 bp -Genome Repeat Length 13,360 bp 13,955 bp -Genome Unique Length 11,703 bp 12,225 bp -Model Fit 47.6072% 48.7581% -Read Error Rate 16.7926% 16.7926% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 44cc4db..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,299 +0,0 @@ -1 1274925 -2 222912 -3 281446 -4 305040 -5 318278 -6 325429 -7 324632 -8 323771 -9 315791 -10 295513 -11 277733 -12 256238 -13 236748 -14 212207 -15 188067 -16 166222 -17 144888 -18 124676 -19 105619 -20 91514 -21 76879 -22 63420 -23 52879 -24 44285 -25 36056 -26 30339 -27 24086 -28 19023 -29 15100 -30 12374 -31 9628 -32 7761 -33 6120 -34 4943 -35 3863 -36 3128 -37 2501 -38 1953 -39 1505 -40 1391 -41 1076 -42 784 -43 768 -44 496 -45 454 -46 471 -47 379 -48 318 -49 309 -50 221 -51 243 -52 259 -53 186 -54 231 -55 187 -56 219 -57 201 -58 262 -59 198 -60 239 -61 224 -62 222 -63 203 -64 198 -65 190 -66 145 -67 165 -68 179 -69 173 -70 158 -71 196 -72 168 -73 198 -74 168 -75 132 -76 154 -77 153 -78 116 -79 137 -80 94 -81 124 -82 93 -83 105 -84 118 -85 124 -86 129 -87 91 -88 92 -89 84 -90 106 -91 69 -92 67 -93 66 -94 84 -95 67 -96 57 -97 45 -98 57 -99 58 -100 67 -101 45 -102 31 -103 48 -104 46 -105 45 -106 45 -107 47 -108 47 -109 45 -110 43 -111 55 -112 43 -113 59 -114 39 -115 42 -116 32 -117 25 -118 50 -119 49 -120 41 -121 27 -122 42 -123 31 -124 30 -125 21 -126 20 -127 23 -128 24 -129 33 -130 21 -131 21 -132 24 -133 23 -134 24 -135 36 -136 26 -137 32 -138 19 -139 28 -140 22 -141 29 -142 34 -143 17 -144 33 -145 38 -146 27 -147 22 -148 33 -149 36 -150 23 -151 21 -152 13 -153 31 -154 13 -155 23 -156 17 -157 26 -158 15 -159 27 -160 19 -161 12 -162 20 -163 14 -164 18 -165 17 -166 15 -167 27 -168 10 -169 20 -170 14 -171 16 -172 17 -173 21 -174 22 -175 9 -176 14 -177 15 -178 13 -179 14 -180 10 -181 15 -182 8 -183 6 -184 12 -185 8 -186 5 -187 9 -188 5 -189 3 -190 10 -191 9 -192 10 -193 9 -194 9 -195 3 -196 9 -197 5 -198 6 -199 8 -200 15 -201 17 -202 12 -203 5 -204 7 -205 13 -206 8 -207 9 -208 2 -209 6 -210 13 -211 4 -212 12 -213 7 -214 2 -215 6 -216 6 -217 3 -218 3 -219 6 -220 1 -221 6 -222 3 -223 1 -225 5 -226 3 -227 7 -228 3 -229 4 -230 3 -231 1 -232 4 -233 4 -234 2 -236 2 -240 1 -244 1 -245 3 -246 1 -247 1 -248 2 -251 1 -252 1 -253 1 -254 4 -255 5 -256 4 -257 3 -259 2 -260 2 -261 1 -262 5 -263 1 -264 1 -267 2 -271 3 -273 1 -276 2 -289 1 -314 1 -330 1 -331 1 -343 1 -431 1 -452 2 -462 1 -464 1 -465 1 -466 2 -468 2 -473 1 -480 1 -483 1 -484 1 -487 2 -490 1 -493 1 -496 1 -497 2 -509 1 -517 1 -524 1 -540 1 -541 1 -561 1 -595 1 -617 1 -618 1 -632 1 -643 1 -679 1 -711 1 -718 1 -781 1 -790 1 -802 1 -818 1 -835 1 -844 1 -865 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d89f7f3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.030e-02 4.584e-03 2.248 0.0254 * -r 2.088e-02 3.732e-03 5.594 5.29e-08 *** -kmercov 6.973e+00 2.295e-01 30.386 < 2e-16 *** -bias 1.934e+00 1.544e-01 12.523 < 2e-16 *** -length 3.881e+06 1.045e+05 37.157 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 147.6 on 279 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 4.015e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 44216ab..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1d50f76..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 250b317..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 3232362066.1823 -round 1 trimming to 20 trying 4peak model... converged. score: 719762124317.822 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e418c9a..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.34144% 2.83443% -Genome Haploid Length 3,674,308 bp 4,192,076 bp -Genome Repeat Length 65,654 bp 74,906 bp -Genome Unique Length 3,608,654 bp 4,117,171 bp -Model Fit 96.4154% 96.6253% -Read Error Rate 0.0984272% 0.0984272% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index c69b074..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,258 +0,0 @@ -1 10395144 -2 493694 -3 364875 -4 382002 -5 389080 -6 386020 -7 378034 -8 358769 -9 328989 -10 299074 -11 265985 -12 233735 -13 205818 -14 174912 -15 148413 -16 123677 -17 101520 -18 83305 -19 68026 -20 54721 -21 43309 -22 33933 -23 26602 -24 20421 -25 15803 -26 12156 -27 9174 -28 6778 -29 4953 -30 3726 -31 2839 -32 2136 -33 1541 -34 1295 -35 1034 -36 862 -37 651 -38 500 -39 418 -40 385 -41 352 -42 269 -43 270 -44 270 -45 259 -46 252 -47 254 -48 248 -49 229 -50 250 -51 203 -52 185 -53 220 -54 230 -55 222 -56 191 -57 213 -58 188 -59 173 -60 194 -61 199 -62 208 -63 186 -64 178 -65 162 -66 144 -67 134 -68 157 -69 148 -70 166 -71 146 -72 138 -73 123 -74 132 -75 111 -76 142 -77 108 -78 98 -79 95 -80 108 -81 67 -82 67 -83 78 -84 69 -85 57 -86 49 -87 68 -88 62 -89 61 -90 42 -91 47 -92 40 -93 68 -94 45 -95 50 -96 64 -97 48 -98 51 -99 49 -100 40 -101 33 -102 52 -103 41 -104 25 -105 25 -106 36 -107 16 -108 33 -109 32 -110 12 -111 15 -112 23 -113 15 -114 10 -115 17 -116 11 -117 18 -118 15 -119 17 -120 9 -121 24 -122 17 -123 25 -124 17 -125 21 -126 24 -127 22 -128 26 -129 20 -130 22 -131 15 -132 10 -133 17 -134 13 -135 12 -136 7 -137 16 -138 21 -139 16 -140 20 -141 14 -142 21 -143 11 -144 31 -145 19 -146 22 -147 12 -148 27 -149 24 -150 23 -151 25 -152 25 -153 26 -154 27 -155 16 -156 19 -157 25 -158 22 -159 20 -160 27 -161 15 -162 19 -163 18 -164 13 -165 21 -166 20 -167 16 -168 10 -169 21 -170 10 -171 9 -172 14 -173 7 -174 13 -175 16 -176 10 -177 11 -178 12 -179 11 -180 15 -181 10 -182 11 -183 7 -184 12 -185 6 -186 10 -187 6 -188 11 -189 2 -190 5 -191 8 -192 7 -193 1 -194 2 -195 1 -196 1 -197 3 -198 4 -199 5 -200 3 -201 5 -202 7 -203 6 -204 4 -205 5 -206 2 -207 2 -209 3 -210 2 -211 1 -212 2 -213 1 -219 1 -231 1 -238 1 -250 1 -281 1 -316 1 -324 1 -325 1 -329 1 -333 1 -359 1 -361 1 -382 1 -383 1 -393 1 -395 1 -396 1 -399 1 -416 1 -422 2 -429 1 -433 1 -434 1 -435 1 -438 1 -443 2 -444 1 -446 1 -448 1 -457 1 -464 1 -469 1 -478 1 -489 1 -509 1 -521 1 -531 1 -576 1 -616 1 -632 1 -649 1 -657 1 -680 1 -691 1 -692 1 -724 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 74663bc..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.322e-02 1.996e-03 11.63 <2e-16 *** -r 4.606e-02 8.002e-04 57.56 <2e-16 *** -kmercov 7.266e+00 4.690e-02 154.93 <2e-16 *** -bias 7.847e-01 4.121e-02 19.04 <2e-16 *** -length 3.282e+06 1.186e+04 276.85 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 88.63 on 238 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.142e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1696aeb..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 562aa21..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1af0b84..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 57510977734.4994 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b7ee695..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 4.44604% 4.76611% -Genome Haploid Length 3,030,197 bp 3,109,454 bp -Genome Repeat Length -164,712 bp -169,020 bp -Genome Unique Length 3,194,909 bp 3,278,474 bp -Model Fit 84.1642% 84.3516% -Read Error Rate 1.05713% 1.05713% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index c154026..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,222 +0,0 @@ -1 18513591 -2 896495 -3 481885 -4 475688 -5 467511 -6 443855 -7 405610 -8 365000 -9 317100 -10 271932 -11 227402 -12 186975 -13 151035 -14 120882 -15 94924 -16 73727 -17 55626 -18 41186 -19 31061 -20 22683 -21 16568 -22 12438 -23 8911 -24 6557 -25 4749 -26 3270 -27 2400 -28 1831 -29 1341 -30 1051 -31 844 -32 648 -33 548 -34 448 -35 438 -36 351 -37 325 -38 354 -39 298 -40 292 -41 272 -42 286 -43 264 -44 263 -45 242 -46 215 -47 217 -48 200 -49 200 -50 188 -51 175 -52 168 -53 168 -54 135 -55 126 -56 119 -57 129 -58 125 -59 107 -60 125 -61 115 -62 107 -63 100 -64 107 -65 110 -66 112 -67 100 -68 86 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-352 1 -354 1 -357 1 -388 1 -408 1 -418 1 -420 1 -437 1 -441 1 -492 1 -501 1 -515 1 -518 1 -540 1 -556 1 -563 1 -570 1 -581 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d8648eb..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6e6b350..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index 658cc8b..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,285 +0,0 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-399 1 -407 1 -422 1 -423 1 -436 1 -438 1 -440 1 -443 1 -446 1 -452 1 -453 1 -458 1 -459 1 -461 2 -462 1 -470 1 -478 1 -481 1 -482 1 -521 1 -547 1 -555 1 -565 1 -588 1 -598 1 -657 1 -667 1 -681 1 -699 1 -715 1 -739 1 -758 1 -768 1 -786 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index b7eb216..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.726e-03 2.181e-03 1.250 0.21232 -r -2.954e-02 2.824e-02 -1.046 0.29660 -kmercov 5.185e+00 3.272e-01 15.847 < 2e-16 *** -bias 1.118e+00 1.286e-01 8.698 3.63e-16 *** -length 2.752e+06 9.313e+05 2.955 0.00341 ** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 148.3 on 265 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 9.95e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3264b99..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 045d0e9..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 92cbf14..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 2026889647744.77 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4aa6f79..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -8.6023% 2.69493% -Genome Haploid Length 3,993,003 bp 5,146,448 bp -Genome Repeat Length 1,551,147 bp 1,999,222 bp -Genome Unique Length 2,441,856 bp 3,147,226 bp -Model Fit 34.8242% 33.0087% -Read Error Rate 0.847228% 0.847228% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index c260d05..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,245 +0,0 @@ -1 10500716 -2 554244 -3 517169 -4 573953 -5 589337 -6 567509 -7 531037 -8 476843 -9 420491 -10 360313 -11 301996 -12 249661 -13 199795 -14 157007 -15 118271 -16 86368 -17 64014 -18 45717 -19 32102 -20 21980 -21 14527 -22 10117 -23 6653 -24 4542 -25 2892 -26 1948 -27 1382 -28 933 -29 839 -30 698 -31 606 -32 503 -33 482 -34 451 -35 391 -36 333 -37 311 -38 363 -39 293 -40 278 -41 269 -42 206 -43 199 -44 190 -45 213 -46 219 -47 225 -48 218 -49 209 -50 249 -51 239 -52 232 -53 204 -54 233 -55 184 -56 193 -57 173 -58 154 -59 177 -60 172 -61 164 -62 148 -63 150 -64 186 -65 159 -66 170 -67 139 -68 148 -69 117 -70 156 -71 114 -72 112 -73 87 -74 83 -75 73 -76 83 -77 50 -78 58 -79 58 -80 48 -81 41 -82 39 -83 45 -84 49 -85 46 -86 42 -87 39 -88 35 -89 37 -90 31 -91 39 -92 26 -93 33 -94 22 -95 27 -96 34 -97 27 -98 18 -99 18 -100 20 -101 20 -102 29 -103 15 -104 18 -105 18 -106 13 -107 11 -108 13 -109 11 -110 8 -111 12 -112 14 -113 13 -114 7 -115 18 -116 12 -117 15 -118 14 -119 12 -120 16 -121 9 -122 13 -123 15 -124 15 -125 14 -126 19 -127 14 -128 22 -129 11 -130 15 -131 17 -132 14 -133 19 -134 13 -135 25 -136 20 -137 28 -138 14 -139 17 -140 24 -141 23 -142 25 -143 24 -144 35 -145 19 -146 15 -147 20 -148 27 -149 24 -150 15 -151 23 -152 25 -153 14 -154 23 -155 18 -156 16 -157 28 -158 13 -159 23 -160 23 -161 22 -162 17 -163 17 -164 16 -165 22 -166 17 -167 18 -168 17 -169 12 -170 15 -171 11 -172 6 -173 14 -174 6 -175 4 -176 6 -177 7 -178 3 -179 3 -180 10 -181 4 -182 2 -183 6 -184 5 -185 3 -186 2 -187 2 -188 2 -189 3 -190 2 -191 1 -192 1 -193 1 -195 4 -196 1 -198 2 -199 3 -200 1 -202 3 -203 1 -207 1 -211 1 -225 1 -234 1 -250 1 -257 1 -323 1 -343 2 -347 1 -356 1 -357 1 -362 1 -366 1 -367 1 -388 1 -390 1 -401 1 -404 1 -405 1 -410 1 -413 1 -414 1 -418 1 -419 1 -420 1 -423 2 -430 1 -431 1 -438 1 -453 1 -465 1 -467 1 -503 2 -504 1 -537 1 -538 1 -549 1 -564 1 -579 1 -590 1 -607 1 -617 1 -644 1 -659 1 -663 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3b81fd3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.927e-01 1.586e-02 12.15 <2e-16 *** -r 3.502e-02 7.601e-04 46.06 <2e-16 *** -kmercov 2.753e+01 2.456e-01 112.09 <2e-16 *** -bias 1.149e+00 5.742e-02 20.01 <2e-16 *** -length 1.279e+04 1.747e+02 73.23 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 15.66 on 210 degrees of freedom - -Number of iterations to convergence: 12 -Achieved convergence tolerance: 8.646e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e7fbba7..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 143705f..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 05dfe0e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 595372.131435837 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c80d580..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.34956% 3.65362% -Genome Haploid Length 17,881 bp 18,530 bp -Genome Repeat Length 7,062 bp 7,319 bp -Genome Unique Length 10,818 bp 11,211 bp -Model Fit 79.5349% 83.8221% -Read Error Rate 17.4175% 17.4175% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 195e1f9..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,200 +0,0 @@ -1 18752189 -2 963778 -3 681966 -4 701756 -5 670741 -6 607578 -7 531753 -8 444673 -9 360368 -10 282316 -11 212813 -12 157485 -13 112489 -14 77785 -15 52965 -16 34527 -17 22478 -18 13987 -19 8866 -20 5707 -21 3536 -22 2323 -23 1573 -24 989 -25 752 -26 593 -27 460 -28 415 -29 341 -30 324 -31 307 -32 329 -33 377 -34 363 -35 345 -36 340 -37 315 -38 323 -39 318 -40 328 -41 244 -42 297 -43 282 -44 300 -45 232 -46 254 -47 257 -48 258 -49 249 -50 216 -51 196 -52 192 -53 186 -54 175 -55 146 -56 136 -57 126 -58 140 -59 112 -60 126 -61 100 -62 85 -63 83 -64 67 -65 72 -66 65 -67 50 -68 52 -69 54 -70 60 -71 46 -72 48 -73 44 -74 30 -75 29 -76 48 -77 33 -78 39 -79 30 -80 24 -81 38 -82 22 -83 26 -84 23 -85 28 -86 27 -87 29 -88 32 -89 29 -90 22 -91 28 -92 19 -93 39 -94 23 -95 36 -96 18 -97 30 -98 29 -99 27 -100 33 -101 32 -102 34 -103 33 -104 42 -105 36 -106 34 -107 40 -108 41 -109 41 -110 39 -111 46 -112 37 -113 30 -114 25 -115 37 -116 30 -117 25 -118 17 -119 30 -120 18 -121 22 -122 11 -123 11 -124 16 -125 5 -126 12 -127 19 -128 12 -129 26 -130 10 -131 11 -132 13 -133 9 -134 13 -135 9 -136 5 -137 3 -138 6 -139 6 -140 6 -141 5 -142 3 -143 2 -144 7 -145 12 -146 3 -147 5 -148 2 -149 4 -151 4 -152 1 -153 4 -155 1 -161 1 -162 1 -165 1 -167 1 -168 1 -172 1 -194 1 -197 1 -214 1 -255 1 -257 1 -263 1 -266 1 -268 1 -273 2 -275 2 -280 1 -282 1 -284 2 -287 1 -288 1 -289 1 -290 1 -294 1 -296 1 -298 1 -305 1 -309 1 -312 1 -317 1 -331 1 -334 1 -335 1 -378 1 -387 1 -408 2 -409 1 -412 1 -415 1 -420 1 -447 1 -451 1 -461 1 -470 1 -476 1 -477 1 -484 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9e50f1e..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.374e-01 1.982e-02 6.934 8.81e-11 *** -r 1.275e-02 3.703e-03 3.443 0.000729 *** -kmercov 2.103e+01 4.237e-01 49.635 < 2e-16 *** -bias 2.621e+00 5.266e-01 4.977 1.61e-06 *** -length 1.255e+04 1.684e+02 74.517 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 14.18 on 165 degrees of freedom - -Number of iterations to convergence: 19 -Achieved convergence tolerance: 2.26e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bf361a0..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 67fb25e..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b5cb5b5..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 45534922.2058949 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5a8c8b3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.534408% 2.01575% -Genome Haploid Length 20,113 bp 21,802 bp -Genome Repeat Length 9,615 bp 10,423 bp -Genome Unique Length 10,497 bp 11,379 bp -Model Fit 44.6184% 45.6249% -Read Error Rate 17.9265% 17.9265% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index c999f02..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,280 +0,0 @@ -1 1382432 -2 327667 -3 386259 -4 424642 -5 439411 -6 444353 -7 430169 -8 409195 -9 380629 -10 351560 -11 318235 -12 279946 -13 247160 -14 213470 -15 180473 -16 156401 -17 128310 -18 108037 -19 88288 -20 71946 -21 58742 -22 46174 -23 36849 -24 28467 -25 22022 -26 17020 -27 13031 -28 9686 -29 7301 -30 5519 -31 4355 -32 3248 -33 2338 -34 1832 -35 1554 -36 1106 -37 758 -38 845 -39 670 -40 434 -41 409 -42 411 -43 378 -44 340 -45 320 -46 270 -47 214 -48 268 -49 212 -50 272 -51 212 -52 206 -53 201 -54 197 -55 179 -56 190 -57 165 -58 196 -59 203 -60 167 -61 169 -62 213 -63 220 -64 179 -65 226 -66 198 -67 152 -68 158 -69 153 -70 167 -71 168 -72 151 -73 169 -74 145 -75 110 -76 112 -77 107 -78 112 -79 94 -80 108 -81 122 -82 113 -83 80 -84 84 -85 76 -86 99 -87 78 -88 57 -89 61 -90 56 -91 66 -92 70 -93 45 -94 57 -95 58 -96 33 -97 48 -98 42 -99 44 -100 40 -101 25 -102 34 -103 28 -104 31 -105 29 -106 41 -107 28 -108 26 -109 43 -110 39 -111 31 -112 17 -113 35 -114 19 -115 28 -116 26 -117 18 -118 17 -119 19 -120 20 -121 18 -122 11 -123 28 -124 15 -125 15 -126 26 -127 18 -128 16 -129 11 -130 19 -131 15 -132 11 -133 18 -134 15 -135 15 -136 14 -137 24 -138 21 -139 16 -140 11 -141 9 -142 16 -143 17 -144 16 -145 11 -146 29 -147 34 -148 19 -149 19 -150 20 -151 16 -152 31 -153 17 -154 18 -155 30 -156 29 -157 17 -158 21 -159 27 -160 28 -161 15 -162 22 -163 13 -164 17 -165 23 -166 12 -167 14 -168 10 -169 11 -170 16 -171 11 -172 9 -173 19 -174 14 -175 15 -176 16 -177 28 -178 19 -179 14 -180 15 -181 11 -182 34 -183 18 -184 30 -185 19 -186 19 -187 14 -188 17 -189 11 -190 21 -191 15 -192 17 -193 10 -194 18 -195 14 -196 12 -197 17 -198 11 -199 8 -200 7 -201 8 -202 8 -203 7 -204 11 -205 7 -206 4 -207 7 -208 4 -209 5 -210 1 -211 4 -212 3 -213 2 -214 3 -215 1 -216 5 -217 3 -219 2 -221 2 -222 5 -223 1 -224 1 -225 1 -226 1 -227 3 -229 1 -230 1 -231 1 -234 1 -237 1 -241 1 -242 1 -243 1 -246 1 -249 1 -253 1 -256 1 -293 1 -304 1 -310 1 -340 1 -343 1 -346 1 -354 1 -362 1 -364 1 -382 1 -403 1 -406 1 -422 1 -429 1 -436 1 -441 1 -444 1 -446 2 -449 1 -460 1 -465 2 -467 1 -472 2 -476 1 -483 1 -485 1 -491 1 -494 1 -517 1 -530 1 -540 1 -559 1 -562 1 -585 1 -692 1 -724 1 -741 1 -748 1 -792 1 -810 1 -829 1 -832 1 -839 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9620d3f..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.437e-03 4.556e-03 2.071 0.0393 * -r 2.354e-02 5.523e-03 4.262 2.83e-05 *** -kmercov 6.544e+00 2.655e-01 24.642 < 2e-16 *** -bias 1.332e+00 1.575e-01 8.455 2.03e-15 *** -length 3.917e+06 7.895e+04 49.615 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 195.9 on 260 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.045e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index c6c97be..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4bdcb89..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2db70de..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 2511799500.71328 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5cbca10..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.2496% 3.45891% -Genome Haploid Length 3,792,417 bp 4,462,398 bp -Genome Repeat Length 198,088 bp 233,083 bp -Genome Unique Length 3,594,329 bp 4,229,315 bp -Model Fit 96.2144% 96.4712% -Read Error Rate 0.183532% 0.183532% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index 6e113b4..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,236 +0,0 @@ -1 10549148 -2 593346 -3 500719 -4 524774 -5 520623 -6 501674 -7 469538 -8 427299 -9 377391 -10 326646 -11 281468 -12 236545 -13 195445 -14 159877 -15 128039 -16 102385 -17 79659 -18 62238 -19 47422 -20 35878 -21 26557 -22 19879 -23 14862 -24 10472 -25 7662 -26 5734 -27 4007 -28 3010 -29 2124 -30 1573 -31 1279 -32 951 -33 715 -34 596 -35 510 -36 388 -37 398 -38 315 -39 312 -40 302 -41 272 -42 296 -43 297 -44 281 -45 238 -46 214 -47 237 -48 213 -49 216 -50 212 -51 190 -52 175 -53 177 -54 166 -55 175 -56 156 -57 165 -58 135 -59 136 -60 170 -61 159 -62 131 -63 133 -64 123 -65 124 -66 91 -67 115 -68 98 -69 100 -70 120 -71 109 -72 130 -73 98 -74 79 -75 108 -76 101 -77 94 -78 60 -79 96 -80 89 -81 83 -82 87 -83 72 -84 62 -85 52 -86 64 -87 43 -88 37 -89 48 -90 46 -91 29 -92 48 -93 34 -94 44 -95 38 -96 37 -97 27 -98 23 -99 31 -100 21 -101 19 -102 30 -103 22 -104 19 -105 17 -106 12 -107 20 -108 18 -109 18 -110 22 -111 26 -112 19 -113 20 -114 19 -115 27 -116 27 -117 18 -118 23 -119 12 -120 31 -121 21 -122 20 -123 20 -124 18 -125 30 -126 19 -127 28 -128 35 -129 33 -130 35 -131 30 -132 25 -133 30 -134 32 -135 25 -136 22 -137 28 -138 29 -139 28 -140 24 -141 19 -142 23 -143 21 -144 16 -145 15 -146 17 -147 15 -148 22 -149 14 -150 22 -151 11 -152 12 -153 16 -154 12 -155 19 -156 19 -157 13 -158 16 -159 13 -160 7 -161 15 -162 9 -163 8 -164 5 -165 11 -166 3 -167 3 -168 9 -169 5 -170 6 -171 6 -172 7 -173 6 -174 2 -175 6 -176 9 -177 4 -178 2 -179 6 -180 4 -181 3 -182 1 -183 3 -184 4 -185 1 -186 2 -187 2 -188 1 -204 3 -208 3 -213 1 -222 1 -246 2 -250 2 -252 2 -255 1 -265 1 -272 1 -302 1 -304 1 -306 2 -307 2 -309 1 -313 2 -319 1 -326 1 -337 1 -340 1 -341 1 -346 1 -347 1 -355 1 -358 1 -359 1 -365 1 -372 1 -376 1 -396 1 -398 1 -413 1 -435 1 -445 1 -488 1 -491 1 -497 1 -505 1 -509 1 -595 1 -604 1 -608 1 -619 1 -658 1 -672 1 -673 1 -706 1 -720 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3ff328c..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.359e-02 3.328e-03 7.087 1.92e-11 *** -r 3.705e-02 5.384e-03 6.883 6.28e-11 *** -kmercov 5.989e+00 1.888e-01 31.730 < 2e-16 *** -bias 7.425e-01 1.018e-01 7.296 5.56e-12 *** -length 3.725e+06 3.686e+04 101.051 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 93.87 on 216 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 9.757e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1f9130a..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 59e664e..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3660584..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 12711726694.7136 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f2dfe80..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.62859% 4.78206% -Genome Haploid Length 3,507,343 bp 3,979,232 bp -Genome Repeat Length 61,323 bp 69,574 bp -Genome Unique Length 3,446,020 bp 3,909,658 bp -Model Fit 93.9014% 94.0806% -Read Error Rate 1.05076% 1.05076% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index 1284b8c..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,226 +0,0 @@ -1 18764178 -2 1004647 -3 640297 -4 630429 -5 594274 -6 542563 -7 478039 -8 404768 -9 334532 -10 270059 -11 212119 -12 166644 -13 126744 -14 95145 -15 70136 -16 50521 -17 36090 -18 25955 -19 17437 -20 12378 -21 8318 -22 5822 -23 3833 -24 2675 -25 1902 -26 1412 -27 1003 -28 759 -29 624 -30 504 -31 492 -32 495 -33 375 -34 361 -35 330 -36 299 -37 314 -38 319 -39 300 -40 298 -41 250 -42 272 -43 278 -44 248 -45 234 -46 258 -47 212 -48 196 -49 159 -50 159 -51 125 -52 138 -53 142 -54 136 -55 148 -56 117 -57 121 -58 101 -59 85 -60 97 -61 101 -62 75 -63 80 -64 55 -65 62 -66 35 -67 46 -68 48 -69 43 -70 60 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1 -339 1 -340 1 -344 1 -349 1 -365 1 -366 1 -373 1 -378 1 -379 1 -387 1 -402 1 -403 1 -406 1 -412 1 -438 1 -445 1 -446 1 -463 1 -464 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 88a26af..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index d0b3aec..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist deleted file mode 100644 index a7d0163..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist +++ /dev/null @@ -1,290 +0,0 @@ -1 1333070 -2 320841 -3 383515 -4 403695 -5 402511 -6 392689 -7 380000 -8 363552 -9 344623 -10 313154 -11 287609 -12 257675 -13 232316 -14 207573 -15 177867 -16 156230 -17 133574 -18 112289 -19 94707 -20 80576 -21 66398 -22 54959 -23 45185 -24 37584 -25 30256 -26 25095 -27 19965 -28 16208 -29 12998 -30 9977 -31 7763 -32 6502 -33 5070 -34 4135 -35 3287 -36 2425 -37 1986 -38 1379 -39 1209 -40 931 -41 724 -42 639 -43 571 -44 413 -45 395 -46 279 -47 285 -48 272 -49 197 -50 236 -51 206 -52 210 -53 234 -54 218 -55 175 -56 180 -57 173 -58 149 -59 157 -60 158 -61 185 -62 163 -63 149 -64 162 -65 134 -66 145 -67 133 -68 170 -69 155 -70 161 -71 162 -72 136 -73 170 -74 163 -75 172 -76 158 -77 166 -78 142 -79 143 -80 132 -81 112 -82 133 -83 107 -84 120 -85 124 -86 110 -87 121 -88 110 -89 96 -90 62 -91 75 -92 69 -93 66 -94 82 -95 82 -96 82 -97 56 -98 60 -99 59 -100 56 -101 46 -102 45 -103 46 -104 38 -105 41 -106 51 -107 47 -108 47 -109 24 -110 33 -111 24 -112 23 -113 30 -114 44 -115 34 -116 33 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-294 1 -313 1 -320 1 -363 1 -370 1 -418 1 -419 1 -423 1 -424 2 -429 1 -430 1 -432 1 -435 2 -437 1 -438 1 -439 1 -444 1 -446 1 -448 1 -455 1 -456 1 -461 1 -462 1 -480 1 -512 1 -524 1 -530 1 -544 1 -557 1 -587 1 -603 1 -609 2 -614 1 -625 1 -627 1 -658 1 -691 1 -698 1 -716 1 -730 1 -752 1 -758 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d7ed109..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.961e-02 3.772e-03 10.500 <2e-16 *** -r 7.546e-02 2.446e-03 30.850 <2e-16 *** -kmercov 9.324e+00 6.662e-02 139.957 <2e-16 *** -bias 6.302e-01 6.476e-02 9.731 <2e-16 *** -length 3.661e+06 8.624e+04 42.457 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 76.13 on 265 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 4.614e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7e5aa1e..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 36d4a1c..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1c2eff6..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... converged. score: 394334615391.184 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a30ae79..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 7.05674% 8.03514% -Genome Haploid Length 2,791,025 bp 2,871,950 bp -Genome Repeat Length -768,968 bp -791,263 bp -Genome Unique Length 3,559,993 bp 3,663,213 bp -Model Fit 55.6528% 55.7562% -Read Error Rate 0.257822% 0.257822% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist deleted file mode 100644 index bf0b97c..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist +++ /dev/null @@ -1,232 +0,0 @@ -1 10474066 -2 596063 -3 478274 -4 483047 -5 469716 -6 453535 -7 421969 -8 387303 -9 345080 -10 301553 -11 260442 -12 225364 -13 193520 -14 162992 -15 134013 -16 110589 -17 90514 -18 73767 -19 58362 -20 46331 -21 36778 -22 28168 -23 21717 -24 16525 -25 12938 -26 9443 -27 7227 -28 5631 -29 4183 -30 3231 -31 2453 -32 1967 -33 1387 -34 1100 -35 886 -36 736 -37 676 -38 560 -39 543 -40 474 -41 407 -42 347 -43 295 -44 263 -45 256 -46 246 -47 268 -48 235 -49 187 -50 228 -51 203 -52 186 -53 172 -54 171 -55 177 -56 159 -57 144 -58 153 -59 145 -60 133 -61 103 -62 124 -63 99 -64 110 -65 107 -66 101 -67 90 -68 83 -69 80 -70 102 -71 87 -72 87 -73 83 -74 86 -75 89 -76 85 -77 75 -78 68 -79 82 -80 56 -81 61 -82 61 -83 57 -84 60 -85 72 -86 61 -87 49 -88 63 -89 57 -90 52 -91 52 -92 48 -93 35 -94 42 -95 40 -96 23 -97 39 -98 36 -99 38 -100 33 -101 28 -102 33 -103 23 -104 25 -105 34 -106 32 -107 23 -108 22 -109 27 -110 24 -111 20 -112 10 -113 15 -114 26 -115 23 -116 23 -117 17 -118 30 -119 27 -120 19 -121 23 -122 27 -123 20 -124 27 -125 32 -126 26 -127 24 -128 25 -129 30 -130 31 -131 28 -132 27 -133 25 -134 24 -135 25 -136 35 -137 23 -138 34 -139 32 -140 26 -141 23 -142 24 -143 19 -144 22 -145 28 -146 24 -147 19 -148 14 -149 18 -150 16 -151 14 -152 16 -153 12 -154 19 -155 20 -156 13 -157 15 -158 10 -159 12 -160 7 -161 9 -162 10 -163 9 -164 5 -165 4 -166 1 -167 3 -168 3 -169 4 -170 5 -171 7 -172 5 -173 3 -174 5 -175 1 -176 4 -177 2 -178 4 -179 3 -180 1 -181 1 -183 2 -189 1 -196 1 -198 1 -206 1 -216 1 -221 1 -224 1 -235 1 -253 1 -257 1 -293 1 -298 1 -300 1 -301 1 -306 2 -316 1 -317 1 -326 1 -334 1 -357 1 -360 1 -361 1 -364 1 -365 1 -367 1 -370 1 -376 1 -377 1 -380 1 -384 1 -387 2 -389 1 -391 1 -397 1 -407 1 -415 1 -441 1 -443 1 -450 1 -464 1 -474 1 -541 1 -563 1 -568 1 -583 1 -594 1 -628 1 -640 1 -654 1 -667 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6112e59..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.551e-02 2.398e-03 14.81 <2e-16 *** -r 4.185e-02 1.747e-03 23.96 <2e-16 *** -kmercov 6.817e+00 7.854e-02 86.80 <2e-16 *** -bias 7.154e-01 5.687e-02 12.58 <2e-16 *** -length 3.164e+06 1.128e+04 280.49 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 88.95 on 212 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.246e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 78b4fe6..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6809525..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ec7a8c3..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 6674564684.79056 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d86c1f0..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.83563% 4.53431% -Genome Haploid Length 3,137,781 bp 3,285,787 bp -Genome Repeat Length 116,155 bp 121,634 bp -Genome Unique Length 3,021,626 bp 3,164,153 bp -Model Fit 94.696% 94.8982% -Read Error Rate 1.14583% 1.14583% diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist deleted file mode 100644 index f65edb2..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist +++ /dev/null @@ -1,218 +0,0 @@ -1 18679354 -2 1001991 -3 603548 -4 576316 -5 536167 -6 484375 -7 427763 -8 370024 -9 314344 -10 259124 -11 213964 -12 172010 -13 135370 -14 105874 -15 82119 -16 63512 -17 48542 -18 35165 -19 26044 -20 19590 -21 14125 -22 10399 -23 7386 -24 5179 -25 3883 -26 2698 -27 1902 -28 1411 -29 1086 -30 902 -31 696 -32 599 -33 505 -34 455 -35 368 -36 337 -37 322 -38 364 -39 314 -40 264 -41 282 -42 281 -43 261 -44 233 -45 251 -46 249 -47 232 -48 235 -49 237 -50 219 -51 226 -52 210 -53 185 -54 180 -55 182 -56 184 -57 130 -58 150 -59 129 -60 122 -61 119 -62 99 -63 99 -64 100 -65 103 -66 71 -67 66 -68 60 -69 66 -70 56 -71 50 -72 55 -73 34 -74 38 -75 36 -76 26 -77 42 -78 44 -79 37 -80 24 -81 20 -82 24 -83 20 -84 12 -85 30 -86 30 -87 23 -88 29 -89 17 -90 26 -91 20 -92 23 -93 22 -94 18 -95 13 -96 20 -97 23 -98 21 -99 13 -100 24 -101 23 -102 24 -103 27 -104 31 -105 21 -106 29 -107 23 -108 24 -109 34 -110 20 -111 25 -112 14 -113 18 -114 23 -115 15 -116 23 -117 17 -118 12 -119 17 -120 16 -121 23 -122 19 -123 18 -124 23 -125 19 -126 16 -127 12 -128 20 -129 12 -130 13 -131 18 -132 16 -133 7 -134 14 -135 8 -136 15 -137 13 -138 8 -139 16 -140 11 -141 13 -142 15 -143 16 -144 7 -145 8 -146 7 -147 8 -148 7 -149 8 -150 7 -151 6 -152 5 -153 7 -154 2 -155 8 -156 14 -157 2 -158 4 -159 6 -160 2 -161 4 -162 5 -163 1 -164 3 -165 3 -166 1 -167 2 -168 4 -169 2 -170 2 -171 2 -172 1 -174 2 -176 2 -177 1 -178 1 -181 1 -182 1 -183 1 -185 2 -189 1 -210 1 -214 1 -226 1 -241 1 -272 1 -273 1 -276 1 -278 1 -279 3 -280 1 -281 2 -282 1 -284 1 -287 3 -289 1 -300 2 -313 1 -321 1 -322 2 -340 1 -346 1 -377 1 -386 1 -406 1 -407 1 -413 1 -423 1 -424 1 -483 1 -502 1 -504 1 -507 1 -527 1 -548 1 -550 1 -560 1 -580 1 diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index ea82b6d..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.996e-01 2.266e-02 8.807 9.71e-16 *** -r 5.996e-02 2.823e-03 21.242 < 2e-16 *** -kmercov 2.345e+01 1.938e-01 120.976 < 2e-16 *** -bias 6.942e-01 3.799e-02 18.275 < 2e-16 *** -length 1.685e+04 2.961e+02 56.897 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13.78 on 183 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 9.171e-06 - diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f2e1928..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 03ffd92..0000000 Binary files a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 965cea7..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... converged. score: 55740379.5471788 -done diff --git a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b3ec7a4..0000000 --- a/analysis/simulation_results_15x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov15_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 5.43158% 6.56069% -Genome Haploid Length 27,028 bp 27,936 bp -Genome Repeat Length 12,013 bp 12,417 bp -Genome Unique Length 15,014 bp 15,519 bp -Model Fit 54.3445% 55.2812% -Read Error Rate 16.4237% 16.4237% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist deleted 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-Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.549e-02 3.970e-04 64.21 <2e-16 *** -r 1.386e-03 1.019e-05 135.97 <2e-16 *** -kmercov 9.892e+00 1.647e-03 6006.21 <2e-16 *** -bias 9.631e-01 2.520e-03 382.26 <2e-16 *** -length 1.069e+08 4.066e+04 2628.62 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5786 on 993 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.114e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dd2fedb..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 5859f5b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0d84c1d..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 33247951722.5357 -round 1 trimming to 8 trying 4peak model... converged. score: 41283664254.6717 -round 2 trimming to 13 trying 4peak model... converged. score: 575970787431.836 -round 3 trimming to 18 trying 4peak model... converged. score: 11402834981349.9 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 93b21c4..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.136543% 0.14062% -Genome Haploid Length 117,297,210 bp 117,375,353 bp -Genome Repeat Length 13,183,025 bp 13,191,807 bp -Genome Unique Length 104,114,185 bp 104,183,546 bp -Model Fit 98.146% 99.3612% -Read Error Rate 0.0997929% 0.0997929% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index b86ec31..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2956 +0,0 @@ -1 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a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.899e-02 5.253e-04 55.18 <2e-16 *** -r 1.742e-03 1.476e-05 118.01 <2e-16 *** -kmercov 8.203e+00 1.905e-03 4306.69 <2e-16 *** -bias 7.555e-01 3.115e-03 242.50 <2e-16 *** -length 1.067e+08 5.097e+04 2093.54 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7700 on 992 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.28e-07 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 78edb93..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2ee92e2..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eae221d..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 31869255455.7306 -round 1 trimming to 9 trying 4peak model... converged. score: 38706629941.636 -round 2 trimming to 14 trying 4peak model... converged. score: 8535976115319.59 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index fbe46cb..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.171257% 0.177162% -Genome Haploid Length 117,565,587 bp 117,674,831 bp -Genome Repeat Length 14,000,770 bp 14,013,780 bp -Genome Unique Length 103,564,817 bp 103,661,051 bp -Model Fit 98.3844% 99.5444% -Read Error Rate 0.987145% 0.987145% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 57ee412..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2567 +0,0 @@ -1 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kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.186e-02 4.181e-04 76.21 <2e-16 *** -r 2.379e-03 7.307e-05 32.56 <2e-16 *** -kmercov 6.659e+00 3.388e-03 1965.53 <2e-16 *** -bias 5.797e-01 4.141e-03 139.98 <2e-16 *** -length 1.068e+08 3.967e+04 2692.35 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5055 on 987 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.473e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b631e6c..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0136e3a..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d68a413..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 69347119421.3129 -round 1 trimming to 9 trying 4peak model... converged. score: 57084118586.724 -round 2 trimming to 14 trying 4peak model... converged. score: 52100820640713.8 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index eca601f..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.22333% 0.25256% -Genome Haploid Length 117,941,871 bp 118,182,136 bp -Genome Repeat Length 14,640,466 bp 14,670,290 bp -Genome Unique Length 103,301,405 bp 103,511,845 bp -Model Fit 98.3205% 99.4863% -Read Error Rate 1.95922% 1.95922% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index bfc8bc5..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,3361 +0,0 @@ -1 48580558 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(1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.097e-02 6.322e-04 33.17 <2e-16 *** -r 2.332e-03 1.775e-05 131.37 <2e-16 *** -kmercov 1.014e+01 2.898e-03 3498.03 <2e-16 *** -bias 1.837e+00 5.861e-03 313.49 <2e-16 *** -length 1.049e+08 4.888e+04 2146.02 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5852 on 993 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 4.85e-07 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cfeaf49..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1bb85d7..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4477cdf..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 34011980107.081 -round 1 trimming to 8 trying 4peak model... converged. score: 60021029974.5022 -round 2 trimming to 13 trying 4peak model... converged. score: 824452123165.179 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9c7b951..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.229697% 0.236799% -Genome Haploid Length 114,446,113 bp 114,577,057 bp -Genome Repeat Length 11,809,538 bp 11,823,050 bp -Genome Unique Length 102,636,575 bp 102,754,007 bp -Model Fit 98.1375% 99.266% -Read Error Rate 0.0997844% 0.0997844% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 443e1d7..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2947 +0,0 @@ -1 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a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.824e-02 6.685e-04 42.24 <2e-16 *** -r 3.101e-03 2.145e-05 144.60 <2e-16 *** -kmercov 8.435e+00 2.678e-03 3149.10 <2e-16 *** -bias 1.411e+00 5.648e-03 249.74 <2e-16 *** -length 1.041e+08 5.197e+04 2003.27 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6253 on 992 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.442e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6820795..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1395c7b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8bbe682..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 26933736241.936 -round 1 trimming to 9 trying 4peak model... converged. score: 76585199157.1039 -round 2 trimming to 14 trying 4peak model... unconverged -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cfead2c..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.305812% 0.31439% -Genome Haploid Length 114,350,081 bp 114,495,421 bp -Genome Repeat Length 13,226,091 bp 13,242,901 bp -Genome Unique Length 101,123,990 bp 101,252,520 bp -Model Fit 98.4361% 99.5408% -Read Error Rate 0.985956% 0.985956% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 0b97dbe..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2587 +0,0 @@ -1 729338683 -2 36530977 -3 4596367 -4 3089508 -5 3620107 -6 4484574 -7 5417472 -8 6287803 -9 6993710 -10 7486577 -11 7734978 -12 7729933 -13 7479485 -14 7049189 -15 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-7654 1 -7702 1 -8200 1 -8225 1 -8260 1 -8286 1 -8366 1 -8402 1 -8601 1 -8864 1 -10383 1 -10653 1 -11347 1 -11760 1 -19232 1 -23719 1 -23778 1 -24052 1 -60048 1 -60650 1 -61966 1 -230329 1 diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5efd468..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.639e-02 1.162e-03 31.31 <2e-16 *** -r 4.470e-03 4.372e-05 102.25 <2e-16 *** -kmercov 6.899e+00 4.137e-03 1667.67 <2e-16 *** -bias 1.020e+00 9.045e-03 112.75 <2e-16 *** -length 1.030e+08 9.436e+04 1091.88 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10610 on 992 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 5.484e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index aa6e89b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c92eb37..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 67455fa..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 55219327415.6253 -round 1 trimming to 9 trying 4peak model... converged. score: 130325808489.063 -round 2 trimming to 14 trying 4peak model... converged. score: 36889017763467.2 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c9473e1..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.438235% 0.455721% -Genome Haploid Length 113,899,695 bp 114,173,217 bp -Genome Repeat Length 14,705,107 bp 14,740,420 bp -Genome Unique Length 99,194,588 bp 99,432,797 bp -Model Fit 98.309% 99.365% -Read Error Rate 1.95566% 1.95566% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 2a6a0e6..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,3387 +0,0 @@ -1 48706852 -2 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1 -10662 1 -10672 1 -10802 1 -10839 1 -10956 1 -11056 1 -11079 1 -11135 1 -11169 1 -11215 1 -11225 1 -11285 1 -11359 1 -11402 1 -11403 1 -11829 1 -12077 1 -12079 1 -12137 1 -12646 1 -12676 1 -12766 1 -12838 1 -13049 1 -13348 1 -13711 1 -15229 1 -15421 1 -26634 1 -33206 1 -33490 1 -33674 1 -87240 1 -89510 1 -91310 1 -342715 1 diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 419d6d5..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.847e-02 8.142e-04 22.68 <2e-16 *** -r 3.767e-03 2.567e-05 146.73 <2e-16 *** -kmercov 1.049e+01 3.868e-03 2711.15 <2e-16 *** -bias 2.597e+00 9.714e-03 267.31 <2e-16 *** -length 1.019e+08 5.586e+04 1825.05 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4981 on 993 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 2.01e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 84ce545..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1e8486d..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bf1fc4e..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 23951404217.1839 -round 1 trimming to 8 trying 4peak model... converged. score: 40170403330.7584 -round 2 trimming to 13 trying 4peak model... converged. score: 617446929435.456 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1a78a02..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.371573% 0.381842% -Genome Haploid Length 110,594,699 bp 110,757,990 bp -Genome Repeat Length 10,594,831 bp 10,610,474 bp -Genome Unique Length 99,999,868 bp 100,147,516 bp -Model Fit 98.3491% 99.4191% -Read Error Rate 0.100033% 0.100033% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index d2faa6e..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2946 +0,0 @@ -1 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a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.893e-02 1.015e-03 28.52 <2e-16 *** -r 4.902e-03 3.740e-05 131.06 <2e-16 *** -kmercov 8.758e+00 4.302e-03 2035.95 <2e-16 *** -bias 1.956e+00 1.094e-02 178.75 <2e-16 *** -length 1.005e+08 7.593e+04 1323.85 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6307 on 992 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 8.455e-07 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3247cc4..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index abe772b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index cae5ea6..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 22615207147.5293 -round 1 trimming to 9 trying 4peak model... converged. score: 45728447565.1957 -round 2 trimming to 14 trying 4peak model... converged. score: 3159670582507.43 -round 3 trimming to 19 trying 4peak model... converged. score: 47189408213355.6 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b0b29e4..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.482679% 0.497638% -Genome Haploid Length 110,081,613 bp 110,298,101 bp -Genome Repeat Length 12,539,695 bp 12,564,355 bp -Genome Unique Length 97,541,918 bp 97,733,746 bp -Model Fit 98.5428% 99.553% -Read Error Rate 0.986574% 0.986574% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 8b253b3..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2574 +0,0 @@ -1 727439052 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d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.770e-02 1.805e-03 20.89 <2e-16 *** -r 6.775e-03 7.957e-05 85.14 <2e-16 *** -kmercov 7.210e+00 7.093e-03 1016.49 <2e-16 *** -bias 1.406e+00 1.783e-02 78.81 <2e-16 *** -length 9.870e+07 1.552e+05 635.74 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10880 on 992 degrees of freedom - -Number of iterations to convergence: 19 -Achieved convergence tolerance: 7.287e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cd1ed67..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9e7a059..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1cfbcf8..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 49809372657.1478 -round 1 trimming to 9 trying 4peak model... converged. score: 63503949250.4522 -round 2 trimming to 14 trying 4peak model... converged. score: 12294552987215.9 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 779c16e..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.661555% 0.693382% -Genome Haploid Length 108,873,757 bp 109,303,033 bp -Genome Repeat Length 14,017,923 bp 14,073,194 bp -Genome Unique Length 94,855,834 bp 95,229,839 bp -Model Fit 98.4479% 99.4159% -Read Error Rate 1.95707% 1.95707% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 44740dc..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,3160 +0,0 @@ -1 48650360 -2 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* d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.710e-02 5.735e-04 47.26 <2e-16 *** -r 1.046e-02 1.708e-05 612.16 <2e-16 *** -kmercov 9.863e+00 3.086e-03 3196.11 <2e-16 *** -bias 9.848e-01 4.453e-03 221.19 <2e-16 *** -length 1.079e+08 4.730e+04 2281.24 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6067 on 989 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 1.442e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4329f71..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e6c4fea..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d0325e4..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 59311037611.8329 -round 1 trimming to 7 trying 4peak model... converged. score: 40639264445.4092 -round 2 trimming to 12 trying 4peak model... converged. score: 239850166223.211 -round 3 trimming to 17 trying 4peak model... converged. score: 5727714422907.8 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ce174c7..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.0424% 1.04924% -Genome Haploid Length 117,747,112 bp 117,894,567 bp -Genome Repeat Length 12,715,260 bp 12,731,184 bp -Genome Unique Length 105,031,851 bp 105,163,384 bp -Model Fit 98.3726% 99.3511% -Read Error Rate 0.10053% 0.10053% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index d439f48..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2784 +0,0 @@ -1 417338412 -2 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3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.077e-02 4.577e-04 67.24 <2e-16 *** -r 1.068e-02 1.939e-05 550.57 <2e-16 *** -kmercov 8.169e+00 2.271e-03 3597.74 <2e-16 *** -bias 7.763e-01 3.531e-03 219.85 <2e-16 *** -length 1.079e+08 3.983e+04 2709.28 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4720 on 988 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.49e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6f4e3a3..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 09b15b6..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d5d06f9..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 214246995050.539 -round 1 trimming to 8 trying 4peak model... converged. score: 38643599256.7591 -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... converged. score: 7938587379410.71 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3d2a86d..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.0637% 1.07145% -Genome Haploid Length 118,190,744 bp 118,322,223 bp -Genome Repeat Length 13,518,471 bp 13,533,509 bp -Genome Unique Length 104,672,273 bp 104,788,713 bp -Model Fit 98.594% 99.5313% -Read Error Rate 0.985876% 0.985876% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 31002e8..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2441 +0,0 @@ -1 738295446 -2 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-10250 1 -11232 1 -17805 1 -20989 1 -21319 1 -21403 1 -52700 1 -54020 1 -54569 1 -206828 1 diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7754405..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.753e-02 1.226e-03 22.45 <2e-16 *** -r 1.085e-02 4.954e-05 219.00 <2e-16 *** -kmercov 6.609e+00 5.094e-03 1297.52 <2e-16 *** -bias 6.768e-01 9.118e-03 74.23 <2e-16 *** -length 1.087e+08 1.170e+05 928.87 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11520 on 992 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 7.71e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5cbe72b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6d13ab1..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8e0d7b2..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 54152941448.7693 -round 1 trimming to 9 trying 4peak model... unconverged -round 2 trimming to 14 trying 4peak model... converged. score: 55675347329869.9 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1a198b7..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.07498% 1.0948% -Genome Haploid Length 118,887,119 bp 119,254,189 bp -Genome Repeat Length 13,237,841 bp 13,278,714 bp -Genome Unique Length 105,649,277 bp 105,975,476 bp -Model Fit 98.3612% 99.4306% -Read Error Rate 1.95698% 1.95698% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index fa4f726..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,3177 +0,0 @@ -1 49183098 -2 1695275 -3 2042725 -4 2653781 -5 3260782 -6 3817366 -7 4315083 -8 4746221 -9 5110335 -10 5386349 -11 5588455 -12 5737815 -13 5825361 -14 5855818 -15 5824337 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* (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.466e-02 9.145e-04 26.96 <2e-16 *** -r 1.096e-02 3.837e-05 285.53 <2e-16 *** -kmercov 1.004e+01 5.473e-03 1834.64 <2e-16 *** -bias 1.868e+00 1.154e-02 161.88 <2e-16 *** -length 1.065e+08 8.624e+04 1234.54 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5475 on 989 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 5.059e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b3bc487..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6a2328b..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 91fc845..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 99396463906.9045 -round 1 trimming to 7 trying 4peak model... converged. score: 33224839773.5237 -round 2 trimming to 12 trying 4peak model... converged. score: 216089201609.691 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 95d4fbf..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08798% 1.10333% -Genome Haploid Length 115,554,677 bp 115,806,891 bp -Genome Repeat Length 11,716,494 bp 11,742,067 bp -Genome Unique Length 103,838,183 bp 104,064,824 bp -Model Fit 98.4634% 99.3528% -Read Error Rate 0.102786% 0.102786% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 5985e5c..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2775 +0,0 @@ -1 416988748 -2 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-269044 1 diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7e6202f..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.037e-02 7.414e-04 40.96 <2e-16 *** -r 1.142e-02 4.291e-05 266.13 <2e-16 *** -kmercov 8.340e+00 4.497e-03 1854.62 <2e-16 *** -bias 1.459e+00 8.762e-03 166.56 <2e-16 *** -length 1.059e+08 8.227e+04 1287.42 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4370 on 988 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 2.634e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d803981..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b4ebbe7..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 96c071b..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... unconverged -round 1 trimming to 8 trying 4peak model... converged. score: 27684619497.6934 -round 2 trimming to 13 trying 4peak model... converged. score: 1293209999218.58 -round 3 trimming to 18 trying 4peak model... converged. score: 58180749411252.9 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e8790f1..0000000 --- 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- r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.339e-02 1.552e-03 34.40 <2e-16 *** -r 2.438e-02 1.216e-03 20.06 <2e-16 *** -kmercov 7.317e+00 4.290e-02 170.57 <2e-16 *** -bias 6.964e-01 3.113e-02 22.37 <2e-16 *** -length 1.050e+08 4.499e+05 233.32 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3606 on 981 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 5.797e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4a6fa96..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c532009..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 87fd3bb..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 46474673677071.8 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7da8538..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 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a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.796e-02 9.885e-04 28.29 <2e-16 *** -r 1.228e-02 5.348e-05 229.54 <2e-16 *** -kmercov 1.037e+01 6.832e-03 1517.42 <2e-16 *** -bias 2.523e+00 1.612e-02 156.50 <2e-16 *** -length 1.030e+08 1.138e+05 905.27 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3735 on 989 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 1.806e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4090d53..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e456437..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b6288f5..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 86003058600.7002 -round 1 trimming to 7 trying 4peak model... converged. score: 13795142602.2828 -round 2 trimming to 12 trying 4peak model... converged. score: 66783726726.0002 -round 3 trimming to 17 trying 4peak model... converged. score: 1529827598102.56 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3d07ef5..0000000 --- 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a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.475e-02 9.106e-04 38.17 <2e-16 *** -r 1.311e-02 7.162e-05 183.03 <2e-16 *** -kmercov 8.649e+00 7.315e-03 1182.48 <2e-16 *** -bias 1.952e+00 1.397e-02 139.79 <2e-16 *** -length 1.019e+08 1.296e+05 786.44 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3354 on 987 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 7.567e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 076c2e8..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 99eba11..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b6c4f09..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 34605870859.7853 -round 1 trimming to 9 trying 4peak model... converged. score: 17754128633.4636 -round 2 trimming to 14 trying 4peak model... converged. score: 851247249447.186 -round 3 trimming to 19 trying 4peak model... converged. score: 26976039320866.2 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9b5bbe8..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.29659% 1.32523% -Genome Haploid Length 111,326,865 bp 111,704,092 bp -Genome Repeat Length 12,880,638 bp 12,924,283 bp -Genome Unique Length 98,446,227 bp 98,779,808 bp -Model Fit 98.813% 99.6613% -Read Error Rate 0.993389% 0.993389% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 01c1960..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,2480 +0,0 @@ -1 734750720 -2 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(2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.784e-02 1.467e-03 39.43 <2e-16 *** -r 2.407e-02 8.252e-04 29.17 <2e-16 *** -kmercov 7.647e+00 4.268e-02 179.16 <2e-16 *** -bias 1.009e+00 3.314e-02 30.44 <2e-16 *** -length 9.618e+07 2.266e+05 424.52 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3087 on 981 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 7.481e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 832f64c..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index dd1ebf4..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0fe9924..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 12352486324458 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9c64e1b..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.24214% 2.57222% -Genome Haploid Length 101,623,301 bp 103,917,822 bp -Genome Repeat Length 11,128,980 bp 11,380,258 bp -Genome Unique Length 90,494,320 bp 92,537,564 bp -Model Fit 91.2294% 91.8633% -Read Error Rate 1.96387% 1.96387% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 4186255..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,2990 +0,0 @@ -1 48827088 -2 1508501 -3 2337424 -4 3590368 -5 4907580 -6 6105919 -7 7078343 -8 7735580 -9 8090615 -10 8168871 -11 8044570 -12 7775714 -13 7471688 -14 7116789 -15 6763398 -16 6429370 -17 6066828 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b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1053dab..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.302e-02 1.089e-03 21.13 <2e-16 *** -r 2.084e-02 4.706e-05 442.79 <2e-16 *** -kmercov 9.917e+00 8.120e-03 1221.35 <2e-16 *** -bias 9.886e-01 8.171e-03 120.98 <2e-16 *** -length 1.082e+08 8.214e+04 1317.69 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8818 on 989 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 8.155e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 10ae710..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index dc86527..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0006207..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 129755865881.275 -round 1 trimming to 7 trying 4peak model... converged. score: 85068452514.9458 -round 2 trimming to 12 trying 4peak model... converged. score: 335413721783.293 -round 3 trimming to 17 trying 4peak model... converged. score: 3920934115692.96 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 743f634..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.0742% 2.09302% -Genome Haploid Length 117,088,306 bp 117,472,406 bp -Genome Repeat Length 11,196,308 bp 11,233,037 bp -Genome Unique Length 105,891,998 bp 106,239,370 bp -Model Fit 98.2833% 99.119% -Read Error Rate 0.101956% 0.101956% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 1f9d8a2..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2629 +0,0 @@ -1 420021345 -2 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b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index de7eb0c..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.076e-02 7.316e-04 42.05 <2e-16 *** -r 2.041e-02 3.283e-05 621.71 <2e-16 *** -kmercov 8.111e+00 4.789e-03 1693.70 <2e-16 *** -bias 8.379e-01 5.956e-03 140.69 <2e-16 *** -length 1.097e+08 6.836e+04 1604.19 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5351 on 988 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 5.096e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b346100..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index da9c0cb..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c7921c7..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 248153955484.814 -round 1 trimming to 8 trying 4peak model... converged. score: 156869177103.313 -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... converged. score: 20067445303279.6 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b9e5759..0000000 --- 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dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.561e-02 1.682e-03 21.17 <2e-16 *** -r 2.035e-02 8.138e-05 249.99 <2e-16 *** -kmercov 9.963e+00 1.409e-02 706.94 <2e-16 *** -bias 1.710e+00 1.950e-02 87.69 <2e-16 *** -length 1.069e+08 1.683e+05 635.05 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7962 on 989 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 4.793e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 39e8fcb..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index d261526..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 772392b..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 229679116742.984 -round 1 trimming to 7 trying 4peak model... converged. score: 65192747727.054 -round 2 trimming to 12 trying 4peak model... converged. score: 334475593336.647 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6aa0703..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.01824% 2.0508% -Genome Haploid Length 116,227,193 bp 116,886,691 bp -Genome Repeat Length 12,985,768 bp 13,059,452 bp -Genome Unique Length 103,241,425 bp 103,827,239 bp -Model Fit 98.4587% 99.206% -Read Error Rate 0.109621% 0.109621% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 6ef3ad9..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2623 +0,0 @@ -1 420181321 -2 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b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 38412b3..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.039e-02 1.436e-03 21.16 <2e-16 *** -r 1.941e-02 8.973e-05 216.35 <2e-16 *** -kmercov 8.083e+00 1.097e-02 736.77 <2e-16 *** -bias 1.652e+00 2.087e-02 79.16 <2e-16 *** -length 1.105e+08 2.423e+05 455.90 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4869 on 988 degrees of freedom - -Number of iterations to convergence: 12 -Achieved convergence tolerance: 6.744e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0ac33af..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8b4f36c..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4064975..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 192832698014.726 -round 1 trimming to 8 trying 4peak model... converged. score: 204259026754.818 -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 0bcc1d2..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ 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-23003 1 -28676 1 -28872 1 -29093 1 -73210 1 -74700 1 -79344 1 -290281 1 diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 620cabf..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.960e-02 1.479e-03 33.54 <2e-16 *** -r 2.079e-02 9.188e-05 226.24 <2e-16 *** -kmercov 1.018e+01 1.544e-02 659.49 <2e-16 *** -bias 2.226e+00 1.917e-02 116.10 <2e-16 *** -length 1.034e+08 1.716e+05 602.53 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5311 on 989 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 5.452e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6a70b24..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 42537b9..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1c870da..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 50951255735.6893 -round 1 trimming to 7 trying 4peak model... converged. score: 27894545248.1279 -round 2 trimming to 12 trying 4peak model... converged. score: 156439712586.42 -round 3 trimming to 17 trying 4peak model... converged. score: 1242053459835.15 -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a6af557..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.06034% 2.0971% -Genome Haploid Length 113,480,599 bp 114,170,985 bp -Genome Repeat Length 14,860,249 bp 14,950,655 bp -Genome Unique Length 98,620,350 bp 99,220,330 bp -Model Fit 98.674% 99.3513% -Read Error Rate 0.119576% 0.119576% diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 45ea3c5..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,2637 +0,0 @@ -1 419778146 -2 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b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7f4c5ca..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.245e-02 2.673e-03 23.36 <2e-16 *** -r 3.284e-02 2.068e-03 15.88 <2e-16 *** -kmercov 9.361e+00 1.067e-01 87.73 <2e-16 *** -bias 1.239e+00 7.457e-02 16.62 <2e-16 *** -length 9.651e+07 3.646e+05 264.71 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2595 on 976 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 1.54e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index c413a1a..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b3a39e6..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 933fc62..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... converged. score: 11171305887919.1 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 980742c..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 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b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index aa3420d..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.602e-02 1.843e-03 35.82 <2e-16 *** -r 3.174e-02 8.317e-04 38.16 <2e-16 *** -kmercov 7.530e+00 4.929e-02 152.75 <2e-16 *** -bias 9.765e-01 4.168e-02 23.43 <2e-16 *** -length 9.611e+07 3.909e+05 245.87 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2865 on 981 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 8.653e-06 - diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 17fcba9..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 26ad87a..0000000 Binary files a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8248170..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 7757253678063.56 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8935783..0000000 --- a/analysis/simulation_results_25x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.00738% 3.34005% -Genome Haploid Length 102,406,753 bp 105,123,946 bp -Genome Repeat Length 12,288,087 bp 12,614,131 bp -Genome Unique Length 90,118,665 bp 92,509,815 bp -Model Fit 93.1397% 93.7484% -Read Error Rate 1.99436% 1.99436% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 0bd9847..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4418 +0,0 @@ -1 54772770 -2 750645 -3 261554 -4 346987 -5 538940 -6 800913 -7 1158054 -8 1606395 -9 2158497 -10 2804352 -11 3538074 -12 4310249 -13 5100677 -14 5817269 -15 6455220 -16 6941743 -17 7257511 -18 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length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.123e-02 3.994e-04 28.12 <2e-16 *** -r 1.430e-03 1.017e-05 140.59 <2e-16 *** -kmercov 9.895e+00 1.606e-03 6159.33 <2e-16 *** -bias 9.629e-01 2.478e-03 388.64 <2e-16 *** -length 1.165e+08 4.399e+04 2648.09 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6284 on 993 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 3.397e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 23ad9d6..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e0d7b9b..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b74daa0..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 36525478494.599 -round 1 trimming to 8 trying 4peak model... converged. score: 46308879925.6625 -round 2 trimming to 13 trying 4peak model... converged. score: 811158894568.959 -round 3 trimming to 18 trying 4peak model... converged. score: 19850422445808.8 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f65534a..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.140967% 0.145035% -Genome Haploid Length 131,786,954 bp 131,872,567 bp -Genome Repeat Length 16,631,154 bp 16,641,958 bp -Genome Unique Length 115,155,800 bp 115,230,609 bp -Model Fit 97.9522% 99.332% -Read Error Rate 0.101655% 0.101655% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 0c70a67..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3882 +0,0 @@ -1 455863826 -2 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~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.709e-02 5.406e-04 31.61 <2e-16 *** -r 2.362e-03 1.607e-05 146.99 <2e-16 *** -kmercov 8.231e+00 1.954e-03 4212.04 <2e-16 *** -bias 7.238e-01 3.187e-03 227.07 <2e-16 *** -length 1.163e+08 5.629e+04 2066.95 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8538 on 991 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.437e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 62315c7..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index c58ed6e..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3fa82e3..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 36622340821.7634 -round 1 trimming to 10 trying 4peak model... converged. score: 41372148998.045 -round 2 trimming to 15 trying 4peak model... converged. score: 10619237337799 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b55f216..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.233024% 0.239453% -Genome Haploid Length 132,437,324 bp 132,563,154 bp -Genome Repeat Length 18,126,710 bp 18,143,932 bp -Genome Unique Length 114,310,614 bp 114,419,222 bp -Model Fit 98.2222% 99.5264% -Read Error Rate 0.984799% 0.984799% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index fe714b6..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3404 +0,0 @@ -1 804840679 -2 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1 -51713 1 -57631 1 -59766 1 -72774 1 -91414 1 diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index c915c66..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.285e-02 7.401e-04 30.87 <2e-16 *** -r 3.524e-03 2.713e-05 129.88 <2e-16 *** -kmercov 6.690e+00 2.442e-03 2739.00 <2e-16 *** -bias 5.217e-01 4.252e-03 122.69 <2e-16 *** -length 1.171e+08 7.390e+04 1584.91 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11370 on 991 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.987e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9d3d537..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6b013d3..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9e409e0..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 74970032877.1832 -round 1 trimming to 10 trying 4peak model... converged. score: 114833502071.208 -round 2 trimming to 15 trying 4peak model... converged. score: 128247513531040 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 361d166..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.346954% 0.357806% -Genome Haploid Length 134,241,084 bp 134,437,271 bp -Genome Repeat Length 19,858,872 bp 19,887,895 bp -Genome Unique Length 114,382,212 bp 114,549,377 bp -Model Fit 97.9775% 99.2887% -Read Error Rate 1.92451% 1.92451% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 123c878..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4446 +0,0 @@ -1 54788691 -2 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.794e-03 6.369e-04 9.099 <2e-16 *** -r 2.381e-03 1.788e-05 133.157 <2e-16 *** -kmercov 1.014e+01 2.839e-03 3571.263 <2e-16 *** -bias 1.858e+00 5.810e-03 319.803 <2e-16 *** -length 1.144e+08 5.289e+04 2162.060 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6364 on 993 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 6.312e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 295d143..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4a6a126..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e09b52c..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 38607405844.019 -round 1 trimming to 8 trying 4peak model... converged. score: 70050334106.5489 -round 2 trimming to 13 trying 4peak model... converged. score: 1181440286277.19 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cbbbf58..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.234557% 0.24171% -Genome Haploid Length 128,572,788 bp 128,716,877 bp -Genome Repeat Length 14,937,199 bp 14,953,939 bp -Genome Unique Length 113,635,589 bp 113,762,938 bp -Model Fit 97.924% 99.2529% -Read Error Rate 0.10149% 0.10149% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 2547f26..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3917 +0,0 @@ -1 454896870 -2 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b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index b0d3f39..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.512e-02 4.701e-04 32.16 <2e-16 *** -r 3.889e-03 4.106e-05 94.73 <2e-16 *** -kmercov 8.476e+00 3.092e-03 2741.53 <2e-16 *** -bias 1.372e+00 5.370e-03 255.55 <2e-16 *** -length 1.134e+08 5.016e+04 2260.65 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4290 on 987 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.662e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index eb1860f..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index dc451fb..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index afb929d..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 104443605766.296 -round 1 trimming to 9 trying 4peak model... converged. score: 25487309085.7571 -round 2 trimming to 14 trying 4peak model... converged. score: 4141936484268.94 -round 3 trimming to 19 trying 4peak model... converged. score: 143636136673710 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2262ae7..0000000 --- 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-13591 1 -13751 1 -13833 1 -14543 1 -14559 1 -16956 1 -17070 1 -17121 1 -17295 1 -17344 1 -17459 1 -17519 1 -18608 1 -18840 1 -27131 1 -27479 1 -28008 1 -36217 1 -36583 1 -36623 1 -39767 1 -40018 1 -40020 1 -40147 1 -40746 1 -40922 1 -41357 1 -41528 1 -41949 1 -51168 1 -52426 1 -59192 1 -61246 1 -72359 1 -90988 1 diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 07832d4..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.062e-02 5.329e-04 38.70 <2e-16 *** -r 5.169e-03 8.533e-05 60.57 <2e-16 *** -kmercov 6.896e+00 4.894e-03 1408.97 <2e-16 *** -bias 1.039e+00 6.652e-03 156.23 <2e-16 *** -length 1.140e+08 7.456e+04 1529.20 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4299 on 987 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.231e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7d15317..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 42a57c9..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8d65a08..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... unconverged -round 1 trimming to 9 trying 4peak model... converged. score: 33638359373.4268 -round 2 trimming to 14 trying 4peak model... converged. score: 39293649290501.2 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 32d6c2d..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.499818% 0.53395% -Genome Haploid Length 130,173,050 bp 130,543,131 bp -Genome Repeat Length 18,633,314 bp 18,686,288 bp -Genome Unique Length 111,539,736 bp 111,856,842 bp -Model Fit 98.3362% 99.6421% -Read Error Rate 1.92311% 1.92311% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index e918cf9..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4443 +0,0 @@ -1 54935926 -2 1285719 -3 991090 -4 1260551 -5 1619794 -6 2030942 -7 2476605 -8 2929207 -9 3369599 -10 3803858 -11 4196132 -12 4549765 -13 4849073 -14 5076303 -15 5252004 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- (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.030e-03 8.426e-04 4.783 1.99e-06 *** -r 3.969e-03 2.696e-05 147.213 < 2e-16 *** -kmercov 1.050e+01 3.934e-03 2669.673 < 2e-16 *** -bias 2.581e+00 9.915e-03 260.286 < 2e-16 *** -length 1.108e+08 6.275e+04 1766.555 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5659 on 993 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 1.866e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 60675b5..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 939fc09..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 783296f..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 26790095472.4055 -round 1 trimming to 8 trying 4peak model... converged. score: 46895097651.122 -round 2 trimming to 13 trying 4peak model... converged. score: 719948542683.474 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index dcd59c2..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.391546% 0.402331% -Genome Haploid Length 124,073,487 bp 124,259,527 bp -Genome Repeat Length 13,752,909 bp 13,773,530 bp -Genome Unique Length 110,320,578 bp 110,485,996 bp -Model Fit 98.1317% 99.4195% -Read Error Rate 0.101734% 0.101734% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 11dc55a..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3915 +0,0 @@ -1 454149183 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b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5c21876..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.707e-02 6.037e-04 28.27 <2e-16 *** -r 6.131e-03 5.107e-05 120.04 <2e-16 *** -kmercov 8.841e+00 4.333e-03 2040.35 <2e-16 *** -bias 1.868e+00 8.260e-03 226.18 <2e-16 *** -length 1.088e+08 7.071e+04 1538.72 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3693 on 987 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 2.574e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8a47ba5..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 501161f..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4d97d8a..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... unconverged -round 1 trimming to 9 trying 4peak model... converged. score: 21372467983.1031 -round 2 trimming to 14 trying 4peak model... converged. score: 1412838604179.68 -round 3 trimming to 19 trying 4peak model... converged. score: 76486468664222.5 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 5bf3722..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.6029% 0.623329% -Genome Haploid Length 123,275,022 bp 123,516,934 bp -Genome Repeat Length 16,412,162 bp 16,444,369 bp -Genome Unique Length 106,862,860 bp 107,072,565 bp -Model Fit 98.4379% 99.6659% -Read Error Rate 0.982846% 0.982846% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index b2ad29c..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3415 +0,0 @@ -1 800428505 -2 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2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.350e-02 7.654e-04 30.71 <2e-16 *** -r 7.720e-03 1.532e-04 50.38 <2e-16 *** -kmercov 7.206e+00 9.754e-03 738.79 <2e-16 *** -bias 1.421e+00 1.231e-02 115.37 <2e-16 *** -length 1.091e+08 1.433e+05 761.56 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3810 on 986 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 2.4e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b6c3876..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index ea362e0..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e1deca9..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 56364382188.9343 -round 1 trimming to 10 trying 4peak model... converged. score: 41804463901.4016 -round 2 trimming to 15 trying 4peak model... converged. score: 30411390384660.1 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c87a493..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.741398% 0.802692% -Genome Haploid Length 124,398,250 bp 125,073,599 bp -Genome Repeat Length 18,056,200 bp 18,154,225 bp -Genome Unique Length 106,342,051 bp 106,919,374 bp -Model Fit 98.3193% 99.5585% -Read Error Rate 1.92383% 1.92383% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 192f204..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4219 +0,0 @@ -1 54799488 -2 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.234e-02 5.774e-04 21.38 <2e-16 *** -r 1.069e-02 1.716e-05 622.91 <2e-16 *** -kmercov 9.859e+00 3.025e-03 3258.73 <2e-16 *** -bias 9.938e-01 4.415e-03 225.08 <2e-16 *** -length 1.184e+08 5.138e+04 2304.91 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6597 on 989 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 1.946e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0df9ab5..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index a51cf77..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6097a60..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 104972203483.533 -round 1 trimming to 7 trying 4peak model... converged. score: 51713983682.9894 -round 2 trimming to 12 trying 4peak model... converged. score: 242227354666.637 -round 3 trimming to 17 trying 4peak model... converged. score: 11237619327293.6 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9b5dc90..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.0652% 1.07206% -Genome Haploid Length 132,736,863 bp 132,899,894 bp -Genome Repeat Length 15,781,339 bp 15,800,722 bp -Genome Unique Length 116,955,524 bp 117,099,172 bp -Model Fit 98.1951% 99.3247% -Read Error Rate 0.101366% 0.101366% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 9eb5248..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3662 +0,0 @@ -1 460591624 -2 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-Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.675e-02 4.337e-04 38.61 <2e-16 *** -r 1.111e-02 2.400e-05 463.01 <2e-16 *** -kmercov 8.175e+00 2.295e-03 3562.66 <2e-16 *** -bias 7.775e-01 3.548e-03 219.13 <2e-16 *** -length 1.187e+08 4.223e+04 2810.18 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4746 on 987 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 5.281e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3e594fc..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index e73908b..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ba2c35b..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 133189826718.367 -round 1 trimming to 9 trying 4peak model... converged. score: 33291202456.7003 -round 2 trimming to 14 trying 4peak model... converged. score: 4768262350491.49 -round 3 trimming to 19 trying 4peak model... converged. score: 80204383227539.6 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4e391d5..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.10635% 1.11595% -Genome Haploid Length 133,770,166 bp 133,920,442 bp -Genome Repeat Length 17,058,397 bp 17,077,560 bp -Genome Unique Length 116,711,769 bp 116,842,881 bp -Model Fit 98.433% 99.5786% -Read Error Rate 0.982361% 0.982361% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index d5be6d5..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3209 +0,0 @@ -1 815040276 -2 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kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.108e-02 1.411e-03 22.03 <2e-16 *** -r 2.470e-02 2.162e-03 11.43 <2e-16 *** -kmercov 6.954e+00 4.311e-02 161.30 <2e-16 *** -bias 3.722e-01 2.755e-02 13.51 <2e-16 *** -length 1.307e+08 2.631e+06 49.66 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4324 on 981 degrees of freedom - -Number of iterations to convergence: 17 -Achieved convergence tolerance: 9.789e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 17a81fc..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index df7cd30..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6eed9ec..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 163477727738671 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c432afa..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.03728% 2.90189% -Genome Haploid Length 129,013,204 bp 132,252,765 bp -Genome Repeat Length 3,289,940 bp 3,372,552 bp -Genome Unique Length 125,723,264 bp 128,880,213 bp -Model Fit 74.61% 75.305% -Read Error Rate 1.88484% 1.88484% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index b17be76..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4183 +0,0 @@ -1 55380954 -2 2129342 -3 2324163 -4 2981253 -5 3659680 -6 4285091 -7 4837615 -8 5314432 -9 5689770 -10 5987028 -11 6238301 -12 6371062 -13 6473609 -14 6494993 -15 6445176 -16 6356585 -17 6176543 -18 5971256 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index c450eb7..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.682e-03 8.666e-04 10.02 <2e-16 *** -r 1.123e-02 3.695e-05 303.84 <2e-16 *** -kmercov 1.005e+01 5.115e-03 1964.12 <2e-16 *** -bias 1.893e+00 1.086e-02 174.36 <2e-16 *** -length 1.168e+08 8.958e+04 1303.98 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5624 on 989 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 2.005e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 50cba3d..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 10decf3..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c30e537..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 171428861359.683 -round 1 trimming to 7 trying 4peak model... converged. score: 34936155444.614 -round 2 trimming to 12 trying 4peak model... converged. score: 224785186609.154 -round 3 trimming to 17 trying 4peak model... converged. score: 4216669390917.5 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 16fdf1d..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.11527% 1.13005% -Genome Haploid Length 130,145,025 bp 130,410,340 bp -Genome Repeat Length 14,416,461 bp 14,445,851 bp -Genome Unique Length 115,728,563 bp 115,964,489 bp -Model Fit 98.3307% 99.4061% -Read Error Rate 0.103503% 0.103503% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 53ffa10..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3707 +0,0 @@ -1 460335626 -2 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b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index f0843aa..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.757e-02 6.497e-04 27.05 <2e-16 *** -r 1.230e-02 4.518e-05 272.25 <2e-16 *** -kmercov 8.388e+00 4.403e-03 1905.08 <2e-16 *** -bias 1.416e+00 7.920e-03 178.82 <2e-16 *** -length 1.158e+08 8.393e+04 1379.73 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4152 on 987 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 1.216e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 873039d..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 65d17e1..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d66ad4b..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 144728125760.631 -round 1 trimming to 9 trying 4peak model... converged. score: 28431419108.8335 -round 2 trimming to 14 trying 4peak model... converged. score: 2658038775464.53 -round 3 trimming to 19 trying 4peak model... converged. score: 83939617839448.8 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6c4e978..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.22112% 1.23919% -Genome Haploid Length 130,269,868 bp 130,543,676 bp -Genome Repeat Length 16,519,881 bp 16,554,603 bp -Genome Unique Length 113,749,988 bp 113,989,073 bp -Model Fit 98.4945% 99.614% -Read Error Rate 0.985212% 0.985212% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 4a20167..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3215 +0,0 @@ -1 813610194 -2 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dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.758e-02 1.261e-03 29.81 <2e-16 *** -r 2.658e-02 1.023e-03 25.99 <2e-16 *** -kmercov 7.369e+00 3.785e-02 194.68 <2e-16 *** -bias 6.951e-01 2.704e-02 25.71 <2e-16 *** -length 1.175e+08 4.116e+05 285.39 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3776 on 981 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 4.055e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d33f066..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c7c2b84..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 09a5456..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 68125577719231.2 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2da6e6b..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.45354% 2.86261% -Genome Haploid Length 121,496,327 bp 124,018,510 bp -Genome Repeat Length 8,780,780 bp 8,963,063 bp -Genome Unique Length 112,715,546 bp 115,055,447 bp -Model Fit 82.6093% 83.391% -Read Error Rate 1.90362% 1.90362% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 80ad74f..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,4219 +0,0 @@ -1 55646352 -2 2696981 -3 2934520 -4 3479968 -5 4005040 -6 4484496 -7 4903147 -8 5283981 -9 5566850 -10 5784849 -11 5933663 -12 6014340 -13 6032940 -14 5996158 -15 5936793 -16 5787032 -17 5605350 -18 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r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.028e-02 1.030e-03 9.98 <2e-16 *** -r 1.236e-02 5.781e-05 213.73 <2e-16 *** -kmercov 1.035e+01 7.086e-03 1460.12 <2e-16 *** -bias 2.589e+00 1.676e-02 154.48 <2e-16 *** -length 1.135e+08 1.315e+05 862.81 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 4234 on 989 degrees of freedom - -Number of iterations to convergence: 12 -Achieved convergence tolerance: 1.612e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6bd03a2..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index c50869e..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7f9ca67..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... unconverged -round 1 trimming to 7 trying 4peak model... converged. score: 17739058425.973 -round 2 trimming to 12 trying 4peak model... converged. score: 75987083376.7822 -round 3 trimming to 17 trying 4peak model... converged. score: 1919738534414.24 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c2e3793..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.22399% 1.24711% -Genome Haploid Length 126,248,860 bp 126,595,193 bp -Genome Repeat Length 14,056,528 bp 14,095,089 bp -Genome Unique Length 112,192,332 bp 112,500,104 bp -Model Fit 98.5448% 99.6109% -Read Error Rate 0.106788% 0.106788% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 3b290be..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3708 +0,0 @@ -1 459713535 -2 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 96f0719..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.998e-02 8.769e-04 22.78 <2e-16 *** -r 1.366e-02 6.832e-05 199.93 <2e-16 *** -kmercov 8.668e+00 6.965e-03 1244.46 <2e-16 *** -bias 1.935e+00 1.323e-02 146.29 <2e-16 *** -length 1.118e+08 1.357e+05 824.18 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3618 on 987 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 5.326e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 40a221f..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4565c9b..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bb30600..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... unconverged -round 1 trimming to 9 trying 4peak model... converged. score: 13045210877.0635 -round 2 trimming to 14 trying 4peak model... unconverged -round 3 trimming to 19 trying 4peak model... converged. score: 40930101735599.1 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 663c931..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.3523% 1.37963% -Genome Haploid Length 125,795,276 bp 126,200,262 bp -Genome Repeat Length 16,263,967 bp 16,316,327 bp -Genome Unique Length 109,531,309 bp 109,883,935 bp -Model Fit 98.6297% 99.7638% -Read Error Rate 0.991793% 0.991793% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index a00d9d4..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3215 +0,0 @@ -1 811363867 -2 44337816 -3 10786208 -4 8582989 -5 8490114 -6 8687577 -7 8883266 -8 8967009 -9 8897878 -10 8667120 -11 8306343 -12 7834653 -13 7281921 -14 6665489 -15 6022789 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mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.241e-02 1.381e-03 30.70 <2e-16 *** -r 2.522e-02 7.843e-04 32.15 <2e-16 *** -kmercov 7.662e+00 4.164e-02 184.00 <2e-16 *** -bias 1.026e+00 3.222e-02 31.83 <2e-16 *** -length 1.068e+08 2.596e+05 411.44 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3336 on 981 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 4.229e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 78c2f70..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 61d37ef..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 814bff4..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 14595126067114.6 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b717922..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.36509% 2.67882% -Genome Haploid Length 116,257,565 bp 118,812,696 bp -Genome Repeat Length 14,323,102 bp 14,637,898 bp -Genome Unique Length 101,934,463 bp 104,174,798 bp -Model Fit 90.9244% 91.8121% -Read Error Rate 1.9245% 1.9245% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 58cf5d7..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,3976 +0,0 @@ -1 55036796 -2 1864374 -3 2633596 -4 4039784 -5 5504514 -6 6859966 -7 7929530 -8 8675754 -9 9071981 -10 9134191 -11 8985458 -12 8699512 -13 8320203 -14 7933338 -15 7512118 -16 7130234 -17 6734229 -18 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-52590 1 -64156 1 -65628 1 -74129 1 -76536 1 -91944 1 -114835 1 diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 75baec3..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 7.663e-03 1.082e-03 7.084 2.66e-12 *** -r 2.134e-02 4.678e-05 456.245 < 2e-16 *** -kmercov 9.926e+00 7.875e-03 1260.409 < 2e-16 *** -bias 9.899e-01 7.922e-03 124.946 < 2e-16 *** -length 1.193e+08 8.849e+04 1348.032 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9569 on 989 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 8.867e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 783ebdd..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 55879ca..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e655a52..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 182751466652.08 -round 1 trimming to 7 trying 4peak model... converged. score: 97782483278.5943 -round 2 trimming to 12 trying 4peak model... converged. score: 420697338614.742 -round 3 trimming to 17 trying 4peak model... converged. score: 5509552663873.83 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 992d220..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12497% 2.14368% -Genome Haploid Length 132,114,177 bp 132,534,117 bp -Genome Repeat Length 13,805,502 bp 13,849,385 bp -Genome Unique Length 118,308,675 bp 118,684,733 bp -Model Fit 98.1581% 99.1486% -Read Error Rate 0.102575% 0.102575% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index ecd155f..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3496 +0,0 @@ -1 465169404 -2 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 22e2976..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.474e-02 7.382e-04 19.97 <2e-16 *** -r 2.087e-02 3.322e-05 628.22 <2e-16 *** -kmercov 8.111e+00 4.728e-03 1715.68 <2e-16 *** -bias 8.630e-01 6.034e-03 143.02 <2e-16 *** -length 1.215e+08 7.733e+04 1571.58 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5819 on 988 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 8.952e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7a60d5e..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 628fbc1..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3eac557..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 744084727487.695 -round 1 trimming to 8 trying 4peak model... converged. score: 122337032711.498 -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2475e03..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08016% 2.09345% -Genome Haploid Length 135,388,076 bp 135,704,094 bp -Genome Repeat Length 15,567,419 bp 15,603,756 bp -Genome Unique Length 119,820,657 bp 120,100,338 bp -Model Fit 98.3069% 99.2611% -Read Error Rate 0.972684% 0.972684% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 84ce16f..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3039 +0,0 @@ -1 825449273 -2 39813504 -3 11780756 -4 11502070 -5 12479340 -6 13071194 -7 13099241 -8 12672192 -9 11973466 -10 11138114 -11 10225350 -12 9271535 -13 8292113 -14 7285044 -15 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-73818 1 -76437 1 -90398 1 -113944 1 diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1eac542..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.013e-02 1.735e-03 11.60 <2e-16 *** -r 2.111e-02 8.400e-05 251.28 <2e-16 *** -kmercov 1.002e+01 1.429e-02 700.65 <2e-16 *** -bias 1.672e+00 1.894e-02 88.28 <2e-16 *** -length 1.172e+08 1.801e+05 650.53 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9253 on 989 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 5.337e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d603fdc..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index ce118ad..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c9e3ed2..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 397257263306.958 -round 1 trimming to 7 trying 4peak model... converged. score: 85279148344.3446 -round 2 trimming to 12 trying 4peak model... converged. score: 473348318015.968 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 854efd5..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.09386% 2.12746% -Genome Haploid Length 130,529,451 bp 131,276,774 bp -Genome Repeat Length 15,754,233 bp 15,844,431 bp -Genome Unique Length 114,775,219 bp 115,432,344 bp -Model Fit 98.2502% 99.1758% -Read Error Rate 0.111522% 0.111522% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index af7a0df..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3469 +0,0 @@ -1 465363662 -2 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a046153..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.253e-02 9.742e-04 33.40 <2e-16 *** -r 2.695e-02 2.660e-04 101.35 <2e-16 *** -kmercov 8.653e+00 1.872e-02 462.27 <2e-16 *** -bias 1.122e+00 1.887e-02 59.43 <2e-16 *** -length 1.148e+08 1.807e+05 635.27 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3386 on 981 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 2.629e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9e86fb2..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index efcfa96..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7cff3d5..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 5428033590603.82 -round 1 trimming to 20 trying 4peak model... converged. score: 165859811929152 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3c7cb7a..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.64227% 2.74865% -Genome Haploid Length 126,024,170 bp 127,119,394 bp -Genome Repeat Length 14,732,347 bp 14,860,380 bp -Genome Unique Length 111,291,823 bp 112,259,014 bp -Model Fit 94.7132% 95.55% -Read Error Rate 0.991009% 0.991009% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 5f71e31..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,3033 +0,0 @@ -1 824152635 -2 42504781 -3 12737739 -4 11550896 -5 11877430 -6 12106640 -7 12021338 -8 11671572 -9 11075669 -10 10332510 -11 9489230 -12 8584282 -13 7673008 -14 6770759 -15 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.587e-02 1.609e-03 28.51 <2e-16 *** -r 3.415e-02 1.081e-03 31.58 <2e-16 *** -kmercov 7.292e+00 4.291e-02 169.93 <2e-16 *** -bias 6.574e-01 3.314e-02 19.84 <2e-16 *** -length 1.160e+08 3.078e+05 376.78 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3594 on 981 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 6.515e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 38c44d0..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4f69151..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 87d10ee..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 42134963779414.5 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2e3d87d..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index fae1543..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.338e-02 1.322e-03 25.24 <2e-16 *** -r 2.166e-02 8.137e-05 266.25 <2e-16 *** -kmercov 1.025e+01 1.350e-02 759.35 <2e-16 *** -bias 2.201e+00 1.595e-02 137.98 <2e-16 *** -length 1.132e+08 1.562e+05 724.64 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5338 on 989 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 5.036e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bb0c880..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index f092a16..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e56f139..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 63993258649.3756 -round 1 trimming to 7 trying 4peak model... converged. score: 28176639492.8947 -round 2 trimming to 12 trying 4peak model... converged. score: 70445685300.5167 -round 3 trimming to 17 trying 4peak model... converged. score: 528526233023.894 -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 875b910..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.15013% 2.18267% -Genome Haploid Length 127,275,246 bp 127,947,457 bp -Genome Repeat Length 17,608,153 bp 17,701,152 bp -Genome Unique Length 109,667,092 bp 110,246,305 bp -Model Fit 98.5446% 99.4281% -Read Error Rate 0.121513% 0.121513% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 383448d..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,3507 +0,0 @@ -1 465176309 -2 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index eca3083..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... unconverged -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -fail diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index abcd927..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity -100% -100% -Genome Haploid Length -1 bp -1 bp -Genome Repeat Length -1 bp -1 bp -Genome Unique Length -1 bp -1 bp -Model Fit 0% 0% -Read Error Rate -100% -100% diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist 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a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7eb208b..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.113e-02 1.728e-03 29.59 <2e-16 *** -r 3.343e-02 7.338e-04 45.55 <2e-16 *** -kmercov 7.614e+00 4.385e-02 173.64 <2e-16 *** -bias 9.495e-01 3.794e-02 25.02 <2e-16 *** -length 1.060e+08 3.730e+05 284.16 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 3229 on 981 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 9.73e-06 - diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 580a349..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6369a87..0000000 Binary files a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d5f0456..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 10118855680752 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7d4a43c..0000000 --- a/analysis/simulation_results_25x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.19595% 3.48948% -Genome Haploid Length 116,101,968 bp 118,807,648 bp -Genome Repeat Length 15,266,852 bp 15,622,636 bp -Genome Unique Length 100,835,116 bp 103,185,012 bp -Model Fit 92.844% 93.6668% -Read Error Rate 1.96709% 1.96709% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 1608371..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,457 +0,0 @@ -1 1911724 -2 10876 -3 7472 -4 11989 -5 19524 -6 29783 -7 44107 -8 61497 -9 82957 -10 108469 -11 138648 -12 169916 -13 199958 -14 229899 -15 254422 -16 271423 -17 283086 -18 285849 -19 283462 -20 277396 -21 259406 -22 241466 -23 220580 -24 198262 -25 171752 -26 145263 -27 123571 -28 102887 -29 85057 -30 67551 -31 54435 -32 43093 -33 33625 -34 25730 -35 19180 -36 14512 -37 10624 -38 8155 -39 5875 -40 4717 -41 3397 -42 2653 -43 2071 -44 1657 -45 1243 -46 916 -47 805 -48 653 -49 645 -50 566 -51 503 -52 468 -53 440 -54 468 -55 479 -56 432 -57 390 -58 357 -59 387 -60 396 -61 320 -62 278 -63 275 -64 250 -65 223 -66 251 -67 230 -68 234 -69 235 -70 220 -71 201 -72 153 -73 173 -74 166 -75 170 -76 147 -77 145 -78 131 -79 115 -80 101 -81 113 -82 121 -83 103 -84 139 -85 103 -86 94 -87 89 -88 103 -89 79 -90 76 -91 69 -92 91 -93 93 -94 108 -95 97 -96 96 -97 97 -98 96 -99 72 -100 93 -101 112 -102 95 -103 109 -104 107 -105 94 -106 92 -107 103 -108 108 -109 115 -110 108 -111 119 -112 93 -113 98 -114 85 -115 92 -116 117 -117 105 -118 114 -119 98 -120 115 -121 106 -122 103 -123 113 -124 94 -125 112 -126 121 -127 98 -128 135 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-392 1 -393 1 -396 1 -397 1 -398 3 -400 3 -401 1 -402 3 -403 1 -405 1 -406 1 -407 1 -417 1 -420 1 -422 1 -430 1 -446 1 -447 1 -449 1 -466 1 -505 1 -538 1 -541 1 -547 1 -552 1 -557 1 -559 1 -568 1 -576 1 -580 1 -721 1 -743 1 -748 1 -763 1 -771 1 -790 1 -810 1 -817 1 -840 1 -885 1 -888 2 -892 1 -893 1 -894 1 -901 1 -902 1 -904 3 -909 1 -912 1 -922 1 -928 1 -935 1 -943 1 -989 1 -1068 1 -1086 1 -1088 1 -1112 1 -1132 1 -1164 1 -1387 1 -1415 1 -1423 1 -1459 1 -1544 1 -1584 1 -1610 1 -1624 1 -1662 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index af802cb..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.961e-03 6.571e-04 -4.507 8.48e-06 *** -r 1.190e-03 1.664e-05 71.508 < 2e-16 *** -kmercov 9.870e+00 2.566e-03 3846.049 < 2e-16 *** -bias 1.016e+00 4.057e-03 250.380 < 2e-16 *** -length 4.503e+06 2.739e+03 1643.976 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 390 on 435 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.264e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1d987c9..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9bbd0e1..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f916416..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 66130641.7270846 -round 1 trimming to 8 trying 4peak model... converged. score: 72931717.9821865 -round 2 trimming to 13 trying 4peak model... converged. score: 1614915608.03402 -round 3 trimming to 18 trying 4peak model... converged. score: 13560215984.2149 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 0cada86..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.115663% 0.122319% -Genome Haploid Length 4,606,645 bp 4,611,439 bp -Genome Repeat Length 92,561 bp 92,657 bp -Genome Unique Length 4,514,084 bp 4,518,781 bp -Model Fit 98.6472% 99.1463% -Read Error Rate 0.0998934% 0.0998934% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index da481f2..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,365 +0,0 @@ -1 16680201 -2 470770 -3 33215 -4 27915 -5 43293 -6 66386 -7 95860 -8 130722 -9 172029 -10 211535 -11 252111 -12 285023 -13 310297 -14 328068 -15 333824 -16 326404 -17 311213 -18 287518 -19 258443 -20 227546 -21 192927 -22 161765 -23 132399 -24 105998 -25 83664 -26 64597 -27 48552 -28 36370 -29 27078 -30 19616 -31 14069 -32 9952 -33 6961 -34 5083 -35 3657 -36 2718 -37 2038 -38 1463 -39 1165 -40 985 -41 808 -42 722 -43 621 -44 661 -45 567 -46 506 -47 440 -48 428 -49 401 -50 382 -51 296 -52 326 -53 259 -54 269 -55 267 -56 243 -57 233 -58 243 -59 241 -60 239 -61 202 -62 199 -63 190 -64 139 -65 143 -66 144 -67 150 -68 126 -69 104 -70 128 -71 145 -72 113 -73 131 -74 110 -75 109 -76 102 -77 127 -78 132 -79 145 -80 147 -81 129 -82 133 -83 136 -84 136 -85 140 -86 148 -87 145 -88 151 -89 144 -90 137 -91 151 -92 144 -93 106 -94 140 -95 134 -96 123 -97 133 -98 125 -99 151 -100 132 -101 141 -102 141 -103 144 -104 136 -105 122 -106 143 -107 128 -108 117 -109 139 -110 129 -111 129 -112 111 -113 115 -114 116 -115 118 -116 146 -117 115 -118 103 -119 118 -120 92 -121 103 -122 97 -123 86 -124 80 -125 79 -126 66 -127 78 -128 61 -129 52 -130 39 -131 28 -132 37 -133 25 -134 26 -135 27 -136 27 -137 13 -138 24 -139 19 -140 21 -141 13 -142 19 -143 18 -144 16 -145 16 -146 18 -147 22 -148 24 -149 23 -150 22 -151 31 -152 33 -153 36 -154 32 -155 14 -156 24 -157 19 -158 20 -159 33 -160 23 -161 36 -162 34 -163 35 -164 33 -165 32 -166 28 -167 33 -168 33 -169 38 -170 33 -171 44 -172 44 -173 23 -174 27 -175 37 -176 16 -177 30 -178 25 -179 22 -180 22 -181 18 -182 14 -183 15 -184 23 -185 17 -186 23 -187 25 -188 20 -189 20 -190 13 -191 24 -192 16 -193 14 -194 17 -195 12 -196 11 -197 7 -198 4 -199 5 -200 9 -201 8 -202 3 -203 5 -204 6 -205 5 -206 5 -207 2 -208 4 -209 3 -210 4 -211 1 -213 1 -214 1 -219 1 -224 1 -225 1 -226 1 -228 1 -230 2 -231 4 -232 4 -233 3 -234 4 -235 7 -236 6 -237 11 -238 14 -239 7 -240 5 -241 11 -242 5 -243 14 -244 14 -245 9 -246 2 -247 5 -248 22 -249 9 -250 10 -251 18 -252 23 -253 21 -254 19 -255 28 -256 25 -257 24 -258 29 -259 29 -260 22 -261 37 -262 42 -263 26 -264 24 -265 22 -266 19 -267 16 -268 23 -269 12 -270 22 -271 23 -272 16 -273 10 -274 26 -275 19 -276 22 -277 20 -278 13 -279 20 -280 14 -281 12 -282 18 -283 14 -284 14 -285 19 -286 13 -287 11 -288 16 -289 11 -290 10 -291 14 -292 15 -293 16 -294 11 -295 11 -296 8 -297 10 -298 6 -299 6 -300 7 -301 10 -302 13 -303 5 -304 14 -305 8 -306 6 -307 9 -308 8 -309 6 -310 9 -311 7 -312 11 -313 3 -314 4 -315 1 -316 1 -317 3 -318 2 -320 2 -323 1 -327 1 -329 1 -331 1 -336 1 -344 1 -345 1 -346 1 -366 1 -391 1 -393 1 -412 1 -413 1 -427 1 -454 1 -471 1 -472 2 -491 2 -493 2 -542 1 -560 1 -561 1 -568 1 -578 2 -588 1 -597 1 -675 1 -694 1 -695 1 -719 1 -762 1 -764 1 -773 1 -774 2 -776 3 -779 1 -785 1 -786 1 -787 1 -799 1 -800 1 -804 1 -816 1 -842 1 -847 1 -855 1 -880 1 -914 1 -922 1 -1109 1 -1135 1 -1169 1 -1186 1 -1222 1 -1256 1 -1288 1 -1308 2 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 78b87f9..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.757e-03 5.697e-04 -3.084 0.00221 ** -r 1.357e-03 1.586e-05 85.533 < 2e-16 *** -kmercov 8.183e+00 1.929e-03 4242.210 < 2e-16 *** -bias 8.031e-01 3.262e-03 246.185 < 2e-16 *** -length 4.492e+06 2.257e+03 1990.591 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 341.8 on 349 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.997e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 416c893..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b956130..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fb59375..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 40782358.7421197 -round 1 trimming to 9 trying 4peak model... converged. score: 351074259.703705 -round 2 trimming to 14 trying 4peak model... converged. score: 7613636785.47989 -round 3 trimming to 19 trying 4peak model... converged. score: 366621046543.727 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 548ec31..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.1325% 0.138845% -Genome Haploid Length 4,596,697 bp 4,601,033 bp -Genome Repeat Length 98,439 bp 98,532 bp -Genome Unique Length 4,498,258 bp 4,502,501 bp -Model Fit 98.947% 99.3804% -Read Error Rate 0.998209% 0.998209% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 4d4c093..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,336 +0,0 @@ -1 29532091 -2 1187466 -3 98575 -4 71727 -5 104123 -6 151237 -7 205527 -8 263374 -9 313020 -10 356030 -11 379959 -12 388799 -13 380629 -14 356565 -15 319617 -16 279090 -17 234148 -18 189523 -19 150395 -20 114655 -21 87123 -22 63898 -23 46367 -24 32016 -25 22678 -26 15625 -27 10717 -28 7425 -29 5013 -30 3580 -31 2497 -32 1892 -33 1340 -34 1057 -35 856 -36 693 -37 651 -38 542 -39 488 -40 534 -41 494 -42 495 -43 401 -44 423 -45 373 -46 341 -47 290 -48 309 -49 270 -50 232 -51 276 -52 215 -53 201 -54 233 -55 198 -56 187 -57 156 -58 160 -59 148 -60 160 -61 135 -62 143 -63 136 -64 129 -65 106 -66 84 -67 97 -68 119 -69 109 -70 118 -71 129 -72 117 -73 123 -74 120 -75 118 -76 137 -77 150 -78 145 -79 151 -80 206 -81 163 -82 158 -83 167 -84 187 -85 154 -86 142 -87 180 -88 139 -89 177 -90 165 -91 161 -92 179 -93 163 -94 149 -95 135 -96 144 -97 148 -98 122 -99 141 -100 122 -101 117 -102 115 -103 112 -104 108 -105 91 -106 85 -107 92 -108 81 -109 77 -110 62 -111 81 -112 69 -113 70 -114 44 -115 41 -116 44 -117 30 -118 34 -119 33 -120 29 -121 26 -122 23 -123 35 -124 15 -125 22 -126 35 -127 22 -128 21 -129 16 -130 24 -131 17 -132 29 -133 35 -134 30 -135 29 -136 33 -137 39 -138 30 -139 27 -140 33 -141 34 -142 23 -143 30 -144 36 -145 31 -146 30 -147 23 -148 29 -149 18 -150 34 -151 27 -152 27 -153 22 -154 22 -155 14 -156 18 -157 11 -158 10 -159 6 -160 10 -161 8 -162 13 -163 13 -164 5 -165 9 -166 5 -167 16 -168 8 -169 4 -170 5 -171 7 -172 6 -173 11 -174 11 -175 12 -176 9 -177 9 -178 14 -179 18 -180 9 -181 11 -182 14 -183 7 -184 5 -185 7 -186 9 -187 15 -188 9 -189 10 -190 15 -191 4 -192 13 -193 9 -194 13 -195 14 -196 10 -197 12 -198 21 -199 12 -200 13 -201 17 -202 21 -203 21 -204 28 -205 34 -206 22 -207 18 -208 21 -209 15 -210 18 -211 27 -212 15 -213 31 -214 23 -215 29 -216 30 -217 18 -218 18 -219 24 -220 23 -221 34 -222 25 -223 23 -224 21 -225 19 -226 17 -227 21 -228 11 -229 16 -230 13 -231 12 -232 13 -233 11 -234 11 -235 8 -236 3 -237 9 -238 9 -239 8 -240 6 -241 10 -242 6 -243 2 -244 7 -245 11 -246 8 -247 6 -248 5 -249 9 -250 10 -251 6 -252 11 -253 6 -254 11 -255 3 -256 7 -257 6 -258 7 -259 3 -260 5 -261 1 -262 3 -263 4 -264 3 -265 3 -266 5 -267 4 -268 6 -269 2 -270 5 -271 6 -272 2 -273 1 -274 3 -275 1 -276 3 -277 4 -278 2 -279 1 -280 1 -281 1 -283 1 -289 2 -294 1 -301 1 -302 1 -308 1 -310 1 -346 1 -347 1 -348 2 -352 1 -356 1 -391 1 -402 1 -432 1 -435 1 -472 1 -486 1 -488 1 -513 1 -517 1 -540 1 -580 1 -581 2 -615 1 -617 1 -626 2 -627 1 -628 2 -629 1 -631 1 -632 1 -634 1 -635 1 -636 1 -645 1 -647 1 -651 1 -664 1 -678 1 -736 1 -747 1 -750 1 -765 1 -795 1 -805 1 -931 1 -965 1 -996 1 -1014 1 -1045 1 -1079 1 -1097 1 -1123 1 -1143 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index be63b8b..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.873e-03 5.199e-04 5.525 6.79e-08 *** -r 1.736e-03 1.692e-05 102.568 < 2e-16 *** -kmercov 6.628e+00 1.537e-03 4312.293 < 2e-16 *** -bias 5.970e-01 2.814e-03 212.147 < 2e-16 *** -length 4.474e+06 1.954e+03 2288.973 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 308.4 on 322 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 7.953e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 22167b3..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8ffd5fb..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 41e581d..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 25626144.1288538 -round 1 trimming to 9 trying 4peak model... converged. score: 298378664.623469 -round 2 trimming to 14 trying 4peak model... converged. score: 34592714891.3704 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 76dfca6..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.170181% 0.176949% -Genome Haploid Length 4,590,974 bp 4,595,235 bp -Genome Repeat Length 132,211 bp 132,333 bp -Genome Unique Length 4,458,764 bp 4,462,902 bp -Model Fit 99.2254% 99.6243% -Read Error Rate 1.99483% 1.99483% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index bb81e01..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,487 +0,0 @@ -1 1922509 -2 19632 -3 19518 -4 28955 -5 41949 -6 58225 -7 77077 -8 94769 -9 116136 -10 136795 -11 161648 -12 177937 -13 196001 -14 212685 -15 224947 -16 233516 -17 236834 -18 237907 -19 233419 -20 225913 -21 217168 -22 203733 -23 190751 -24 171313 -25 157596 -26 139398 -27 125990 -28 109465 -29 95469 -30 82580 -31 69563 -32 58897 -33 49383 -34 40106 -35 34278 -36 26984 -37 21584 -38 18155 -39 14473 -40 11920 -41 9217 -42 7437 -43 5831 -44 4600 -45 3466 -46 2956 -47 2372 -48 1723 -49 1560 -50 1241 -51 1098 -52 866 -53 779 -54 706 -55 551 -56 486 -57 444 -58 400 -59 372 -60 335 -61 312 -62 340 -63 340 -64 316 -65 314 -66 297 -67 323 -68 267 -69 306 -70 231 -71 242 -72 237 -73 192 -74 229 -75 157 -76 154 -77 148 -78 159 -79 194 -80 144 -81 168 -82 118 -83 144 -84 114 -85 128 -86 108 -87 105 -88 121 -89 102 -90 92 -91 97 -92 82 -93 119 -94 128 -95 111 -96 88 -97 117 -98 107 -99 121 -100 111 -101 105 -102 90 -103 108 -104 80 -105 127 -106 102 -107 130 -108 110 -109 118 -110 121 -111 124 -112 105 -113 108 -114 113 -115 119 -116 94 -117 121 -118 104 -119 99 -120 105 -121 100 -122 116 -123 108 -124 105 -125 120 -126 96 -127 104 -128 148 -129 150 -130 126 -131 118 -132 108 -133 97 -134 110 -135 105 -136 103 -137 91 -138 100 -139 93 -140 93 -141 98 -142 91 -143 84 -144 79 -145 85 -146 82 -147 70 -148 92 -149 94 -150 82 -151 67 -152 46 -153 61 -154 61 -155 61 -156 62 -157 68 -158 42 -159 34 -160 43 -161 31 -162 31 -163 26 -164 21 -165 22 -166 19 -167 19 -168 12 -169 20 -170 30 -171 21 -172 35 -173 21 -174 25 -175 20 -176 17 -177 28 -178 22 -179 30 -180 18 -181 15 -182 17 -183 15 -184 19 -185 16 -186 23 -187 16 -188 19 -189 15 -190 27 -191 13 -192 28 -193 20 -194 12 -195 15 -196 15 -197 16 -198 17 -199 19 -200 19 -201 26 -202 16 -203 22 -204 18 -205 13 -206 21 -207 23 -208 23 -209 23 -210 27 -211 17 -212 20 -213 28 -214 16 -215 24 -216 24 -217 14 -218 16 -219 31 -220 24 -221 21 -222 16 -223 11 -224 15 -225 8 -226 18 -227 15 -228 19 -229 18 -230 15 -231 14 -232 13 -233 10 -234 17 -235 9 -236 16 -237 21 -238 13 -239 9 -240 10 -241 12 -242 10 -243 9 -244 8 -245 9 -246 7 -247 7 -248 4 -249 7 -250 5 -251 12 -252 7 -253 6 -254 5 -255 12 -256 5 -257 6 -258 4 -259 5 -260 6 -261 4 -262 5 -263 6 -264 2 -265 11 -266 8 -267 5 -268 7 -269 4 -270 3 -271 9 -272 6 -273 6 -274 8 -275 3 -276 5 -277 2 -278 1 -279 5 -280 6 -281 3 -282 6 -283 7 -284 4 -285 5 -286 4 -287 7 -288 9 -289 5 -290 11 -291 11 -292 4 -293 3 -294 7 -295 4 -296 6 -297 1 -298 2 -299 4 -300 7 -301 7 -302 7 -303 6 -304 6 -305 10 -306 8 -307 10 -308 13 -309 10 -310 7 -311 8 -312 12 -313 9 -314 13 -315 17 -316 6 -317 14 -318 13 -319 14 -320 12 -321 11 -322 9 -323 8 -324 10 -325 9 -326 9 -327 12 -328 9 -329 4 -330 5 -331 9 -332 8 -333 7 -334 6 -335 9 -336 11 -337 10 -338 8 -339 12 -340 11 -341 14 -342 11 -343 11 -344 14 -345 18 -346 14 -347 13 -348 11 -349 14 -350 10 -351 5 -352 13 -353 11 -354 13 -355 6 -356 12 -357 7 -358 14 -359 10 -360 8 -361 5 -362 7 -363 10 -364 4 -365 8 -366 6 -367 9 -368 8 -369 6 -370 11 -371 8 -372 12 -373 10 -374 6 -375 9 -376 11 -377 9 -378 7 -379 16 -380 4 -381 4 -382 6 -383 5 -384 7 -385 10 -386 4 -387 1 -388 3 -389 3 -390 2 -391 3 -392 2 -393 3 -394 1 -395 6 -396 3 -397 4 -398 4 -399 2 -400 1 -401 2 -402 4 -403 3 -404 1 -405 1 -406 2 -407 1 -408 6 -411 4 -413 1 -414 2 -415 3 -416 1 -417 2 -418 1 -419 2 -420 1 -421 2 -422 3 -423 1 -424 3 -425 2 -426 3 -428 2 -429 2 -430 2 -431 3 -432 2 -433 2 -434 1 -435 7 -436 1 -437 1 -439 2 -440 2 -441 1 -442 3 -444 1 -446 1 -447 1 -449 1 -519 1 -533 1 -534 2 -543 1 -571 1 -581 1 -598 1 -651 1 -743 1 -751 2 -760 1 -763 1 -777 1 -789 1 -805 1 -814 1 -875 1 -878 2 -881 1 -886 2 -891 1 -910 1 -915 1 -918 1 -921 1 -927 1 -956 1 -1046 1 -1054 1 -1066 1 -1069 1 -1071 1 -1081 1 -1083 1 -1093 2 -1106 1 -1141 1 -1168 1 -1435 2 -1503 1 -1525 1 -1532 1 -1577 1 -1643 1 -1655 1 -1672 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 55df93f..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -8.932e-03 1.071e-03 -8.343 8.46e-16 *** -r 2.503e-03 3.010e-05 83.130 < 2e-16 *** -kmercov 1.017e+01 4.660e-03 2181.893 < 2e-16 *** -bias 1.859e+00 9.597e-03 193.728 < 2e-16 *** -length 4.391e+06 3.381e+03 1298.577 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 409.7 on 461 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.136e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ffa1776..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6078553..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8475618..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 77396812.1440472 -round 1 trimming to 8 trying 4peak model... converged. score: 128548271.181895 -round 2 trimming to 13 trying 4peak model... converged. score: 704686857.904633 -round 3 trimming to 18 trying 4peak model... converged. score: 17913869137.7363 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4e6208a..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.244236% 0.256277% -Genome Haploid Length 4,469,337 bp 4,477,538 bp -Genome Repeat Length 43,574 bp 43,654 bp -Genome Unique Length 4,425,763 bp 4,433,884 bp -Model Fit 98.4963% 99.0075% -Read Error Rate 0.100261% 0.100261% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index f2e6c8b..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,389 +0,0 @@ -1 16672905 -2 502003 -3 52806 -4 55046 -5 76280 -6 103488 -7 132661 -8 164342 -9 191784 -10 217271 -11 240917 -12 260264 -13 274121 -14 278067 -15 277912 -16 271177 -17 259394 -18 242629 -19 224336 -20 200922 -21 178807 -22 156457 -23 135682 -24 114980 -25 96927 -26 80756 -27 65975 -28 53872 -29 42978 -30 34319 -31 26792 -32 20807 -33 16098 -34 12854 -35 9809 -36 7411 -37 5647 -38 4409 -39 3229 -40 2472 -41 2059 -42 1537 -43 1331 -44 931 -45 775 -46 693 -47 630 -48 559 -49 466 -50 402 -51 403 -52 354 -53 313 -54 272 -55 290 -56 232 -57 246 -58 255 -59 227 -60 237 -61 215 -62 187 -63 184 -64 178 -65 165 -66 172 -67 194 -68 182 -69 184 -70 176 -71 139 -72 151 -73 156 -74 112 -75 111 -76 126 -77 143 -78 142 -79 130 -80 120 -81 133 -82 150 -83 134 -84 115 -85 127 -86 127 -87 115 -88 120 -89 115 -90 109 -91 120 -92 141 -93 116 -94 138 -95 144 -96 121 -97 120 -98 114 -99 121 -100 123 -101 125 -102 114 -103 111 -104 117 -105 140 -106 142 -107 145 -108 158 -109 155 -110 155 -111 142 -112 132 -113 136 -114 139 -115 119 -116 130 -117 124 -118 107 -119 111 -120 104 -121 93 -122 108 -123 82 -124 70 -125 85 -126 76 -127 57 -128 65 -129 62 -130 60 -131 56 -132 70 -133 59 -134 53 -135 64 -136 31 -137 51 -138 41 -139 46 -140 44 -141 47 -142 34 -143 34 -144 24 -145 32 -146 22 -147 16 -148 31 -149 22 -150 32 -151 31 -152 36 -153 34 -154 32 -155 35 -156 24 -157 23 -158 27 -159 27 -160 41 -161 23 -162 25 -163 39 -164 41 -165 49 -166 31 -167 44 -168 36 -169 39 -170 33 -171 33 -172 20 -173 18 -174 22 -175 28 -176 24 -177 24 -178 27 -179 23 -180 25 -181 32 -182 28 -183 21 -184 19 -185 22 -186 14 -187 15 -188 7 -189 6 -190 7 -191 2 -192 5 -193 5 -194 4 -195 3 -196 5 -197 6 -198 5 -199 5 -200 6 -201 3 -202 5 -203 2 -204 6 -205 2 -206 5 -207 6 -208 8 -209 1 -210 1 -211 3 -212 3 -213 1 -214 3 -216 1 -218 1 -219 1 -220 1 -221 2 -222 2 -227 1 -232 1 -233 2 -234 3 -235 1 -236 1 -237 5 -238 7 -239 5 -240 9 -241 8 -242 14 -243 12 -244 8 -245 7 -246 13 -247 10 -248 11 -249 8 -250 13 -251 11 -252 15 -253 10 -254 11 -255 18 -256 14 -257 16 -258 7 -259 20 -260 21 -261 10 -262 15 -263 26 -264 20 -265 21 -266 23 -267 15 -268 26 -269 30 -270 16 -271 24 -272 19 -273 22 -274 14 -275 12 -276 15 -277 13 -278 11 -279 25 -280 9 -281 17 -282 18 -283 23 -284 14 -285 18 -286 15 -287 17 -288 16 -289 15 -290 15 -291 15 -292 16 -293 14 -294 21 -295 23 -296 20 -297 17 -298 13 -299 14 -300 10 -301 14 -302 7 -303 13 -304 12 -305 11 -306 13 -307 7 -308 16 -309 9 -310 11 -311 12 -312 5 -313 6 -314 8 -315 10 -316 5 -317 5 -318 7 -319 5 -320 2 -321 5 -322 4 -323 4 -324 3 -325 4 -326 3 -327 1 -328 2 -329 2 -331 2 -333 1 -334 2 -335 1 -336 1 -337 1 -339 2 -340 1 -341 1 -344 2 -346 2 -348 1 -352 1 -366 1 -367 1 -391 1 -399 1 -402 1 -404 1 -407 1 -410 1 -431 1 -456 1 -480 1 -481 1 -484 1 -491 1 -492 1 -515 1 -584 1 -592 1 -598 1 -602 1 -608 1 -609 1 -610 1 -634 1 -691 1 -694 1 -696 1 -699 1 -700 1 -702 1 -708 1 -711 1 -717 1 -718 1 -730 1 -733 2 -738 1 -747 1 -751 1 -755 1 -756 1 -794 1 -831 1 -854 1 -861 1 -867 1 -871 1 -898 1 -1068 1 -1108 1 -1121 1 -1142 1 -1208 1 -1214 1 -1251 1 -1281 1 -1330 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8854b87..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.774e-03 2.051e-03 -1.353 0.177 -r 3.060e-03 6.254e-05 48.928 <2e-16 *** -kmercov 8.444e+00 7.658e-03 1102.639 <2e-16 *** -bias 1.439e+00 1.648e-02 87.320 <2e-16 *** -length 4.362e+06 6.437e+03 677.725 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 801 on 373 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 5.092e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 716a214..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6b199dd..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d9ef8db..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 69827381.7968608 -round 1 trimming to 8 trying 4peak model... converged. score: 237165230.198275 -round 2 trimming to 13 trying 4peak model... converged. score: 3900731622.13305 -round 3 trimming to 18 trying 4peak model... converged. score: 99396885872.1985 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 30596bb..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.293512% 0.31853% -Genome Haploid Length 4,448,376 bp 4,464,542 bp -Genome Repeat Length 82,043 bp 82,342 bp -Genome Unique Length 4,366,333 bp 4,382,201 bp -Model Fit 98.9674% 99.397% -Read Error Rate 0.998571% 0.998571% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 47cfb70..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,342 +0,0 @@ -1 29453888 -2 1252903 -3 130397 -4 110228 -5 145652 -6 187259 -7 229236 -8 269016 -9 300616 -10 325091 -11 334074 -12 330778 -13 318948 -14 299846 -15 274548 -16 246876 -17 216581 -18 184809 -19 154324 -20 126880 -21 102840 -22 81992 -23 64396 -24 49546 -25 37515 -26 28186 -27 21070 -28 15784 -29 11588 -30 8402 -31 6126 -32 4645 -33 3421 -34 2414 -35 1880 -36 1385 -37 1087 -38 909 -39 726 -40 580 -41 549 -42 459 -43 445 -44 394 -45 384 -46 322 -47 299 -48 243 -49 275 -50 221 -51 232 -52 222 -53 230 -54 193 -55 179 -56 168 -57 174 -58 151 -59 145 -60 141 -61 146 -62 164 -63 134 -64 153 -65 171 -66 182 -67 182 -68 176 -69 167 -70 184 -71 186 -72 171 -73 205 -74 165 -75 187 -76 212 -77 175 -78 197 -79 211 -80 171 -81 158 -82 156 -83 161 -84 135 -85 166 -86 151 -87 152 -88 151 -89 182 -90 160 -91 170 -92 161 -93 167 -94 136 -95 111 -96 140 -97 141 -98 103 -99 115 -100 95 -101 117 -102 96 -103 87 -104 87 -105 73 -106 70 -107 61 -108 71 -109 64 -110 41 -111 39 -112 45 -113 41 -114 33 -115 39 -116 36 -117 27 -118 35 -119 23 -120 34 -121 33 -122 22 -123 29 -124 35 -125 39 -126 37 -127 36 -128 40 -129 41 -130 49 -131 30 -132 31 -133 28 -134 29 -135 31 -136 29 -137 31 -138 25 -139 24 -140 22 -141 24 -142 29 -143 25 -144 20 -145 26 -146 27 -147 25 -148 14 -149 14 -150 22 -151 24 -152 14 -153 13 -154 12 -155 13 -156 13 -157 4 -158 13 -159 14 -160 12 -161 14 -162 10 -163 6 -164 6 -165 12 -166 8 -167 11 -168 5 -169 8 -170 8 -171 5 -172 4 -173 9 -174 8 -175 3 -176 9 -177 10 -178 9 -179 8 -180 5 -181 4 -182 5 -183 6 -184 7 -185 14 -186 9 -187 10 -188 7 -189 7 -190 5 -191 8 -192 6 -193 9 -194 16 -195 13 -196 14 -197 15 -198 15 -199 9 -200 14 -201 9 -202 13 -203 11 -204 17 -205 13 -206 20 -207 13 -208 22 -209 19 -210 19 -211 18 -212 10 -213 21 -214 16 -215 28 -216 17 -217 25 -218 20 -219 15 -220 25 -221 13 -222 21 -223 20 -224 14 -225 18 -226 21 -227 23 -228 18 -229 14 -230 18 -231 21 -232 10 -233 15 -234 13 -235 16 -236 13 -237 18 -238 15 -239 11 -240 8 -241 6 -242 10 -243 11 -244 13 -245 12 -246 15 -247 13 -248 13 -249 18 -250 5 -251 11 -252 9 -253 14 -254 16 -255 10 -256 8 -257 8 -258 7 -259 7 -260 6 -261 7 -262 8 -263 4 -264 4 -265 4 -266 4 -267 5 -268 3 -269 7 -270 3 -271 7 -272 3 -273 1 -274 5 -275 3 -276 3 -277 3 -278 3 -279 3 -280 1 -281 4 -282 3 -283 1 -284 2 -285 1 -286 1 -287 1 -288 1 -317 1 -319 1 -320 1 -323 1 -326 1 -327 1 -330 2 -331 2 -339 1 -375 2 -379 2 -381 1 -392 1 -443 1 -479 1 -489 1 -491 1 -493 1 -498 1 -520 1 -536 1 -542 1 -558 1 -565 1 -570 1 -583 1 -585 1 -588 1 -589 1 -590 1 -591 1 -593 1 -594 1 -604 1 -608 1 -615 1 -617 1 -631 1 -648 1 -663 1 -702 1 -750 1 -762 1 -763 1 -787 1 -792 1 -864 2 -900 1 -929 1 -948 1 -963 1 -984 1 -1001 1 -1002 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 758b727..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.602e-03 9.838e-04 -2.645 0.00855 ** -r 2.883e-03 3.778e-05 76.316 < 2e-16 *** -kmercov 6.798e+00 3.187e-03 2132.822 < 2e-16 *** -bias 1.183e+00 7.394e-03 159.999 < 2e-16 *** -length 4.385e+06 3.196e+03 1371.849 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 370.1 on 332 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 9.289e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index df505f3..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 57e75cb..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ea76074..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 39600932.5236357 -round 1 trimming to 9 trying 4peak model... converged. score: 563423789.89398 -round 2 trimming to 14 trying 4peak model... converged. score: 11820624983.4558 -round 3 trimming to 19 trying 4peak model... converged. score: 2207111232410.81 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 05a8f19..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.280774% 0.295887% -Genome Haploid Length 4,474,560 bp 4,482,959 bp -Genome Repeat Length 82,550 bp 82,705 bp -Genome Unique Length 4,392,009 bp 4,400,254 bp -Model Fit 99.0305% 99.4694% -Read Error Rate 1.99432% 1.99432% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index f3b6a43..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,491 +0,0 @@ -1 1927538 -2 31381 -3 35086 -4 48402 -5 63873 -6 79923 -7 93779 -8 113845 -9 127575 -10 145931 -11 164254 -12 175064 -13 189359 -14 197827 -15 203171 -16 206541 -17 210660 -18 207483 -19 204614 -20 195275 -21 189660 -22 178535 -23 168261 -24 156992 -25 144619 -26 133705 -27 122546 -28 109493 -29 98235 -30 86401 -31 76577 -32 67256 -33 57084 -34 49195 -35 44175 -36 36851 -37 31347 -38 26114 -39 22347 -40 18621 -41 15104 -42 12361 -43 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a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.477e-02 1.369e-03 -10.79 <2e-16 *** -r 3.886e-03 6.121e-05 63.48 <2e-16 *** -kmercov 1.053e+01 7.088e-03 1486.04 <2e-16 *** -bias 2.613e+00 1.731e-02 150.92 <2e-16 *** -length 4.268e+06 4.345e+03 982.21 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 345.9 on 469 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 6.285e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4fd255b..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6e9d920..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bb122ff..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 59734784.4878979 -round 1 trimming to 7 trying 4peak model... converged. score: 57007709.0561005 -round 2 trimming to 12 trying 4peak model... converged. score: 381114628.737622 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f9202c8..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.376316% 0.400801% -Genome Haploid Length 4,312,706 bp 4,324,330 bp -Genome Repeat Length -11,730 bp -11,761 bp -Genome Unique Length 4,324,436 bp 4,336,092 bp -Model Fit 98.6482% 99.1613% -Read Error Rate 0.100321% 0.100321% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 8f00ddc..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,402 +0,0 @@ -1 16587857 -2 542330 -3 77252 -4 79953 -5 100611 -6 125402 -7 150716 -8 174335 -9 195300 -10 212793 -11 229153 -12 240048 -13 245225 -14 248477 -15 245284 -16 237665 -17 228936 -18 215728 -19 201627 -20 184906 -21 166351 -22 149925 -23 131852 -24 115993 -25 101498 -26 86356 -27 74072 -28 62586 -29 53049 -30 44683 -31 36531 -32 30114 -33 24343 -34 19374 -35 16192 -36 12702 -37 10273 -38 8218 -39 6203 -40 5020 -41 3828 -42 3036 -43 2380 -44 1941 -45 1546 -46 1297 -47 1073 -48 876 -49 714 -50 612 -51 519 -52 464 -53 428 -54 397 -55 362 -56 352 -57 293 -58 310 -59 285 -60 241 -61 244 -62 230 -63 219 -64 237 -65 209 -66 185 -67 165 -68 160 -69 182 -70 197 -71 203 -72 189 -73 143 -74 155 -75 127 -76 136 -77 140 -78 139 -79 126 -80 146 -81 110 -82 112 -83 128 -84 118 -85 126 -86 128 -87 105 -88 108 -89 101 -90 112 -91 98 -92 104 -93 95 -94 112 -95 107 -96 122 -97 130 -98 112 -99 101 -100 115 -101 97 -102 112 -103 101 -104 120 -105 105 -106 120 -107 106 -108 110 -109 113 -110 93 -111 83 -112 67 -113 89 -114 87 -115 95 -116 95 -117 102 -118 90 -119 88 -120 98 -121 103 -122 118 -123 101 -124 98 -125 98 -126 119 -127 115 -128 74 -129 94 -130 80 -131 79 -132 102 -133 78 -134 87 -135 77 -136 55 -137 69 -138 64 -139 65 -140 50 -141 58 -142 60 -143 52 -144 46 -145 48 -146 42 -147 37 -148 43 -149 50 -150 32 -151 47 -152 46 -153 34 -154 28 -155 39 -156 49 -157 31 -158 37 -159 33 -160 48 -161 44 -162 53 -163 43 -164 35 -165 33 -166 34 -167 33 -168 41 -169 35 -170 22 -171 34 -172 32 -173 40 -174 20 -175 19 -176 29 -177 28 -178 19 -179 18 -180 20 -181 13 -182 8 -183 10 -184 10 -185 8 -186 9 -187 13 -188 7 -189 12 -190 6 -191 9 -192 7 -193 3 -194 5 -195 12 -196 9 -197 10 -198 4 -199 4 -200 6 -201 2 -202 5 -203 2 -204 15 -205 8 -206 4 -207 7 -208 2 -209 3 -211 2 -212 2 -213 1 -214 5 -215 2 -216 1 -217 2 -218 3 -222 1 -223 1 -224 2 -225 2 -226 3 -227 8 -228 6 -229 1 -230 9 -231 2 -232 8 -233 5 -234 2 -235 4 -236 5 -237 8 -238 7 -239 5 -240 8 -241 4 -242 5 -243 9 -244 5 -245 9 -246 4 -247 4 -248 6 -249 10 -250 13 -251 9 -252 9 -253 11 -254 8 -255 5 -256 9 -257 12 -258 12 -259 10 -260 5 -261 5 -262 13 -263 13 -264 6 -265 15 -266 10 -267 14 -268 15 -269 21 -270 12 -271 9 -272 16 -273 15 -274 17 -275 19 -276 23 -277 22 -278 32 -279 23 -280 20 -281 21 -282 23 -283 14 -284 23 -285 26 -286 13 -287 15 -288 21 -289 12 -290 19 -291 5 -292 12 -293 15 -294 11 -295 15 -296 11 -297 13 -298 20 -299 11 -300 16 -301 16 -302 5 -303 8 -304 11 -305 8 -306 9 -307 10 -308 10 -309 7 -310 9 -311 11 -312 11 -313 7 -314 10 -315 7 -316 8 -317 10 -318 8 -319 12 -320 3 -321 9 -322 12 -323 6 -324 12 -325 8 -326 9 -327 3 -328 13 -329 4 -330 4 -331 10 -332 8 -333 7 -334 3 -335 5 -336 6 -337 6 -338 3 -339 3 -340 1 -341 5 -342 2 -343 4 -344 4 -345 1 -346 1 -347 1 -348 1 -350 1 -352 1 -359 2 -363 1 -365 1 -367 1 -375 1 -382 1 -388 1 -411 1 -412 1 -414 2 -437 1 -497 1 -549 1 -555 1 -598 1 -647 1 -671 1 -676 1 -686 1 -694 1 -706 1 -707 1 -709 1 -735 1 -747 1 -750 2 -751 1 -754 1 -755 1 -759 1 -760 1 -764 1 -766 1 -768 1 -783 1 -788 1 -808 1 -813 1 -814 1 -832 1 -866 1 -891 1 -908 1 -911 1 -929 1 -969 1 -987 1 -1149 1 -1164 1 -1226 1 -1255 1 -1275 1 -1279 1 -1336 1 -1342 1 -1350 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0b1c883..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.152e-03 3.517e-03 -1.465 0.144 -r 4.897e-03 1.264e-04 38.736 <2e-16 *** -kmercov 8.765e+00 1.396e-02 627.844 <2e-16 *** -bias 1.970e+00 3.615e-02 54.481 <2e-16 *** -length 4.216e+06 1.059e+04 397.915 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 943.4 on 386 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 5.325e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 39199e2..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index bf06538..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 36aba4f..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 65565076.1898837 -round 1 trimming to 8 trying 4peak model... converged. score: 78025430.7676291 -round 2 trimming to 13 trying 4peak model... converged. score: 172119456.231243 -round 3 trimming to 18 trying 4peak model... converged. score: 648725090.921298 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c3f801e..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.464455% 0.515028% -Genome Haploid Length 4,281,365 bp 4,308,729 bp -Genome Repeat Length 57,774 bp 58,143 bp -Genome Unique Length 4,223,591 bp 4,250,585 bp -Model Fit 98.9838% 99.3939% -Read Error Rate 0.996397% 0.996397% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index b270258..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,321 +0,0 @@ -1 29375975 -2 1320116 -3 165149 -4 140271 -5 169521 -6 203009 -7 234326 -8 263706 -9 282033 -10 293450 -11 296272 -12 291947 -13 283397 -14 265744 -15 246861 -16 223853 -17 200554 -18 176011 -19 151489 -20 129924 -21 109002 -22 90595 -23 74313 -24 59825 -25 47838 -26 38843 -27 30909 -28 24170 -29 19127 -30 14633 -31 11272 -32 8647 -33 6638 -34 5226 -35 3992 -36 2978 -37 2285 -38 1807 -39 1358 -40 1078 -41 933 -42 708 -43 624 -44 527 -45 465 -46 385 -47 346 -48 290 -49 271 -50 239 -51 210 -52 198 -53 174 -54 165 -55 171 -56 171 -57 160 -58 152 -59 201 -60 156 -61 175 -62 163 -63 151 -64 169 -65 151 -66 165 -67 152 -68 151 -69 138 -70 155 -71 133 -72 140 -73 144 -74 130 -75 155 -76 148 -77 141 -78 152 -79 143 -80 143 -81 148 -82 119 -83 123 -84 132 -85 160 -86 134 -87 143 -88 143 -89 129 -90 133 -91 129 -92 136 -93 143 -94 118 -95 119 -96 126 -97 128 -98 129 -99 94 -100 99 -101 102 -102 89 -103 95 -104 81 -105 74 -106 68 -107 78 -108 77 -109 59 -110 53 -111 52 -112 64 -113 53 -114 58 -115 70 -116 44 -117 43 -118 58 -119 47 -120 52 -121 46 -122 54 -123 43 -124 59 -125 49 -126 40 -127 46 -128 41 -129 32 -130 50 -131 46 -132 32 -133 30 -134 22 -135 32 -136 31 -137 22 -138 18 -139 39 -140 27 -141 34 -142 27 -143 29 -144 26 -145 32 -146 33 -147 27 -148 32 -149 25 -150 24 -151 36 -152 28 -153 33 -154 18 -155 20 -156 25 -157 18 -158 33 -159 17 -160 19 -161 25 -162 25 -163 15 -164 11 -165 6 -166 14 -167 14 -168 10 -169 10 -170 4 -171 7 -172 9 -173 7 -174 4 -175 15 -176 10 -177 8 -178 11 -179 8 -180 18 -181 9 -182 15 -183 13 -184 9 -185 10 -186 13 -187 9 -188 17 -189 16 -190 13 -191 11 -192 14 -193 11 -194 10 -195 15 -196 12 -197 18 -198 17 -199 15 -200 20 -201 16 -202 10 -203 16 -204 17 -205 15 -206 21 -207 14 -208 17 -209 23 -210 15 -211 22 -212 22 -213 18 -214 35 -215 22 -216 36 -217 28 -218 31 -219 33 -220 23 -221 26 -222 26 -223 26 -224 25 -225 21 -226 14 -227 12 -228 17 -229 16 -230 18 -231 17 -232 13 -233 10 -234 14 -235 16 -236 20 -237 17 -238 15 -239 7 -240 11 -241 11 -242 13 -243 12 -244 17 -245 5 -246 5 -247 3 -248 4 -249 5 -250 3 -251 5 -252 2 -253 3 -254 3 -256 3 -257 6 -258 5 -259 4 -260 5 -261 2 -262 3 -263 1 -264 2 -265 1 -266 2 -267 2 -269 1 -271 1 -273 1 -274 1 -281 1 -309 1 -310 1 -311 1 -332 3 -334 1 -351 1 -357 1 -363 1 -427 1 -428 1 -457 1 -484 1 -486 1 -496 1 -510 1 -525 1 -526 2 -558 1 -580 1 -593 1 -595 1 -598 2 -604 1 -607 1 -611 1 -618 1 -631 1 -640 2 -643 1 -644 1 -658 1 -662 1 -671 1 -681 1 -691 1 -693 1 -702 1 -704 1 -705 1 -725 1 -744 1 -900 1 -938 1 -967 1 -979 1 -1006 1 -1025 1 -1056 1 -1075 1 -1089 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index e59c5ef..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.664e-04 1.402e-03 -0.119 0.906 -r 4.855e-03 6.087e-05 79.758 <2e-16 *** -kmercov 7.060e+00 4.922e-03 1434.426 <2e-16 *** -bias 1.600e+00 1.303e-02 122.774 <2e-16 *** -length 4.219e+06 4.655e+03 906.386 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 362 on 308 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 6.54e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0470247..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 5212c16..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5e39816..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 30260574.7733534 -round 1 trimming to 9 trying 4peak model... converged. score: 636605064.986765 -round 2 trimming to 14 trying 4peak model... converged. score: 656005889.313007 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ebb5e07..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.473326% 0.497675% -Genome Haploid Length 4,305,634 bp 4,317,657 bp -Genome Repeat Length 91,401 bp 91,656 bp -Genome Unique Length 4,214,233 bp 4,226,001 bp -Model Fit 99.1752% 99.524% -Read Error Rate 1.99539% 1.99539% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index a8bddad..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,432 +0,0 @@ -1 1931361 -2 35511 -3 53691 -4 82177 -5 114887 -6 145209 -7 175071 -8 196365 -9 214144 -10 225766 -11 240284 -12 251165 -13 257214 -14 263168 -15 267085 -16 269398 -17 267138 -18 264131 -19 254765 -20 242810 -21 227269 -22 209224 -23 188001 -24 166606 -25 144664 -26 125070 -27 104771 -28 85843 -29 70527 -30 55614 -31 44957 -32 34776 -33 26860 -34 20762 -35 15922 -36 11820 -37 9220 -38 6917 -39 5118 -40 3707 -41 2951 -42 2314 -43 1695 -44 1240 -45 968 -46 793 -47 635 -48 605 -49 528 -50 491 -51 463 -52 394 -53 377 -54 355 -55 326 -56 263 -57 297 -58 249 -59 263 -60 245 -61 230 -62 212 -63 216 -64 237 -65 242 -66 195 -67 180 -68 224 -69 182 -70 152 -71 178 -72 157 -73 129 -74 153 -75 121 -76 143 -77 101 -78 113 -79 91 -80 87 -81 104 -82 87 -83 106 -84 110 -85 98 -86 122 -87 100 -88 100 -89 97 -90 92 -91 89 -92 81 -93 98 -94 93 -95 98 -96 97 -97 95 -98 93 -99 118 -100 111 -101 100 -102 104 -103 131 -104 119 -105 132 -106 140 -107 145 -108 120 -109 154 -110 166 -111 133 -112 138 -113 148 -114 126 -115 129 -116 141 -117 124 -118 156 -119 156 -120 144 -121 132 -122 152 -123 136 -124 131 -125 131 -126 121 -127 116 -128 117 -129 109 -130 111 -131 102 -132 93 -133 76 -134 69 -135 72 -136 67 -137 73 -138 66 -139 64 -140 65 -141 66 -142 59 -143 42 -144 57 -145 70 -146 39 -147 41 -148 26 -149 28 -150 33 -151 26 -152 34 -153 40 -154 31 -155 32 -156 32 -157 26 -158 24 -159 30 -160 31 -161 34 -162 31 -163 25 -164 18 -165 25 -166 13 -167 26 -168 23 -169 21 -170 28 -171 18 -172 32 -173 26 -174 38 -175 30 -176 16 -177 10 -178 25 -179 21 -180 14 -181 15 -182 17 -183 22 -184 20 -185 20 -186 16 -187 18 -188 26 -189 20 -190 24 -191 21 -192 27 -193 32 -194 30 -195 20 -196 27 -197 27 -198 27 -199 21 -200 34 -201 21 -202 22 -203 14 -204 12 -205 14 -206 18 -207 18 -208 18 -209 13 -210 15 -211 11 -212 12 -213 19 -214 13 -215 10 -216 16 -217 12 -218 11 -219 14 -220 15 -221 12 -222 11 -223 9 -224 9 -225 13 -226 3 -227 4 -228 1 -229 10 -230 8 -231 14 -232 9 -233 7 -234 3 -235 8 -236 8 -237 8 -238 8 -239 7 -240 7 -241 5 -242 7 -243 8 -244 10 -245 11 -246 11 -247 10 -248 5 -249 7 -250 8 -251 6 -252 7 -253 12 -254 5 -255 10 -256 15 -257 12 -258 12 -259 5 -260 10 -261 13 -262 22 -263 15 -264 15 -265 12 -266 10 -267 8 -268 19 -269 9 -270 15 -271 10 -272 7 -273 11 -274 14 -275 13 -276 5 -277 5 -278 7 -279 9 -280 4 -281 10 -282 11 -283 13 -284 8 -285 11 -286 13 -287 13 -288 9 -289 11 -290 23 -291 8 -292 16 -293 13 -294 11 -295 10 -296 7 -297 19 -298 16 -299 11 -300 7 -301 12 -302 11 -303 11 -304 15 -305 11 -306 19 -307 10 -308 15 -309 12 -310 17 -311 13 -312 15 -313 11 -314 11 -315 9 -316 18 -317 9 -318 9 -319 12 -320 12 -321 12 -322 8 -323 13 -324 6 -325 11 -326 12 -327 11 -328 13 -329 5 -330 17 -331 6 -332 13 -333 8 -334 7 -335 8 -336 4 -337 6 -338 10 -339 6 -340 6 -341 7 -342 8 -343 8 -344 5 -345 4 -346 7 -348 4 -349 5 -350 6 -351 6 -352 3 -353 4 -354 5 -355 1 -356 3 -357 1 -358 3 -359 1 -360 1 -361 4 -362 2 -363 2 -364 3 -365 3 -367 1 -368 4 -369 3 -370 2 -372 1 -373 3 -374 1 -375 4 -376 1 -379 1 -381 2 -382 1 -400 1 -444 1 -446 1 -454 1 -457 1 -459 1 -466 1 -479 1 -480 1 -488 1 -516 1 -525 1 -532 2 -533 1 -537 1 -554 1 -667 1 -672 1 -683 1 -689 1 -690 1 -693 1 -742 1 -747 1 -766 1 -789 1 -794 1 -795 1 -803 1 -805 1 -807 1 -809 1 -810 1 -811 1 -825 1 -840 1 -847 1 -848 1 -872 3 -911 1 -919 1 -950 1 -986 1 -991 1 -993 1 -1011 1 -1032 1 -1269 1 -1303 1 -1352 1 -1380 1 -1418 1 -1481 1 -1506 1 -1525 1 -1532 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1a2c0b1..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.424e-03 9.856e-04 -3.474 0.000566 *** -r 1.046e-02 2.867e-05 364.859 < 2e-16 *** -kmercov 9.912e+00 4.950e-03 2002.252 < 2e-16 *** -bias 9.767e-01 7.216e-03 135.344 < 2e-16 *** -length 4.498e+06 3.290e+03 1367.083 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 435.4 on 410 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 3.29e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f0a4668..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 67ece77..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9192db0..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 107526833.23201 -round 1 trimming to 7 trying 4peak model... converged. score: 88701632.1241001 -round 2 trimming to 12 trying 4peak model... converged. score: 889994664.220667 -round 3 trimming to 17 trying 4peak model... converged. score: 6554118331.57308 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 386c920..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04017% 1.05164% -Genome Haploid Length 4,583,482 bp 4,592,648 bp -Genome Repeat Length 75,190 bp 75,340 bp -Genome Unique Length 4,508,292 bp 4,517,308 bp -Model Fit 98.7073% 99.0978% -Read Error Rate 0.101689% 0.101689% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index cbbce64..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,370 +0,0 @@ -1 16747690 -2 485783 -3 110487 -4 140649 -5 181991 -6 219780 -7 249180 -8 272684 -9 289652 -10 302336 -11 314640 -12 319088 -13 320598 -14 315358 -15 307062 -16 291954 -17 273018 -18 245510 -19 218108 -20 188701 -21 162821 -22 135094 -23 110431 -24 88216 -25 70090 -26 53747 -27 41137 -28 30644 -29 22517 -30 16642 -31 11913 -32 8523 -33 6157 -34 4459 -35 3396 -36 2477 -37 1904 -38 1455 -39 1214 -40 948 -41 799 -42 678 -43 640 -44 576 -45 557 -46 452 -47 412 -48 355 -49 309 -50 325 -51 255 -52 263 -53 257 -54 261 -55 222 -56 247 -57 208 -58 176 -59 187 -60 192 -61 165 -62 156 -63 145 -64 124 -65 123 -66 138 -67 150 -68 115 -69 128 -70 132 -71 126 -72 111 -73 122 -74 128 -75 115 -76 113 -77 154 -78 140 -79 134 -80 102 -81 136 -82 126 -83 137 -84 108 -85 134 -86 125 -87 107 -88 115 -89 111 -90 109 -91 126 -92 111 -93 116 -94 115 -95 109 -96 126 -97 126 -98 134 -99 121 -100 127 -101 134 -102 155 -103 141 -104 135 -105 133 -106 119 -107 130 -108 138 -109 122 -110 126 -111 129 -112 134 -113 104 -114 96 -115 96 -116 85 -117 65 -118 78 -119 71 -120 61 -121 74 -122 69 -123 54 -124 58 -125 52 -126 50 -127 45 -128 43 -129 49 -130 59 -131 58 -132 46 -133 42 -134 44 -135 33 -136 42 -137 37 -138 44 -139 31 -140 37 -141 39 -142 34 -143 39 -144 33 -145 46 -146 34 -147 42 -148 29 -149 41 -150 27 -151 35 -152 35 -153 39 -154 25 -155 26 -156 26 -157 27 -158 26 -159 20 -160 20 -161 13 -162 17 -163 15 -164 19 -165 17 -166 12 -167 14 -168 12 -169 15 -170 6 -171 19 -172 17 -173 20 -174 14 -175 25 -176 18 -177 24 -178 19 -179 19 -180 22 -181 21 -182 18 -183 10 -184 15 -185 24 -186 12 -187 11 -188 16 -189 7 -190 6 -191 2 -192 7 -193 7 -194 11 -195 8 -196 10 -197 13 -198 4 -199 16 -200 11 -201 7 -202 13 -203 12 -204 9 -205 10 -206 12 -207 8 -208 10 -209 14 -210 4 -211 13 -212 13 -213 9 -214 17 -215 15 -216 7 -217 13 -218 19 -219 12 -220 11 -221 15 -222 14 -223 12 -224 7 -225 11 -226 14 -227 9 -228 13 -229 14 -230 14 -231 23 -232 10 -233 13 -234 14 -235 6 -236 9 -237 6 -238 12 -239 12 -240 9 -241 12 -242 6 -243 9 -244 11 -245 14 -246 11 -247 14 -248 12 -249 13 -250 17 -251 18 -252 21 -253 8 -254 14 -255 22 -256 16 -257 13 -258 11 -259 9 -260 11 -261 14 -262 16 -263 19 -264 22 -265 19 -266 19 -267 25 -268 25 -269 15 -270 18 -271 11 -272 20 -273 13 -274 19 -275 17 -276 12 -277 20 -278 12 -279 16 -280 17 -281 10 -282 10 -283 8 -284 15 -285 9 -286 8 -287 9 -288 9 -289 4 -290 3 -291 1 -292 5 -293 2 -294 1 -295 5 -296 1 -297 1 -298 5 -299 1 -300 2 -302 1 -303 2 -307 1 -309 1 -310 1 -311 1 -312 1 -313 1 -315 1 -316 1 -317 2 -319 3 -320 1 -321 1 -338 1 -345 1 -347 1 -351 1 -358 1 -360 1 -362 1 -364 1 -387 1 -422 1 -435 1 -449 1 -455 1 -456 1 -458 1 -461 1 -472 1 -489 1 -572 1 -578 1 -580 1 -595 1 -639 2 -641 1 -657 1 -691 1 -694 1 -703 1 -706 1 -714 1 -723 1 -729 1 -752 1 -753 1 -757 1 -758 2 -761 3 -766 1 -769 1 -770 1 -793 1 -815 1 -863 1 -882 1 -890 1 -905 1 -916 1 -1029 1 -1042 1 -1049 1 -1092 1 -1149 1 -1171 1 -1213 1 -1235 1 -1239 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6616f6a..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -9.608e-03 1.885e-03 -5.098 5.59e-07 *** -r 9.878e-03 6.779e-05 145.732 < 2e-16 *** -kmercov 8.125e+00 8.641e-03 940.279 < 2e-16 *** -bias 9.525e-01 1.319e-02 72.235 < 2e-16 *** -length 4.562e+06 6.582e+03 693.062 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 806.2 on 354 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 9.269e-07 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5ad6c05..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index d96e78a..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f97cb87..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 100944982.156774 -round 1 trimming to 8 trying 4peak model... unconverged -round 2 trimming to 13 trying 4peak model... unconverged -round 3 trimming to 18 trying 4peak model... converged. score: 514403198280.328 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6465c32..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.97429% 1.0014% -Genome Haploid Length 4,624,159 bp 4,643,872 bp -Genome Repeat Length 29,851 bp 29,978 bp -Genome Unique Length 4,594,308 bp 4,613,894 bp -Model Fit 98.6769% 99.0852% -Read Error Rate 0.995923% 0.995923% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index dbe8ed1..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,315 +0,0 @@ -1 29735138 -2 1181116 -3 215508 -4 231584 -5 280396 -6 319976 -7 348820 -8 369832 -9 382374 -10 387571 -11 382332 -12 368870 -13 343490 -14 312591 -15 277084 -16 239702 -17 198185 -18 160241 -19 127497 -20 96659 -21 72763 -22 53652 -23 38359 -24 27193 -25 19096 -26 12945 -27 8887 -28 5868 -29 4067 -30 2771 -31 1991 -32 1563 -33 1122 -34 916 -35 791 -36 702 -37 592 -38 474 -39 447 -40 399 -41 408 -42 370 -43 363 -44 318 -45 258 -46 262 -47 236 -48 203 -49 194 -50 210 -51 237 -52 206 -53 180 -54 159 -55 166 -56 162 -57 155 -58 153 -59 139 -60 164 -61 157 -62 167 -63 141 -64 169 -65 152 -66 154 -67 138 -68 147 -69 176 -70 174 -71 191 -72 166 -73 206 -74 204 -75 197 -76 205 -77 205 -78 202 -79 189 -80 173 -81 175 -82 167 -83 165 -84 203 -85 172 -86 175 -87 157 -88 130 -89 112 -90 140 -91 130 -92 107 -93 118 -94 115 -95 110 -96 113 -97 87 -98 75 -99 82 -100 73 -101 59 -102 54 -103 38 -104 46 -105 46 -106 40 -107 67 -108 34 -109 38 -110 38 -111 37 -112 26 -113 41 -114 41 -115 28 -116 41 -117 39 -118 37 -119 39 -120 35 -121 31 -122 41 -123 36 -124 31 -125 19 -126 14 -127 26 -128 33 -129 22 -130 22 -131 33 -132 33 -133 15 -134 18 -135 21 -136 16 -137 18 -138 18 -139 13 -140 16 -141 21 -142 18 -143 19 -144 16 -145 19 -146 19 -147 14 -148 15 -149 7 -150 13 -151 13 -152 15 -153 6 -154 10 -155 8 -156 10 -157 9 -158 11 -159 12 -160 3 -161 14 -162 6 -163 9 -164 4 -165 8 -166 8 -167 8 -168 5 -169 8 -170 10 -171 8 -172 5 -173 7 -174 7 -175 11 -176 8 -177 8 -178 10 -179 16 -180 9 -181 14 -182 15 -183 14 -184 9 -185 8 -186 20 -187 15 -188 16 -189 14 -190 11 -191 19 -192 25 -193 14 -194 21 -195 18 -196 23 -197 29 -198 26 -199 20 -200 25 -201 27 -202 25 -203 20 -204 23 -205 19 -206 22 -207 24 -208 26 -209 23 -210 29 -211 28 -212 23 -213 14 -214 25 -215 24 -216 20 -217 15 -218 20 -219 14 -220 15 -221 11 -222 10 -223 11 -224 18 -225 12 -226 17 -227 12 -228 11 -229 12 -230 11 -231 14 -232 3 -233 6 -234 6 -235 5 -236 5 -237 5 -238 6 -239 2 -240 3 -241 6 -242 5 -243 6 -244 5 -245 5 -246 5 -247 6 -248 5 -249 6 -250 5 -251 4 -252 1 -253 3 -254 4 -255 3 -256 1 -257 3 -258 1 -260 1 -261 5 -263 2 -264 3 -266 1 -268 1 -272 1 -277 1 -288 1 -306 1 -316 1 -322 1 -323 1 -324 1 -329 1 -333 1 -380 1 -397 1 -401 1 -408 1 -409 1 -423 1 -454 1 -465 1 -507 1 -516 1 -520 1 -524 1 -525 1 -533 2 -536 1 -539 1 -542 1 -544 2 -547 1 -549 1 -552 2 -555 1 -567 1 -587 1 -609 1 -620 1 -641 1 -670 1 -675 1 -677 1 -702 1 -705 1 -748 1 -779 1 -790 1 -802 1 -848 1 -881 1 -910 1 -929 1 -933 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 37520ae..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.223e-02 6.559e-03 -4.913 1.46e-06 *** -r 9.623e-03 3.173e-04 30.330 < 2e-16 *** -kmercov 6.585e+00 2.587e-02 254.570 < 2e-16 *** -bias 9.635e-01 5.239e-02 18.389 < 2e-16 *** -length 4.636e+06 2.743e+04 169.021 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 2307 on 307 degrees of freedom - -Number of iterations to convergence: 12 -Achieved convergence tolerance: 8.646e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 018d440..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2ba8089..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f11f444..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 481532325.258483 -round 1 trimming to 8 trying 4peak model... unconverged -round 2 trimming to 13 trying 4peak model... converged. score: 10876485654.2124 -round 3 trimming to 18 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index fcb6b22..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.898796% 1.0257% -Genome Haploid Length 4,597,261 bp 4,670,068 bp -Genome Repeat Length -145,921 bp -148,232 bp -Genome Unique Length 4,743,182 bp 4,818,300 bp -Model Fit 97.3811% 98.1705% -Read Error Rate 1.98437% 1.98437% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 6e0a501..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,428 +0,0 @@ -1 1938892 -2 64830 -3 85001 -4 111076 -5 137379 -6 158995 -7 181161 -8 201036 -9 216530 -10 225852 -11 235025 -12 243463 -13 245897 -14 246827 -15 244166 -16 244301 -17 238869 -18 229323 -19 217950 -20 207849 -21 193574 -22 179927 -23 164754 -24 148474 -25 134803 -26 120139 -27 106076 -28 92799 -29 80287 -30 67416 -31 57676 -32 49147 -33 41345 -34 34694 -35 28784 -36 23338 -37 19227 -38 15497 -39 12194 -40 10054 -41 7867 -42 6683 -43 4904 -44 3923 -45 3206 -46 2619 -47 2007 -48 1528 -49 1286 -50 1188 -51 749 -52 772 -53 608 -54 538 -55 462 -56 422 -57 425 -58 391 -59 351 -60 298 -61 307 -62 342 -63 266 -64 255 -65 216 -66 204 -67 232 -68 232 -69 243 -70 239 -71 193 -72 208 -73 190 -74 203 -75 161 -76 145 -77 179 -78 136 -79 146 -80 144 -81 133 -82 128 -83 105 -84 116 -85 116 -86 107 -87 91 -88 116 -89 109 -90 110 -91 124 -92 123 -93 127 -94 134 -95 105 -96 122 -97 111 -98 106 -99 93 -100 116 -101 116 -102 105 -103 95 -104 107 -105 91 -106 95 -107 121 -108 107 -109 112 -110 107 -111 105 -112 116 -113 109 -114 112 -115 111 -116 106 -117 112 -118 100 -119 91 -120 93 -121 98 -122 117 -123 91 -124 99 -125 110 -126 79 -127 81 -128 85 -129 80 -130 83 -131 82 -132 77 -133 85 -134 59 -135 78 -136 64 -137 71 -138 62 -139 64 -140 70 -141 76 -142 82 -143 81 -144 73 -145 82 -146 73 -147 58 -148 64 -149 53 -150 49 -151 42 -152 46 -153 51 -154 46 -155 47 -156 39 -157 46 -158 34 -159 33 -160 31 -161 39 -162 35 -163 33 -164 18 -165 24 -166 34 -167 42 -168 36 -169 22 -170 28 -171 33 -172 24 -173 28 -174 28 -175 34 -176 32 -177 24 -178 32 -179 26 -180 23 -181 29 -182 23 -183 23 -184 25 -185 21 -186 12 -187 25 -188 18 -189 18 -190 19 -191 29 -192 26 -193 21 -194 23 -195 21 -196 34 -197 23 -198 26 -199 28 -200 18 -201 15 -202 26 -203 18 -204 14 -205 9 -206 14 -207 10 -208 12 -209 16 -210 12 -211 7 -212 13 -213 16 -214 12 -215 12 -216 15 -217 8 -218 11 -219 12 -220 9 -221 9 -222 9 -223 13 -224 17 -225 17 -226 11 -227 11 -228 11 -229 13 -230 10 -231 12 -232 10 -233 10 -234 3 -235 9 -236 6 -237 3 -238 13 -240 3 -241 4 -242 5 -243 3 -244 5 -245 1 -246 3 -247 3 -248 4 -249 4 -250 2 -252 3 -253 6 -254 3 -255 4 -256 6 -257 6 -258 6 -259 3 -260 5 -261 9 -262 9 -263 7 -264 7 -265 7 -266 12 -267 7 -268 4 -269 10 -270 5 -271 2 -272 6 -273 13 -274 11 -275 4 -276 8 -277 5 -278 16 -279 15 -280 15 -281 19 -282 14 -283 11 -284 11 -285 16 -286 10 -287 14 -288 12 -289 12 -290 15 -291 13 -292 17 -293 17 -294 22 -295 17 -296 12 -297 16 -298 17 -299 14 -300 16 -301 13 -302 11 -303 13 -304 14 -305 13 -306 18 -307 20 -308 12 -309 8 -310 7 -311 11 -312 19 -313 9 -314 10 -315 8 -316 14 -317 18 -318 14 -319 11 -320 15 -321 7 -322 18 -323 11 -324 13 -325 8 -326 14 -327 16 -328 7 -329 14 -330 6 -331 11 -332 10 -333 7 -334 9 -335 7 -336 10 -337 7 -338 7 -339 7 -340 7 -341 10 -342 3 -343 9 -344 5 -345 13 -346 6 -347 9 -348 5 -349 5 -350 3 -351 9 -352 6 -353 8 -354 5 -355 5 -356 8 -357 4 -358 4 -359 1 -360 4 -361 3 -362 1 -363 1 -364 1 -366 1 -368 2 -369 2 -370 1 -371 2 -374 1 -376 2 -377 1 -378 2 -382 1 -414 1 -420 1 -423 1 -425 1 -427 1 -453 1 -465 1 -480 1 -483 1 -489 1 -495 1 -509 1 -537 1 -563 1 -568 1 -569 1 -572 1 -581 1 -586 1 -587 1 -596 1 -600 1 -651 1 -710 1 -720 1 -737 2 -738 1 -740 1 -744 1 -750 1 -753 1 -756 1 -757 1 -760 1 -761 1 -771 1 -782 1 -786 1 -795 1 -807 1 -808 1 -822 1 -832 1 -839 1 -875 2 -904 1 -911 1 -1158 1 -1195 1 -1234 1 -1261 1 -1283 1 -1322 1 -1343 1 -1376 1 -1389 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d9036b0..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.479e-03 1.262e-03 -4.34 1.8e-05 *** -r 1.109e-02 5.378e-05 206.26 < 2e-16 *** -kmercov 1.007e+01 7.283e-03 1383.34 < 2e-16 *** -bias 1.903e+00 1.549e-02 122.79 < 2e-16 *** -length 4.440e+06 4.857e+03 914.03 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 316.9 on 408 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 4.44e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 898c20a..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e0e20b6..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a2093a5..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 118912554.790659 -round 1 trimming to 7 trying 4peak model... converged. score: 57772920.0920493 -round 2 trimming to 12 trying 4peak model... converged. score: 317385849.29348 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 61dfa72..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.09847% 1.11999% -Genome Haploid Length 4,506,579 bp 4,519,629 bp -Genome Repeat Length 50,071 bp 50,216 bp -Genome Unique Length 4,456,508 bp 4,469,413 bp -Model Fit 98.9968% 99.3504% -Read Error Rate 0.102603% 0.102603% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index a019ded..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,372 +0,0 @@ -1 16738603 -2 538040 -3 140913 -4 161940 -5 195783 -6 224160 -7 247734 -8 267250 -9 283399 -10 291353 -11 294869 -12 295289 -13 292855 -14 282519 -15 270326 -16 254955 -17 236832 -18 218789 -19 198034 -20 177634 -21 156268 -22 133028 -23 115089 -24 98150 -25 80903 -26 67680 -27 54638 -28 44615 -29 35782 -30 28018 -31 22202 -32 17166 -33 13587 -34 10398 -35 7928 -36 6054 -37 4604 -38 3529 -39 2635 -40 2071 -41 1534 -42 1205 -43 989 -44 816 -45 712 -46 632 -47 588 -48 459 -49 408 -50 402 -51 305 -52 301 -53 272 -54 235 -55 220 -56 239 -57 234 -58 231 -59 217 -60 219 -61 216 -62 211 -63 200 -64 195 -65 160 -66 163 -67 133 -68 138 -69 143 -70 135 -71 128 -72 122 -73 126 -74 123 -75 108 -76 131 -77 113 -78 95 -79 128 -80 135 -81 123 -82 126 -83 121 -84 129 -85 109 -86 122 -87 133 -88 146 -89 108 -90 135 -91 120 -92 137 -93 108 -94 128 -95 121 -96 138 -97 134 -98 137 -99 120 -100 133 -101 130 -102 137 -103 120 -104 143 -105 141 -106 111 -107 100 -108 94 -109 89 -110 94 -111 78 -112 70 -113 76 -114 99 -115 79 -116 97 -117 84 -118 59 -119 66 -120 65 -121 73 -122 76 -123 53 -124 63 -125 52 -126 58 -127 56 -128 48 -129 46 -130 41 -131 38 -132 51 -133 53 -134 55 -135 41 -136 42 -137 40 -138 39 -139 40 -140 42 -141 41 -142 35 -143 36 -144 32 -145 35 -146 32 -147 25 -148 29 -149 27 -150 25 -151 19 -152 29 -153 24 -154 24 -155 21 -156 25 -157 32 -158 27 -159 18 -160 40 -161 23 -162 22 -163 21 -164 36 -165 26 -166 28 -167 22 -168 22 -169 21 -170 16 -171 20 -172 21 -173 25 -174 20 -175 21 -176 24 -177 22 -178 22 -179 19 -180 19 -181 23 -182 13 -183 18 -184 13 -185 7 -186 15 -187 21 -188 21 -189 17 -190 13 -191 12 -192 9 -193 12 -194 6 -195 11 -196 8 -197 6 -198 6 -199 10 -200 7 -201 6 -202 3 -203 10 -204 4 -205 6 -206 9 -207 6 -208 5 -209 6 -210 10 -211 6 -212 8 -213 4 -214 8 -215 6 -216 9 -217 5 -218 4 -219 5 -220 7 -221 10 -222 9 -223 6 -224 9 -225 8 -226 9 -227 12 -228 17 -229 12 -230 12 -231 14 -232 10 -233 18 -234 12 -235 14 -236 19 -237 17 -238 16 -239 18 -240 14 -241 11 -242 24 -243 15 -244 19 -245 17 -246 12 -247 12 -248 18 -249 8 -250 14 -251 6 -252 10 -253 3 -254 18 -255 6 -256 8 -257 7 -258 9 -259 15 -260 9 -261 12 -262 21 -263 13 -264 9 -265 9 -266 10 -267 10 -268 8 -269 9 -270 11 -271 6 -272 11 -273 9 -274 19 -275 14 -276 16 -277 11 -278 18 -279 16 -280 12 -281 18 -282 18 -283 16 -284 14 -285 18 -286 22 -287 15 -288 15 -289 19 -290 6 -291 10 -292 8 -293 18 -294 2 -295 5 -296 5 -297 9 -298 8 -299 6 -300 6 -301 4 -302 4 -303 4 -304 3 -305 4 -306 3 -307 6 -308 5 -309 3 -310 3 -311 2 -312 4 -313 1 -314 1 -315 1 -318 1 -324 2 -330 1 -336 1 -342 2 -357 1 -388 1 -400 1 -401 1 -402 2 -409 1 -429 1 -468 1 -482 1 -487 1 -504 1 -583 1 -586 1 -588 1 -596 1 -603 1 -624 1 -625 1 -635 1 -659 1 -669 1 -676 1 -679 1 -696 1 -699 1 -710 1 -712 2 -722 1 -731 1 -732 1 -740 1 -744 1 -751 1 -755 1 -759 1 -761 1 -790 1 -806 1 -816 1 -825 1 -847 1 -874 1 -902 1 -1004 1 -1009 1 -1056 1 -1093 1 -1105 1 -1124 1 -1150 1 -1156 1 -1171 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9c6bf72..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.299e-03 1.228e-03 -4.317 2.06e-05 *** -r 1.135e-02 7.388e-05 153.569 < 2e-16 *** -kmercov 8.361e+00 7.234e-03 1155.683 < 2e-16 *** -bias 1.499e+00 1.414e-02 105.998 < 2e-16 *** -length 4.432e+06 5.568e+03 795.899 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 307.6 on 351 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 3.127e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 658dc65..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9c13a09..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c7a7184..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... unconverged -round 1 trimming to 8 trying 4peak model... converged. score: 111845777.663552 -round 2 trimming to 13 trying 4peak model... converged. score: 6270500177.14802 -round 3 trimming to 18 trying 4peak model... converged. score: 812521377.404174 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2130b23..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.11974% 1.14929% -Genome Haploid Length 4,492,105 bp 4,507,679 bp -Genome Repeat Length 45,806 bp 45,965 bp -Genome Unique Length 4,446,298 bp 4,461,714 bp -Model Fit 98.8448% 99.1953% -Read Error Rate 0.999571% 0.999571% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 92280f1..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,311 +0,0 @@ -1 29672875 -2 1259606 -3 251270 -4 250427 -5 286611 -6 320075 -7 341173 -8 350618 -9 359113 -10 355611 -11 343927 -12 326033 -13 304628 -14 278009 -15 247283 -16 218637 -17 187816 -18 157284 -19 131224 -20 108167 -21 86912 -22 68826 -23 53862 -24 42188 -25 32070 -26 24041 -27 17822 -28 13116 -29 9859 -30 7116 -31 5274 -32 3818 -33 2721 -34 1986 -35 1472 -36 1136 -37 966 -38 787 -39 753 -40 648 -41 603 -42 499 -43 410 -44 311 -45 299 -46 270 -47 220 -48 224 -49 224 -50 190 -51 202 -52 218 -53 196 -54 180 -55 160 -56 147 -57 188 -58 176 -59 180 -60 174 -61 195 -62 216 -63 190 -64 169 -65 168 -66 167 -67 150 -68 165 -69 170 -70 177 -71 175 -72 143 -73 152 -74 174 -75 181 -76 152 -77 171 -78 174 -79 171 -80 158 -81 161 -82 144 -83 138 -84 163 -85 136 -86 134 -87 108 -88 131 -89 158 -90 146 -91 124 -92 102 -93 108 -94 93 -95 101 -96 103 -97 95 -98 96 -99 84 -100 89 -101 93 -102 82 -103 77 -104 66 -105 41 -106 64 -107 55 -108 47 -109 51 -110 46 -111 37 -112 47 -113 43 -114 34 -115 33 -116 33 -117 23 -118 25 -119 32 -120 22 -121 25 -122 26 -123 20 -124 31 -125 27 -126 22 -127 15 -128 20 -129 18 -130 25 -131 11 -132 18 -133 14 -134 23 -135 19 -136 20 -137 25 -138 21 -139 20 -140 16 -141 32 -142 20 -143 23 -144 21 -145 17 -146 22 -147 20 -148 17 -149 19 -150 17 -151 13 -152 9 -153 9 -154 17 -155 19 -156 12 -157 9 -158 8 -159 9 -160 9 -161 11 -162 8 -163 7 -164 15 -165 12 -166 9 -167 10 -168 7 -169 15 -170 12 -171 9 -172 14 -173 13 -174 21 -175 18 -176 19 -177 18 -178 23 -179 13 -180 22 -181 25 -182 15 -183 20 -184 18 -185 12 -186 9 -187 10 -188 11 -189 19 -190 21 -191 13 -192 17 -193 19 -194 13 -195 26 -196 13 -197 19 -198 18 -199 25 -200 22 -201 18 -202 21 -203 22 -204 21 -205 25 -206 17 -207 17 -208 20 -209 20 -210 24 -211 18 -212 16 -213 22 -214 18 -215 15 -216 20 -217 15 -218 13 -219 21 -220 9 -221 15 -222 10 -223 14 -224 15 -225 13 -226 14 -227 15 -228 12 -229 5 -230 18 -231 7 -232 9 -233 10 -234 8 -235 4 -236 7 -237 6 -238 7 -239 7 -240 5 -241 6 -242 2 -243 3 -244 4 -245 5 -246 4 -247 3 -248 6 -249 4 -250 1 -251 2 -252 1 -253 3 -254 1 -257 1 -259 1 -263 1 -267 1 -274 1 -276 1 -289 1 -300 1 -301 1 -310 1 -314 1 -324 1 -325 1 -327 1 -331 1 -351 1 -374 1 -399 1 -452 1 -458 1 -465 1 -469 2 -474 1 -482 2 -484 1 -485 1 -486 1 -490 2 -496 1 -498 1 -507 1 -516 1 -547 1 -550 1 -552 1 -554 1 -562 1 -566 1 -567 1 -580 1 -596 1 -630 1 -697 1 -714 1 -716 1 -723 1 -729 1 -751 1 -816 1 -850 1 -874 1 -907 1 -919 1 -924 1 -960 1 -975 1 -994 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 37d52e9..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.338e-03 1.246e-03 2.678 0.007818 ** -r 9.799e-03 2.521e-03 3.886 0.000126 *** -kmercov 6.756e+00 8.618e-02 78.393 < 2e-16 *** -bias 1.132e+00 4.747e-02 23.844 < 2e-16 *** -length 4.291e+06 4.053e+04 105.879 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 147 on 291 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.582e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index fd235b4..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6be3abb..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6790fbe..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 3053992546.90685 -round 1 trimming to 20 trying 4peak model... converged. score: 5576225651127.54 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ba0e6c9..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.475606% 1.48411% -Genome Haploid Length 4,350,993 bp 4,578,813 bp -Genome Repeat Length 180,019 bp 189,445 bp -Genome Unique Length 4,170,974 bp 4,389,369 bp -Model Fit 96.4261% 96.7311% -Read Error Rate 2.04175% 2.04175% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index f5d906e..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,469 +0,0 @@ -1 1953746 -2 86896 -3 109455 -4 127371 -5 150090 -6 170427 -7 183701 -8 198406 -9 211712 -10 221058 -11 225325 -12 229640 -13 229325 -14 231794 -15 230022 -16 220272 -17 214851 -18 207419 -19 198038 -20 189952 -21 174652 -22 164928 -23 151775 -24 139246 -25 128712 -26 115290 -27 103298 -28 92326 -29 83311 -30 72912 -31 64665 -32 56886 -33 48993 -34 42767 -35 36027 -36 31459 -37 25851 -38 22268 -39 18381 -40 15262 -41 13397 -42 10582 -43 8797 -44 6358 -45 5952 -46 4955 -47 3823 -48 3420 -49 2750 -50 2089 -51 1846 -52 1500 -53 1211 -54 1024 -55 673 -56 723 -57 629 -58 499 -59 458 -60 472 -61 437 -62 366 -63 324 -64 297 -65 314 -66 269 -67 268 -68 269 -69 242 -70 174 -71 193 -72 161 -73 170 -74 169 -75 157 -76 162 -77 156 -78 191 -79 148 -80 147 -81 143 -82 143 -83 165 -84 139 -85 107 -86 119 -87 117 -88 120 -89 113 -90 114 -91 89 -92 127 -93 126 -94 104 -95 88 -96 97 -97 102 -98 105 -99 144 -100 126 -101 122 -102 85 -103 113 -104 78 -105 111 -106 113 -107 96 -108 98 -109 108 -110 99 -111 105 -112 128 -113 121 -114 118 -115 105 -116 125 -117 115 -118 96 -119 93 -120 89 -121 93 -122 101 -123 89 -124 90 -125 69 -126 82 -127 86 -128 103 -129 77 -130 82 -131 76 -132 81 -133 78 -134 52 -135 89 -136 65 -137 80 -138 81 -139 63 -140 73 -141 87 -142 66 -143 62 -144 71 -145 71 -146 72 -147 77 -148 70 -149 65 -150 47 -151 49 -152 63 -153 65 -154 63 -155 56 -156 61 -157 48 -158 46 -159 55 -160 48 -161 37 -162 41 -163 48 -164 45 -165 32 -166 36 -167 27 -168 31 -169 37 -170 26 -171 28 -172 27 -173 22 -174 16 -175 17 -176 31 -177 21 -178 18 -179 22 -180 24 -181 24 -182 13 -183 18 -184 20 -185 19 -186 13 -187 14 -188 19 -189 14 -190 11 -191 19 -192 17 -193 20 -194 25 -195 21 -196 21 -197 19 -198 22 -199 30 -200 14 -201 15 -202 16 -203 14 -204 20 -205 18 -206 17 -207 12 -208 13 -209 16 -210 12 -211 20 -212 19 -213 17 -214 4 -215 13 -216 6 -217 6 -218 8 -219 8 -220 8 -221 11 -222 8 -223 5 -224 1 -225 6 -226 3 -227 4 -228 3 -229 6 -230 4 -231 5 -232 5 -233 8 -234 2 -235 5 -236 4 -237 1 -238 5 -239 8 -240 3 -241 2 -242 2 -243 3 -244 2 -245 9 -246 2 -247 3 -248 3 -249 10 -250 6 -251 8 -252 5 -253 5 -254 6 -255 1 -256 5 -257 4 -259 8 -260 7 -261 5 -262 8 -263 2 -264 6 -265 7 -266 9 -267 5 -268 7 -269 8 -270 5 -271 2 -272 7 -273 8 -274 11 -275 6 -276 10 -277 9 -278 5 -279 6 -280 7 -281 9 -282 8 -283 8 -284 16 -285 8 -286 8 -287 12 -288 12 -289 10 -290 9 -291 11 -292 10 -293 6 -294 10 -295 15 -296 10 -297 16 -298 4 -299 9 -300 14 -301 11 -302 14 -303 6 -304 10 -305 13 -306 9 -307 15 -308 13 -309 11 -310 9 -311 10 -312 15 -313 11 -314 19 -315 9 -316 25 -317 5 -318 16 -319 4 -320 11 -321 7 -322 15 -323 13 -324 16 -325 6 -326 17 -327 14 -328 14 -329 16 -330 13 -331 12 -332 17 -333 28 -334 9 -335 13 -336 10 -337 12 -338 14 -339 8 -340 16 -341 12 -342 12 -343 9 -344 9 -345 8 -346 10 -347 8 -348 5 -349 5 -350 12 -351 8 -352 7 -353 7 -354 12 -355 6 -356 5 -357 3 -358 6 -359 3 -360 5 -361 2 -362 8 -363 6 -364 9 -365 4 -366 3 -367 5 -368 7 -369 2 -370 1 -371 3 -372 6 -373 3 -374 7 -375 2 -376 3 -377 6 -378 3 -379 4 -380 3 -382 2 -383 4 -384 2 -385 4 -386 2 -387 4 -388 1 -389 3 -390 4 -391 2 -392 4 -393 5 -394 3 -395 4 -396 2 -397 3 -398 1 -399 2 -400 2 -401 2 -402 2 -403 2 -404 1 -405 3 -407 1 -409 1 -410 3 -413 2 -414 1 -416 1 -417 1 -418 2 -419 2 -428 1 -430 1 -432 1 -435 1 -438 1 -440 1 -447 1 -487 1 -492 1 -494 1 -504 1 -509 1 -522 1 -528 1 -538 1 -574 1 -597 1 -683 1 -686 1 -713 1 -717 1 -718 1 -724 1 -726 1 -776 1 -823 1 -854 1 -871 1 -873 1 -880 1 -882 1 -883 1 -886 1 -887 2 -889 1 -900 2 -902 1 -912 1 -929 1 -930 1 -939 1 -949 1 -1023 1 -1045 1 -1054 1 -1063 1 -1116 1 -1134 1 -1233 1 -1274 1 -1310 1 -1316 1 -1354 1 -1408 1 -1412 1 -1447 1 -1451 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1a7ab7c..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.583e-02 2.147e-03 -7.373 8.29e-13 *** -r 1.128e-02 1.267e-04 89.071 < 2e-16 *** -kmercov 1.028e+01 1.416e-02 725.656 < 2e-16 *** -bias 2.797e+00 3.458e-02 80.877 < 2e-16 *** -length 4.392e+06 1.030e+04 426.254 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 339.4 on 443 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 2.448e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 818d28f..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6caa76a..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5897de4..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 126785040.288619 -round 1 trimming to 7 trying 4peak model... converged. score: 51015500.0893544 -round 2 trimming to 12 trying 4peak model... converged. score: 94948228.2491456 -round 3 trimming to 17 trying 4peak model... converged. score: 123262988.698301 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 17f86f3..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.10279% 1.15345% -Genome Haploid Length 4,409,241 bp 4,433,613 bp -Genome Repeat Length -36,541 bp -36,743 bp -Genome Unique Length 4,445,782 bp 4,470,356 bp -Model Fit 98.8501% 99.2705% -Read Error Rate 0.104929% 0.104929% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index beafa27..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,404 +0,0 @@ -1 16733726 -2 580907 -3 168466 -4 181763 -5 205780 -6 229077 -7 249371 -8 263313 -9 270258 -10 273772 -11 272796 -12 272648 -13 263210 -14 254739 -15 243943 -16 230212 -17 215690 -18 199242 -19 180887 -20 165012 -21 147211 -22 129805 -23 115611 -24 100572 -25 87692 -26 75615 -27 63898 -28 53486 -29 44563 -30 37250 -31 30725 -32 25389 -33 21002 -34 16906 -35 13352 -36 10485 -37 8255 -38 6780 -39 5419 -40 4272 -41 3402 -42 2751 -43 2212 -44 1770 -45 1484 -46 1136 -47 881 -48 713 -49 653 -50 527 -51 474 -52 361 -53 349 -54 325 -55 265 -56 240 -57 208 -58 223 -59 238 -60 213 -61 204 -62 170 -63 160 -64 146 -65 152 -66 156 -67 163 -68 128 -69 129 -70 129 -71 122 -72 115 -73 127 -74 109 -75 132 -76 134 -77 123 -78 113 -79 127 -80 105 -81 107 -82 139 -83 118 -84 99 -85 103 -86 109 -87 118 -88 125 -89 124 -90 138 -91 105 -92 116 -93 129 -94 140 -95 148 -96 153 -97 129 -98 132 -99 145 -100 133 -101 115 -102 125 -103 120 -104 128 -105 117 -106 107 -107 121 -108 98 -109 123 -110 119 -111 124 -112 108 -113 100 -114 106 -115 103 -116 87 -117 92 -118 66 -119 65 -120 75 -121 54 -122 55 -123 66 -124 45 -125 56 -126 44 -127 35 -128 43 -129 48 -130 52 -131 46 -132 51 -133 48 -134 51 -135 53 -136 37 -137 46 -138 32 -139 37 -140 45 -141 48 -142 42 -143 45 -144 32 -145 43 -146 26 -147 19 -148 30 -149 28 -150 34 -151 25 -152 22 -153 15 -154 30 -155 16 -156 22 -157 20 -158 17 -159 19 -160 22 -161 21 -162 22 -163 15 -164 11 -165 10 -166 13 -167 12 -168 9 -169 19 -170 12 -171 17 -172 20 -173 18 -174 18 -175 28 -176 8 -177 19 -178 18 -179 15 -180 7 -181 16 -182 16 -183 21 -184 21 -185 14 -186 11 -187 8 -188 14 -189 17 -190 11 -191 14 -192 16 -193 13 -194 14 -195 12 -196 11 -197 8 -198 8 -199 7 -200 6 -201 11 -202 6 -203 5 -204 4 -205 8 -206 7 -207 9 -208 6 -209 6 -210 8 -211 2 -212 6 -213 9 -214 3 -215 10 -216 6 -217 5 -218 2 -219 9 -220 9 -221 7 -222 10 -223 12 -224 13 -225 10 -226 12 -227 11 -228 12 -229 11 -230 12 -231 14 -232 16 -233 14 -234 17 -235 15 -236 21 -237 22 -238 13 -239 20 -240 15 -241 21 -242 10 -243 22 -244 15 -245 19 -246 13 -247 11 -248 12 -249 15 -250 7 -251 9 -252 11 -253 8 -254 8 -255 20 -256 11 -257 7 -258 8 -259 14 -260 10 -261 13 -262 11 -263 7 -264 9 -265 8 -266 11 -267 7 -268 13 -269 11 -270 16 -271 4 -272 8 -273 10 -274 10 -275 7 -276 6 -277 11 -278 12 -279 10 -280 9 -281 8 -282 14 -283 10 -284 11 -285 5 -286 8 -287 13 -288 13 -289 5 -290 13 -291 10 -292 6 -293 7 -294 7 -295 14 -296 9 -297 9 -298 10 -299 10 -300 5 -301 10 -302 7 -303 5 -304 5 -305 4 -306 2 -307 6 -308 4 -309 7 -310 8 -311 1 -312 3 -313 3 -314 3 -315 2 -316 2 -317 1 -318 4 -319 2 -321 4 -322 4 -323 3 -324 1 -327 1 -328 3 -329 2 -330 2 -332 3 -333 5 -334 4 -335 5 -336 2 -337 5 -338 6 -339 2 -340 1 -341 2 -342 1 -343 3 -344 1 -345 1 -346 3 -347 4 -348 1 -349 1 -351 1 -352 1 -355 1 -356 1 -366 1 -367 1 -369 1 -372 1 -376 1 -378 1 -395 1 -398 1 -400 1 -416 1 -421 1 -432 1 -435 1 -456 1 -461 1 -585 1 -648 1 -657 1 -658 1 -659 1 -664 1 -667 2 -669 2 -674 1 -684 1 -685 1 -687 1 -703 1 -708 1 -715 1 -733 1 -740 1 -742 1 -743 1 -747 1 -751 1 -754 1 -757 1 -766 1 -767 1 -850 1 -855 1 -893 1 -896 1 -901 1 -918 1 -922 1 -983 1 -1000 1 -1030 1 -1047 1 -1068 1 -1090 1 -1125 1 -1130 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 13e4d1c..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.617e-03 1.186e-03 -3.049 0.00246 ** -r 1.319e-02 2.979e-04 44.262 < 2e-16 *** -kmercov 8.712e+00 2.340e-02 372.347 < 2e-16 *** -bias 2.006e+00 2.632e-02 76.211 < 2e-16 *** -length 4.236e+06 1.119e+04 378.479 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 152.1 on 381 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 4.958e-07 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8e3d308..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7878f58..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5e674e4..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 179897740.188654 -round 1 trimming to 8 trying 4peak model... converged. score: 48677376.8717261 -round 2 trimming to 13 trying 4peak model... converged. score: 48167860.0949004 -round 3 trimming to 18 trying 4peak model... converged. score: 45842116897.9925 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 86c68c3..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.25919% 1.37836% -Genome Haploid Length 4,289,187 bp 4,335,513 bp -Genome Repeat Length 61,466 bp 62,130 bp -Genome Unique Length 4,227,721 bp 4,273,383 bp -Model Fit 99.1317% 99.4523% -Read Error Rate 1.00647% 1.00647% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 197efa5..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,324 +0,0 @@ -1 29572702 -2 1341796 -3 277128 -4 261150 -5 291357 -6 311887 -7 325834 -8 333366 -9 333422 -10 326069 -11 315702 -12 297480 -13 277388 -14 253586 -15 229577 -16 205060 -17 179249 -18 155144 -19 132269 -20 111760 -21 93903 -22 77668 -23 64083 -24 51669 -25 41076 -26 32305 -27 25622 -28 19777 -29 15428 -30 12048 -31 8949 -32 6758 -33 4972 -34 3955 -35 2924 -36 2265 -37 1812 -38 1362 -39 1106 -40 890 -41 749 -42 619 -43 473 -44 415 -45 373 -46 287 -47 300 -48 307 -49 296 -50 280 -51 269 -52 277 -53 224 -54 195 -55 212 -56 181 -57 180 -58 162 -59 160 -60 184 -61 168 -62 164 -63 186 -64 160 -65 161 -66 198 -67 167 -68 139 -69 157 -70 141 -71 147 -72 125 -73 159 -74 153 -75 136 -76 134 -77 142 -78 123 -79 146 -80 142 -81 140 -82 141 -83 145 -84 158 -85 101 -86 120 -87 127 -88 111 -89 109 -90 121 -91 124 -92 90 -93 104 -94 106 -95 101 -96 94 -97 110 -98 109 -99 104 -100 96 -101 85 -102 63 -103 74 -104 70 -105 58 -106 57 -107 45 -108 55 -109 61 -110 49 -111 33 -112 44 -113 34 -114 43 -115 42 -116 35 -117 37 -118 38 -119 35 -120 41 -121 38 -122 30 -123 33 -124 28 -125 20 -126 28 -127 28 -128 42 -129 27 -130 47 -131 29 -132 25 -133 38 -134 29 -135 37 -136 25 -137 37 -138 32 -139 31 -140 29 -141 31 -142 40 -143 25 -144 32 -145 19 -146 26 -147 32 -148 22 -149 32 -150 24 -151 23 -152 19 -153 28 -154 30 -155 19 -156 29 -157 28 -158 23 -159 11 -160 18 -161 21 -162 15 -163 20 -164 23 -165 14 -166 12 -167 20 -168 14 -169 16 -170 10 -171 14 -172 9 -173 11 -174 8 -175 6 -176 6 -177 10 -178 12 -179 5 -180 8 -181 10 -182 14 -183 12 -184 13 -185 9 -186 14 -187 10 -188 17 -189 18 -190 18 -191 10 -192 19 -193 13 -194 14 -195 16 -196 23 -197 17 -198 10 -199 4 -200 21 -201 13 -202 9 -203 19 -204 15 -205 23 -206 15 -207 15 -208 18 -209 21 -210 12 -211 16 -212 13 -213 9 -214 22 -215 21 -216 25 -217 12 -218 17 -219 14 -220 16 -221 9 -222 9 -223 11 -224 12 -225 18 -226 11 -227 21 -228 13 -229 14 -230 10 -231 17 -232 6 -233 12 -234 7 -235 8 -236 7 -237 8 -238 4 -239 8 -240 9 -241 7 -242 9 -243 5 -244 8 -245 5 -246 8 -247 6 -248 3 -249 4 -250 2 -251 2 -252 1 -253 4 -254 5 -255 2 -256 2 -257 3 -258 2 -259 2 -260 5 -261 2 -262 2 -263 1 -264 1 -265 1 -266 4 -267 1 -268 1 -269 1 -271 1 -272 2 -274 1 -275 1 -278 1 -290 2 -297 1 -313 1 -333 1 -338 1 -345 1 -346 1 -347 1 -348 1 -351 2 -353 1 -402 1 -471 2 -498 1 -505 1 -508 1 -512 1 -518 1 -527 1 -528 1 -536 1 -539 1 -540 1 -544 1 -545 2 -549 2 -550 2 -563 1 -565 1 -566 1 -578 1 -581 1 -583 1 -589 1 -595 1 -676 1 -692 1 -700 1 -712 1 -721 1 -725 1 -764 1 -793 1 -819 1 -833 1 -851 1 -854 1 -873 1 -895 1 -905 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 4ea5853..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.072e-03 1.402e-03 3.617 0.000349 *** -r 2.192e-02 1.055e-03 20.783 < 2e-16 *** -kmercov 7.467e+00 5.810e-02 128.519 < 2e-16 *** -bias 1.322e+00 4.092e-02 32.298 < 2e-16 *** -length 4.170e+06 1.674e+04 249.076 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 118.8 on 304 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 9.934e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3f184db..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4b95e44..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4d9866c..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 20560080087.9438 -round 1 trimming to 20 trying 4peak model... converged. score: 99144553163.7783 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c556f49..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.98112% 2.40302% -Genome Haploid Length 4,022,056 bp 4,149,216 bp -Genome Repeat Length -66,518 bp -68,621 bp -Genome Unique Length 4,088,574 bp 4,217,837 bp -Model Fit 91.4744% 91.7082% -Read Error Rate 1.98641% 1.98641% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 64b8b76..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,423 +0,0 @@ -1 1937736 -2 58608 -3 95450 -4 146356 -5 202791 -6 249773 -7 294968 -8 319877 -9 335532 -10 341940 -11 334052 -12 326144 -13 309764 -14 296460 -15 284120 -16 269687 -17 255629 -18 242722 -19 227368 -20 209025 -21 194390 -22 176699 -23 155885 -24 136618 -25 118075 -26 101715 -27 85365 -28 70262 -29 57486 -30 46774 -31 36598 -32 28894 -33 22058 -34 16812 -35 13102 -36 9557 -37 7204 -38 5514 -39 3937 -40 2907 -41 2228 -42 1673 -43 1380 -44 1188 -45 884 -46 820 -47 651 -48 586 -49 512 -50 492 -51 419 -52 388 -53 423 -54 362 -55 324 -56 329 -57 248 -58 269 -59 276 -60 263 -61 258 -62 208 -63 239 -64 238 -65 225 -66 186 -67 172 -68 134 -69 173 -70 149 -71 135 -72 141 -73 131 -74 124 -75 146 -76 119 -77 135 -78 111 -79 135 -80 108 -81 112 -82 113 -83 122 -84 131 -85 131 -86 103 -87 99 -88 108 -89 125 -90 116 -91 142 -92 113 -93 128 -94 115 -95 106 -96 106 -97 119 -98 99 -99 103 -100 123 -101 114 -102 130 -103 122 -104 134 -105 149 -106 114 -107 123 -108 130 -109 121 -110 123 -111 129 -112 114 -113 109 -114 110 -115 116 -116 89 -117 117 -118 108 -119 94 -120 101 -121 116 -122 114 -123 84 -124 78 -125 91 -126 84 -127 88 -128 95 -129 76 -130 91 -131 76 -132 73 -133 82 -134 71 -135 60 -136 78 -137 67 -138 62 -139 50 -140 41 -141 32 -142 47 -143 36 -144 33 -145 32 -146 31 -147 34 -148 25 -149 32 -150 24 -151 26 -152 37 -153 33 -154 23 -155 37 -156 47 -157 33 -158 25 -159 37 -160 20 -161 42 -162 30 -163 39 -164 28 -165 24 -166 20 -167 24 -168 22 -169 28 -170 14 -171 19 -172 26 -173 22 -174 26 -175 23 -176 24 -177 23 -178 24 -179 14 -180 19 -181 23 -182 28 -183 12 -184 23 -185 14 -186 16 -187 12 -188 17 -189 17 -190 10 -191 8 -192 19 -193 10 -194 13 -195 8 -196 8 -197 10 -198 11 -199 10 -200 10 -201 10 -202 12 -203 14 -204 8 -205 9 -206 17 -207 14 -208 5 -209 6 -210 7 -211 3 -212 7 -213 6 -214 5 -215 6 -216 6 -217 2 -218 2 -219 3 -220 3 -221 3 -222 7 -223 2 -224 1 -225 3 -226 4 -227 3 -228 3 -229 8 -230 3 -231 4 -232 3 -233 2 -234 8 -235 4 -236 4 -237 6 -238 7 -239 4 -240 5 -241 3 -242 5 -243 3 -244 4 -245 7 -246 2 -247 3 -248 7 -249 16 -250 10 -251 6 -252 10 -253 9 -254 18 -255 6 -256 12 -257 13 -258 8 -259 16 -260 19 -261 16 -262 14 -263 14 -264 9 -265 16 -266 11 -267 17 -268 14 -269 16 -270 16 -271 15 -272 14 -273 20 -274 13 -275 12 -276 14 -277 13 -278 15 -279 17 -280 14 -281 16 -282 4 -283 12 -284 12 -285 23 -286 17 -287 15 -288 11 -289 19 -290 21 -291 15 -292 22 -293 15 -294 14 -295 15 -296 17 -297 22 -298 12 -299 18 -300 15 -301 12 -302 20 -303 3 -304 6 -305 11 -306 7 -307 9 -308 6 -309 6 -310 5 -311 7 -312 8 -313 6 -314 11 -315 8 -316 8 -317 4 -318 4 -319 9 -320 8 -321 5 -322 5 -323 6 -324 7 -325 7 -326 6 -327 4 -328 5 -329 5 -330 4 -331 6 -332 5 -333 5 -334 4 -335 6 -336 4 -337 4 -338 3 -339 4 -340 4 -341 2 -342 1 -343 9 -344 4 -345 2 -346 7 -347 1 -348 1 -349 1 -350 2 -351 3 -352 6 -353 4 -354 4 -355 1 -356 1 -357 4 -358 2 -359 1 -360 1 -361 3 -362 3 -363 1 -365 3 -366 1 -368 1 -370 2 -371 1 -372 1 -380 1 -383 2 -388 2 -389 1 -393 2 -397 1 -399 1 -425 1 -442 1 -465 1 -466 1 -469 1 -472 1 -483 1 -485 1 -497 1 -603 1 -674 1 -680 1 -682 1 -688 1 -701 1 -710 1 -724 1 -727 1 -738 1 -739 1 -740 1 -752 1 -758 3 -760 2 -763 1 -775 1 -776 1 -779 1 -780 1 -781 2 -793 1 -814 1 -895 1 -932 1 -958 1 -998 1 -1008 1 -1010 1 -1056 1 -1095 1 -1103 1 -1127 1 -1198 1 -1228 1 -1266 1 -1295 1 -1304 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index ca249b2..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.339e-03 1.349e-03 -4.701 3.57e-06 *** -r 2.085e-02 5.493e-05 379.621 < 2e-16 *** -kmercov 9.961e+00 9.348e-03 1065.530 < 2e-16 *** -bias 9.650e-01 9.509e-03 101.483 < 2e-16 *** -length 4.490e+06 4.098e+03 1095.724 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 462.8 on 401 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 5.305e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1d2277d..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9270257..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 357d422..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 181746373.154229 -round 1 trimming to 7 trying 4peak model... converged. score: 107161766.798881 -round 2 trimming to 12 trying 4peak model... converged. score: 371295263.552571 -round 3 trimming to 17 trying 4peak model... converged. score: 2442028254.69416 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c36b737..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.07428% 2.09626% -Genome Haploid Length 4,554,258 bp 4,571,386 bp -Genome Repeat Length 47,733 bp 47,912 bp -Genome Unique Length 4,506,525 bp 4,523,474 bp -Model Fit 98.8706% 99.236% -Read Error Rate 0.104551% 0.104551% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index f08b335..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,338 +0,0 @@ -1 16810568 -2 491358 -3 180979 -4 244878 -5 306547 -6 356999 -7 389164 -8 401523 -9 397804 -10 387972 -11 369119 -12 347928 -13 328807 -14 307557 -15 284034 -16 260144 -17 235081 -18 210227 -19 184416 -20 158599 -21 134896 -22 111421 -23 90777 -24 72193 -25 56296 -26 44194 -27 33248 -28 24992 -29 18648 -30 13756 -31 10200 -32 7264 -33 5260 -34 3730 -35 2565 -36 2062 -37 1567 -38 1234 -39 1034 -40 825 -41 632 -42 592 -43 519 -44 486 -45 444 -46 442 -47 401 -48 336 -49 310 -50 297 -51 285 -52 199 -53 190 -54 189 -55 212 -56 186 -57 190 -58 187 -59 158 -60 169 -61 186 -62 159 -63 172 -64 155 -65 126 -66 147 -67 137 -68 155 -69 173 -70 160 -71 159 -72 184 -73 147 -74 132 -75 151 -76 169 -77 162 -78 139 -79 119 -80 110 -81 152 -82 130 -83 144 -84 132 -85 133 -86 161 -87 148 -88 150 -89 131 -90 174 -91 165 -92 132 -93 150 -94 155 -95 144 -96 120 -97 111 -98 108 -99 137 -100 91 -101 115 -102 95 -103 86 -104 61 -105 81 -106 99 -107 96 -108 86 -109 78 -110 75 -111 95 -112 74 -113 70 -114 69 -115 67 -116 76 -117 63 -118 67 -119 55 -120 54 -121 52 -122 41 -123 41 -124 48 -125 35 -126 38 -127 47 -128 27 -129 35 -130 41 -131 32 -132 43 -133 36 -134 30 -135 42 -136 40 -137 41 -138 26 -139 25 -140 25 -141 32 -142 38 -143 29 -144 27 -145 27 -146 15 -147 24 -148 20 -149 13 -150 22 -151 20 -152 19 -153 23 -154 20 -155 22 -156 18 -157 8 -158 14 -159 21 -160 16 -161 16 -162 11 -163 15 -164 3 -165 7 -166 13 -167 8 -168 5 -169 8 -170 8 -171 9 -172 7 -173 5 -174 2 -175 1 -177 1 -178 1 -179 4 -180 2 -182 3 -183 2 -184 1 -186 5 -187 2 -188 1 -189 4 -190 6 -191 7 -192 7 -193 8 -194 5 -195 4 -196 8 -197 12 -198 8 -199 6 -200 5 -201 7 -202 15 -203 17 -204 6 -205 8 -206 10 -207 6 -208 15 -209 12 -210 17 -211 16 -212 17 -213 6 -214 17 -215 15 -216 11 -217 22 -218 12 -219 14 -220 26 -221 29 -222 19 -223 25 -224 20 -225 20 -226 23 -227 15 -228 16 -229 20 -230 20 -231 24 -232 17 -233 20 -234 16 -235 13 -236 21 -237 19 -238 19 -239 20 -240 19 -241 25 -242 11 -243 22 -244 16 -245 21 -246 18 -247 14 -248 10 -249 21 -250 11 -251 14 -252 10 -253 15 -254 9 -255 13 -256 17 -257 7 -258 16 -259 12 -260 15 -261 13 -262 11 -263 10 -264 21 -265 13 -266 6 -267 11 -268 7 -269 5 -270 7 -271 10 -272 5 -273 7 -274 7 -275 3 -276 4 -277 2 -278 4 -279 2 -280 2 -281 1 -283 1 -284 3 -285 1 -286 3 -287 2 -297 1 -308 1 -311 1 -312 1 -315 1 -322 1 -323 1 -334 1 -342 1 -353 1 -368 1 -400 1 -418 1 -437 1 -520 1 -531 1 -534 2 -550 1 -552 1 -563 1 -571 1 -618 1 -621 1 -629 1 -631 1 -634 1 -635 1 -640 1 -642 1 -644 1 -645 1 -648 1 -651 1 -654 1 -655 1 -656 1 -660 1 -671 1 -674 1 -676 1 -720 1 -723 1 -726 1 -730 1 -758 1 -786 1 -891 1 -895 1 -932 1 -956 1 -957 1 -975 1 -981 1 -1000 1 -1024 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 4c64bd1..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.182e-02 3.011e-03 -3.927 0.000105 *** -r 2.044e-02 1.407e-04 145.322 < 2e-16 *** -kmercov 8.187e+00 1.947e-02 420.587 < 2e-16 *** -bias 9.022e-01 1.147e-02 78.643 < 2e-16 *** -length 4.546e+06 7.051e+03 644.686 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 1019 on 330 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 4.753e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4512cbd..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index fe7cf0c..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f83b479..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 252942670.803957 -round 1 trimming to 8 trying 4peak model... converged. score: 469121491.735223 -round 2 trimming to 13 trying 4peak model... converged. score: 3858885294.8179 -round 3 trimming to 18 trying 4peak model... converged. score: 53142321435.2771 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 83f3bce..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.01595% 2.07221% -Genome Haploid Length 4,579,161 bp 4,622,919 bp -Genome Repeat Length 8,120 bp 8,197 bp -Genome Unique Length 4,571,041 bp 4,614,721 bp -Model Fit 98.5843% 98.9164% -Read Error Rate 0.993997% 0.993997% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 1d200dc..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,299 +0,0 @@ -1 29937114 -2 1178651 -3 325614 -4 380994 -5 441985 -6 475657 -7 482449 -8 471029 -9 447027 -10 417119 -11 383977 -12 348456 -13 314477 -14 276907 -15 238594 -16 200179 -17 164033 -18 132507 -19 103061 -20 78473 -21 58775 -22 42736 -23 31297 -24 21857 -25 15201 -26 10635 -27 7250 -28 5021 -29 3530 -30 2516 -31 1744 -32 1278 -33 1041 -34 775 -35 626 -36 526 -37 515 -38 435 -39 382 -40 376 -41 301 -42 338 -43 287 -44 272 -45 262 -46 230 -47 220 -48 193 -49 185 -50 185 -51 176 -52 166 -53 183 -54 190 -55 180 -56 193 -57 185 -58 193 -59 170 -60 139 -61 177 -62 176 -63 151 -64 168 -65 173 -66 151 -67 164 -68 178 -69 168 -70 168 -71 162 -72 186 -73 180 -74 161 -75 163 -76 173 -77 182 -78 150 -79 163 -80 163 -81 167 -82 136 -83 165 -84 170 -85 155 -86 126 -87 113 -88 119 -89 110 -90 91 -91 94 -92 78 -93 78 -94 62 -95 69 -96 67 -97 63 -98 41 -99 49 -100 57 -101 43 -102 46 -103 45 -104 40 -105 37 -106 45 -107 35 -108 37 -109 45 -110 36 -111 41 -112 45 -113 39 -114 35 -115 30 -116 40 -117 36 -118 39 -119 32 -120 22 -121 28 -122 36 -123 37 -124 28 -125 33 -126 33 -127 33 -128 26 -129 25 -130 13 -131 22 -132 14 -133 21 -134 13 -135 14 -136 9 -137 9 -138 8 -139 8 -140 9 -141 11 -142 6 -143 4 -144 4 -145 5 -146 5 -147 5 -148 2 -149 4 -150 2 -151 5 -152 12 -153 9 -154 7 -155 8 -156 14 -157 11 -158 15 -159 10 -160 15 -161 5 -162 15 -163 15 -164 12 -165 19 -166 21 -167 15 -168 22 -169 22 -170 22 -171 8 -172 27 -173 24 -174 17 -175 28 -176 13 -177 24 -178 20 -179 23 -180 17 -181 32 -182 15 -183 24 -184 23 -185 25 -186 18 -187 28 -188 16 -189 21 -190 12 -191 19 -192 22 -193 29 -194 23 -195 19 -196 20 -197 21 -198 24 -199 20 -200 28 -201 24 -202 25 -203 15 -204 12 -205 16 -206 21 -207 17 -208 13 -209 11 -210 7 -211 9 -212 11 -213 6 -214 8 -215 6 -216 8 -217 5 -218 5 -219 2 -220 5 -221 5 -222 6 -223 3 -224 5 -225 3 -226 4 -227 1 -228 4 -229 4 -230 2 -231 1 -232 4 -233 4 -234 2 -235 2 -236 1 -237 2 -238 3 -239 2 -240 4 -241 1 -242 1 -243 1 -246 1 -248 2 -249 1 -251 1 -279 1 -282 1 -311 1 -314 1 -319 1 -324 1 -328 1 -330 1 -332 1 -333 1 -371 1 -396 1 -401 1 -402 1 -405 1 -406 1 -430 1 -433 1 -438 1 -470 1 -476 1 -482 1 -487 1 -488 1 -489 1 -497 1 -498 1 -502 1 -508 1 -524 1 -542 1 -551 1 -556 1 -565 1 -568 1 -580 1 -606 1 -614 1 -633 1 -634 1 -660 1 -666 1 -702 1 -761 1 -790 1 -824 1 -826 1 -862 1 -902 1 -928 1 -945 1 -961 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 18d6ae6..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.180e-02 7.182e-04 16.43 <2e-16 *** -r 3.243e-02 1.226e-03 26.45 <2e-16 *** -kmercov 6.892e+00 2.954e-02 233.25 <2e-16 *** -bias 4.093e-01 1.726e-02 23.71 <2e-16 *** -length 4.917e+06 4.894e+04 100.47 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 99.72 on 279 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 3.875e-07 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ac7f706..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6afe75e..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b06847b..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 196708038974.272 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e1d632c..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.99756% 3.48802% -Genome Haploid Length 4,394,856 bp 4,470,874 bp -Genome Repeat Length -437,453 bp -445,020 bp -Genome Unique Length 4,832,310 bp 4,915,894 bp -Model Fit 78.8965% 79.0427% -Read Error Rate 1.97888% 1.97888% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 17376df..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,422 +0,0 @@ -1 1967367 -2 109610 -3 142624 -4 185399 -5 224760 -6 253623 -7 275202 -8 293220 -9 297141 -10 304366 -11 303188 -12 299340 -13 288029 -14 276281 -15 265925 -16 252689 -17 240862 -18 223694 -19 207140 -20 192251 -21 176607 -22 161570 -23 143936 -24 130974 -25 114738 -26 102345 -27 87836 -28 76881 -29 66782 -30 57136 -31 48770 -32 40530 -33 33601 -34 27759 -35 22530 -36 18662 -37 15316 -38 12458 -39 9710 -40 7616 -41 6221 -42 4805 -43 3985 -44 3005 -45 2725 -46 2153 -47 1672 -48 1283 -49 1027 -50 933 -51 705 -52 635 -53 566 -54 517 -55 364 -56 424 -57 351 -58 346 -59 306 -60 303 -61 252 -62 259 -63 207 -64 226 -65 148 -66 174 -67 175 -68 169 -69 179 -70 194 -71 168 -72 170 -73 138 -74 140 -75 152 -76 133 -77 118 -78 120 -79 135 -80 110 -81 103 -82 106 -83 100 -84 110 -85 133 -86 123 -87 130 -88 143 -89 141 -90 139 -91 138 -92 148 -93 141 -94 159 -95 133 -96 128 -97 116 -98 121 -99 117 -100 100 -101 107 -102 119 -103 108 -104 125 -105 102 -106 126 -107 108 -108 119 -109 91 -110 108 -111 105 -112 115 -113 138 -114 105 -115 103 -116 90 -117 95 -118 101 -119 83 -120 84 -121 112 -122 114 -123 81 -124 100 -125 89 -126 78 -127 77 -128 61 -129 65 -130 79 -131 54 -132 61 -133 55 -134 65 -135 61 -136 64 -137 60 -138 60 -139 56 -140 76 -141 48 -142 57 -143 37 -144 42 -145 39 -146 41 -147 40 -148 36 -149 40 -150 28 -151 33 -152 28 -153 39 -154 39 -155 30 -156 28 -157 29 -158 23 -159 32 -160 22 -161 36 -162 16 -163 15 -164 25 -165 21 -166 20 -167 10 -168 23 -169 22 -170 21 -171 27 -172 24 -173 19 -174 19 -175 27 -176 17 -177 15 -178 16 -179 22 -180 22 -181 19 -182 23 -183 15 -184 20 -185 8 -186 17 -187 20 -188 21 -189 18 -190 17 -191 21 -192 14 -193 18 -194 18 -195 19 -196 25 -197 21 -198 15 -199 11 -200 18 -201 25 -202 11 -203 13 -204 23 -205 13 -206 9 -207 13 -208 16 -209 12 -210 7 -211 12 -212 11 -213 12 -214 10 -215 18 -216 8 -217 4 -218 3 -219 7 -220 6 -221 4 -222 7 -223 7 -224 10 -225 4 -226 5 -227 6 -228 10 -229 7 -230 11 -231 9 -232 7 -233 18 -234 17 -235 9 -236 4 -237 8 -238 11 -239 10 -240 11 -241 6 -242 13 -243 12 -244 16 -245 13 -246 11 -247 18 -248 8 -249 9 -250 14 -251 5 -252 6 -253 7 -254 15 -255 9 -256 7 -257 11 -258 14 -259 12 -260 16 -261 22 -262 14 -263 13 -264 10 -265 14 -266 16 -267 16 -268 14 -269 18 -270 8 -271 20 -272 16 -273 13 -274 8 -275 12 -276 10 -277 11 -278 12 -279 13 -280 10 -281 11 -282 6 -283 11 -284 9 -285 9 -286 9 -287 7 -288 9 -289 7 -290 13 -291 3 -292 6 -293 10 -294 4 -295 6 -296 4 -297 1 -298 5 -299 5 -300 4 -301 3 -302 4 -303 5 -304 14 -305 2 -306 7 -307 6 -308 3 -309 3 -310 3 -311 8 -312 6 -313 3 -314 5 -315 10 -316 7 -317 10 -318 4 -319 7 -320 7 -321 4 -322 11 -323 8 -324 2 -325 4 -326 5 -327 8 -328 7 -329 4 -330 5 -331 8 -332 3 -333 2 -334 4 -335 3 -336 2 -337 6 -338 4 -339 6 -340 2 -341 4 -342 4 -343 3 -344 3 -345 3 -346 1 -347 4 -348 2 -349 3 -350 5 -351 2 -352 3 -353 2 -354 2 -355 5 -356 4 -357 3 -358 1 -360 4 -361 1 -362 1 -363 6 -364 3 -365 1 -366 1 -367 1 -369 1 -370 2 -371 3 -373 1 -374 2 -376 2 -378 1 -391 1 -457 1 -462 1 -467 1 -470 1 -472 1 -476 1 -485 1 -492 1 -519 1 -613 1 -614 1 -620 1 -635 2 -642 1 -647 1 -657 1 -681 1 -706 1 -716 1 -722 1 -725 1 -727 1 -732 1 -733 1 -736 1 -739 1 -743 1 -747 1 -752 2 -764 1 -787 1 -808 1 -824 1 -838 1 -851 2 -856 1 -897 1 -904 1 -919 1 -1068 1 -1072 1 -1130 1 -1161 1 -1162 1 -1167 1 -1219 1 -1244 1 -1248 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index cfb3c68..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.533e-03 2.573e-03 -0.596 0.552 -r 1.910e-02 1.310e-04 145.826 <2e-16 *** -kmercov 9.877e+00 2.028e-02 487.136 <2e-16 *** -bias 1.869e+00 3.376e-02 55.368 <2e-16 *** -length 4.523e+06 1.293e+04 349.827 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 495.6 on 402 degrees of freedom - -Number of iterations to convergence: 16 -Achieved convergence tolerance: 4.431e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d584812..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4273756..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c0ba0df..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 224313642.374299 -round 1 trimming to 7 trying 4peak model... converged. score: 101558763.109122 -round 2 trimming to 12 trying 4peak model... converged. score: 422585240.665206 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b734ed0..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.88413% 1.93653% -Genome Haploid Length 4,580,637 bp 4,618,405 bp -Genome Repeat Length 70,046 bp 70,624 bp -Genome Unique Length 4,510,590 bp 4,547,781 bp -Model Fit 98.9163% 99.2048% -Read Error Rate 0.10668% 0.10668% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index fb27208..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,355 +0,0 @@ -1 16796930 -2 570606 -3 227051 -4 267481 -5 310033 -6 337870 -7 357320 -8 361501 -9 363184 -10 355212 -11 340178 -12 323274 -13 303278 -14 285194 -15 261944 -16 239827 -17 217441 -18 193889 -19 171009 -20 151844 -21 131970 -22 114217 -23 97064 -24 81748 -25 68426 -26 57112 -27 45751 -28 37445 -29 29788 -30 23414 -31 18415 -32 14596 -33 11229 -34 8684 -35 6678 -36 5120 -37 3989 -38 2894 -39 2183 -40 1772 -41 1385 -42 1091 -43 900 -44 748 -45 625 -46 531 -47 455 -48 346 -49 313 -50 281 -51 280 -52 288 -53 251 -54 252 -55 262 -56 182 -57 215 -58 217 -59 192 -60 193 -61 174 -62 189 -63 178 -64 152 -65 180 -66 128 -67 111 -68 125 -69 118 -70 132 -71 123 -72 126 -73 119 -74 137 -75 146 -76 143 -77 109 -78 113 -79 130 -80 129 -81 132 -82 129 -83 134 -84 121 -85 128 -86 136 -87 128 -88 168 -89 140 -90 131 -91 135 -92 136 -93 121 -94 138 -95 125 -96 139 -97 123 -98 120 -99 115 -100 123 -101 115 -102 107 -103 111 -104 123 -105 108 -106 93 -107 117 -108 81 -109 66 -110 87 -111 84 -112 75 -113 81 -114 71 -115 73 -116 62 -117 73 -118 59 -119 65 -120 60 -121 44 -122 51 -123 57 -124 57 -125 61 -126 48 -127 45 -128 38 -129 41 -130 35 -131 33 -132 32 -133 32 -134 28 -135 53 -136 34 -137 32 -138 33 -139 30 -140 24 -141 37 -142 34 -143 30 -144 32 -145 27 -146 33 -147 34 -148 35 -149 22 -150 27 -151 27 -152 20 -153 26 -154 22 -155 17 -156 17 -157 28 -158 14 -159 18 -160 15 -161 24 -162 16 -163 17 -164 12 -165 15 -166 16 -167 10 -168 14 -169 10 -170 16 -171 14 -172 17 -173 13 -174 12 -175 5 -176 12 -177 9 -178 12 -179 7 -180 8 -181 7 -182 4 -183 6 -184 11 -185 5 -186 10 -187 13 -188 6 -189 12 -190 8 -191 10 -192 13 -193 6 -194 10 -195 17 -196 15 -197 10 -198 12 -199 13 -200 13 -201 12 -202 16 -203 10 -204 11 -205 9 -206 19 -207 16 -208 13 -209 19 -210 13 -211 13 -212 16 -213 11 -214 15 -215 12 -216 14 -217 18 -218 21 -219 18 -220 22 -221 19 -222 24 -223 22 -224 22 -225 16 -226 16 -227 15 -228 21 -229 21 -230 19 -231 23 -232 25 -233 16 -234 19 -235 15 -236 25 -237 23 -238 16 -239 13 -240 11 -241 15 -242 10 -243 11 -244 22 -245 21 -246 12 -247 15 -248 19 -249 12 -250 17 -251 6 -252 14 -253 8 -254 9 -255 10 -256 5 -257 5 -258 12 -259 7 -260 7 -261 5 -262 1 -263 2 -264 9 -265 4 -266 9 -267 5 -269 1 -270 6 -271 4 -272 5 -273 6 -274 7 -275 2 -276 4 -277 2 -278 6 -279 1 -280 5 -281 3 -282 3 -283 5 -284 5 -285 4 -286 4 -287 1 -288 2 -289 2 -290 1 -291 4 -292 4 -293 1 -294 4 -295 3 -297 5 -298 2 -299 3 -300 4 -301 2 -302 3 -303 1 -304 2 -314 1 -318 1 -326 1 -329 1 -337 1 -338 1 -372 1 -382 1 -384 1 -396 2 -397 1 -399 1 -425 1 -438 1 -520 1 -551 1 -555 1 -559 1 -565 1 -568 1 -575 1 -583 1 -593 1 -602 1 -612 1 -616 1 -624 1 -626 2 -627 1 -631 1 -635 2 -636 1 -646 1 -655 1 -661 1 -663 2 -665 1 -674 1 -743 1 -761 1 -765 1 -776 1 -783 1 -802 1 -904 1 -921 1 -966 1 -989 1 -1025 1 -1028 1 -1039 1 -1043 1 -1057 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index d948568..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -7.032e-03 3.218e-03 -2.185 0.0296 * -r 1.767e-02 1.922e-04 91.911 <2e-16 *** -kmercov 7.994e+00 2.580e-02 309.897 <2e-16 *** -bias 1.776e+00 1.643e-02 108.085 <2e-16 *** -length 4.661e+06 1.101e+04 423.374 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 822.9 on 343 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 3.092e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ad220d1..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7ba6d7d..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 955d885..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 191550271.138404 -round 1 trimming to 8 trying 4peak model... converged. score: 424836208.035234 -round 2 trimming to 13 trying 4peak model... converged. score: 659521813.175654 -round 3 trimming to 18 trying 4peak model... converged. score: 54792896711.2222 -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f9f90f0..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.72848% 1.80538% -Genome Haploid Length 4,683,422 bp 4,744,266 bp -Genome Repeat Length 22,745 bp 23,041 bp -Genome Unique Length 4,660,677 bp 4,721,225 bp -Model Fit 98.72% 99.0028% -Read Error Rate 0.992417% 0.992417% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 8726fd9..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,298 +0,0 @@ -1 29885613 -2 1278586 -3 365921 -4 378971 -5 419273 -6 440050 -7 442825 -8 433279 -9 412653 -10 383957 -11 354612 -12 323465 -13 289404 -14 256363 -15 222967 -16 191625 -17 160860 -18 134031 -19 111176 -20 89278 -21 72192 -22 56641 -23 43901 -24 33667 -25 26094 -26 19610 -27 14263 -28 10592 -29 7738 -30 5724 -31 4008 -32 3020 -33 2247 -34 1587 -35 1225 -36 1027 -37 774 -38 643 -39 610 -40 474 -41 408 -42 353 -43 306 -44 255 -45 235 -46 192 -47 219 -48 187 -49 189 -50 203 -51 222 -52 222 -53 162 -54 212 -55 186 -56 188 -57 186 -58 165 -59 176 -60 165 -61 176 -62 144 -63 152 -64 159 -65 174 -66 157 -67 195 -68 177 -69 166 -70 175 -71 174 -72 151 -73 154 -74 149 -75 139 -76 184 -77 146 -78 144 -79 136 -80 140 -81 93 -82 121 -83 126 -84 119 -85 117 -86 108 -87 118 -88 111 -89 130 -90 108 -91 111 -92 111 -93 95 -94 99 -95 86 -96 95 -97 98 -98 70 -99 71 -100 80 -101 90 -102 70 -103 89 -104 64 -105 56 -106 64 -107 56 -108 67 -109 45 -110 46 -111 53 -112 44 -113 44 -114 43 -115 34 -116 44 -117 41 -118 30 -119 45 -120 36 -121 28 -122 19 -123 26 -124 30 -125 28 -126 22 -127 14 -128 16 -129 20 -130 14 -131 16 -132 22 -133 23 -134 12 -135 13 -136 24 -137 17 -138 11 -139 14 -140 18 -141 15 -142 21 -143 14 -144 14 -145 19 -146 21 -147 13 -148 17 -149 11 -150 10 -151 8 -152 14 -153 3 -154 9 -155 13 -156 19 -157 11 -158 24 -159 24 -160 13 -161 15 -162 15 -163 24 -164 11 -165 22 -166 27 -167 21 -168 18 -169 22 -170 14 -171 25 -172 18 -173 17 -174 23 -175 21 -176 20 -177 16 -178 27 -179 21 -180 23 -181 18 -182 17 -183 15 -184 20 -185 21 -186 19 -187 21 -188 27 -189 19 -190 27 -191 32 -192 22 -193 33 -194 19 -195 22 -196 18 -197 18 -198 20 -199 15 -200 20 -201 20 -202 28 -203 11 -204 14 -205 16 -206 17 -207 16 -208 17 -209 17 -210 7 -211 8 -212 8 -213 17 -214 6 -215 3 -216 7 -217 10 -218 7 -219 9 -220 4 -221 2 -222 2 -223 6 -224 3 -225 1 -226 3 -227 1 -228 2 -229 3 -230 3 -231 2 -232 5 -233 6 -234 4 -235 3 -236 3 -238 1 -239 2 -240 3 -241 1 -244 1 -245 1 -247 2 -248 2 -249 1 -251 1 -279 1 -286 1 -319 1 -326 1 -331 1 -332 1 -333 1 -335 1 -338 1 -351 1 -399 1 -437 1 -439 1 -453 1 -458 1 -459 1 -488 1 -489 1 -492 1 -497 1 -500 1 -504 2 -509 1 -515 1 -516 1 -517 1 -524 1 -526 1 -534 1 -537 1 -538 1 -539 1 -542 1 -544 1 -546 1 -550 1 -563 1 -624 1 -626 1 -639 1 -668 1 -680 1 -702 1 -707 1 -716 1 -741 1 -767 1 -779 1 -785 1 -826 1 -835 1 -838 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index f3e5eaa..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.278e-03 1.291e-03 7.188 6.06e-12 *** -r 3.220e-02 9.910e-04 32.493 < 2e-16 *** -kmercov 7.202e+00 4.721e-02 152.553 < 2e-16 *** -bias 8.745e-01 3.282e-02 26.644 < 2e-16 *** -length 4.433e+06 1.043e+04 425.074 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 115.3 on 278 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.202e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9fd9fcd..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6ae4d0d..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6097b99..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 53723261163.1238 -round 1 trimming to 20 trying 4peak model... unconverged -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c1af785..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 3.02187% 3.41827% -Genome Haploid Length 4,173,405 bp 4,284,287 bp -Genome Repeat Length -171,307 bp -175,858 bp -Genome Unique Length 4,344,712 bp 4,460,145 bp -Model Fit 87.7336% 87.929% -Read Error Rate 1.99363% 1.99363% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist deleted file mode 100644 index 9d9f73e..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist +++ /dev/null @@ -1,401 +0,0 @@ -1 1987474 -2 139380 -3 176890 -4 203426 -5 230154 -6 250179 -7 270068 -8 278003 -9 284542 -10 282744 -11 279231 -12 275984 -13 269781 -14 258884 -15 243994 -16 234470 -17 220081 -18 205232 -19 193220 -20 180592 -21 164583 -22 148683 -23 137896 -24 125484 -25 111380 -26 99932 -27 89070 -28 79219 -29 69851 -30 60740 -31 54722 -32 47454 -33 41246 -34 35046 -35 30003 -36 26384 -37 21272 -38 17993 -39 15067 -40 13170 -41 10898 -42 9048 -43 7610 -44 6252 -45 5173 -46 4021 -47 3382 -48 2835 -49 2289 -50 1861 -51 1543 -52 1227 -53 1079 -54 939 -55 822 -56 715 -57 610 -58 518 -59 435 -60 382 -61 327 -62 299 -63 264 -64 265 -65 248 -66 239 -67 190 -68 182 -69 215 -70 214 -71 164 -72 175 -73 162 -74 168 -75 147 -76 167 -77 189 -78 136 -79 169 -80 127 -81 150 -82 154 -83 136 -84 143 -85 165 -86 126 -87 139 -88 141 -89 120 -90 122 -91 126 -92 111 -93 121 -94 111 -95 113 -96 86 -97 123 -98 117 -99 103 -100 126 -101 117 -102 113 -103 103 -104 107 -105 90 -106 101 -107 103 -108 98 -109 100 -110 131 -111 106 -112 123 -113 92 -114 100 -115 102 -116 96 -117 91 -118 105 -119 95 -120 77 -121 88 -122 79 -123 86 -124 99 -125 80 -126 84 -127 70 -128 90 -129 77 -130 78 -131 86 -132 71 -133 73 -134 82 -135 64 -136 56 -137 62 -138 48 -139 58 -140 45 -141 53 -142 61 -143 59 -144 49 -145 51 -146 42 -147 53 -148 34 -149 38 -150 34 -151 40 -152 27 -153 38 -154 25 -155 31 -156 27 -157 23 -158 29 -159 29 -160 32 -161 28 -162 35 -163 25 -164 28 -165 30 -166 21 -167 19 -168 25 -169 21 -170 24 -171 22 -172 28 -173 17 -174 29 -175 22 -176 26 -177 32 -178 32 -179 21 -180 20 -181 28 -182 24 -183 23 -184 17 -185 16 -186 25 -187 35 -188 17 -189 20 -190 28 -191 17 -192 15 -193 15 -194 22 -195 14 -196 21 -197 17 -198 13 -199 13 -200 8 -201 5 -202 11 -203 3 -204 7 -205 6 -206 2 -207 7 -208 4 -209 9 -210 9 -211 7 -212 7 -213 1 -214 3 -215 4 -216 7 -217 7 -218 2 -220 3 -221 4 -222 3 -223 4 -224 4 -225 4 -226 2 -227 10 -228 10 -229 11 -230 7 -231 7 -232 10 -233 5 -234 7 -235 7 -236 10 -237 7 -238 8 -239 15 -240 11 -241 13 -242 11 -243 14 -244 15 -245 12 -246 14 -247 12 -248 9 -249 9 -250 16 -251 9 -252 8 -253 7 -254 16 -255 18 -256 15 -257 17 -258 13 -259 21 -260 19 -261 16 -262 11 -263 15 -264 24 -265 14 -266 16 -267 12 -268 17 -269 9 -270 11 -271 13 -272 18 -273 18 -274 15 -275 12 -276 16 -277 18 -278 15 -279 24 -280 24 -281 16 -282 17 -283 20 -284 13 -285 11 -286 14 -287 14 -288 14 -289 16 -290 9 -291 12 -292 18 -293 9 -294 7 -295 4 -296 7 -297 7 -298 11 -299 10 -300 8 -301 10 -302 8 -303 9 -304 12 -305 11 -306 9 -307 14 -308 11 -309 5 -310 9 -311 10 -312 6 -313 10 -314 8 -315 5 -316 5 -317 7 -318 8 -319 5 -320 5 -321 5 -322 5 -323 5 -324 4 -325 9 -326 4 -327 3 -328 4 -329 6 -330 3 -331 3 -332 2 -333 3 -335 2 -338 2 -339 3 -340 1 -341 2 -342 1 -343 2 -344 4 -346 1 -347 2 -348 3 -350 3 -351 2 -352 2 -353 1 -354 5 -355 1 -357 2 -358 1 -360 1 -362 1 -365 2 -366 1 -367 2 -368 3 -426 1 -429 1 -447 2 -455 1 -566 1 -576 1 -618 1 -638 1 -649 1 -670 1 -691 1 -697 1 -705 1 -726 1 -735 2 -736 1 -737 1 -750 1 -753 1 -755 2 -759 1 -761 1 -764 1 -766 1 -769 2 -786 1 -788 1 -819 1 -833 1 -871 1 -879 1 -882 1 -889 1 -907 1 -917 1 -1130 1 -1132 1 -1158 1 -1167 1 -1186 1 -1233 1 -1239 1 -1284 1 -1312 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0beafb4..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -9.205e-03 3.083e-03 -2.986 0.00301 ** -r 1.387e-02 2.132e-04 65.050 < 2e-16 *** -kmercov 9.341e+00 3.220e-02 290.124 < 2e-16 *** -bias 3.294e+00 2.455e-02 134.187 < 2e-16 *** -length 4.843e+06 1.419e+04 341.337 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 674.1 on 386 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 8.417e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8755225..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index f177abf..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c38ffde..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 2 trying 4peak model... converged. score: 169177778.233563 -round 1 trimming to 7 trying 4peak model... converged. score: 141720440.165503 -round 2 trimming to 12 trying 4peak model... converged. score: 335486016.037086 -round 3 trimming to 17 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 61ef813..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.34423% 1.42951% -Genome Haploid Length 4,838,307 bp 4,905,476 bp -Genome Repeat Length -12,936 bp -13,116 bp -Genome Unique Length 4,851,243 bp 4,918,592 bp -Model Fit 98.6197% 98.9031% -Read Error Rate 0.0986752% 0.0986752% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist deleted file mode 100644 index 7912931..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist +++ /dev/null @@ -1,362 +0,0 @@ -1 16801448 -2 613659 -3 249614 -4 272934 -5 302050 -6 322562 -7 333779 -8 339245 -9 335045 -10 327990 -11 316206 -12 299945 -13 284737 -14 264862 -15 244087 -16 224132 -17 205355 -18 185256 -19 166871 -20 147379 -21 130103 -22 114323 -23 100085 -24 85845 -25 73900 -26 63224 -27 53594 -28 45028 -29 37122 -30 30739 -31 25072 -32 20772 -33 16910 -34 13519 -35 10909 -36 8719 -37 6887 -38 5559 -39 4283 -40 3304 -41 2816 -42 2320 -43 1859 -44 1474 -45 1230 -46 922 -47 740 -48 589 -49 575 -50 489 -51 465 -52 416 -53 395 -54 379 -55 286 -56 264 -57 226 -58 224 -59 207 -60 184 -61 171 -62 174 -63 177 -64 171 -65 178 -66 153 -67 170 -68 170 -69 161 -70 170 -71 150 -72 168 -73 172 -74 177 -75 153 -76 140 -77 137 -78 144 -79 135 -80 136 -81 147 -82 132 -83 119 -84 129 -85 109 -86 108 -87 124 -88 89 -89 118 -90 105 -91 90 -92 104 -93 117 -94 130 -95 135 -96 118 -97 101 -98 134 -99 106 -100 94 -101 93 -102 112 -103 96 -104 99 -105 107 -106 107 -107 97 -108 96 -109 97 -110 79 -111 73 -112 72 -113 60 -114 96 -115 79 -116 79 -117 76 -118 63 -119 66 -120 61 -121 71 -122 60 -123 45 -124 54 -125 49 -126 58 -127 45 -128 43 -129 31 -130 40 -131 38 -132 36 -133 24 -134 44 -135 35 -136 31 -137 30 -138 19 -139 32 -140 32 -141 26 -142 27 -143 29 -144 26 -145 21 -146 24 -147 18 -148 23 -149 11 -150 19 -151 21 -152 15 -153 16 -154 11 -155 12 -156 16 -157 14 -158 8 -159 13 -160 6 -161 10 -162 7 -163 3 -164 4 -165 4 -166 5 -167 4 -168 3 -169 4 -170 2 -171 4 -172 3 -173 8 -174 5 -175 5 -176 6 -177 6 -178 9 -179 4 -180 4 -181 2 -182 8 -183 8 -184 4 -185 11 -186 1 -187 2 -188 5 -189 9 -190 5 -191 14 -192 6 -193 11 -194 6 -195 8 -196 2 -197 11 -198 10 -199 7 -200 8 -201 8 -202 5 -203 8 -204 12 -205 9 -206 13 -207 7 -208 7 -209 11 -210 20 -211 16 -212 12 -213 13 -214 21 -215 18 -216 16 -217 22 -218 19 -219 24 -220 23 -221 18 -222 24 -223 14 -224 14 -225 17 -226 15 -227 19 -228 17 -229 25 -230 11 -231 23 -232 20 -233 24 -234 15 -235 21 -236 17 -237 11 -238 20 -239 19 -240 13 -241 13 -242 12 -243 13 -244 14 -245 20 -246 13 -247 18 -248 15 -249 10 -250 14 -251 15 -252 20 -253 12 -254 8 -255 6 -256 19 -257 12 -258 6 -259 7 -260 15 -261 8 -262 11 -263 9 -264 9 -265 6 -266 8 -267 3 -268 5 -269 4 -270 7 -271 5 -272 5 -273 5 -274 4 -275 7 -276 4 -277 10 -278 4 -279 3 -280 7 -281 5 -282 5 -283 6 -284 3 -285 5 -286 9 -287 5 -288 5 -290 4 -292 2 -293 4 -294 3 -295 2 -296 3 -297 5 -298 3 -300 1 -301 1 -302 1 -303 1 -304 2 -307 2 -308 2 -310 2 -311 2 -312 1 -313 1 -315 1 -318 1 -324 1 -325 1 -326 1 -332 1 -333 1 -338 2 -344 1 -362 1 -387 1 -395 1 -417 1 -422 1 -425 1 -432 1 -450 1 -486 1 -487 1 -500 2 -518 1 -526 1 -530 1 -534 1 -538 1 -540 1 -547 1 -550 1 -554 1 -556 3 -562 1 -563 1 -564 1 -570 1 -573 1 -585 1 -589 1 -618 1 -619 1 -623 1 -729 1 -748 1 -752 1 -761 1 -795 1 -801 1 -802 1 -848 1 -862 1 -868 1 -900 1 -929 1 -941 1 -973 1 -992 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 02288a2..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.785e-04 1.563e-03 0.626 0.532 -r 2.337e-02 4.991e-04 46.816 <2e-16 *** -kmercov 8.711e+00 4.284e-02 203.331 <2e-16 *** -bias 1.912e+00 4.064e-02 47.052 <2e-16 *** -length 4.248e+06 2.187e+04 194.225 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 122 on 342 degrees of freedom - -Number of iterations to convergence: 18 -Achieved convergence tolerance: 5.033e-06 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9ce6403..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6c5e7df..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index df04d37..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 269089095.817849 -round 1 trimming to 20 trying 4peak model... converged. score: 39482450862.7917 -round 2 trimming to 25 trying 4peak model... converged. score: 17700079227.2043 -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a55523e..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.23685% 2.4365% -Genome Haploid Length 4,268,183 bp 4,352,983 bp -Genome Repeat Length 64,603 bp 65,886 bp -Genome Unique Length 4,203,581 bp 4,287,097 bp -Model Fit 98.8122% 99.0623% -Read Error Rate 1.00957% 1.00957% diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist deleted file mode 100644 index 75826b6..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist +++ /dev/null @@ -1,295 +0,0 @@ -1 29800579 -2 1350107 -3 379273 -4 374606 -5 400039 -6 411142 -7 406593 -8 399443 -9 379902 -10 357895 -11 331646 -12 300505 -13 270536 -14 239972 -15 212852 -16 185787 -17 161314 -18 137298 -19 115503 -20 97218 -21 80148 -22 65157 -23 53282 -24 43043 -25 33704 -26 26622 -27 20529 -28 16075 -29 12624 -30 9779 -31 7613 -32 5581 -33 4124 -34 3207 -35 2484 -36 1910 -37 1454 -38 1152 -39 923 -40 704 -41 611 -42 541 -43 484 -44 463 -45 385 -46 344 -47 317 -48 293 -49 250 -50 226 -51 238 -52 234 -53 227 -54 214 -55 215 -56 215 -57 205 -58 203 -59 181 -60 168 -61 198 -62 212 -63 193 -64 208 -65 200 -66 183 -67 194 -68 165 -69 164 -70 180 -71 165 -72 143 -73 153 -74 143 -75 117 -76 116 -77 138 -78 133 -79 133 -80 136 -81 137 -82 129 -83 148 -84 112 -85 123 -86 119 -87 102 -88 134 -89 102 -90 95 -91 96 -92 75 -93 87 -94 85 -95 74 -96 85 -97 74 -98 74 -99 71 -100 66 -101 60 -102 67 -103 54 -104 45 -105 38 -106 43 -107 47 -108 32 -109 37 -110 42 -111 39 -112 52 -113 31 -114 48 -115 27 -116 25 -117 33 -118 33 -119 31 -120 32 -121 24 -122 18 -123 23 -124 25 -125 17 -126 13 -127 12 -128 10 -129 12 -130 10 -131 16 -132 8 -133 5 -134 12 -135 9 -136 12 -137 11 -138 12 -139 9 -140 11 -141 12 -142 12 -143 7 -144 14 -145 23 -146 13 -147 7 -148 18 -149 11 -150 11 -151 11 -152 12 -153 11 -154 20 -155 14 -156 14 -157 10 -158 14 -159 8 -160 13 -161 6 -162 15 -163 10 -164 15 -165 8 -166 9 -167 12 -168 7 -169 17 -170 18 -171 11 -172 16 -173 17 -174 11 -175 14 -176 14 -177 16 -178 20 -179 13 -180 22 -181 22 -182 18 -183 31 -184 19 -185 25 -186 20 -187 27 -188 21 -189 24 -190 28 -191 20 -192 27 -193 17 -194 23 -195 20 -196 18 -197 20 -198 16 -199 18 -200 20 -201 19 -202 24 -203 29 -204 19 -205 15 -206 26 -207 10 -208 10 -209 9 -210 14 -211 10 -212 6 -213 13 -214 9 -215 7 -216 14 -217 10 -218 12 -219 6 -220 2 -221 8 -222 6 -223 7 -224 7 -225 1 -226 2 -227 3 -228 5 -229 3 -230 1 -232 2 -233 1 -235 2 -236 1 -238 1 -240 1 -244 1 -249 1 -253 1 -255 1 -256 1 -258 1 -259 1 -265 1 -272 1 -276 1 -279 1 -283 1 -291 1 -323 1 -331 1 -346 1 -349 1 -351 1 -352 1 -355 1 -389 1 -405 1 -407 2 -411 1 -414 1 -451 2 -454 1 -455 1 -462 1 -463 1 -465 1 -468 1 -469 1 -470 1 -478 1 -480 1 -490 1 -491 1 -492 1 -520 1 -536 1 -539 2 -567 1 -585 1 -626 1 -629 1 -649 1 -657 1 -663 1 -670 1 -738 1 -750 1 -775 1 -783 1 -822 1 -883 1 -896 1 -909 1 -913 1 diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index dfdc882..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.217e-02 1.522e-03 7.994 3.64e-14 *** -r 2.676e-02 1.040e-03 25.728 < 2e-16 *** -kmercov 7.336e+00 5.965e-02 122.980 < 2e-16 *** -bias 1.234e+00 4.260e-02 28.961 < 2e-16 *** -length 4.046e+06 2.037e+04 198.645 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 104.5 on 275 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.301e-07 - diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 35adbc6..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index ae4b00e..0000000 Binary files a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2da4094..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 15 trying 4peak model... converged. score: 959881195.771882 -round 1 trimming to 20 trying 4peak model... converged. score: 640519278191.865 -round 2 trimming to 25 trying 4peak model... unconverged -round 3 trimming to 30 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6568e25..0000000 --- a/analysis/simulation_results_25x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov25_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.46774% 2.88374% -Genome Haploid Length 4,060,156 bp 4,194,398 bp -Genome Repeat Length 118,319 bp 122,231 bp -Genome Unique Length 3,941,837 bp 4,072,167 bp -Model Fit 98.2518% 98.4829% -Read Error Rate 2.02218% 2.02218% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist 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dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.661e-02 4.318e-04 61.63 <2e-16 *** -r 1.153e-03 8.560e-06 134.70 <2e-16 *** -kmercov 1.966e+01 2.551e-03 7708.02 <2e-16 *** -bias 9.810e-01 2.369e-03 414.19 <2e-16 *** -length 1.074e+08 6.075e+04 1767.33 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6820 on 591 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 7.301e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3e0c411..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index efcff7c..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2c054b6..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 27457006373.6692 -round 1 trimming to 10 trying 4peak model... converged. score: 27457085777.7051 -round 2 trimming to 15 trying 4peak model... converged. score: 27875827853.0472 -round 3 trimming to 20 trying 4peak model... converged. score: 45270644210.1247 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index dbb905a..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.113592% 0.117016% -Genome Haploid Length 116,242,163 bp 116,302,502 bp -Genome Repeat Length 11,761,661 bp 11,767,766 bp -Genome Unique Length 104,480,502 bp 104,534,735 bp -Model Fit 97.9357% 99.0852% -Read Error Rate 0.101315% 0.101315% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 9e89c4e..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index f8fe8aa..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.692e-02 3.707e-04 72.62 <2e-16 *** -r 1.201e-03 8.971e-06 133.90 <2e-16 *** -kmercov 1.627e+01 1.936e-03 8405.04 <2e-16 *** -bias 8.056e-01 1.959e-03 411.31 <2e-16 *** -length 1.074e+08 5.071e+04 2118.45 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6192 on 583 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 4.781e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dcea30b..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8bb7f9f..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fea10ca..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 22964217210.2027 -round 1 trimming to 13 trying 4peak model... converged. score: 22726342247.2541 -round 2 trimming to 18 trying 4peak model... converged. score: 45379427368.5794 -round 3 trimming to 23 trying 4peak model... converged. score: 506253480993.983 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index da8e79b..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.118325% 0.121913% -Genome Haploid Length 116,866,865 bp 116,922,496 bp -Genome Repeat Length 12,364,385 bp 12,370,271 bp -Genome Unique Length 104,502,480 bp 104,552,225 bp -Model Fit 98.1625% 99.344% -Read Error Rate 1.00249% 1.00249% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 6685eed..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1342104362 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-518 174 -519 205 -520 161 -521 181 -522 198 -523 157 -524 212 -525 211 -526 183 -527 174 -528 167 -529 197 -530 194 -531 169 -532 169 -533 165 -534 167 -535 157 -536 189 -537 152 -538 168 -539 167 -540 178 -541 162 -542 193 -543 155 -544 136 -545 175 -546 159 -547 186 -548 137 -549 161 -550 148 -551 136 -552 161 -553 164 -554 148 -555 162 -556 169 -557 175 -558 132 -559 145 -560 145 -561 155 -562 140 -563 157 -564 138 -565 131 -566 154 -567 163 -568 142 -569 145 -570 140 -571 156 -572 128 -573 140 -574 137 -575 145 -576 157 -577 142 -578 154 -579 149 -580 159 -581 154 -582 129 -583 151 -584 120 -585 146 -586 112 -587 137 -588 151 -589 146 -590 129 -591 123 -592 156 -593 134 -594 142 -595 134 -596 146 -597 137 -598 137 -599 156 -600 129 -601 42935 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1eae9ff..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.792e-02 3.365e-04 82.97 <2e-16 *** -r 1.352e-03 1.288e-05 104.92 <2e-16 *** -kmercov 1.316e+01 1.614e-03 8157.65 <2e-16 *** -bias 6.465e-01 1.865e-03 346.56 <2e-16 *** -length 1.076e+08 4.388e+04 2453.11 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5880 on 583 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 6.928e-07 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7e758ed..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index b7c46f5..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 31426c5..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 24217567482.4418 -round 1 trimming to 13 trying 4peak model... converged. score: 20847516741.1483 -round 2 trimming to 18 trying 4peak model... converged. score: 152010927235.933 -round 3 trimming to 23 trying 4peak model... converged. score: 2903212779333.1 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e3b008b..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.132582% 0.137735% -Genome Haploid Length 117,730,106 bp 117,787,848 bp -Genome Repeat Length 13,108,920 bp 13,115,349 bp -Genome Unique Length 104,621,186 bp 104,672,498 bp -Model Fit 98.3452% 99.5675% -Read Error Rate 1.98922% 1.98922% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index e98e364..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95662522 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a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index bdfdd8d..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.277e-02 6.991e-04 32.57 <2e-16 *** -r 1.420e-03 1.560e-05 91.03 <2e-16 *** -kmercov 1.982e+01 5.082e-03 3900.05 <2e-16 *** -bias 1.942e+00 6.180e-03 314.24 <2e-16 *** -length 1.068e+08 8.364e+04 1276.53 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8981 on 592 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 7.847e-07 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cf2922a..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e467138..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bef7028..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 47428976007.299 -round 1 trimming to 9 trying 4peak model... converged. score: 47431517647.8824 -round 2 trimming to 14 trying 4peak model... converged. score: 49867661829.6786 -round 3 trimming to 19 trying 4peak model... converged. score: 102697994860.007 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b14e779..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.138884% 0.145124% -Genome Haploid Length 115,301,957 bp 115,420,274 bp -Genome Repeat Length 11,012,908 bp 11,024,208 bp -Genome Unique Length 104,289,049 bp 104,396,066 bp -Model Fit 97.4196% 98.5789% -Read Error Rate 0.1013% 0.1013% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 740f5da..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 776461215 -2 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-513 301 -514 285 -515 270 -516 274 -517 290 -518 290 -519 254 -520 259 -521 282 -522 283 -523 253 -524 258 -525 240 -526 247 -527 305 -528 238 -529 237 -530 289 -531 242 -532 219 -533 216 -534 241 -535 243 -536 243 -537 250 -538 227 -539 243 -540 218 -541 260 -542 250 -543 268 -544 243 -545 225 -546 235 -547 234 -548 233 -549 225 -550 221 -551 213 -552 224 -553 241 -554 200 -555 223 -556 244 -557 203 -558 213 -559 203 -560 207 -561 205 -562 239 -563 225 -564 205 -565 218 -566 221 -567 211 -568 189 -569 197 -570 217 -571 189 -572 204 -573 189 -574 197 -575 162 -576 205 -577 184 -578 209 -579 171 -580 216 -581 191 -582 196 -583 192 -584 217 -585 182 -586 187 -587 186 -588 177 -589 200 -590 183 -591 184 -592 172 -593 180 -594 196 -595 174 -596 194 -597 192 -598 183 -599 153 -600 178 -601 61817 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 27a636b..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.397e-02 5.748e-04 41.69 <2e-16 *** -r 1.547e-03 1.600e-05 96.68 <2e-16 *** -kmercov 1.641e+01 3.658e-03 4485.43 <2e-16 *** -bias 1.590e+00 4.778e-03 332.85 <2e-16 *** -length 1.068e+08 6.628e+04 1611.51 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7739 on 584 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.303e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 492ef41..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 417627e..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ee06c28..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 36968300732.8438 -round 1 trimming to 12 trying 4peak model... converged. score: 36705878854.1682 -round 2 trimming to 17 trying 4peak model... converged. score: 95900008941.481 -round 3 trimming to 22 trying 4peak model... converged. score: 992546261682.972 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 89b7da2..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.151488% 0.157888% -Genome Haploid Length 115,917,416 bp 116,020,834 bp -Genome Repeat Length 11,711,796 bp 11,722,245 bp -Genome Unique Length 104,205,620 bp 104,298,589 bp -Model Fit 97.7595% 98.9412% -Read Error Rate 1.00132% 1.00132% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 148c599..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1337588080 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192 -519 205 -520 187 -521 191 -522 184 -523 200 -524 173 -525 172 -526 173 -527 169 -528 189 -529 173 -530 173 -531 174 -532 169 -533 165 -534 195 -535 180 -536 174 -537 165 -538 188 -539 187 -540 189 -541 169 -542 184 -543 182 -544 186 -545 168 -546 145 -547 176 -548 175 -549 179 -550 164 -551 164 -552 164 -553 165 -554 133 -555 153 -556 139 -557 160 -558 138 -559 175 -560 152 -561 168 -562 169 -563 126 -564 145 -565 167 -566 165 -567 153 -568 158 -569 122 -570 139 -571 156 -572 158 -573 151 -574 140 -575 130 -576 140 -577 142 -578 145 -579 150 -580 130 -581 141 -582 114 -583 144 -584 144 -585 146 -586 145 -587 137 -588 150 -589 152 -590 133 -591 130 -592 124 -593 127 -594 124 -595 156 -596 125 -597 136 -598 115 -599 148 -600 129 -601 43254 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3a423c9..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.636e-02 5.494e-04 47.98 <2e-16 *** -r 1.849e-03 1.409e-05 131.26 <2e-16 *** -kmercov 1.329e+01 2.929e-03 4536.14 <2e-16 *** -bias 1.252e+00 3.977e-03 314.85 <2e-16 *** -length 1.070e+08 6.065e+04 1763.53 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7772 on 588 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 1.717e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d669ce1..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8e6ecf1..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e8136ef..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 8 trying 4peak model... converged. score: 27939878874.133 -round 1 trimming to 13 trying 4peak model... converged. score: 31781024424.6197 -round 2 trimming to 18 trying 4peak model... converged. score: 530819607177.367 -round 3 trimming to 23 trying 4peak model... converged. score: 12013456540287.2 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7ec866b..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.1821% 0.187735% -Genome Haploid Length 116,709,873 bp 116,812,834 bp -Genome Repeat Length 12,615,312 bp 12,626,441 bp -Genome Unique Length 104,094,562 bp 104,186,393 bp -Model Fit 98.1222% 99.3244% -Read Error Rate 1.98553% 1.98553% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 10f082e..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95734618 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354 -506 330 -507 341 -508 356 -509 384 -510 388 -511 341 -512 359 -513 353 -514 319 -515 329 -516 333 -517 328 -518 354 -519 346 -520 344 -521 345 -522 366 -523 344 -524 344 -525 341 -526 337 -527 370 -528 354 -529 361 -530 315 -531 328 -532 303 -533 336 -534 354 -535 327 -536 327 -537 341 -538 320 -539 315 -540 328 -541 310 -542 302 -543 306 -544 314 -545 317 -546 303 -547 284 -548 320 -549 323 -550 283 -551 300 -552 291 -553 320 -554 325 -555 296 -556 302 -557 282 -558 279 -559 312 -560 299 -561 332 -562 300 -563 262 -564 287 -565 283 -566 282 -567 280 -568 272 -569 253 -570 263 -571 280 -572 258 -573 267 -574 262 -575 286 -576 294 -577 257 -578 279 -579 264 -580 270 -581 283 -582 236 -583 263 -584 265 -585 240 -586 248 -587 242 -588 272 -589 227 -590 252 -591 203 -592 256 -593 255 -594 266 -595 223 -596 298 -597 261 -598 261 -599 250 -600 253 -601 85469 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0518254..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.862e-02 8.979e-04 20.74 <2e-16 *** -r 1.808e-03 2.145e-05 84.31 <2e-16 *** -kmercov 2.004e+01 7.316e-03 2739.66 <2e-16 *** -bias 2.874e+00 1.084e-02 265.07 <2e-16 *** -length 1.059e+08 8.982e+04 1179.36 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9179 on 592 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 8.36e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 474609b..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index dc2f805..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1154b5c..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 49458909592.907 -round 1 trimming to 9 trying 4peak model... converged. score: 49507631910.7758 -round 2 trimming to 14 trying 4peak model... converged. score: 57901263587.5879 -round 3 trimming to 19 trying 4peak model... converged. score: 148022009172.704 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b2d5f5e..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.176557% 0.185138% -Genome Haploid Length 113,968,991 bp 114,135,511 bp -Genome Repeat Length 10,082,705 bp 10,097,436 bp -Genome Unique Length 103,886,286 bp 104,038,074 bp -Model Fit 97.3326% 98.4477% -Read Error Rate 0.101433% 0.101433% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 47efcd5..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 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309 -511 289 -512 305 -513 299 -514 294 -515 267 -516 303 -517 267 -518 264 -519 278 -520 264 -521 278 -522 303 -523 280 -524 276 -525 294 -526 261 -527 281 -528 265 -529 254 -530 280 -531 260 -532 218 -533 273 -534 262 -535 254 -536 202 -537 239 -538 239 -539 245 -540 233 -541 221 -542 258 -543 240 -544 226 -545 261 -546 199 -547 220 -548 226 -549 217 -550 261 -551 199 -552 211 -553 258 -554 219 -555 230 -556 244 -557 225 -558 226 -559 210 -560 219 -561 209 -562 202 -563 221 -564 223 -565 199 -566 175 -567 191 -568 207 -569 172 -570 209 -571 185 -572 167 -573 200 -574 203 -575 199 -576 206 -577 202 -578 188 -579 200 -580 207 -581 203 -582 220 -583 206 -584 214 -585 190 -586 192 -587 172 -588 191 -589 195 -590 162 -591 190 -592 188 -593 172 -594 193 -595 171 -596 195 -597 166 -598 166 -599 184 -600 181 -601 61807 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6417676..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.106e-02 7.892e-04 26.69 <2e-16 *** -r 2.052e-03 1.968e-05 104.28 <2e-16 *** -kmercov 1.661e+01 5.477e-03 3033.04 <2e-16 *** -bias 2.329e+00 8.387e-03 277.66 <2e-16 *** -length 1.058e+08 7.661e+04 1381.56 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8495 on 589 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.497e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 95e4f59..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 55559af..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3434531..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 35503729009.0135 -round 1 trimming to 12 trying 4peak model... converged. score: 36497761848.9268 -round 2 trimming to 17 trying 4peak model... converged. score: 144710678705.975 -round 3 trimming to 22 trying 4peak model... converged. score: 1047802184934.89 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 6f9b9e5..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.201262% 0.209133% -Genome Haploid Length 114,500,119 bp 114,651,222 bp -Genome Repeat Length 10,953,685 bp 10,968,141 bp -Genome Unique Length 103,546,434 bp 103,683,082 bp -Model Fit 97.7895% 98.9762% -Read Error Rate 1.00039% 1.00039% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index a98c3a0..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1333970867 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 296a4c8..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.499e-02 5.776e-04 43.27 <2e-16 *** -r 2.526e-03 2.727e-05 92.60 <2e-16 *** -kmercov 1.346e+01 3.847e-03 3498.67 <2e-16 *** -bias 1.812e+00 6.338e-03 285.89 <2e-16 *** -length 1.059e+08 5.426e+04 1951.14 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6317 on 584 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.024e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 43c05e6..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index b0ac7f4..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 48144ee..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 31357752845.0414 -round 1 trimming to 12 trying 4peak model... converged. score: 27504710604.7111 -round 2 trimming to 17 trying 4peak model... converged. score: 375481700243.223 -round 3 trimming to 22 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b939daf..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.247111% 0.25802% -Genome Haploid Length 115,230,687 bp 115,362,504 bp -Genome Repeat Length 12,061,426 bp 12,075,224 bp -Genome Unique Length 103,169,261 bp 103,287,281 bp -Model Fit 98.1332% 99.3179% -Read Error Rate 1.98391% 1.98391% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 42646fe..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95682758 -2 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-510 369 -511 329 -512 302 -513 330 -514 340 -515 296 -516 328 -517 288 -518 312 -519 334 -520 291 -521 341 -522 303 -523 329 -524 301 -525 304 -526 296 -527 299 -528 278 -529 292 -530 281 -531 292 -532 291 -533 261 -534 307 -535 297 -536 266 -537 268 -538 284 -539 248 -540 284 -541 289 -542 270 -543 277 -544 271 -545 235 -546 274 -547 312 -548 271 -549 273 -550 308 -551 277 -552 267 -553 241 -554 271 -555 280 -556 266 -557 258 -558 269 -559 248 -560 267 -561 244 -562 273 -563 244 -564 251 -565 266 -566 260 -567 277 -568 234 -569 275 -570 257 -571 234 -572 227 -573 227 -574 256 -575 219 -576 243 -577 209 -578 247 -579 246 -580 236 -581 219 -582 225 -583 227 -584 217 -585 208 -586 210 -587 213 -588 209 -589 229 -590 238 -591 251 -592 199 -593 208 -594 215 -595 227 -596 208 -597 208 -598 237 -599 260 -600 213 -601 73664 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index f0142d4..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.595e-02 6.426e-04 40.38 <2e-16 *** -r 1.040e-02 1.322e-05 786.46 <2e-16 *** -kmercov 1.968e+01 4.546e-03 4329.66 <2e-16 *** -bias 9.965e-01 3.127e-03 318.71 <2e-16 *** -length 1.080e+08 6.519e+04 1657.18 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8237 on 587 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.805e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 0630665..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 79c69f0..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index cb23c80..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 39300755800.9425 -round 1 trimming to 9 trying 4peak model... converged. score: 39103275301.4913 -round 2 trimming to 14 trying 4peak model... converged. score: 39202138240.6595 -round 3 trimming to 19 trying 4peak model... converged. score: 54219062012.6152 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 08f2f01..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03696% 1.04225% -Genome Haploid Length 116,478,801 bp 116,586,461 bp -Genome Repeat Length 11,196,767 bp 11,207,116 bp -Genome Unique Length 105,282,034 bp 105,379,345 bp -Model Fit 98.0943% 99.0101% -Read Error Rate 0.101646% 0.101646% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 6b1a63c..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 786594957 -2 44361545 -3 3780035 -4 977316 -5 601614 -6 620472 -7 811799 -8 1104883 -9 1474317 -10 1883397 -11 2296109 -12 2670400 -13 2989305 -14 3228352 -15 3374426 -16 3444040 -17 3464073 -18 3440568 -19 3412246 -20 3398365 -21 3413689 -22 3469022 -23 3567807 -24 3711486 -25 3882661 -26 4054076 -27 4230746 -28 4379045 -29 4496400 -30 4560579 -31 4571086 -32 4516645 -33 4396854 -34 4222867 -35 4002809 -36 3735140 -37 3445322 -38 3133206 -39 2817850 -40 2499180 -41 2191726 -42 1900476 -43 1633249 -44 1389608 -45 1169323 -46 977653 -47 812223 -48 670112 -49 551749 -50 453418 -51 373767 -52 311870 -53 259446 -54 219062 -55 188028 -56 164800 -57 145612 -58 132353 -59 121465 -60 114026 -61 107227 -62 102161 -63 97842 -64 94002 -65 90529 -66 87213 -67 83999 -68 80774 -69 77872 -70 75079 -71 70827 -72 67489 -73 63664 -74 59909 -75 56443 -76 53712 -77 50343 -78 46822 -79 43948 -80 41018 -81 38052 -82 35895 -83 33584 -84 31833 -85 29681 -86 28100 -87 26567 -88 25317 -89 23982 -90 23092 -91 22135 -92 21198 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9cd2124..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.651e-02 6.637e-04 39.94 <2e-16 *** -r 1.036e-02 1.421e-05 728.93 <2e-16 *** -kmercov 1.627e+01 4.238e-03 3838.94 <2e-16 *** -bias 8.373e-01 3.298e-03 253.86 <2e-16 *** -length 1.083e+08 6.574e+04 1647.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8927 on 586 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 9.397e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a679375..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 705c9e5..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ada3012..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 55799493370.1995 -round 1 trimming to 10 trying 4peak model... converged. score: 46718734112.2084 -round 2 trimming to 15 trying 4peak model... converged. score: 59604305393.2986 -round 3 trimming to 20 trying 4peak model... converged. score: 247922184500.908 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ed927b8..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03319% 1.03887% -Genome Haploid Length 117,281,239 bp 117,403,504 bp -Genome Repeat Length 11,772,093 bp 11,784,366 bp -Genome Unique Length 105,509,146 bp 105,619,139 bp -Model Fit 98.1155% 99.0425% -Read Error Rate 0.996697% 0.996697% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index e0885d3..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1362349271 -2 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-520 188 -521 154 -522 169 -523 164 -524 162 -525 156 -526 178 -527 153 -528 151 -529 195 -530 153 -531 162 -532 148 -533 132 -534 130 -535 166 -536 164 -537 160 -538 152 -539 144 -540 150 -541 140 -542 129 -543 141 -544 157 -545 171 -546 148 -547 118 -548 153 -549 103 -550 132 -551 144 -552 141 -553 131 -554 136 -555 171 -556 133 -557 129 -558 133 -559 126 -560 129 -561 116 -562 163 -563 145 -564 126 -565 150 -566 129 -567 135 -568 135 -569 133 -570 116 -571 154 -572 132 -573 142 -574 121 -575 120 -576 145 -577 141 -578 136 -579 137 -580 117 -581 136 -582 149 -583 134 -584 115 -585 130 -586 112 -587 127 -588 120 -589 139 -590 114 -591 131 -592 135 -593 129 -594 130 -595 120 -596 109 -597 130 -598 117 -599 99 -600 121 -601 36858 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 918360d..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.778e-02 5.905e-04 47.05 <2e-16 *** -r 1.040e-02 1.368e-05 760.38 <2e-16 *** -kmercov 1.314e+01 3.361e-03 3909.28 <2e-16 *** -bias 6.814e-01 2.947e-03 231.19 <2e-16 *** -length 1.088e+08 5.653e+04 1924.95 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8268 on 586 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.028e-07 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d18b0a5..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1bce062..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 28f0a33..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 155284031026.936 -round 1 trimming to 10 trying 4peak model... converged. score: 40872840043.3504 -round 2 trimming to 15 trying 4peak model... converged. score: 120116639000.759 -round 3 trimming to 20 trying 4peak model... converged. score: 1585595593242.17 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 26b4996..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03736% 1.04283% -Genome Haploid Length 118,369,583 bp 118,490,761 bp -Genome Repeat Length 12,517,066 bp 12,529,880 bp -Genome Unique Length 105,852,517 bp 105,960,881 bp -Model Fit 98.2137% 99.193% -Read Error Rate 1.97858% 1.97858% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index a032052..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95667204 -2 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-508 290 -509 288 -510 340 -511 336 -512 317 -513 326 -514 302 -515 318 -516 285 -517 300 -518 320 -519 322 -520 316 -521 289 -522 300 -523 330 -524 291 -525 281 -526 335 -527 297 -528 265 -529 303 -530 282 -531 328 -532 320 -533 286 -534 306 -535 290 -536 309 -537 298 -538 310 -539 287 -540 309 -541 281 -542 281 -543 299 -544 273 -545 267 -546 304 -547 270 -548 281 -549 253 -550 263 -551 282 -552 278 -553 263 -554 281 -555 257 -556 260 -557 269 -558 263 -559 280 -560 247 -561 269 -562 254 -563 255 -564 279 -565 236 -566 256 -567 274 -568 272 -569 278 -570 242 -571 262 -572 284 -573 247 -574 252 -575 200 -576 253 -577 261 -578 236 -579 264 -580 243 -581 246 -582 247 -583 217 -584 223 -585 213 -586 197 -587 235 -588 206 -589 235 -590 221 -591 244 -592 241 -593 214 -594 196 -595 207 -596 212 -597 239 -598 226 -599 227 -600 210 -601 73182 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7c418b7..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.095e-02 1.167e-03 17.95 <2e-16 *** -r 1.059e-02 2.796e-05 378.78 <2e-16 *** -kmercov 1.982e+01 1.098e-02 1805.73 <2e-16 *** -bias 2.012e+00 1.040e-02 193.41 <2e-16 *** -length 1.076e+08 9.980e+04 1078.55 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11610 on 588 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 5.748e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 181c261..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4f6dade..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 7167759..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 80604751286.1218 -round 1 trimming to 8 trying 4peak model... converged. score: 77732468941.1027 -round 2 trimming to 13 trying 4peak model... converged. score: 78422203780.77 -round 3 trimming to 18 trying 4peak model... converged. score: 116159932675.044 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f103679..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05348% 1.06466% -Genome Haploid Length 115,561,654 bp 115,817,927 bp -Genome Repeat Length 10,203,201 bp 10,225,828 bp -Genome Unique Length 105,358,453 bp 105,592,099 bp -Model Fit 97.5826% 98.516% -Read Error Rate 0.102625% 0.102625% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 933b719..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 784899162 -2 45221343 -3 4016517 -4 1212121 -5 915001 -6 991121 -7 1197844 -8 1468148 -9 1768841 -10 2065517 -11 2349893 -12 2618710 -13 2839017 -14 3021348 -15 3171538 -16 3292208 -17 3377362 -18 3451117 -19 3518205 -20 3575775 -21 3636190 -22 3706038 -23 3777877 -24 3838809 -25 3913811 -26 3972526 -27 4016788 -28 4040540 -29 4044159 -30 4017204 -31 3962964 -32 3879533 -33 3762292 -34 3618731 -35 3450442 -36 3265015 -37 3062998 -38 2851272 -39 2632749 -40 2408266 -41 2183419 -42 1972977 -43 1766239 -44 1566387 -45 1383302 -46 1215880 -47 1060146 -48 923938 -49 799800 -50 690460 -51 593353 -52 509067 -53 437996 -54 377250 -55 323885 -56 280211 -57 243539 -58 212432 -59 187282 -60 165374 -61 148712 -62 133806 -63 121019 -64 112534 -65 103766 -66 95848 -67 89697 -68 83958 -69 79856 -70 75236 -71 71212 -72 66902 -73 63539 -74 59624 -75 57166 -76 54346 -77 51438 -78 48452 -79 46421 -80 43734 -81 40938 -82 38835 -83 37103 -84 34893 -85 32797 -86 31234 -87 30122 -88 28570 -89 27171 -90 25784 -91 24704 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465 -403 484 -404 432 -405 438 -406 439 -407 395 -408 392 -409 399 -410 416 -411 446 -412 425 -413 398 -414 404 -415 427 -416 399 -417 394 -418 388 -419 408 -420 385 -421 407 -422 405 -423 408 -424 355 -425 431 -426 406 -427 383 -428 397 -429 386 -430 368 -431 359 -432 409 -433 372 -434 347 -435 412 -436 328 -437 360 -438 327 -439 360 -440 381 -441 334 -442 331 -443 378 -444 351 -445 366 -446 369 -447 392 -448 338 -449 377 -450 369 -451 355 -452 374 -453 368 -454 351 -455 321 -456 383 -457 318 -458 335 -459 326 -460 340 -461 343 -462 343 -463 344 -464 300 -465 326 -466 320 -467 313 -468 332 -469 365 -470 340 -471 307 -472 309 -473 295 -474 308 -475 287 -476 323 -477 273 -478 314 -479 308 -480 285 -481 280 -482 303 -483 289 -484 258 -485 284 -486 274 -487 312 -488 267 -489 287 -490 278 -491 263 -492 295 -493 275 -494 286 -495 271 -496 257 -497 259 -498 279 -499 266 -500 272 -501 253 -502 239 -503 223 -504 233 -505 270 -506 253 -507 260 -508 252 -509 246 -510 259 -511 273 -512 255 -513 238 -514 238 -515 238 -516 222 -517 255 -518 237 -519 225 -520 249 -521 242 -522 220 -523 217 -524 240 -525 242 -526 253 -527 221 -528 220 -529 202 -530 206 -531 217 -532 220 -533 223 -534 199 -535 194 -536 194 -537 204 -538 200 -539 202 -540 195 -541 168 -542 213 -543 189 -544 216 -545 196 -546 208 -547 196 -548 201 -549 217 -550 191 -551 177 -552 170 -553 181 -554 209 -555 188 -556 182 -557 183 -558 185 -559 186 -560 180 -561 188 -562 165 -563 185 -564 183 -565 178 -566 162 -567 192 -568 177 -569 188 -570 156 -571 173 -572 145 -573 144 -574 163 -575 184 -576 176 -577 161 -578 177 -579 166 -580 164 -581 157 -582 170 -583 161 -584 182 -585 182 -586 149 -587 158 -588 165 -589 157 -590 174 -591 152 -592 145 -593 162 -594 165 -595 160 -596 159 -597 177 -598 148 -599 153 -600 160 -601 53337 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7016821..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.243e-02 1.102e-03 20.36 <2e-16 *** -r 1.051e-02 2.726e-05 385.62 <2e-16 *** -kmercov 1.638e+01 8.818e-03 1857.17 <2e-16 *** -bias 1.657e+00 9.833e-03 168.47 <2e-16 *** -length 1.080e+08 9.345e+04 1155.40 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11360 on 586 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 4.405e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ad0b6da..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 76f3630..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9bc9c40..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 110215760111.561 -round 1 trimming to 10 trying 4peak model... converged. score: 76221663686.7478 -round 2 trimming to 15 trying 4peak model... converged. score: 115097996263.946 -round 3 trimming to 20 trying 4peak model... converged. score: 526683237558.011 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index bcd45aa..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04591% 1.05682% -Genome Haploid Length 116,438,416 bp 116,689,473 bp -Genome Repeat Length 10,906,580 bp 10,930,096 bp -Genome Unique Length 105,531,836 bp 105,759,378 bp -Model Fit 97.7165% 98.6606% -Read Error Rate 0.997774% 0.997774% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index d7fac70..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1358409043 -2 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0acb4f2..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.428e-02 8.475e-04 28.65 <2e-16 *** -r 1.061e-02 2.308e-05 459.82 <2e-16 *** -kmercov 1.323e+01 5.764e-03 2295.01 <2e-16 *** -bias 1.340e+00 7.107e-03 188.50 <2e-16 *** -length 1.085e+08 7.048e+04 1538.81 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8954 on 586 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 5.451e-07 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 26b4b67..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9db989b..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fdbcc7a..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 239288863241.346 -round 1 trimming to 10 trying 4peak model... converged. score: 49094653214.985 -round 2 trimming to 15 trying 4peak model... converged. score: 195530515077.534 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9d80070..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05665% 1.06588% -Genome Haploid Length 117,546,689 bp 117,751,742 bp -Genome Repeat Length 11,704,810 bp 11,725,228 bp -Genome Unique Length 105,841,879 bp 106,026,513 bp -Model Fit 98.0201% 99.0153% -Read Error Rate 1.97851% 1.97851% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index c862b8f..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95680330 -2 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-507 307 -508 330 -509 312 -510 333 -511 340 -512 319 -513 307 -514 321 -515 310 -516 297 -517 303 -518 332 -519 336 -520 312 -521 319 -522 311 -523 313 -524 306 -525 277 -526 287 -527 314 -528 308 -529 303 -530 331 -531 279 -532 317 -533 294 -534 270 -535 277 -536 289 -537 305 -538 296 -539 299 -540 299 -541 248 -542 290 -543 308 -544 278 -545 252 -546 272 -547 276 -548 287 -549 308 -550 277 -551 267 -552 269 -553 241 -554 275 -555 278 -556 248 -557 269 -558 273 -559 273 -560 252 -561 231 -562 270 -563 249 -564 253 -565 279 -566 259 -567 248 -568 248 -569 273 -570 261 -571 234 -572 249 -573 224 -574 248 -575 235 -576 236 -577 249 -578 260 -579 225 -580 215 -581 215 -582 233 -583 255 -584 220 -585 223 -586 239 -587 224 -588 233 -589 223 -590 223 -591 227 -592 230 -593 261 -594 203 -595 216 -596 200 -597 201 -598 222 -599 195 -600 227 -601 74246 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 50403b6..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.815e-02 1.421e-03 12.77 <2e-16 *** -r 1.064e-02 3.944e-05 269.73 <2e-16 *** -kmercov 1.995e+01 1.518e-02 1313.87 <2e-16 *** -bias 2.979e+00 1.886e-02 157.91 <2e-16 *** -length 1.073e+08 1.097e+05 978.17 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 10900 on 588 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 4.505e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a92bd86..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6410200..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index c67d5ad..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 83384464601.5071 -round 1 trimming to 8 trying 4peak model... converged. score: 68841018846.7598 -round 2 trimming to 13 trying 4peak model... converged. score: 70746697823.3308 -round 3 trimming to 18 trying 4peak model... converged. score: 116794109801.447 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 06bd6a1..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.05586% 1.07163% -Genome Haploid Length 114,738,308 bp 115,088,155 bp -Genome Repeat Length 9,480,635 bp 9,509,543 bp -Genome Unique Length 105,257,673 bp 105,578,613 bp -Model Fit 97.6506% 98.5965% -Read Error Rate 0.10368% 0.10368% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 0ed82e2..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 783030633 -2 46092259 -3 4328474 -4 1473334 -5 1193149 -6 1266615 -7 1451893 -8 1683707 -9 1926652 -10 2172965 -11 2405549 -12 2613771 -13 2809966 -14 2979329 -15 3115985 -16 3238792 -17 3349115 -18 3442993 -19 3523488 -20 3596184 -21 3652374 -22 3708062 -23 3747464 -24 3778717 -25 3797505 -26 3803732 -27 3797355 -28 3778419 -29 3732977 -30 3673406 -31 3595534 -32 3499269 -33 3381241 -34 3256740 -35 3119354 -36 2967062 -37 2802686 -38 2639747 -39 2471771 -40 2296872 -41 2125016 -42 1954779 -43 1788225 -44 1626063 -45 1474837 -46 1328253 -47 1192233 -48 1067002 -49 951667 -50 844023 -51 746309 -52 658049 -53 580165 -54 509942 -55 450414 -56 395002 -57 345849 -58 304966 -59 268699 -60 238011 -61 210637 -62 186508 -63 167031 -64 148801 -65 134842 -66 121576 -67 111608 -68 101219 -69 93211 -70 86059 -71 79855 -72 74408 -73 69606 -74 65690 -75 61305 -76 57735 -77 54747 -78 51783 -79 49014 -80 46635 -81 44143 -82 41676 -83 39460 -84 37292 -85 35528 -86 33933 -87 32458 -88 30850 -89 29082 -90 27652 -91 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428 -403 451 -404 418 -405 383 -406 447 -407 443 -408 425 -409 463 -410 457 -411 368 -412 437 -413 434 -414 426 -415 434 -416 422 -417 405 -418 434 -419 403 -420 415 -421 404 -422 366 -423 419 -424 385 -425 356 -426 385 -427 386 -428 373 -429 366 -430 381 -431 371 -432 373 -433 375 -434 387 -435 363 -436 352 -437 383 -438 364 -439 384 -440 357 -441 384 -442 376 -443 331 -444 339 -445 347 -446 329 -447 382 -448 335 -449 335 -450 344 -451 324 -452 353 -453 325 -454 356 -455 352 -456 329 -457 347 -458 351 -459 311 -460 302 -461 336 -462 314 -463 327 -464 322 -465 309 -466 326 -467 332 -468 323 -469 309 -470 290 -471 313 -472 290 -473 287 -474 303 -475 289 -476 305 -477 319 -478 302 -479 268 -480 294 -481 308 -482 301 -483 305 -484 304 -485 268 -486 285 -487 297 -488 305 -489 264 -490 272 -491 292 -492 276 -493 265 -494 244 -495 236 -496 259 -497 246 -498 261 -499 266 -500 270 -501 287 -502 293 -503 276 -504 302 -505 247 -506 249 -507 262 -508 228 -509 254 -510 259 -511 260 -512 225 -513 224 -514 221 -515 234 -516 231 -517 212 -518 226 -519 238 -520 222 -521 231 -522 258 -523 260 -524 217 -525 215 -526 236 -527 230 -528 227 -529 240 -530 206 -531 236 -532 253 -533 228 -534 218 -535 199 -536 201 -537 205 -538 251 -539 201 -540 195 -541 211 -542 220 -543 202 -544 206 -545 205 -546 229 -547 199 -548 203 -549 195 -550 205 -551 200 -552 217 -553 210 -554 216 -555 192 -556 213 -557 194 -558 193 -559 175 -560 178 -561 192 -562 203 -563 172 -564 185 -565 195 -566 182 -567 181 -568 175 -569 190 -570 191 -571 164 -572 179 -573 167 -574 194 -575 177 -576 187 -577 168 -578 181 -579 158 -580 160 -581 156 -582 175 -583 187 -584 145 -585 174 -586 138 -587 194 -588 161 -589 168 -590 173 -591 143 -592 144 -593 162 -594 165 -595 172 -596 181 -597 151 -598 141 -599 166 -600 145 -601 53583 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index d47f18c..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.913e-02 1.299e-03 14.73 <2e-16 *** -r 1.057e-02 3.735e-05 282.96 <2e-16 *** -kmercov 1.648e+01 1.134e-02 1453.30 <2e-16 *** -bias 2.483e+00 1.726e-02 143.82 <2e-16 *** -length 1.077e+08 1.022e+05 1053.83 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9948 on 586 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 6.502e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 84cb610..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b423432..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1965ec9..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 109873870447.766 -round 1 trimming to 10 trying 4peak model... converged. score: 59843186307.2625 -round 2 trimming to 15 trying 4peak model... converged. score: 98798374728.6514 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 62867ca..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04939% 1.06433% -Genome Haploid Length 115,677,121 bp 115,995,945 bp -Genome Repeat Length 10,085,889 bp 10,113,688 bp -Genome Unique Length 105,591,232 bp 105,882,257 bp -Model Fit 97.8112% 98.7805% -Read Error Rate 0.997924% 0.997924% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 732b7e5..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1354558907 -2 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167 -520 156 -521 142 -522 160 -523 164 -524 159 -525 162 -526 166 -527 168 -528 171 -529 200 -530 152 -531 150 -532 169 -533 148 -534 162 -535 143 -536 152 -537 163 -538 172 -539 163 -540 138 -541 161 -542 147 -543 153 -544 164 -545 142 -546 153 -547 158 -548 138 -549 173 -550 136 -551 136 -552 118 -553 140 -554 118 -555 158 -556 157 -557 159 -558 142 -559 134 -560 121 -561 132 -562 159 -563 136 -564 123 -565 124 -566 164 -567 152 -568 131 -569 137 -570 130 -571 147 -572 141 -573 122 -574 118 -575 114 -576 137 -577 141 -578 121 -579 147 -580 108 -581 111 -582 119 -583 131 -584 116 -585 124 -586 124 -587 128 -588 137 -589 118 -590 114 -591 111 -592 123 -593 148 -594 125 -595 128 -596 125 -597 95 -598 114 -599 113 -600 114 -601 36528 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 75f8762..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.345e-02 9.593e-04 24.45 <2e-16 *** -r 1.094e-02 3.296e-05 331.81 <2e-16 *** -kmercov 1.334e+01 7.187e-03 1856.26 <2e-16 *** -bias 1.947e+00 1.141e-02 170.65 <2e-16 *** -length 1.078e+08 7.769e+04 1388.02 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7574 on 585 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 1.875e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d255244..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 54fc11f..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f230d44..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 71922331222.8494 -round 1 trimming to 11 trying 4peak model... converged. score: 41947419944.8451 -round 2 trimming to 16 trying 4peak model... unconverged -round 3 trimming to 21 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f535f2d..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08709% 1.10028% -Genome Haploid Length 116,528,692 bp 116,780,067 bp -Genome Repeat Length 11,230,764 bp 11,254,991 bp -Genome Unique Length 105,297,928 bp 105,525,076 bp -Model Fit 98.1507% 99.1485% -Read Error Rate 1.97883% 1.97883% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 1554f24..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95733011 -2 857842 -3 60711 -4 73491 -5 147637 -6 279009 -7 483685 -8 769026 -9 1141994 -10 1601120 -11 2122952 -12 2684881 -13 3252102 -14 3797140 -15 4269342 -16 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265 -528 262 -529 259 -530 276 -531 281 -532 250 -533 270 -534 258 -535 241 -536 251 -537 266 -538 265 -539 260 -540 254 -541 261 -542 242 -543 240 -544 233 -545 267 -546 243 -547 241 -548 223 -549 244 -550 235 -551 255 -552 240 -553 232 -554 233 -555 241 -556 235 -557 216 -558 217 -559 220 -560 201 -561 207 -562 227 -563 201 -564 197 -565 223 -566 217 -567 218 -568 224 -569 190 -570 201 -571 220 -572 193 -573 203 -574 191 -575 212 -576 199 -577 181 -578 192 -579 194 -580 223 -581 211 -582 201 -583 187 -584 220 -585 181 -586 210 -587 189 -588 188 -589 176 -590 185 -591 165 -592 191 -593 175 -594 196 -595 189 -596 174 -597 175 -598 205 -599 190 -600 154 -601 62909 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index cc6ba0b..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.299e-02 7.890e-04 29.14 <2e-16 *** -r 2.085e-02 2.226e-05 936.84 <2e-16 *** -kmercov 1.977e+01 6.140e-03 3220.56 <2e-16 *** -bias 1.010e+00 3.397e-03 297.42 <2e-16 *** -length 1.083e+08 6.198e+04 1747.45 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8765 on 583 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 5.663e-07 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1b38de0..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 42c1c8f..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 64e55d4..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 48599321576.0208 -round 1 trimming to 8 trying 4peak model... converged. score: 47123086110.4786 -round 2 trimming to 13 trying 4peak model... converged. score: 44786479929.7658 -round 3 trimming to 18 trying 4peak model... converged. score: 63402970975.2679 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 482fb99..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08104% 2.08994% -Genome Haploid Length 116,227,333 bp 116,371,779 bp -Genome Repeat Length 10,159,326 bp 10,171,952 bp -Genome Unique Length 106,068,007 bp 106,199,827 bp -Model Fit 98.1732% 98.9433% -Read Error Rate 0.10329% 0.10329% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 70c33ea..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 794823719 -2 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index aab080e..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.086e-02 1.015e-03 20.55 <2e-16 *** -r 2.079e-02 3.045e-05 682.72 <2e-16 *** -kmercov 1.638e+01 7.302e-03 2242.50 <2e-16 *** -bias 8.562e-01 4.275e-03 200.29 <2e-16 *** -length 1.086e+08 7.690e+04 1412.82 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11740 on 586 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.916e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6a25e9f..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index fbed531..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d2158a8..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 96552188094.7224 -round 1 trimming to 10 trying 4peak model... converged. score: 80834045473.418 -round 2 trimming to 15 trying 4peak model... converged. score: 142616249411.086 -round 3 trimming to 20 trying 4peak model... converged. score: 491035895515.56 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3bba787..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.07268% 2.08486% -Genome Haploid Length 116,803,000 bp 117,011,531 bp -Genome Repeat Length 10,226,778 bp 10,245,036 bp -Genome Unique Length 106,576,223 bp 106,766,495 bp -Model Fit 97.8983% 98.6685% -Read Error Rate 0.993881% 0.993881% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 22fe4f4..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1382158403 -2 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162 -523 147 -524 153 -525 165 -526 149 -527 149 -528 132 -529 135 -530 151 -531 140 -532 152 -533 145 -534 128 -535 123 -536 145 -537 141 -538 149 -539 118 -540 127 -541 115 -542 115 -543 137 -544 119 -545 135 -546 129 -547 149 -548 137 -549 150 -550 115 -551 116 -552 128 -553 139 -554 140 -555 141 -556 143 -557 114 -558 146 -559 126 -560 116 -561 123 -562 119 -563 121 -564 103 -565 106 -566 112 -567 109 -568 115 -569 107 -570 115 -571 107 -572 120 -573 90 -574 117 -575 109 -576 108 -577 120 -578 102 -579 131 -580 101 -581 92 -582 110 -583 81 -584 100 -585 100 -586 85 -587 124 -588 95 -589 108 -590 104 -591 90 -592 82 -593 116 -594 93 -595 78 -596 92 -597 95 -598 99 -599 98 -600 98 -601 31147 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index dff3421..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.206e-02 9.932e-04 22.21 <2e-16 *** -r 2.077e-02 3.269e-05 635.42 <2e-16 *** -kmercov 1.321e+01 7.247e-03 1822.37 <2e-16 *** -bias 7.201e-01 4.619e-03 155.91 <2e-16 *** -length 1.095e+08 7.777e+04 1407.76 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11690 on 586 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 2.841e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 02f074b..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index d2a763e..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 37d1c4c..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 206006947590.048 -round 1 trimming to 10 trying 4peak model... converged. score: 98179469319.526 -round 2 trimming to 15 trying 4peak model... converged. score: 331163131035.451 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e88590f..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.07059% 2.08367% -Genome Haploid Length 118,057,203 bp 118,316,617 bp -Genome Repeat Length 10,805,027 bp 10,828,769 bp -Genome Unique Length 107,252,176 bp 107,487,847 bp -Model Fit 98.0179% 98.8055% -Read Error Rate 1.97126% 1.97126% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 2df9d05..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95747005 -2 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259 -510 275 -511 299 -512 313 -513 305 -514 279 -515 299 -516 274 -517 282 -518 261 -519 271 -520 255 -521 275 -522 271 -523 273 -524 287 -525 234 -526 290 -527 264 -528 271 -529 251 -530 256 -531 276 -532 264 -533 253 -534 234 -535 256 -536 268 -537 291 -538 256 -539 249 -540 240 -541 245 -542 263 -543 299 -544 263 -545 263 -546 254 -547 244 -548 244 -549 239 -550 238 -551 232 -552 249 -553 232 -554 241 -555 212 -556 208 -557 230 -558 258 -559 238 -560 210 -561 191 -562 267 -563 251 -564 213 -565 219 -566 227 -567 220 -568 228 -569 216 -570 215 -571 226 -572 231 -573 221 -574 201 -575 206 -576 225 -577 189 -578 235 -579 219 -580 194 -581 220 -582 200 -583 211 -584 185 -585 202 -586 204 -587 190 -588 174 -589 185 -590 153 -591 178 -592 190 -593 214 -594 213 -595 216 -596 187 -597 194 -598 172 -599 195 -600 162 -601 63479 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6aa8ccf..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.012e-02 1.677e-03 6.034 2.85e-09 *** -r 2.151e-02 6.170e-05 348.669 < 2e-16 *** -kmercov 2.010e+01 2.011e-02 999.627 < 2e-16 *** -bias 2.034e+00 1.493e-02 136.242 < 2e-16 *** -length 1.074e+08 1.166e+05 920.987 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13680 on 583 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 7.407e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index af9e212..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index b8acd81..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fc4aa88..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 137706481842.183 -round 1 trimming to 8 trying 4peak model... converged. score: 116911989425.342 -round 2 trimming to 13 trying 4peak model... converged. score: 110281352821.771 -round 3 trimming to 18 trying 4peak model... converged. score: 211870128079.571 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8d6ce3a..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.13884% 2.16351% -Genome Haploid Length 114,078,635 bp 114,536,035 bp -Genome Repeat Length 7,816,798 bp 7,848,140 bp -Genome Unique Length 106,261,836 bp 106,687,895 bp -Model Fit 97.5229% 98.2583% -Read Error Rate 0.106266% 0.106266% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index d9b742e..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 793101203 -2 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177 -517 220 -518 193 -519 188 -520 164 -521 212 -522 193 -523 180 -524 186 -525 184 -526 194 -527 193 -528 183 -529 160 -530 165 -531 162 -532 170 -533 187 -534 197 -535 160 -536 190 -537 172 -538 183 -539 161 -540 176 -541 192 -542 174 -543 181 -544 175 -545 163 -546 156 -547 170 -548 173 -549 161 -550 180 -551 186 -552 190 -553 167 -554 173 -555 156 -556 169 -557 151 -558 167 -559 130 -560 167 -561 167 -562 169 -563 159 -564 149 -565 154 -566 172 -567 143 -568 174 -569 176 -570 139 -571 149 -572 154 -573 170 -574 157 -575 151 -576 134 -577 172 -578 153 -579 163 -580 149 -581 158 -582 124 -583 122 -584 151 -585 150 -586 161 -587 149 -588 157 -589 124 -590 152 -591 151 -592 132 -593 139 -594 151 -595 137 -596 160 -597 154 -598 125 -599 135 -600 156 -601 46047 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index edc6c61..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.796e-03 1.970e-03 4.466 9.57e-06 *** -r 2.137e-02 7.551e-05 282.980 < 2e-16 *** -kmercov 1.663e+01 2.041e-02 814.519 < 2e-16 *** -bias 1.700e+00 1.567e-02 108.441 < 2e-16 *** -length 1.079e+08 1.299e+05 830.518 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 16350 on 586 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 4.67e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ceee293..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6e1fe8a..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e6a55bd..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 214801540565.232 -round 1 trimming to 10 trying 4peak model... converged. score: 156952837277.472 -round 2 trimming to 15 trying 4peak model... converged. score: 348130481346.039 -round 3 trimming to 20 trying 4peak model... converged. score: 889934821640.277 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 965f104..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12174% 2.15194% -Genome Haploid Length 114,789,566 bp 115,354,670 bp -Genome Repeat Length 8,024,119 bp 8,063,621 bp -Genome Unique Length 106,765,447 bp 107,291,049 bp -Model Fit 97.3069% 98.125% -Read Error Rate 0.996748% 0.996748% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index f1b4035..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1377666795 -2 99610534 -3 10635913 -4 3337682 -5 2830082 -6 3237842 -7 3869822 -8 4549051 -9 5183769 -10 5691606 -11 6065121 -12 6269835 -13 6338445 -14 6296307 -15 6169486 -16 5996119 -17 5793156 -18 5573974 -19 5364227 -20 5154217 -21 4971190 -22 4798367 -23 4623703 -24 4438409 -25 4245837 -26 4043352 -27 3819590 -28 3585903 -29 3329047 -30 3072032 -31 2800998 -32 2531998 -33 2266341 -34 2013415 -35 1770581 -36 1538984 -37 1335873 -38 1149289 -39 980265 -40 830543 -41 702152 -42 592148 -43 500029 -44 419184 -45 354344 -46 298239 -47 252218 -48 216374 -49 186884 -50 161974 -51 141976 -52 125907 -53 113213 -54 102379 -55 92744 -56 84787 -57 78064 -58 73046 -59 67853 -60 63324 -61 59057 -62 55339 -63 51896 -64 48448 -65 45344 -66 42505 -67 39843 -68 37391 -69 35387 -70 33265 -71 31553 -72 30027 -73 28242 -74 26633 -75 25440 -76 24378 -77 23292 -78 21977 -79 21001 -80 19967 -81 19212 -82 18419 -83 17751 -84 16965 -85 16108 -86 15785 -87 15296 -88 14853 -89 14113 -90 13700 -91 13258 -92 12792 -93 12210 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-521 135 -522 156 -523 159 -524 146 -525 161 -526 153 -527 145 -528 172 -529 136 -530 141 -531 137 -532 138 -533 170 -534 161 -535 142 -536 136 -537 144 -538 126 -539 135 -540 132 -541 131 -542 131 -543 133 -544 136 -545 137 -546 132 -547 126 -548 141 -549 151 -550 122 -551 118 -552 124 -553 141 -554 144 -555 137 -556 119 -557 132 -558 135 -559 132 -560 128 -561 110 -562 147 -563 127 -564 148 -565 111 -566 122 -567 110 -568 118 -569 112 -570 123 -571 122 -572 124 -573 117 -574 109 -575 125 -576 123 -577 114 -578 125 -579 106 -580 119 -581 118 -582 100 -583 114 -584 127 -585 115 -586 109 -587 111 -588 102 -589 107 -590 109 -591 96 -592 121 -593 115 -594 98 -595 101 -596 113 -597 93 -598 121 -599 134 -600 96 -601 30901 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8208a61..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.515e-02 1.712e-03 8.85 <2e-16 *** -r 2.095e-02 6.987e-05 299.88 <2e-16 *** -kmercov 1.329e+01 1.644e-02 808.39 <2e-16 *** -bias 1.442e+00 1.516e-02 95.11 <2e-16 *** -length 1.095e+08 1.324e+05 827.31 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13780 on 586 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 3.402e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index fcea8e0..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index fd24707..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 0ac4565..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 297451434574.205 -round 1 trimming to 10 trying 4peak model... converged. score: 163339550829.694 -round 2 trimming to 15 trying 4peak model... converged. score: 493713894976.028 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4eed264..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.0813% 2.10925% -Genome Haploid Length 117,177,063 bp 117,758,303 bp -Genome Repeat Length 9,376,979 bp 9,423,492 bp -Genome Unique Length 107,800,084 bp 108,334,811 bp -Model Fit 97.7568% 98.5637% -Read Error Rate 1.9702% 1.9702% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 0038a02..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 95850370 -2 1164507 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 3d99d82..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 5.448e-03 2.707e-03 2.013 0.0446 * -r 2.168e-02 1.132e-04 191.464 <2e-16 *** -kmercov 2.029e+01 3.870e-02 524.129 <2e-16 *** -bias 2.973e+00 3.743e-02 79.429 <2e-16 *** -length 1.069e+08 1.829e+05 584.446 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 15440 on 583 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 9.774e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 338e1bb..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index b8bd6b9..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2d46176..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 223922931586.928 -round 1 trimming to 8 trying 4peak model... converged. score: 155515191635.315 -round 2 trimming to 13 trying 4peak model... converged. score: 149946375488.118 -round 3 trimming to 18 trying 4peak model... converged. score: 406888864018.233 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1ccffe5..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.14517% 2.19046% -Genome Haploid Length 112,797,885 bp 113,662,023 bp -Genome Repeat Length 6,800,383 bp 6,852,481 bp -Genome Unique Length 105,997,502 bp 106,809,543 bp -Model Fit 97.2179% 98.0014% -Read Error Rate 0.108434% 0.108434% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index a504f10..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 791456792 -2 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-515 206 -516 201 -517 201 -518 215 -519 194 -520 172 -521 187 -522 188 -523 224 -524 196 -525 184 -526 185 -527 184 -528 190 -529 182 -530 184 -531 192 -532 213 -533 181 -534 183 -535 193 -536 187 -537 168 -538 172 -539 188 -540 155 -541 194 -542 190 -543 173 -544 166 -545 182 -546 217 -547 164 -548 190 -549 183 -550 181 -551 158 -552 156 -553 171 -554 192 -555 178 -556 163 -557 160 -558 171 -559 160 -560 158 -561 176 -562 149 -563 158 -564 148 -565 170 -566 139 -567 157 -568 145 -569 176 -570 151 -571 161 -572 161 -573 136 -574 163 -575 147 -576 156 -577 149 -578 177 -579 141 -580 162 -581 144 -582 155 -583 159 -584 141 -585 165 -586 151 -587 152 -588 151 -589 148 -590 155 -591 160 -592 145 -593 153 -594 149 -595 162 -596 154 -597 155 -598 155 -599 135 -600 141 -601 45850 diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index f9f8c11..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.733e-03 2.733e-03 3.561 4e-04 *** -r 2.149e-02 1.163e-04 184.815 <2e-16 *** -kmercov 1.676e+01 3.275e-02 511.612 <2e-16 *** -bias 2.377e+00 3.004e-02 79.128 <2e-16 *** -length 1.070e+08 1.719e+05 622.350 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 16550 on 586 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 8.984e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bf45fe8..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 934a995..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a8aef58..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 258100421649.425 -round 1 trimming to 10 trying 4peak model... converged. score: 160625195938.942 -round 2 trimming to 15 trying 4peak model... converged. score: 478249977848.703 -round 3 trimming to 20 trying 4peak model... converged. score: 790344070563.255 -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9cc41e7..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12556% 2.17207% -Genome Haploid Length 113,629,264 bp 114,521,153 bp -Genome Repeat Length 7,937,095 bp 7,999,394 bp -Genome Unique Length 105,692,170 bp 106,521,759 bp -Model Fit 97.3255% 98.1636% -Read Error Rate 1.00105% 1.00105% diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 5d7975f..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1373682395 -2 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b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1309ec2..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.677e-02 2.527e-03 6.636 7.36e-11 *** -r 2.049e-02 1.062e-04 192.880 < 2e-16 *** -kmercov 1.325e+01 2.526e-02 524.556 < 2e-16 *** -bias 2.109e+00 3.410e-02 61.849 < 2e-16 *** -length 1.101e+08 2.304e+05 477.720 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 13690 on 586 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 4.695e-06 - diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 982efaa..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index bc1515d..0000000 Binary files a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f5f2025..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 311979033221.409 -round 1 trimming to 10 trying 4peak model... converged. score: 200900991838.612 -round 2 trimming to 15 trying 4peak model... converged. score: 514463910286.701 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4e4b821..0000000 --- a/analysis/simulation_results_50x/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.02745% 2.06994% -Genome Haploid Length 117,402,277 bp 118,300,953 bp -Genome Repeat Length 9,362,604 bp 9,434,271 bp -Genome Unique Length 108,039,673 bp 108,866,682 bp -Model Fit 97.7415% 98.5497% -Read Error Rate 1.96933% 1.96933% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 904978d..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107074290 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5926258..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.330e-02 4.168e-04 31.91 <2e-16 *** -r 1.181e-03 8.151e-06 144.87 <2e-16 *** -kmercov 1.966e+01 2.393e-03 8214.05 <2e-16 *** -bias 9.801e-01 2.230e-03 439.45 <2e-16 *** -length 1.171e+08 6.299e+04 1859.02 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7085 on 590 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 6.982e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index de6c6a7..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index e175aa4..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d0c2c4b..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 29504725715.3336 -round 1 trimming to 11 trying 4peak model... converged. score: 29505917191.3279 -round 2 trimming to 16 trying 4peak model... converged. score: 30732664548.4402 -round 3 trimming to 21 trying 4peak model... converged. score: 64230023518.0287 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index acaf30c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.116452% 0.119712% -Genome Haploid Length 126,489,680 bp 126,551,291 bp -Genome Repeat Length 10,976,684 bp 10,982,031 bp -Genome Unique Length 115,512,996 bp 115,569,261 bp -Model Fit 97.9245% 99.072% -Read Error Rate 0.106695% 0.106695% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index b538a22..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 850482960 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 8915d14..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.366e-02 3.187e-04 42.87 <2e-16 *** -r 1.419e-03 8.285e-06 171.24 <2e-16 *** -kmercov 1.628e+01 1.634e-03 9962.30 <2e-16 *** -bias 8.056e-01 1.672e-03 481.79 <2e-16 *** -length 1.174e+08 4.658e+04 2520.01 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5709 on 582 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 4.121e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cf4528b..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index d15981c..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 25c9425..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 26248115701.1291 -round 1 trimming to 14 trying 4peak model... converged. score: 18968072025.8013 -round 2 trimming to 19 trying 4peak model... converged. score: 31485993430.3546 -round 3 trimming to 24 trying 4peak model... converged. score: 1161608267972.09 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1cc5309..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.140211% 0.143524% -Genome Haploid Length 128,049,808 bp 128,101,233 bp -Genome Repeat Length 12,291,196 bp 12,296,132 bp -Genome Unique Length 115,758,613 bp 115,805,101 bp -Model Fit 98.2204% 99.4532% -Read Error Rate 1.03316% 1.03316% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index a3a4de7..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1474051311 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index e37ed4b..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.476e-02 2.962e-04 49.84 <2e-16 *** -r 1.666e-03 1.848e-05 90.15 <2e-16 *** -kmercov 1.315e+01 1.560e-03 8426.61 <2e-16 *** -bias 6.509e-01 1.840e-03 353.82 <2e-16 *** -length 1.187e+08 4.194e+04 2830.30 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5544 on 581 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 4.148e-07 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 8d11593..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index a9abb83..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 8081d0e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 10 trying 4peak model... converged. score: 29374927882.4979 -round 1 trimming to 15 trying 4peak model... converged. score: 18444415414.3688 -round 2 trimming to 20 trying 4peak model... converged. score: 470660238124.428 -round 3 trimming to 25 trying 4peak model... converged. score: 7579842253196.91 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 60ab1ae..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.162868% 0.170258% -Genome Haploid Length 130,877,772 bp 130,939,913 bp -Genome Repeat Length 13,954,902 bp 13,961,528 bp -Genome Unique Length 116,922,870 bp 116,978,385 bp -Model Fit 98.3155% 99.6317% -Read Error Rate 2.01146% 2.01146% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 7a30c9c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107048205 -2 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--git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1c988a5..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.969e-03 6.977e-04 12.85 <2e-16 *** -r 1.455e-03 1.540e-05 94.49 <2e-16 *** -kmercov 1.981e+01 4.924e-03 4024.01 <2e-16 *** -bias 1.949e+00 6.041e-03 322.63 <2e-16 *** -length 1.164e+08 8.956e+04 1299.99 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9635 on 591 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.948e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e6340b4..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 1dbd7e2..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 341f9b2..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 54025670176.0851 -round 1 trimming to 10 trying 4peak model... converged. score: 54051705233.1479 -round 2 trimming to 15 trying 4peak model... converged. score: 60696031227.0579 -round 3 trimming to 20 trying 4peak model... converged. score: 166391130181.302 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7a94413..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.142462% 0.148623% -Genome Haploid Length 125,433,817 bp 125,558,564 bp -Genome Repeat Length 10,109,402 bp 10,119,456 bp -Genome Unique Length 115,324,415 bp 115,439,108 bp -Model Fit 97.3861% 98.564% -Read Error Rate 0.106709% 0.106709% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index c391f3c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 848807412 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index c809982..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.127e-02 4.705e-04 23.96 <2e-16 *** -r 1.954e-03 1.559e-05 125.36 <2e-16 *** -kmercov 1.644e+01 3.000e-03 5479.71 <2e-16 *** -bias 1.552e+00 3.967e-03 391.17 <2e-16 *** -length 1.166e+08 5.783e+04 2016.02 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6802 on 582 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.593e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ac2bcb6..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2e9f9ed..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 240602e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 30265970877.7343 -round 1 trimming to 14 trying 4peak model... converged. score: 27495492479.8378 -round 2 trimming to 19 trying 4peak model... converged. score: 124242575823.18 -round 3 trimming to 24 trying 4peak model... converged. score: 2401878594114.94 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index fa3628a..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.192298% 0.198533% -Genome Haploid Length 126,910,477 bp 127,003,151 bp -Genome Repeat Length 11,670,328 bp 11,678,850 bp -Genome Unique Length 115,240,149 bp 115,324,301 bp -Model Fit 97.9715% 99.2005% -Read Error Rate 1.02882% 1.02882% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index a2a621f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1469651819 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9f6e207..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.352e-02 4.022e-04 33.61 <2e-16 *** -r 2.287e-03 2.446e-05 93.49 <2e-16 *** -kmercov 1.327e+01 2.597e-03 5111.16 <2e-16 *** -bias 1.243e+00 3.652e-03 340.48 <2e-16 *** -length 1.180e+08 4.645e+04 2539.26 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5963 on 582 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.485e-07 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 395bd5d..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index e70b584..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ed20480..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 45186340125.0844 -round 1 trimming to 14 trying 4peak model... converged. score: 21879887272.156 -round 2 trimming to 19 trying 4peak model... converged. score: 625767905149.054 -round 3 trimming to 24 trying 4peak model... converged. score: 21082305383617.4 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d08e37e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.223796% 0.23358% -Genome Haploid Length 129,804,420 bp 129,906,045 bp -Genome Repeat Length 13,489,989 bp 13,500,550 bp -Genome Unique Length 116,314,431 bp 116,405,495 bp -Model Fit 98.1834% 99.4872% -Read Error Rate 2.00427% 2.00427% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 66de623..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107009395 -2 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diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9f02301..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 4.885e-03 8.973e-04 5.444 7.65e-08 *** -r 1.835e-03 2.128e-05 86.231 < 2e-16 *** -kmercov 2.003e+01 7.097e-03 2822.275 < 2e-16 *** -bias 2.888e+00 1.063e-02 271.744 < 2e-16 *** -length 1.155e+08 9.638e+04 1198.578 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9872 on 591 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 6.082e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 10e8e15..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7c09f1a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bba9f19..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 57035551884.8646 -round 1 trimming to 10 trying 4peak model... converged. score: 57275815309.8858 -round 2 trimming to 15 trying 4peak model... converged. score: 75812930622.7317 -round 3 trimming to 20 trying 4peak model... converged. score: 253527580433.194 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b425908..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.179249% 0.187761% -Genome Haploid Length 124,063,834 bp 124,239,794 bp -Genome Repeat Length 9,191,779 bp 9,204,816 bp -Genome Unique Length 114,872,054 bp 115,034,978 bp -Model Fit 97.3083% 98.4636% -Read Error Rate 0.106655% 0.106655% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index eb62ad5..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 846797599 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 5cc81b4..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 9.451e-03 5.762e-04 16.4 <2e-16 *** -r 2.654e-03 2.263e-05 117.3 <2e-16 *** -kmercov 1.665e+01 4.260e-03 3909.3 <2e-16 *** -bias 2.254e+00 6.724e-03 335.2 <2e-16 *** -length 1.154e+08 5.977e+04 1931.0 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 6589 on 582 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.045e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ec61006..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index fb67108..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ce2d633..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 27941313461.1352 -round 1 trimming to 14 trying 4peak model... converged. score: 27849588459.3573 -round 2 trimming to 19 trying 4peak model... converged. score: 177943547527.061 -round 3 trimming to 24 trying 4peak model... converged. score: 2665199213842.26 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cf9b762..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.260864% 0.269918% -Genome Haploid Length 125,325,069 bp 125,453,368 bp -Genome Repeat Length 11,060,798 bp 11,072,121 bp -Genome Unique Length 114,264,271 bp 114,381,247 bp -Model Fit 97.9602% 99.195% -Read Error Rate 1.02584% 1.02584% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index d25e8a3..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1465353739 -2 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618 -507 571 -508 620 -509 583 -510 628 -511 597 -512 582 -513 621 -514 581 -515 535 -516 595 -517 589 -518 569 -519 583 -520 599 -521 528 -522 550 -523 549 -524 513 -525 532 -526 556 -527 530 -528 551 -529 549 -530 518 -531 511 -532 499 -533 515 -534 509 -535 509 -536 522 -537 540 -538 539 -539 502 -540 480 -541 463 -542 472 -543 534 -544 483 -545 461 -546 491 -547 457 -548 498 -549 517 -550 454 -551 487 -552 455 -553 511 -554 503 -555 482 -556 470 -557 464 -558 405 -559 450 -560 437 -561 462 -562 442 -563 435 -564 383 -565 420 -566 442 -567 420 -568 419 -569 421 -570 430 -571 386 -572 406 -573 438 -574 389 -575 404 -576 444 -577 410 -578 360 -579 458 -580 379 -581 396 -582 395 -583 410 -584 411 -585 364 -586 373 -587 352 -588 344 -589 343 -590 364 -591 371 -592 340 -593 349 -594 332 -595 371 -596 342 -597 357 -598 346 -599 328 -600 394 -601 164619 diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9eeb0d8..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.292e-02 4.903e-04 26.34 <2e-16 *** -r 3.119e-03 3.405e-05 91.61 <2e-16 *** -kmercov 1.346e+01 3.809e-03 3533.04 <2e-16 *** -bias 1.783e+00 5.966e-03 298.84 <2e-16 *** -length 1.167e+08 4.916e+04 2373.16 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 5673 on 582 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 9.461e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 24b5116..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 8953e6a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index df30a99..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 9 trying 4peak model... converged. score: 37005452398.4432 -round 1 trimming to 14 trying 4peak model... converged. score: 20707977479.7134 -round 2 trimming to 19 trying 4peak model... converged. score: 595414016539.515 -round 3 trimming to 24 trying 4peak model... converged. score: 16563350797707.7 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 367e05f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.305111% 0.318731% -Genome Haploid Length 128,136,025 bp 128,281,179 bp -Genome Repeat Length 13,034,054 bp 13,048,819 bp -Genome Unique Length 115,101,971 bp 115,232,360 bp -Model Fit 98.2108% 99.5166% -Read Error Rate 1.9993% 1.9993% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 931bbce..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107130410 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 19b7701..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.210e-02 6.777e-04 17.86 <2e-16 *** -r 1.068e-02 1.385e-05 771.13 <2e-16 *** -kmercov 1.968e+01 4.678e-03 4207.20 <2e-16 *** -bias 9.988e-01 3.213e-03 310.86 <2e-16 *** -length 1.185e+08 7.365e+04 1608.54 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9367 on 587 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 8.229e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index b27f6e0..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 85e95d2..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index dd8c475..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 51196011878.5621 -round 1 trimming to 9 trying 4peak model... converged. score: 50938397927.8995 -round 2 trimming to 14 trying 4peak model... converged. score: 51365820760.4841 -round 3 trimming to 19 trying 4peak model... converged. score: 74523683657.823 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cf02178..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.06517% 1.07071% -Genome Haploid Length 127,532,931 bp 127,654,241 bp -Genome Repeat Length 10,488,848 bp 10,498,825 bp -Genome Unique Length 117,044,084 bp 117,155,416 bp -Model Fit 97.9846% 98.9335% -Read Error Rate 0.105618% 0.105618% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 9e38272..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 863711920 -2 50672344 -3 6427892 -4 2510583 -5 1511629 -6 1190072 -7 1207888 -8 1433519 -9 1792215 -10 2214452 -11 2642281 -12 3044971 -13 3384110 -14 3632407 -15 3792776 -16 3867113 -17 3880026 -18 3860173 -19 3819891 -20 3801676 -21 3818705 -22 3880861 -23 3990765 -24 4140931 -25 4323343 -26 4519529 -27 4701318 -28 4865697 -29 4991313 -30 5059530 -31 5065141 -32 4987532 -33 4860364 -34 4668918 -35 4420207 -36 4127561 -37 3810863 -38 3455663 -39 3104579 -40 2752114 -41 2409057 -42 2085133 -43 1783056 -44 1511812 -45 1265166 -46 1052364 -47 867967 -48 709979 -49 578166 -50 468682 -51 378825 -52 304756 -53 246147 -54 200601 -55 164680 -56 138342 -57 116548 -58 99768 -59 88351 -60 78817 -61 71781 -62 67003 -63 63280 -64 59875 -65 57546 -66 55116 -67 52735 -68 50395 -69 48436 -70 46420 -71 44455 -72 42422 -73 40276 -74 37878 -75 36462 -76 34493 -77 32577 -78 30901 -79 29160 -80 27786 -81 26261 -82 25015 -83 23558 -84 22707 -85 21488 -86 20778 -87 19943 -88 19219 -89 18564 -90 18000 -91 17578 -92 16772 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 0c98b89..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.276e-02 5.638e-04 22.64 <2e-16 *** -r 1.065e-02 1.206e-05 882.74 <2e-16 *** -kmercov 1.626e+01 3.529e-03 4608.35 <2e-16 *** -bias 8.459e-01 2.773e-03 305.04 <2e-16 *** -length 1.193e+08 6.019e+04 1981.79 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 8195 on 585 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.621e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 31b3777..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index e047ad9..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1da2b79..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 105687304397.633 -round 1 trimming to 11 trying 4peak model... converged. score: 39286850558.1896 -round 2 trimming to 16 trying 4peak model... converged. score: 54514453765.5258 -round 3 trimming to 21 trying 4peak model... converged. score: 371648547436.97 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d4c2b61..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.06215% 1.06697% -Genome Haploid Length 129,575,155 bp 129,687,674 bp -Genome Repeat Length 11,796,344 bp 11,806,588 bp -Genome Unique Length 117,778,811 bp 117,881,086 bp -Model Fit 98.1185% 99.1364% -Read Error Rate 1.01758% 1.01758% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 0034c20..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1501871039 -2 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487 -510 486 -511 507 -512 508 -513 462 -514 500 -515 510 -516 471 -517 472 -518 483 -519 490 -520 468 -521 464 -522 454 -523 422 -524 466 -525 463 -526 440 -527 444 -528 501 -529 429 -530 450 -531 408 -532 458 -533 423 -534 474 -535 399 -536 430 -537 406 -538 415 -539 443 -540 410 -541 443 -542 377 -543 443 -544 389 -545 396 -546 383 -547 368 -548 364 -549 411 -550 374 -551 368 -552 356 -553 375 -554 364 -555 364 -556 362 -557 376 -558 351 -559 393 -560 365 -561 387 -562 323 -563 372 -564 382 -565 378 -566 336 -567 360 -568 356 -569 340 -570 358 -571 355 -572 370 -573 328 -574 382 -575 359 -576 371 -577 317 -578 377 -579 381 -580 350 -581 378 -582 336 -583 325 -584 363 -585 358 -586 310 -587 339 -588 373 -589 328 -590 346 -591 330 -592 342 -593 342 -594 338 -595 328 -596 343 -597 329 -598 345 -599 288 -600 314 -601 146685 diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index c4f6ec1..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.465e-02 5.030e-04 29.12 <2e-16 *** -r 1.072e-02 1.205e-05 889.72 <2e-16 *** -kmercov 1.312e+01 2.805e-03 4677.00 <2e-16 *** -bias 6.915e-01 2.486e-03 278.19 <2e-16 *** -length 1.207e+08 5.207e+04 2318.73 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7645 on 585 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.476e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 04fe708..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7fb7dd9..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1264b8f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 507287967948.709 -round 1 trimming to 11 trying 4peak model... converged. score: 34189447653.8188 -round 2 trimming to 16 trying 4peak model... converged. score: 160493315447.243 -round 3 trimming to 21 trying 4peak model... converged. score: 3695209060493.69 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a149219..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.06958% 1.07439% -Genome Haploid Length 132,457,930 bp 132,571,263 bp -Genome Repeat Length 13,469,996 bp 13,481,521 bp -Genome Unique Length 118,987,934 bp 119,089,742 bp -Model Fit 98.1622% 99.2978% -Read Error Rate 1.98896% 1.98896% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 91bb20c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107087750 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2b16dd4..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.807e-03 1.204e-03 5.653 2.47e-08 *** -r 1.083e-02 2.852e-05 379.772 < 2e-16 *** -kmercov 1.982e+01 1.097e-02 1806.745 < 2e-16 *** -bias 2.001e+00 1.065e-02 187.877 < 2e-16 *** -length 1.180e+08 1.109e+05 1064.318 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12950 on 587 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 8.138e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 38c4e0e..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index acac942..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e370b8e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 102196855553.432 -round 1 trimming to 9 trying 4peak model... converged. score: 98236738694.1196 -round 2 trimming to 14 trying 4peak model... converged. score: 101856086629.818 -round 3 trimming to 19 trying 4peak model... converged. score: 179991146823.965 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 910a686..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.07757% 1.08898% -Genome Haploid Length 126,512,140 bp 126,792,539 bp -Genome Repeat Length 9,396,453 bp 9,417,280 bp -Genome Unique Length 117,115,687 bp 117,375,260 bp -Model Fit 97.4845% 98.4632% -Read Error Rate 0.106821% 0.106821% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 8b9d700..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 861703503 -2 51550982 -3 6683657 -4 2773097 -5 1856088 -6 1597988 -7 1636782 -8 1838593 -9 2113749 -10 2422009 -11 2724652 -12 2989616 -13 3221573 -14 3423122 -15 3572649 -16 3693987 -17 3781752 -18 3862082 -19 3934145 -20 4000897 -21 4069525 -22 4141815 -23 4212220 -24 4290423 -25 4363615 -26 4422337 -27 4473385 -28 4492496 -29 4487799 -30 4454708 -31 4385780 -32 4290116 -33 4160970 -34 4001621 -35 3818307 -36 3604555 -37 3377385 -38 3141048 -39 2888359 -40 2643103 -41 2393355 -42 2151641 -43 1925890 -44 1704506 -45 1502524 -46 1311902 -47 1140097 -48 987949 -49 848360 -50 727051 -51 621768 -52 527455 -53 447332 -54 378921 -55 320208 -56 271206 -57 228991 -58 194584 -59 166873 -60 143525 -61 124137 -62 108514 -63 94884 -64 83456 -65 75542 -66 67972 -67 62380 -68 57216 -69 52875 -70 49353 -71 46241 -72 43554 -73 41876 -74 39182 -75 37329 -76 35554 -77 33646 -78 32137 -79 30356 -80 29281 -81 28262 -82 26764 -83 25320 -84 24212 -85 23566 -86 22483 -87 21384 -88 20782 -89 19867 -90 19118 -91 18395 -92 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 7f69abf..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.940e-03 8.899e-04 10.05 <2e-16 *** -r 1.086e-02 2.206e-05 492.49 <2e-16 *** -kmercov 1.636e+01 6.966e-03 2348.93 <2e-16 *** -bias 1.660e+00 7.816e-03 212.36 <2e-16 *** -length 1.189e+08 8.141e+04 1460.44 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9920 on 585 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.669e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 747ce45..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index efdc2b8..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2c3cbd3..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 184876176296.389 -round 1 trimming to 11 trying 4peak model... converged. score: 57572613605.4178 -round 2 trimming to 16 trying 4peak model... converged. score: 98366962425.486 -round 3 trimming to 21 trying 4peak model... converged. score: 749978937272.069 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a188f99..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08208% 1.0909% -Genome Haploid Length 128,715,771 bp 128,935,148 bp -Genome Repeat Length 10,939,518 bp 10,958,163 bp -Genome Unique Length 117,776,253 bp 117,976,985 bp -Model Fit 97.8655% 98.8991% -Read Error Rate 1.01724% 1.01724% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index b554962..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1497071952 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 4a01a82..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.212e-02 6.844e-04 17.71 <2e-16 *** -r 1.110e-02 2.152e-05 515.52 <2e-16 *** -kmercov 1.321e+01 4.605e-03 2868.95 <2e-16 *** -bias 1.335e+00 5.799e-03 230.13 <2e-16 *** -length 1.203e+08 6.159e+04 1952.76 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7818 on 584 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 2.015e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a8baf8b..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 949207c..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2171c2f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 166767358191.559 -round 1 trimming to 12 trying 4peak model... converged. score: 38014164631.9611 -round 2 trimming to 17 trying 4peak model... converged. score: 446413160532.048 -round 3 trimming to 22 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index a473e9c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.10531% 1.11392% -Genome Haploid Length 131,531,585 bp 131,715,099 bp -Genome Repeat Length 12,747,561 bp 12,765,347 bp -Genome Unique Length 118,784,023 bp 118,949,752 bp -Model Fit 98.0758% 99.2341% -Read Error Rate 1.98717% 1.98717% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 534828e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107098899 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 976cf1f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.834e-03 1.549e-03 2.475 0.0136 * -r 1.095e-02 4.257e-05 257.329 <2e-16 *** -kmercov 1.996e+01 1.599e-02 1247.988 <2e-16 *** -bias 2.970e+00 2.079e-02 142.882 <2e-16 *** -length 1.176e+08 1.291e+05 910.979 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12750 on 587 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 3.268e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1be0ea2..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index db9890a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 42ec20a..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 109366396097.27 -round 1 trimming to 9 trying 4peak model... converged. score: 95410466156.742 -round 2 trimming to 14 trying 4peak model... converged. score: 103120809233.916 -round 3 trimming to 19 trying 4peak model... converged. score: 201223771146.9 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 563b69b..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.08687% 1.1039% -Genome Haploid Length 125,539,316 bp 125,942,335 bp -Genome Repeat Length 8,589,406 bp 8,616,980 bp -Genome Unique Length 116,949,910 bp 117,325,355 bp -Model Fit 97.4796% 98.4813% -Read Error Rate 0.107764% 0.107764% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 7f5161a..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 859757618 -2 52566257 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index e755a90..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.093e-03 1.087e-03 5.606 3.2e-08 *** -r 1.113e-02 3.112e-05 357.629 < 2e-16 *** -kmercov 1.651e+01 9.356e-03 1764.322 < 2e-16 *** -bias 2.430e+00 1.393e-02 174.536 < 2e-16 *** -length 1.182e+08 9.232e+04 1280.687 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9139 on 585 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 1.623e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f5cd5a8..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index da11b0a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1b173aa..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 195587023657.06 -round 1 trimming to 11 trying 4peak model... converged. score: 48952978288.0315 -round 2 trimming to 16 trying 4peak model... converged. score: 95682126009.393 -round 3 trimming to 21 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index b737d9e..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.10681% 1.11926% -Genome Haploid Length 127,506,866 bp 127,796,272 bp -Genome Repeat Length 10,099,613 bp 10,122,537 bp -Genome Unique Length 117,407,252 bp 117,673,735 bp -Model Fit 97.9063% 98.9691% -Read Error Rate 1.01799% 1.01799% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index ecde8c8..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1492767035 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index eb85945..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.042e-02 8.257e-04 12.62 <2e-16 *** -r 1.149e-02 3.125e-05 367.69 <2e-16 *** -kmercov 1.334e+01 6.209e-03 2148.61 <2e-16 *** -bias 1.934e+00 9.856e-03 196.27 <2e-16 *** -length 1.194e+08 7.391e+04 1615.82 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 7077 on 584 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 9.264e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 949b7f7..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 13cb8c8..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index df474a7..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... unconverged -round 1 trimming to 12 trying 4peak model... converged. score: 30530123683.0377 -round 2 trimming to 17 trying 4peak model... converged. score: 323219811005.846 -round 3 trimming to 22 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9799d1c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.1429% 1.1554% -Genome Haploid Length 130,237,477 bp 130,480,162 bp -Genome Repeat Length 12,115,601 bp 12,138,177 bp -Genome Unique Length 118,121,876 bp 118,341,985 bp -Model Fit 98.1422% 99.3206% -Read Error Rate 1.98738% 1.98738% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 5347285..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107260247 -2 1455907 -3 172922 -4 106995 -5 168367 -6 312081 -7 535885 -8 855951 -9 1274217 -10 1790128 -11 2370191 -12 3013732 -13 3650838 -14 4247465 -15 4784377 -16 5210537 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-516 655 -517 594 -518 594 -519 592 -520 658 -521 627 -522 647 -523 586 -524 622 -525 636 -526 644 -527 605 -528 614 -529 632 -530 631 -531 623 -532 624 -533 611 -534 559 -535 632 -536 611 -537 584 -538 595 -539 638 -540 600 -541 576 -542 564 -543 607 -544 648 -545 579 -546 592 -547 553 -548 596 -549 604 -550 612 -551 553 -552 603 -553 584 -554 601 -555 543 -556 605 -557 538 -558 537 -559 599 -560 554 -561 575 -562 566 -563 580 -564 525 -565 512 -566 582 -567 556 -568 531 -569 569 -570 592 -571 524 -572 573 -573 559 -574 580 -575 531 -576 519 -577 523 -578 524 -579 546 -580 515 -581 570 -582 575 -583 575 -584 540 -585 574 -586 530 -587 556 -588 503 -589 565 -590 511 -591 546 -592 535 -593 532 -594 527 -595 514 -596 525 -597 575 -598 545 -599 578 -600 535 -601 224225 diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index f71be5d..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.541e-03 8.036e-04 10.63 <2e-16 *** -r 2.128e-02 2.255e-05 943.70 <2e-16 *** -kmercov 1.977e+01 6.277e-03 3150.23 <2e-16 *** -bias 1.013e+00 3.453e-03 293.33 <2e-16 *** -length 1.195e+08 6.904e+04 1730.27 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 9703 on 582 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 4.151e-07 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d9e602d..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index be84102..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a070023..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 59065370453.4542 -round 1 trimming to 9 trying 4peak model... converged. score: 56544592240.3038 -round 2 trimming to 14 trying 4peak model... converged. score: 55182533727.0908 -round 3 trimming to 19 trying 4peak model... converged. score: 98686617731.1235 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cdcdb40..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.1239% 2.13292% -Genome Haploid Length 128,040,277 bp 128,202,960 bp -Genome Repeat Length 9,545,559 bp 9,557,687 bp -Genome Unique Length 118,494,718 bp 118,645,272 bp -Model Fit 98.1056% 98.9377% -Read Error Rate 0.105982% 0.105982% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 304c4a7..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 875919099 -2 47300820 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index bcaba3c..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 6.235e-03 1.025e-03 6.081 2.16e-09 *** -r 2.121e-02 3.076e-05 689.541 < 2e-16 *** -kmercov 1.637e+01 7.433e-03 2202.653 < 2e-16 *** -bias 8.714e-01 4.439e-03 196.305 < 2e-16 *** -length 1.203e+08 8.556e+04 1405.897 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12900 on 585 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.804e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f0d4786..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3c1c3eb..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a6fcf9d..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 168600261837.031 -round 1 trimming to 11 trying 4peak model... converged. score: 97429437301.7421 -round 2 trimming to 16 trying 4peak model... converged. score: 198458739872.798 -round 3 trimming to 21 trying 4peak model... converged. score: 924031334151.492 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 13d6bcc..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.11478% 2.12708% -Genome Haploid Length 129,727,859 bp 129,963,658 bp -Genome Repeat Length 10,200,103 bp 10,218,643 bp -Genome Unique Length 119,527,757 bp 119,745,015 bp -Model Fit 97.8486% 98.7069% -Read Error Rate 1.00845% 1.00845% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index ab2391d..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1528589493 -2 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b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6ff558f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 8.066e-03 1.010e-03 7.987 7.37e-15 *** -r 2.113e-02 3.349e-05 630.870 < 2e-16 *** -kmercov 1.318e+01 7.326e-03 1799.711 < 2e-16 *** -bias 7.489e-01 4.752e-03 157.598 < 2e-16 *** -length 1.221e+08 8.642e+04 1412.752 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 12940 on 586 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 3.208e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index d23d152..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9e40b4a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9195d62..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 690472789634.262 -round 1 trimming to 10 trying 4peak model... converged. score: 98360029740.6915 -round 2 trimming to 15 trying 4peak model... converged. score: 369410451024.703 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d5a2563..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.10611% 2.11951% -Genome Haploid Length 132,807,158 bp 133,102,660 bp -Genome Repeat Length 11,712,703 bp 11,738,765 bp -Genome Unique Length 121,094,454 bp 121,363,895 bp -Model Fit 97.9262% 98.8612% -Read Error Rate 1.9725% 1.9725% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 800a80f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107232139 -2 1568411 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index e411c57..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.882e-03 1.741e-03 -3.379 0.000776 *** -r 2.202e-02 6.414e-05 343.371 < 2e-16 *** -kmercov 2.012e+01 2.043e-02 984.716 < 2e-16 *** -bias 2.051e+00 1.526e-02 134.412 < 2e-16 *** -length 1.185e+08 1.304e+05 908.130 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 15390 on 583 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 8.856e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 936c881..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3e0c3b8..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5551c0d..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 176852277205.117 -round 1 trimming to 8 trying 4peak model... converged. score: 148285075658.049 -round 2 trimming to 13 trying 4peak model... converged. score: 141910703238.876 -round 3 trimming to 18 trying 4peak model... converged. score: 283456843404.136 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 7227c54..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.18953% 2.21519% -Genome Haploid Length 125,591,578 bp 126,102,780 bp -Genome Repeat Length 6,774,520 bp 6,802,095 bp -Genome Unique Length 118,817,058 bp 119,300,685 bp -Model Fit 97.39% 98.2079% -Read Error Rate 0.108846% 0.108846% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index cd4ac70..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 874074979 -2 48284757 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2e4cbe9..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -4.203e-03 1.818e-03 -2.312 0.0212 * -r 2.170e-02 6.974e-05 311.213 <2e-16 *** -kmercov 1.659e+01 1.852e-02 895.400 <2e-16 *** -bias 1.718e+00 1.438e-02 119.424 <2e-16 *** -length 1.195e+08 1.304e+05 916.667 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 16420 on 586 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 3.209e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e1981f7..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b3d36bf..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f2a1d1a..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 536637585763.974 -round 1 trimming to 10 trying 4peak model... converged. score: 158057788956.642 -round 2 trimming to 15 trying 4peak model... converged. score: 316757107318.416 -round 3 trimming to 20 trying 4peak model... converged. score: 894876060384.562 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 31ed3d9..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.1564% 2.18429% -Genome Haploid Length 127,822,297 bp 128,394,593 bp -Genome Repeat Length 8,117,010 bp 8,153,352 bp -Genome Unique Length 119,705,287 bp 120,241,241 bp -Model Fit 97.3425% 98.2751% -Read Error Rate 1.01043% 1.01043% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 13c7d23..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1523758677 -2 109886192 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b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index e847b3f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.475e-03 1.626e-03 0.907 0.365 -r 2.136e-02 6.668e-05 320.370 <2e-16 *** -kmercov 1.326e+01 1.536e-02 863.358 <2e-16 *** -bias 1.472e+00 1.447e-02 101.707 <2e-16 *** -length 1.222e+08 1.394e+05 876.650 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 14210 on 586 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 3.488e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2da50f1..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 2b8fa7a..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 885c060..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 863322108767.786 -round 1 trimming to 10 trying 4peak model... converged. score: 126095483755.49 -round 2 trimming to 15 trying 4peak model... converged. score: 439899590398.598 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index d218285..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.12287% 2.14955% -Genome Haploid Length 131,919,385 bp 132,531,996 bp -Genome Repeat Length 10,161,275 bp 10,208,463 bp -Genome Unique Length 121,758,110 bp 122,323,534 bp -Model Fit 97.7339% 98.7219% -Read Error Rate 1.96986% 1.96986% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 2f9caa7..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 107393986 -2 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index d51f013..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.059e-02 2.755e-03 -3.844 0.000134 *** -r 2.218e-02 1.153e-04 192.418 < 2e-16 *** -kmercov 2.031e+01 3.849e-02 527.525 < 2e-16 *** -bias 2.987e+00 3.733e-02 80.002 < 2e-16 *** -length 1.178e+08 2.018e+05 583.871 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 17110 on 583 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 4.071e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 77b46c1..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index a4a2425..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index fa25efa..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 288332915962.743 -round 1 trimming to 8 trying 4peak model... converged. score: 187935700565.483 -round 2 trimming to 13 trying 4peak model... converged. score: 182697883258.315 -round 3 trimming to 18 trying 4peak model... converged. score: 518786121517.436 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1881250..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.1953% 2.24142% -Genome Haploid Length 124,124,658 bp 125,069,426 bp -Genome Repeat Length 5,661,717 bp 5,704,811 bp -Genome Unique Length 118,462,941 bp 119,364,615 bp -Model Fit 97.153% 98.0113% -Read Error Rate 0.111313% 0.111313% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index c02fe5f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 872449563 -2 49408730 -3 6673390 -4 3249810 -5 2670132 -6 2696390 -7 2983224 -8 3374358 -9 3800052 -10 4208369 -11 4581015 -12 4897390 -13 5135173 -14 5309328 -15 5417327 -16 5461983 -17 5458275 -18 5404942 -19 5329212 -20 5226499 -21 5107737 -22 4963539 -23 4826616 -24 4679135 -25 4529449 -26 4381940 -27 4238504 -28 4091270 -29 3938578 -30 3793447 -31 3633897 -32 3472510 -33 3318833 -34 3152274 -35 2979996 -36 2802196 -37 2627896 -38 2456065 -39 2281265 -40 2110792 -41 1943163 -42 1780679 -43 1619939 -44 1468051 -45 1327238 -46 1193653 -47 1066845 -48 948871 -49 842323 -50 744840 -51 658542 -52 577359 -53 505878 -54 440002 -55 384745 -56 333453 -57 290157 -58 251237 -59 219082 -60 189703 -61 165951 -62 144832 -63 127233 -64 111418 -65 97537 -66 87155 -67 77750 -68 69524 -69 62595 -70 56626 -71 51592 -72 47319 -73 43267 -74 40522 -75 37698 -76 36297 -77 33763 -78 31482 -79 29706 -80 28488 -81 27014 -82 25642 -83 24293 -84 23569 -85 22404 -86 21678 -87 20448 -88 19742 -89 19071 -90 18370 -91 17871 -92 17102 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a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index b65ea31..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.841e-03 2.589e-03 -1.483 0.139 -r 2.169e-02 1.092e-04 198.512 <2e-16 *** -kmercov 1.668e+01 3.032e-02 550.150 <2e-16 *** -bias 2.423e+00 2.858e-02 84.780 <2e-16 *** -length 1.189e+08 1.804e+05 659.138 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 16920 on 586 degrees of freedom - -Number of iterations to convergence: 14 -Achieved convergence tolerance: 4.415e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2639c52..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 56fc85d..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index ea5ff1f..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 607617538348.945 -round 1 trimming to 10 trying 4peak model... converged. score: 167827122303.668 -round 2 trimming to 15 trying 4peak model... converged. score: 422247684488.971 -round 3 trimming to 20 trying 4peak model... converged. score: 873826803257.463 -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 65907a6..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.14666% 2.19035% -Genome Haploid Length 126,805,631 bp 127,730,966 bp -Genome Repeat Length 7,929,291 bp 7,987,154 bp -Genome Unique Length 118,876,339 bp 119,743,813 bp -Model Fit 97.3458% 98.307% -Read Error Rate 1.01381% 1.01381% diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index e8d79fa..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,601 +0,0 @@ -1 1518996375 -2 112065996 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-512 458 -513 414 -514 428 -515 438 -516 441 -517 431 -518 426 -519 462 -520 444 -521 401 -522 442 -523 417 -524 415 -525 414 -526 411 -527 433 -528 384 -529 404 -530 413 -531 442 -532 368 -533 416 -534 407 -535 399 -536 386 -537 405 -538 399 -539 385 -540 380 -541 428 -542 403 -543 431 -544 380 -545 367 -546 414 -547 352 -548 379 -549 361 -550 376 -551 335 -552 343 -553 353 -554 392 -555 332 -556 339 -557 349 -558 323 -559 383 -560 336 -561 313 -562 335 -563 358 -564 342 -565 336 -566 300 -567 338 -568 348 -569 309 -570 304 -571 351 -572 308 -573 323 -574 338 -575 353 -576 343 -577 284 -578 367 -579 327 -580 305 -581 306 -582 326 -583 329 -584 336 -585 308 -586 313 -587 279 -588 306 -589 318 -590 302 -591 306 -592 329 -593 328 -594 314 -595 308 -596 326 -597 344 -598 317 -599 340 -600 317 -601 129996 diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 36367fe..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 3.529e-03 1.973e-03 1.789 0.0741 . -r 2.081e-02 8.344e-05 249.363 <2e-16 *** -kmercov 1.317e+01 1.933e-02 681.352 <2e-16 *** -bias 2.192e+00 2.782e-02 78.794 <2e-16 *** -length 1.235e+08 2.135e+05 578.466 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 11310 on 585 degrees of freedom - -Number of iterations to convergence: 11 -Achieved convergence tolerance: 7.248e-06 - diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9650d85..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 6c2e691..0000000 Binary files a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1f2c6b1..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 274630064107.047 -round 1 trimming to 11 trying 4peak model... converged. score: 127179768458.624 -round 2 trimming to 16 trying 4peak model... converged. score: 485682614855.927 -round 3 trimming to 21 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 88dbab6..0000000 --- a/analysis/simulation_results_50x/Drosophila_melanogaster.BDGP6.dna_sm.main_chr.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.06405% 2.09743% -Genome Haploid Length 132,958,527 bp 133,741,382 bp -Genome Repeat Length 10,192,296 bp 10,252,308 bp -Genome Unique Length 122,766,231 bp 123,489,074 bp -Model Fit 97.9302% 98.8922% -Read Error Rate 1.96362% 1.96362% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 0b38cbf..0000000 --- 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-465 7 -466 7 -467 6 -468 10 -469 9 -470 10 -471 4 -472 3 -473 7 -474 1 -475 4 -476 1 -477 4 -478 2 -479 1 -480 1 -481 1 -482 1 -487 1 -488 1 -489 2 -491 1 -492 3 -493 1 -494 1 -495 1 -497 3 -502 1 -503 1 -518 1 -524 1 -537 1 -544 1 -545 1 -553 1 -558 2 -586 1 -589 4 -591 1 -592 1 -594 2 -595 1 -601 1248 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 70a1ebc..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.314e-03 4.648e-04 2.826 0.0049 ** -r 1.121e-03 8.994e-06 124.642 <2e-16 *** -kmercov 1.965e+01 2.598e-03 7560.932 <2e-16 *** -bias 9.805e-01 2.435e-03 402.651 <2e-16 *** -length 4.517e+06 2.681e+03 1684.626 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 301.8 on 497 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 2.015e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5bb675f..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4e4905a..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 9c552e9..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... round 0 trimming to 118 trying 4peak model... converged. score: 45252776.8158785 -round 1 trimming to 9 trying 4peak model... round 1 trimming to 123 trying 4peak model... converged. score: 45252808.1569478 -round 2 trimming to 14 trying 4peak model... round 2 trimming to 128 trying 4peak model... converged. score: 45425153.8364137 -round 3 trimming to 19 trying 4peak model... round 3 trimming to 133 trying 4peak model... converged. score: 56751282.0669025 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index ec66ca6..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.110301% 0.113898% -Genome Haploid Length 4,606,838 bp 4,609,276 bp -Genome Repeat Length 97,336 bp 97,388 bp -Genome Unique Length 4,509,502 bp 4,511,888 bp -Model Fit 98.6048% 98.9789% -Read Error Rate 0.100669% 0.100669% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 6180f64..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,581 +0,0 @@ -1 31621802 -2 1670819 -3 95286 -4 13006 -5 4517 -6 3027 -7 3674 -8 4975 -9 6988 -10 9201 -11 11736 -12 14644 -13 18028 -14 21668 -15 26427 -16 31974 -17 39112 -18 48435 -19 60746 -20 73287 -21 89166 -22 106151 -23 125753 -24 143957 -25 162752 -26 181443 -27 197807 -28 212404 -29 222301 -30 229200 -31 230958 -32 231380 -33 225386 -34 216475 -35 206205 -36 192191 -37 176595 -38 160744 -39 144242 -40 127742 -41 111480 -42 96438 -43 82680 -44 69490 -45 58501 -46 47792 -47 38815 -48 31132 -49 25041 -50 19686 -51 15707 -52 12402 -53 9756 -54 7590 -55 5996 -56 4687 -57 3494 -58 2687 -59 2178 -60 1711 -61 1475 -62 1093 -63 1015 -64 853 -65 719 -66 676 -67 617 -68 537 -69 530 -70 492 -71 433 -72 444 -73 399 -74 354 -75 340 -76 307 -77 285 -78 293 -79 255 -80 257 -81 250 -82 248 -83 234 -84 203 -85 205 -86 214 -87 224 -88 228 -89 208 -90 233 -91 206 -92 212 -93 212 -94 195 -95 229 -96 214 -97 215 -98 228 -99 211 -100 213 -101 172 -102 203 -103 189 -104 208 -105 185 -106 175 -107 179 -108 168 -109 195 -110 150 -111 161 -112 173 -113 142 -114 144 -115 149 -116 118 -117 139 -118 121 -119 121 -120 113 -121 107 -122 112 -123 86 -124 94 -125 90 -126 76 -127 78 -128 85 -129 83 -130 74 -131 73 -132 71 -133 75 -134 77 -135 71 -136 85 -137 70 -138 100 -139 80 -140 79 -141 82 -142 87 -143 60 -144 79 -145 52 -146 62 -147 53 -148 54 -149 63 -150 52 -151 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-567 10 -568 8 -569 6 -570 10 -571 12 -572 12 -573 7 -574 3 -575 9 -576 5 -577 5 -578 6 -579 4 -580 4 -581 4 -582 3 -583 7 -584 5 -585 9 -586 3 -587 6 -588 9 -589 6 -590 8 -591 5 -592 6 -593 6 -594 10 -595 4 -596 8 -597 5 -598 13 -599 5 -600 7 -601 152 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index c86e2b5..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.733e-03 3.225e-04 5.374 1.12e-07 *** -r 1.130e-03 6.509e-06 173.604 < 2e-16 *** -kmercov 1.625e+01 1.582e-03 10274.376 < 2e-16 *** -bias 8.142e-01 1.595e-03 510.474 < 2e-16 *** -length 4.514e+06 1.808e+03 2496.052 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 221.3 on 570 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 7.613e-07 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a49233e..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index 78ef272..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e97fb66..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 27012728.7637801 -round 1 trimming to 11 trying 4peak model... converged. score: 27146338.2452587 -round 2 trimming to 16 trying 4peak model... converged. score: 42955806.526208 -round 3 trimming to 21 trying 4peak model... converged. score: 331751196.433023 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 06106ae..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.111691% 0.114295% -Genome Haploid Length 4,626,115 bp 4,627,916 bp -Genome Repeat Length 120,759 bp 120,806 bp -Genome Unique Length 4,505,355 bp 4,507,110 bp -Model Fit 98.906% 99.3005% -Read Error Rate 0.999462% 0.999462% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 274f6e9..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,516 +0,0 @@ -1 54870523 -2 4025802 -3 318344 -4 44579 -5 17440 -6 11390 -7 10674 -8 12896 -9 17420 -10 22165 -11 28420 -12 36758 -13 47333 -14 60159 -15 77355 -16 97650 -17 120310 -18 143903 -19 169889 -20 196111 -21 219809 -22 240236 -23 257084 -24 266628 -25 270635 -26 267904 -27 259922 -28 246305 -29 230216 -30 209109 -31 186880 -32 164270 -33 142056 -34 120851 -35 100522 -36 82678 -37 66876 -38 53727 -39 42181 -40 32911 -41 25360 -42 19287 -43 14379 -44 10860 -45 7983 -46 5951 -47 4378 -48 3458 -49 2569 -50 1972 -51 1538 -52 1208 -53 1009 -54 843 -55 790 -56 709 -57 655 -58 627 -59 567 -60 496 -61 503 -62 464 -63 487 -64 451 -65 443 -66 414 -67 359 -68 351 -69 326 -70 312 -71 273 -72 272 -73 287 -74 284 -75 284 -76 295 -77 287 -78 257 -79 265 -80 239 -81 254 -82 236 -83 215 -84 232 -85 221 -86 186 -87 200 -88 215 -89 174 -90 191 -91 190 -92 200 -93 171 -94 162 -95 153 -96 109 -97 111 -98 116 -99 94 -100 105 -101 107 -102 101 -103 102 -104 90 -105 94 -106 105 -107 86 -108 84 -109 87 -110 79 -111 79 -112 91 -113 76 -114 59 -115 62 -116 71 -117 68 -118 58 -119 58 -120 61 -121 62 -122 55 -123 65 -124 57 -125 44 -126 50 -127 53 -128 69 -129 56 -130 62 -131 58 -132 58 -133 48 -134 56 -135 62 -136 65 -137 56 -138 80 -139 55 -140 49 -141 57 -142 60 -143 48 -144 56 -145 56 -146 46 -147 52 -148 44 -149 56 -150 55 -151 51 -152 47 -153 36 -154 53 -155 63 -156 57 -157 63 -158 79 -159 61 -160 67 -161 74 -162 92 -163 89 -164 79 -165 74 -166 68 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13 -443 7 -444 12 -445 11 -446 9 -447 13 -448 16 -449 10 -450 11 -451 13 -452 12 -453 9 -454 12 -455 8 -456 14 -457 10 -458 7 -459 7 -460 5 -461 8 -462 12 -463 8 -464 15 -465 10 -466 8 -467 5 -468 5 -469 8 -470 9 -471 13 -472 9 -473 7 -474 11 -475 13 -476 13 -477 9 -478 7 -479 9 -480 8 -481 10 -482 8 -483 5 -484 8 -485 7 -486 8 -487 5 -488 6 -489 4 -490 4 -491 8 -492 6 -493 7 -494 5 -495 14 -496 7 -497 3 -498 7 -499 6 -500 7 -501 6 -502 4 -503 5 -504 5 -505 7 -506 4 -507 6 -508 3 -509 3 -510 5 -511 1 -512 2 -513 3 -514 3 -515 4 -516 1 -517 1 -520 5 -524 1 -525 1 -540 1 -553 1 -555 1 -577 1 -581 1 -584 1 -585 1 -601 55 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index ae31c94..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 1.684e-03 3.431e-04 4.909 1.24e-06 *** -r 1.203e-03 7.370e-06 163.214 < 2e-16 *** -kmercov 1.314e+01 1.453e-03 9043.747 < 2e-16 *** -bias 6.426e-01 1.593e-03 403.266 < 2e-16 *** -length 4.512e+06 1.848e+03 2441.337 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 248.3 on 504 degrees of freedom - -Number of iterations to convergence: 5 -Achieved convergence tolerance: 1.517e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 7d69e37..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index fed8781..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 052cae8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 7 trying 4peak model... converged. score: 30482031.3036778 -round 1 trimming to 12 trying 4peak model... converged. score: 40502095.9234742 -round 2 trimming to 17 trying 4peak model... converged. score: 435166110.279603 -round 3 trimming to 22 trying 4peak model... converged. score: 3771873045.02734 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index c84da50..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.118812% 0.12176% -Genome Haploid Length 4,627,290 bp 4,629,337 bp -Genome Repeat Length 124,246 bp 124,301 bp -Genome Unique Length 4,503,045 bp 4,505,037 bp -Model Fit 98.9279% 99.323% -Read Error Rate 1.99845% 1.99845% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index b242f10..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,551 +0,0 @@ -1 3800992 -2 28884 -3 883 -4 953 -5 1447 -6 1973 -7 2896 -8 4067 -9 5170 -10 6508 -11 8450 -12 10011 -13 12574 -14 15182 -15 17463 -16 21296 -17 25290 -18 29923 -19 35847 -20 41193 -21 48516 -22 55925 -23 63841 -24 73107 -25 82710 -26 92352 -27 101129 -28 112276 -29 122031 -30 131732 -31 140255 -32 147333 -33 153469 -34 158965 -35 162777 -36 162561 -37 165949 -38 162776 -39 161323 -40 159799 -41 155947 -42 149427 -43 144315 -44 139174 -45 131588 -46 123318 -47 114365 -48 106032 -49 97618 -50 89770 -51 82367 -52 73083 -53 66295 -54 59250 -55 52417 -56 45998 -57 40152 -58 35100 -59 31172 -60 26948 -61 22996 -62 19166 -63 16677 -64 14092 -65 12091 -66 9849 -67 8497 -68 7252 -69 5758 -70 5032 -71 4274 -72 3673 -73 2911 -74 2393 -75 2125 -76 1726 -77 1494 -78 1289 -79 1047 -80 973 -81 741 -82 630 -83 578 -84 483 -85 531 -86 475 -87 374 -88 336 -89 349 -90 275 -91 327 -92 264 -93 286 -94 289 -95 250 -96 235 -97 251 -98 261 -99 209 -100 233 -101 240 -102 254 -103 227 -104 208 -105 224 -106 194 -107 234 -108 203 -109 189 -110 179 -111 194 -112 178 -113 186 -114 219 -115 200 -116 157 -117 142 -118 142 -119 132 -120 151 -121 134 -122 128 -123 132 -124 128 -125 119 -126 145 -127 120 -128 143 -129 140 -130 141 -131 148 -132 155 -133 123 -134 129 -135 133 -136 114 -137 114 -138 97 -139 95 -140 75 -141 79 -142 104 -143 79 -144 76 -145 83 -146 101 -147 95 -148 89 -149 89 -150 94 -151 95 -152 89 -153 87 -154 80 -155 76 -156 71 -157 76 -158 95 -159 78 -160 72 -161 56 -162 76 -163 59 -164 70 -165 60 -166 65 -167 76 -168 68 -169 78 -170 67 -171 63 -172 83 -173 78 -174 64 -175 62 -176 55 -177 75 -178 42 -179 61 -180 50 -181 42 -182 40 -183 47 -184 50 -185 47 -186 49 -187 32 -188 39 -189 45 -190 39 -191 25 -192 33 -193 42 -194 40 -195 37 -196 36 -197 42 -198 30 -199 35 -200 26 -201 33 -202 28 -203 44 -204 33 -205 34 -206 27 -207 34 -208 24 -209 42 -210 33 -211 22 -212 38 -213 33 -214 27 -215 34 -216 39 -217 30 -218 45 -219 31 -220 26 -221 29 -222 35 -223 29 -224 35 -225 39 -226 32 -227 28 -228 33 -229 34 -230 33 -231 24 -232 36 -233 35 -234 45 -235 40 -236 42 -237 64 -238 41 -239 34 -240 49 -241 33 -242 43 -243 40 -244 42 -245 38 -246 46 -247 38 -248 51 -249 52 -250 50 -251 50 -252 61 -253 53 -254 54 -255 45 -256 54 -257 69 -258 52 -259 65 -260 68 -261 64 -262 76 -263 72 -264 83 -265 65 -266 76 -267 68 -268 87 -269 62 -270 86 -271 64 -272 67 -273 68 -274 58 -275 64 -276 63 -277 66 -278 77 -279 63 -280 79 -281 55 -282 84 -283 73 -284 82 -285 82 -286 70 -287 72 -288 61 -289 63 -290 53 -291 63 -292 58 -293 44 -294 70 -295 71 -296 57 -297 53 -298 50 -299 60 -300 43 -301 41 -302 30 -303 44 -304 32 -305 38 -306 31 -307 28 -308 31 -309 37 -310 23 -311 24 -312 22 -313 35 -314 25 -315 25 -316 16 -317 23 -318 18 -319 18 -320 11 -321 18 -322 15 -323 14 -324 11 -325 7 -326 14 -327 12 -328 11 -329 6 -330 6 -331 8 -332 14 -333 9 -334 12 -335 8 -336 4 -337 4 -338 10 -339 10 -340 5 -341 6 -342 3 -343 6 -344 6 -345 5 -346 6 -347 7 -348 8 -349 5 -350 7 -351 3 -352 2 -354 4 -355 2 -356 5 -357 2 -358 2 -359 3 -360 5 -361 10 -362 3 -363 10 -364 11 -365 7 -366 5 -367 8 -368 10 -369 9 -370 8 -371 3 -372 11 -373 18 -374 11 -375 9 -376 12 -377 9 -378 11 -379 19 -380 9 -381 8 -382 14 -383 19 -384 17 -385 12 -386 14 -387 14 -388 21 -389 16 -390 16 -391 13 -392 14 -393 9 -394 10 -395 14 -396 8 -397 12 -398 15 -399 12 -400 16 -401 8 -402 12 -403 19 -404 10 -405 11 -406 11 -407 11 -408 13 -409 14 -410 12 -411 16 -412 5 -413 11 -414 8 -415 16 -416 11 -417 11 -418 8 -419 14 -420 8 -421 12 -422 9 -423 6 -424 11 -425 11 -426 13 -427 11 -428 3 -429 8 -430 18 -431 5 -432 10 -433 5 -434 16 -435 11 -436 7 -437 12 -438 13 -439 10 -440 10 -441 7 -442 11 -443 10 -444 10 -445 11 -446 7 -447 14 -448 9 -449 7 -450 13 -451 11 -452 8 -453 6 -454 15 -455 8 -456 8 -457 8 -458 6 -459 5 -460 12 -461 9 -462 8 -463 11 -464 6 -465 10 -466 10 -467 10 -468 10 -469 6 -470 8 -471 6 -472 7 -473 4 -474 1 -475 6 -476 4 -477 2 -478 7 -479 7 -480 7 -481 7 -482 8 -483 4 -484 5 -485 6 -486 5 -487 3 -488 5 -489 1 -490 3 -491 2 -492 2 -493 1 -494 1 -495 1 -497 1 -498 2 -499 1 -502 1 -503 1 -505 1 -508 1 -510 2 -518 1 -524 2 -536 1 -546 1 -548 1 -549 1 -552 2 -553 1 -554 1 -556 1 -557 2 -558 1 -561 3 -562 1 -564 1 -565 1 -566 1 -567 2 -568 5 -569 1 -570 1 -572 3 -573 4 -574 4 -575 1 -576 1 -577 3 -578 1 -579 3 -580 3 -581 1 -582 2 -583 1 -584 4 -587 2 -588 4 -589 3 -590 1 -591 3 -592 1 -593 3 -594 6 -595 2 -596 4 -597 1 -598 4 -599 7 -600 3 -601 1158 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2a2a455..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -5.067e-03 8.150e-04 -6.217 1.02e-09 *** -r 1.388e-03 1.786e-05 77.686 < 2e-16 *** -kmercov 1.984e+01 5.582e-03 3553.557 < 2e-16 *** -bias 1.962e+00 6.912e-03 283.850 < 2e-16 *** -length 4.486e+06 3.981e+03 1126.798 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 428.3 on 538 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 7.877e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e343b63..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 4f0ea84..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 6e9651f..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 98730803.3300178 -round 1 trimming to 8 trying 4peak model... converged. score: 98730693.1023668 -round 2 trimming to 13 trying 4peak model... converged. score: 100146915.366856 -round 3 trimming to 18 trying 4peak model... converged. score: 145739147.692941 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2bf5cf7..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.135198% 0.142343% -Genome Haploid Length 4,563,624 bp 4,568,764 bp -Genome Repeat Length 57,703 bp 57,768 bp -Genome Unique Length 4,505,921 bp 4,510,996 bp -Model Fit 97.9298% 98.3909% -Read Error Rate 0.100641% 0.100641% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 0c35084..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,524 +0,0 @@ -1 31562792 -2 1690155 -3 99031 -4 14983 -5 6312 -6 5264 -7 6285 -8 8537 -9 11024 -10 13604 -11 17693 -12 21628 -13 26736 -14 33797 -15 40685 -16 49819 -17 59580 -18 69758 -19 82430 -20 94891 -21 108856 -22 122870 -23 135976 -24 147303 -25 159312 -26 169225 -27 178355 -28 184799 -29 188856 -30 192104 -31 192527 -32 190614 -33 186788 -34 181884 -35 175458 -36 166200 -37 156168 -38 144364 -39 133160 -40 121391 -41 110515 -42 98937 -43 88442 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b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index e6a07e7..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -3.513e-03 7.718e-04 -4.552 6.63e-06 *** -r 1.421e-03 1.751e-05 81.164 < 2e-16 *** -kmercov 1.639e+01 4.539e-03 3609.937 < 2e-16 *** -bias 1.634e+00 5.954e-03 274.361 < 2e-16 *** -length 4.488e+06 3.638e+03 1233.867 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 425.5 on 513 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.98e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 9f736f0..0000000 Binary files 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a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a549407..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 92667122.3719823 -round 1 trimming to 11 trying 4peak model... converged. score: 95070977.6944061 -round 2 trimming to 16 trying 4peak model... converged. score: 235805130.797832 -round 3 trimming to 21 trying 4peak model... converged. score: 2584079852.87162 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 3b0f3b5..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.138579% 0.145581% -Genome Haploid Length 4,582,358 bp 4,587,439 bp -Genome Repeat Length 80,829 bp 80,919 bp -Genome Unique Length 4,501,529 bp 4,506,520 bp -Model Fit 98.0808% 98.5185% -Read Error Rate 0.999863% 0.999863% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 501bfb5..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,523 +0,0 @@ -1 54735593 -2 4088509 -3 332711 -4 49806 -5 20436 -6 14470 -7 15401 -8 19310 -9 25500 -10 33152 -11 41855 -12 53698 -13 67515 -14 83029 -15 99685 -16 118817 -17 137811 -18 157337 -19 176240 -20 192931 -21 208013 -22 218319 -23 224490 -24 228069 -25 230833 -26 226245 -27 218606 -28 209623 -29 197337 -30 185142 -31 169461 -32 152956 -33 136922 -34 120964 -35 106496 -36 92395 -37 79064 -38 67440 -39 57018 -40 47259 -41 39282 -42 32104 -43 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b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 2ccca17..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.536e-03 5.234e-04 -4.846 1.68e-06 *** -r 1.432e-03 1.253e-05 114.244 < 2e-16 *** -kmercov 1.323e+01 2.590e-03 5108.408 < 2e-16 *** -bias 1.306e+00 3.627e-03 360.018 < 2e-16 *** -length 4.492e+06 2.365e+03 1899.095 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 303 on 512 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 1.945e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 60bf3cb..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 7b56c7f..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 37d7563..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 35664117.065729 -round 1 trimming to 11 trying 4peak model... converged. score: 39318195.2881278 -round 2 trimming to 16 trying 4peak model... converged. score: 293010483.737241 -round 3 trimming to 21 trying 4peak model... converged. score: 12547258621.8013 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index aa4b828..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.140675% 0.145688% -Genome Haploid Length 4,594,468 bp 4,598,067 bp -Genome Repeat Length 92,976 bp 93,049 bp -Genome Unique Length 4,501,492 bp 4,505,018 bp -Model Fit 98.8203% 99.2613% -Read Error Rate 1.99927% 1.99927% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 81af929..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,570 +0,0 @@ -1 3808645 -2 29597 -3 1633 -4 1903 -5 2682 -6 3610 -7 5054 -8 6194 -9 7982 -10 9990 -11 12185 -12 14835 -13 17921 -14 21980 -15 25946 -16 31025 -17 35949 -18 42700 -19 47937 -20 53503 -21 62325 -22 68534 -23 77163 -24 84669 -25 92242 -26 100558 -27 107657 -28 112614 -29 118391 -30 123896 -31 130562 -32 134797 -33 137742 -34 141761 -35 142741 -36 144106 -37 145151 -38 143893 -39 140539 -40 138179 -41 134687 -42 131382 -43 125314 -44 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-577 4 -578 4 -579 3 -580 2 -581 8 -582 4 -583 2 -584 4 -585 2 -586 5 -587 4 -588 3 -589 3 -590 6 -591 6 -592 3 -593 3 -594 3 -595 5 -596 8 -597 4 -598 1 -599 2 -600 3 -601 1120 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 20644bc..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -9.626e-03 1.044e-03 -9.223 <2e-16 *** -r 1.671e-03 2.457e-05 67.999 <2e-16 *** -kmercov 2.000e+01 8.009e-03 2497.238 <2e-16 *** -bias 2.964e+00 1.224e-02 242.108 <2e-16 *** -length 4.457e+06 4.245e+03 1049.911 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 434.1 on 562 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 1.011e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 1994879..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 96cc231..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 961f983..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 105324468.137518 -round 1 trimming to 8 trying 4peak model... converged. score: 105335931.712512 -round 2 trimming to 13 trying 4peak model... converged. score: 114159914.784131 -round 3 trimming to 18 trying 4peak model... converged. score: 260365495.644669 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index cd28be1..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.162185% 0.172014% -Genome Haploid Length 4,524,596 bp 4,531,849 bp -Genome Repeat Length 28,686 bp 28,732 bp -Genome Unique Length 4,495,910 bp 4,503,117 bp -Model Fit 97.7358% 98.2878% -Read Error Rate 0.100827% 0.100827% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index b532db4..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,580 +0,0 @@ -1 31492210 -2 1729868 -3 105454 -4 16125 -5 8309 -6 7673 -7 9680 -8 13013 -9 16245 -10 19835 -11 25302 -12 30942 -13 37478 -14 45018 -15 53572 -16 62963 -17 72123 -18 82660 -19 92661 -20 103419 -21 114940 -22 125443 -23 135354 -24 143101 -25 151864 -26 158543 -27 165880 -28 167719 -29 168770 -30 170624 -31 169393 -32 167318 -33 164673 -34 158987 -35 153868 -36 148061 -37 141086 -38 132238 -39 123821 -40 114822 -41 106563 -42 96809 -43 88636 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4 -578 10 -579 5 -580 11 -581 8 -582 8 -583 8 -584 7 -585 8 -586 5 -587 7 -588 4 -589 2 -590 5 -591 3 -592 5 -593 5 -594 2 -595 4 -596 4 -597 6 -598 8 -599 8 -600 7 -601 189 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index ca0aef9..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -7.416e-03 7.669e-04 -9.671 <2e-16 *** -r 1.743e-03 1.863e-05 93.583 <2e-16 *** -kmercov 1.655e+01 4.966e-03 3332.819 <2e-16 *** -bias 2.376e+00 7.790e-03 305.023 <2e-16 *** -length 4.453e+06 3.061e+03 1454.956 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 340.7 on 569 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.76e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4d50f62..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index db3b520..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3a39ad7..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 66051473.9684249 -round 1 trimming to 11 trying 4peak model... converged. score: 72344107.5750002 -round 2 trimming to 16 trying 4peak model... converged. score: 224189027.498615 -round 3 trimming to 21 trying 4peak model... converged. score: 1634029581.42928 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index da0f4e4..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.170585% 0.178036% -Genome Haploid Length 4,540,283 bp 4,545,735 bp -Genome Repeat Length 57,083 bp 57,152 bp -Genome Unique Length 4,483,199 bp 4,488,583 bp -Model Fit 98.257% 98.7739% -Read Error Rate 0.999675% 0.999675% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index da50f95..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,516 +0,0 @@ -1 54529638 -2 4150262 -3 349517 -4 53838 -5 24014 -6 20364 -7 23316 -8 28205 -9 36429 -10 45185 -11 56606 -12 68964 -13 83385 -14 98062 -15 112350 -16 128423 -17 144074 -18 159283 -19 172008 -20 183117 -21 191073 -22 198503 -23 202304 -24 204152 -25 202983 -26 200165 -27 195049 -28 186143 -29 176465 -30 166686 -31 155322 -32 142581 -33 130523 -34 118460 -35 106325 -36 95054 -37 84002 -38 73879 -39 65045 -40 55839 -41 47317 -42 40439 -43 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b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 14da0c4..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -4.757e-03 6.524e-04 -7.293 1.18e-12 *** -r 1.912e-03 1.688e-05 113.265 < 2e-16 *** -kmercov 1.338e+01 3.539e-03 3781.837 < 2e-16 *** -bias 1.905e+00 5.866e-03 324.802 < 2e-16 *** -length 4.450e+06 2.495e+03 1783.673 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 301.7 on 505 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 6.466e-07 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index dd2d9f2..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index bc52376..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index e133ccd..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 6 trying 4peak model... converged. score: 37979236.8079642 -round 1 trimming to 11 trying 4peak model... converged. score: 50969682.4083413 -round 2 trimming to 16 trying 4peak model... converged. score: 551110718.028905 -round 3 trimming to 21 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 4d14065..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.001_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 0.187812% 0.194564% -Genome Haploid Length 4,543,569 bp 4,548,377 bp -Genome Repeat Length 75,240 bp 75,319 bp -Genome Unique Length 4,468,329 bp 4,473,058 bp -Model Fit 98.7431% 99.2108% -Read Error Rate 1.99717% 1.99717% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index c17ec20..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,536 +0,0 @@ -1 3807603 -2 26852 -3 920 -4 1446 -5 3280 -6 5964 -7 10597 -8 17203 -9 25055 -10 35913 -11 47659 -12 60134 -13 74449 -14 87518 -15 97890 -16 105274 -17 112876 -18 117123 -19 119247 -20 120861 -21 119284 -22 117784 -23 116374 -24 114568 -25 113944 -26 113298 -27 115819 -28 119773 -29 126160 -30 132576 -31 139799 -32 146502 -33 154003 -34 161373 -35 165892 -36 169363 -37 170144 -38 170649 -39 168214 -40 163095 -41 156583 -42 150479 -43 141601 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a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index b331125..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d 2.589e-04 6.652e-04 0.389 0.697 -r 1.015e-02 1.330e-05 762.928 <2e-16 *** -kmercov 1.966e+01 4.414e-03 4454.889 <2e-16 *** -bias 9.827e-01 3.213e-03 305.885 <2e-16 *** -length 4.522e+06 2.800e+03 1615.289 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 352.1 on 518 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 4.639e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f9dfa59..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 9deb736..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index bc5035d..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 66132551.6667527 -round 1 trimming to 8 trying 4peak model... converged. score: 65976012.4651438 -round 2 trimming to 13 trying 4peak model... converged. score: 65967737.2284071 -round 3 trimming to 18 trying 4peak model... converged. score: 80456729.7067624 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 778a0b8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.01231% 1.01763% -Genome Haploid Length 4,610,238 bp 4,614,380 bp -Genome Repeat Length 91,387 bp 91,469 bp -Genome Unique Length 4,518,851 bp 4,522,911 bp -Model Fit 98.6974% 99.0108% -Read Error Rate 0.101453% 0.101453% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 3ecc998..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,576 +0,0 @@ -1 31860550 -2 1537187 -3 83988 -4 14814 -5 12923 -6 18441 -7 29123 -8 43502 -9 59095 -10 75712 -11 92811 -12 108341 -13 123216 -14 132439 -15 138799 -16 143515 -17 143083 -18 142855 -19 143098 -20 141973 -21 143550 -22 146692 -23 152230 -24 159402 -25 166294 -26 173699 -27 181563 -28 187477 -29 193204 -30 196664 -31 197147 -32 195684 -33 189615 -34 181057 -35 171318 -36 159657 -37 148237 -38 134926 -39 121430 -40 106057 -41 92775 -42 79937 -43 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-582 1 -583 1 -584 1 -585 1 -586 3 -587 2 -588 2 -589 3 -591 2 -592 1 -593 3 -594 1 -597 2 -598 2 -599 3 -600 2 -601 81 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 1b5c7e8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.489e-03 8.484e-04 -1.755 0.0798 . -r 1.012e-02 1.759e-05 575.435 <2e-16 *** -kmercov 1.626e+01 5.049e-03 3220.521 <2e-16 *** -bias 8.328e-01 4.030e-03 206.660 <2e-16 *** -length 4.532e+06 3.448e+03 1314.306 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 470.1 on 561 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 1.486e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 5f68a60..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a92c7e8..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 59a6f39..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 126619340.421417 -round 1 trimming to 10 trying 4peak model... converged. score: 126464756.013213 -round 2 trimming to 15 trying 4peak model... converged. score: 172307876.192373 -round 3 trimming to 20 trying 4peak model... converged. score: 591669868.039505 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 0df039a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.00893% 1.01597% -Genome Haploid Length 4,625,620 bp 4,631,368 bp -Genome Repeat Length 89,992 bp 90,103 bp -Genome Unique Length 4,535,628 bp 4,541,265 bp -Model Fit 98.3236% 98.6478% -Read Error Rate 0.996841% 0.996841% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 102d8e5..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,507 +0,0 @@ -1 55499201 -2 3735600 -3 285624 -4 53494 -5 41734 -6 53328 -7 73750 -8 97782 -9 120296 -10 141046 -11 157817 -12 168715 -13 174427 -14 178313 -15 180054 -16 181337 -17 184709 -18 190853 -19 196953 -20 205180 -21 214480 -22 222074 -23 226870 -24 231367 -25 231020 -26 225951 -27 217363 -28 205659 -29 191388 -30 173240 -31 155966 -32 135991 -33 118148 -34 100035 -35 83178 -36 68890 -37 56045 -38 44477 -39 34782 -40 27621 -41 20728 -42 16062 -43 12103 -44 8972 -45 6848 -46 5070 -47 3938 -48 2846 -49 2272 -50 1654 -51 1295 -52 1062 -53 880 -54 761 -55 724 -56 611 -57 577 -58 479 -59 491 -60 433 -61 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-454 9 -455 4 -456 8 -457 4 -458 3 -459 3 -460 5 -461 7 -462 2 -463 5 -464 5 -465 4 -466 2 -467 5 -468 1 -469 6 -470 2 -471 2 -472 1 -474 2 -475 3 -476 4 -477 3 -478 1 -481 3 -482 2 -483 2 -486 3 -487 1 -488 4 -490 3 -491 1 -492 3 -493 1 -494 1 -495 2 -496 2 -497 2 -499 2 -500 2 -503 1 -505 2 -506 2 -507 1 -509 3 -522 1 -526 1 -529 3 -533 1 -534 1 -537 1 -541 1 -544 1 -545 1 -555 1 -557 1 -587 1 -601 51 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index c848e61..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.181e-03 6.921e-04 -1.707 0.0884 . -r 1.031e-02 1.562e-05 660.151 <2e-16 *** -kmercov 1.314e+01 3.675e-03 3575.106 <2e-16 *** -bias 6.842e-01 3.307e-03 206.931 <2e-16 *** -length 4.536e+06 2.691e+03 1686.051 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 396 on 492 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 5.479e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 6d3a27f..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index f3f11a5..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index a21be58..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 109831740.989456 -round 1 trimming to 10 trying 4peak model... converged. score: 107352895.651356 -round 2 trimming to 15 trying 4peak model... converged. score: 352217410.294461 -round 3 trimming to 20 trying 4peak model... converged. score: 5236724833.39124 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 0e8fa84..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.028% 1.03424% -Genome Haploid Length 4,632,185 bp 4,637,371 bp -Genome Repeat Length 93,215 bp 93,320 bp -Genome Unique Length 4,538,970 bp 4,544,051 bp -Model Fit 98.5787% 98.9071% -Read Error Rate 1.99313% 1.99313% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 5da176c..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,597 +0,0 @@ -1 3788591 -2 29306 -3 4288 -4 7321 -5 11429 -6 17496 -7 23791 -8 32016 -9 41073 -10 49817 -11 59773 -12 68109 -13 77288 -14 87044 -15 93497 -16 100108 -17 105380 -18 110963 -19 111353 -20 115320 -21 117283 -22 120063 -23 121030 -24 122252 -25 124251 -26 128739 -27 128828 -28 131797 -29 135422 -30 138181 -31 140343 -32 141722 -33 144780 -34 144868 -35 147608 -36 144858 -37 143477 -38 142415 -39 139935 -40 135905 -41 132341 -42 126261 -43 122415 -44 114615 -45 108980 -46 102311 -47 94908 -48 88158 -49 80486 -50 72853 -51 67480 -52 60218 -53 54285 -54 48477 -55 43642 -56 38638 -57 33362 -58 29919 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3 -435 3 -436 1 -437 2 -438 4 -439 4 -440 3 -441 3 -442 1 -443 2 -444 4 -445 4 -446 6 -447 4 -448 4 -449 2 -450 3 -451 2 -452 4 -453 8 -454 6 -455 8 -456 5 -457 1 -458 2 -459 3 -460 4 -461 3 -462 5 -463 4 -464 4 -465 4 -466 2 -467 5 -468 2 -469 1 -470 4 -471 5 -472 1 -473 1 -474 1 -475 3 -476 3 -477 2 -478 6 -479 3 -480 1 -481 2 -482 1 -483 2 -484 7 -485 2 -487 3 -488 1 -489 2 -490 2 -491 1 -492 4 -493 3 -494 2 -495 2 -496 2 -497 1 -498 4 -499 4 -500 3 -501 5 -502 1 -503 4 -504 5 -505 5 -506 2 -507 3 -508 3 -510 4 -511 4 -512 3 -513 1 -516 3 -517 3 -518 1 -519 1 -520 2 -521 1 -522 1 -523 1 -524 2 -525 1 -526 3 -527 2 -528 1 -529 8 -530 7 -531 2 -532 6 -533 6 -534 3 -535 4 -536 3 -537 7 -538 2 -539 7 -540 9 -541 6 -542 6 -543 8 -544 7 -545 6 -546 5 -547 6 -548 6 -549 1 -550 6 -551 6 -552 8 -553 5 -554 7 -555 3 -556 5 -557 10 -558 4 -559 3 -560 3 -561 7 -562 2 -563 4 -564 1 -565 9 -566 6 -567 4 -568 4 -569 9 -570 7 -571 10 -572 3 -573 9 -574 12 -575 9 -576 5 -577 7 -578 15 -579 7 -580 12 -581 2 -582 10 -583 4 -584 12 -585 4 -586 12 -587 6 -588 6 -589 8 -590 9 -591 9 -592 12 -593 9 -594 6 -595 3 -596 5 -597 7 -598 8 -599 12 -600 9 -601 687 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index fe6fbec..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.862e-03 1.179e-03 -5.818 9.8e-09 *** -r 1.043e-02 2.748e-05 379.472 < 2e-16 *** -kmercov 1.982e+01 1.033e-02 1917.725 < 2e-16 *** -bias 2.014e+00 1.015e-02 198.400 < 2e-16 *** -length 4.505e+06 4.138e+03 1088.806 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 484.4 on 584 degrees of freedom - -Number of iterations to convergence: 8 -Achieved convergence tolerance: 3.175e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 33c88d8..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 55888d3..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 3a181d3..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 138047271.427273 -round 1 trimming to 8 trying 4peak model... converged. score: 132712185.637323 -round 2 trimming to 13 trying 4peak model... converged. score: 133975660.228567 -round 3 trimming to 18 trying 4peak model... converged. score: 191876558.954417 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index de314fa..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03725% 1.04824% -Genome Haploid Length 4,572,800 bp 4,582,348 bp -Genome Repeat Length 42,881 bp 42,971 bp -Genome Unique Length 4,529,919 bp 4,539,377 bp -Model Fit 98.0728% 98.4474% -Read Error Rate 0.102404% 0.102404% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index ac43774..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,584 +0,0 @@ -1 31829034 -2 1563635 -3 93477 -4 24145 -5 26065 -6 34381 -7 44950 -8 58387 -9 70663 -10 84063 -11 96179 -12 108220 -13 118142 -14 125833 -15 133105 -16 137524 -17 141513 -18 144337 -19 147350 -20 151022 -21 154140 -22 156272 -23 159010 -24 162723 -25 165099 -26 169128 -27 171538 -28 172286 -29 173293 -30 172561 -31 170356 -32 166503 -33 161221 -34 155007 -35 148029 -36 139354 -37 129963 -38 120485 -39 111923 -40 101856 -41 92416 -42 82379 -43 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-571 3 -572 2 -573 3 -574 2 -575 4 -576 1 -579 2 -580 2 -581 4 -582 1 -583 1 -584 5 -585 1 -586 2 -587 2 -588 1 -589 1 -591 1 -593 1 -594 2 -595 1 -596 1 -598 1 -599 1 -600 2 -601 76 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 45bf637..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -4.480e-03 1.194e-03 -3.751 0.000194 *** -r 1.043e-02 2.867e-05 363.977 < 2e-16 *** -kmercov 1.639e+01 8.897e-03 1841.838 < 2e-16 *** -bias 1.620e+00 9.851e-03 164.434 < 2e-16 *** -length 4.501e+06 4.140e+03 1087.157 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 514.1 on 570 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 2.529e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 86c1db7..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index e938ef8..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 525fb9c..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 169351711.606638 -round 1 trimming to 9 trying 4peak model... converged. score: 150882464.476247 -round 2 trimming to 14 trying 4peak model... converged. score: 205281272.814124 -round 3 trimming to 19 trying 4peak model... converged. score: 740593090.612353 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 9be125b..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03771% 1.04917% -Genome Haploid Length 4,585,443 bp 4,595,413 bp -Genome Repeat Length 70,224 bp 70,376 bp -Genome Unique Length 4,515,220 bp 4,525,036 bp -Model Fit 98.2922% 98.6549% -Read Error Rate 0.999128% 0.999128% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index cf175ac..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,517 +0,0 @@ -1 55334162 -2 3815770 -3 310024 -4 68969 -5 58078 -6 68958 -7 86315 -8 104740 -9 121720 -10 136597 -11 150289 -12 161491 -13 171216 -14 176588 -15 182282 -16 188399 -17 192023 -18 197170 -19 201372 -20 204643 -21 207466 -22 209296 -23 208990 -24 207646 -25 203146 -26 198008 -27 189811 -28 179092 -29 168670 -30 156050 -31 143100 -32 129201 -33 115306 -34 102998 -35 88712 -36 76630 -37 66011 -38 55911 -39 46645 -40 38722 -41 31900 -42 25819 -43 20906 -44 16823 -45 13366 -46 10801 -47 8486 -48 6668 -49 5392 -50 4208 -51 3290 -52 2578 -53 2101 -54 1708 -55 1410 -56 1147 -57 988 -58 807 -59 766 -60 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8 -465 4 -466 4 -467 10 -468 5 -469 3 -470 2 -471 6 -472 9 -473 3 -474 2 -475 2 -476 4 -477 6 -478 4 -479 5 -480 1 -481 1 -482 3 -483 3 -484 1 -485 3 -486 1 -487 1 -488 3 -489 1 -490 2 -491 2 -492 4 -493 1 -494 1 -495 2 -497 1 -498 2 -499 1 -500 1 -501 3 -502 2 -504 3 -505 3 -507 2 -509 2 -510 1 -511 1 -512 1 -513 1 -515 1 -517 2 -518 1 -520 1 -521 1 -523 2 -530 2 -532 1 -533 1 -535 1 -542 1 -549 1 -551 1 -558 1 -568 1 -570 1 -572 1 -585 1 -591 1 -600 1 -601 50 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index cdfa0fe..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -9.665e-03 1.691e-03 -5.714 1.89e-08 *** -r 1.018e-02 4.463e-05 228.165 < 2e-16 *** -kmercov 1.320e+01 1.080e-02 1222.193 < 2e-16 *** -bias 1.409e+00 1.276e-02 110.393 < 2e-16 *** -length 4.536e+06 5.656e+03 802.042 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 740.6 on 507 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 3.831e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 2703d47..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index ba71dc3..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 16e632c..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 193618910.930709 -round 1 trimming to 10 trying 4peak model... converged. score: 197417935.480277 -round 2 trimming to 15 trying 4peak model... converged. score: 764608080.35155 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 36a206a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.00947% 1.02732% -Genome Haploid Length 4,603,700 bp 4,618,792 bp -Genome Repeat Length 32,793 bp 32,901 bp -Genome Unique Length 4,570,907 bp 4,585,891 bp -Model Fit 97.983% 98.3787% -Read Error Rate 1.99357% 1.99357% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index e952ef1..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,570 +0,0 @@ -1 3793670 -2 34677 -3 10929 -4 15196 -5 20052 -6 26689 -7 33263 -8 41009 -9 49624 -10 58424 -11 65393 -12 71712 -13 80785 -14 85985 -15 93100 -16 99033 -17 104101 -18 108781 -19 111177 -20 114693 -21 116404 -22 120700 -23 121578 -24 125115 -25 125597 -26 128568 -27 129070 -28 132776 -29 132572 -30 133973 -31 136007 -32 135334 -33 137077 -34 135586 -35 135808 -36 132323 -37 129510 -38 128220 -39 125505 -40 122645 -41 116731 -42 114037 -43 109536 -44 104668 -45 98919 -46 94162 -47 88840 -48 82765 -49 76818 -50 71106 -51 66033 -52 60945 -53 55986 -54 51874 -55 46484 -56 42336 -57 37770 -58 35187 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a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index decc224..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.547e-03 1.318e-03 -4.968 9.03e-07 *** -r 1.054e-02 3.553e-05 296.629 < 2e-16 *** -kmercov 1.991e+01 1.312e-02 1517.918 < 2e-16 *** -bias 2.907e+00 1.659e-02 175.254 < 2e-16 *** -length 4.483e+06 4.190e+03 1069.718 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 427.6 on 557 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 7.048e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 4a86a35..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index b88f730..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 2278d47..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 121346398.084138 -round 1 trimming to 8 trying 4peak model... converged. score: 100590798.408306 -round 2 trimming to 13 trying 4peak model... converged. score: 103152435.35168 -round 3 trimming to 18 trying 4peak model... converged. score: 168840805.054055 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f7521d1..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.04688% 1.06109% -Genome Haploid Length 4,544,672 bp 4,556,664 bp -Genome Repeat Length 39,921 bp 40,027 bp -Genome Unique Length 4,504,750 bp 4,516,637 bp -Model Fit 98.3717% 98.7582% -Read Error Rate 0.103491% 0.103491% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index fb966a4..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,590 +0,0 @@ -1 31690666 -2 1607261 -3 109423 -4 36989 -5 37034 -6 46748 -7 56232 -8 68273 -9 79267 -10 90686 -11 98955 -12 107912 -13 115769 -14 123096 -15 129175 -16 135579 -17 140115 -18 143823 -19 148275 -20 150668 -21 154130 -22 157852 -23 160224 -24 160952 -25 162474 -26 162765 -27 161094 -28 160277 -29 159448 -30 157028 -31 153089 -32 148361 -33 143833 -34 139049 -35 133736 -36 127213 -37 120151 -38 112331 -39 104839 -40 96962 -41 89773 -42 82355 -43 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= kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.101e-02 1.345e-03 -8.184 1.77e-15 *** -r 1.029e-02 3.832e-05 268.415 < 2e-16 *** -kmercov 1.646e+01 1.092e-02 1507.397 < 2e-16 *** -bias 2.512e+00 1.708e-02 147.022 < 2e-16 *** -length 4.504e+06 4.312e+03 1044.493 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 430.1 on 576 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 7.536e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index bdc65b8..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index ad26049..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index b34ade6..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 156557949.176095 -round 1 trimming to 9 trying 4peak model... converged. score: 107245994.688643 -round 2 trimming to 14 trying 4peak model... converged. score: 148636867.084846 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 26c5c2b..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.02096% 1.03628% -Genome Haploid Length 4,563,880 bp 4,576,007 bp -Genome Repeat Length 18,420 bp 18,469 bp -Genome Unique Length 4,545,460 bp 4,557,538 bp -Model Fit 98.2201% 98.6397% -Read Error Rate 0.998661% 0.998661% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 521723c..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,509 +0,0 @@ -1 55183779 -2 3886368 -3 333688 -4 83726 -5 71883 -6 82181 -7 94859 -8 110158 -9 126379 -10 138890 -11 149629 -12 159865 -13 168941 -14 176083 -15 182108 -16 186995 -17 191108 -18 194677 -19 197633 -20 198199 -21 199185 -22 198215 -23 196201 -24 191871 -25 185439 -26 179382 -27 172665 -28 164562 -29 155034 -30 143335 -31 132213 -32 121412 -33 109958 -34 98981 -35 88965 -36 78411 -37 69684 -38 60968 -39 52260 -40 45458 -41 39479 -42 33410 -43 28373 -44 23985 -45 19797 -46 16533 -47 13817 -48 11474 -49 9705 -50 8007 -51 6516 -52 5281 -53 4183 -54 3502 -55 2819 -56 2227 -57 1793 -58 1521 -59 1165 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a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.042e-03 1.002e-03 -6.029 3.24e-09 *** -r 1.038e-02 3.251e-05 319.385 < 2e-16 *** -kmercov 1.326e+01 6.863e-03 1931.977 < 2e-16 *** -bias 1.976e+00 1.136e-02 173.906 < 2e-16 *** -length 4.513e+06 3.294e+03 1370.242 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 333 on 494 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 1.736e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index a1a3d5d..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 020017a..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index cca795f..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 5 trying 4peak model... converged. score: 112261452.425704 -round 1 trimming to 10 trying 4peak model... converged. score: 99810072.5395364 -round 2 trimming to 15 trying 4peak model... converged. score: 461367470.472039 -round 3 trimming to 20 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 1d04237..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.01_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 1.03175% 1.04475% -Genome Haploid Length 4,585,003 bp 4,594,505 bp -Genome Repeat Length 50,029 bp 50,132 bp -Genome Unique Length 4,534,974 bp 4,544,373 bp -Model Fit 98.6115% 98.9894% -Read Error Rate 1.99573% 1.99573% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index abe2e15..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,577 +0,0 @@ -1 3790068 -2 24004 -3 1366 -4 2839 -5 5971 -6 11283 -7 19979 -8 31579 -9 46817 -10 65994 -11 88175 -12 110820 -13 133040 -14 154453 -15 177530 -16 193231 -17 204480 -18 209971 -19 211902 -20 207006 -21 200834 -22 190526 -23 180699 -24 171784 -25 161624 -26 152612 -27 143599 -28 138706 -29 135292 -30 132992 -31 134847 -32 136674 -33 137674 -34 138797 -35 140210 -36 140898 -37 141412 -38 140496 -39 136855 -40 132563 -41 129442 -42 122887 -43 116285 -44 107232 -45 99314 -46 91662 -47 82407 -48 73564 -49 65551 -50 57664 -51 50248 -52 43362 -53 37201 -54 31677 -55 26541 -56 22433 -57 18945 -58 15777 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330 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 6d77d27..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -4.391e-03 8.545e-04 -5.139 3.83e-07 *** -r 2.050e-02 2.301e-05 891.162 < 2e-16 *** -kmercov 1.975e+01 6.312e-03 3128.635 < 2e-16 *** -bias 9.935e-01 3.534e-03 281.128 < 2e-16 *** -length 4.518e+06 2.747e+03 1644.862 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 391.6 on 559 degrees of freedom - -Number of iterations to convergence: 6 -Achieved convergence tolerance: 6.306e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index ca3b024..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index 3c9ccc2..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 83b5651..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 93570772.8513277 -round 1 trimming to 8 trying 4peak model... converged. score: 90847692.1498788 -round 2 trimming to 13 trying 4peak model... converged. score: 85711217.6866161 -round 3 trimming to 18 trying 4peak model... converged. score: 122312656.451776 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 2c397d5..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.04575% 2.05495% -Genome Haploid Length 4,595,517 bp 4,601,396 bp -Genome Repeat Length 62,657 bp 62,737 bp -Genome Unique Length 4,532,860 bp 4,538,659 bp -Model Fit 98.6049% 98.8945% -Read Error Rate 0.10348% 0.10348% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 30e7ff1..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,557 +0,0 @@ -1 32115142 -2 1422196 -3 74301 -4 16748 -5 20524 -6 33014 -7 53281 -8 78733 -9 108506 -10 139507 -11 170662 -12 198430 -13 220820 -14 235364 -15 243821 -16 244065 -17 238925 -18 229861 -19 219103 -20 205132 -21 192655 -22 182017 -23 175531 -24 169829 -25 167203 -26 166470 -27 166567 -28 166387 -29 165945 -30 165786 -31 164330 -32 159867 -33 155665 -34 147347 -35 140233 -36 130395 -37 119780 -38 108124 -39 97213 -40 87187 -41 75876 -42 65040 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a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index 4b090dd..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -6.759e-03 8.765e-04 -7.711 6.02e-14 *** -r 2.055e-02 2.511e-05 818.538 < 2e-16 *** -kmercov 1.636e+01 5.921e-03 2763.011 < 2e-16 *** -bias 8.447e-01 3.396e-03 248.692 < 2e-16 *** -length 4.522e+06 2.665e+03 1696.558 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 416.5 on 543 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 6.341e-07 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index fba1f42..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index b2c20fc..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index db2bf01..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 99172168.4330828 -round 1 trimming to 9 trying 4peak model... converged. score: 94191860.6306628 -round 2 trimming to 14 trying 4peak model... converged. score: 133118185.495264 -round 3 trimming to 19 trying 4peak model... converged. score: 456230895.59308 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f30fdbf..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.05003% 2.06007% -Genome Haploid Length 4,596,941 bp 4,603,601 bp -Genome Repeat Length 51,481 bp 51,556 bp -Genome Unique Length 4,545,460 bp 4,552,045 bp -Model Fit 98.5938% 98.8735% -Read Error Rate 0.996991% 0.996991% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index e1656ed..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,473 +0,0 @@ -1 56112430 -2 3482833 -3 256687 -4 59384 -5 64358 -6 91916 -7 128520 -8 172546 -9 213111 -10 247920 -11 273584 -12 286388 -13 289302 -14 282029 -15 270311 -16 257056 -17 241680 -18 229898 -19 220316 -20 214083 -21 209679 -22 205784 -23 204448 -24 200693 -25 195790 -26 189283 -27 180572 -28 169963 -29 156921 -30 142441 -31 126730 -32 109809 -33 95250 -34 80741 -35 67381 -36 55533 -37 44673 -38 36032 -39 28635 -40 22256 -41 17307 -42 13296 -43 10157 -44 7903 -45 5797 -46 4250 -47 3245 -48 2428 -49 1938 -50 1414 -51 1167 -52 990 -53 844 -54 825 -55 669 -56 635 -57 554 -58 527 -59 465 -60 457 -61 371 -62 378 -63 319 -64 342 -65 304 -66 281 -67 298 -68 284 -69 276 -70 233 -71 242 -72 245 -73 236 -74 255 -75 233 -76 227 -77 214 -78 189 -79 195 -80 191 -81 177 -82 172 -83 180 -84 154 -85 181 -86 125 -87 128 -88 137 -89 144 -90 125 -91 125 -92 127 -93 108 -94 93 -95 94 -96 95 -97 106 -98 93 -99 101 -100 88 -101 94 -102 101 -103 90 -104 83 -105 85 -106 90 -107 82 -108 73 -109 65 -110 71 -111 81 -112 72 -113 76 -114 78 -115 79 -116 86 -117 83 -118 90 -119 87 -120 88 -121 84 -122 86 -123 60 -124 80 -125 83 -126 88 -127 83 -128 86 -129 100 -130 79 -131 78 -132 90 -133 85 -134 86 -135 85 -136 75 -137 79 -138 102 -139 126 -140 104 -141 89 -142 100 -143 113 -144 93 -145 87 -146 88 -147 77 -148 90 -149 83 -150 84 -151 83 -152 110 -153 100 -154 80 -155 92 -156 108 -157 94 -158 89 -159 99 -160 72 -161 66 -162 91 -163 87 -164 86 -165 77 -166 82 -167 73 -168 81 -169 74 -170 78 -171 61 -172 70 -173 56 -174 55 -175 56 -176 52 -177 44 -178 49 -179 47 -180 48 -181 59 -182 54 -183 45 -184 55 -185 37 -186 41 -187 40 -188 26 -189 32 -190 29 -191 33 -192 25 -193 26 -194 19 -195 18 -196 21 -197 25 -198 13 -199 22 -200 24 -201 13 -202 15 -203 23 -204 15 -205 13 -206 8 -207 9 -208 12 -209 21 -210 22 -211 19 -212 12 -213 23 -214 18 -215 14 -216 9 -217 16 -218 15 -219 17 -220 16 -221 17 -222 12 -223 11 -224 7 -225 15 -226 12 -227 11 -228 11 -229 10 -230 14 -231 15 -232 16 -233 8 -234 18 -235 20 -236 9 -237 16 -238 12 -239 16 -240 11 -241 19 -242 21 -243 18 -244 24 -245 16 -246 15 -247 13 -248 12 -249 12 -250 7 -251 11 -252 12 -253 13 -254 6 -255 10 -256 9 -257 8 -258 15 -259 14 -260 14 -261 12 -262 8 -263 4 -264 5 -265 12 -266 11 -267 12 -268 6 -269 9 -270 11 -271 5 -272 6 -273 5 -274 6 -275 5 -276 10 -277 6 -278 4 -279 6 -280 6 -281 3 -282 4 -283 4 -284 6 -285 7 -286 7 -287 4 -288 5 -289 1 -290 6 -292 5 -293 8 -294 2 -296 4 -297 3 -298 7 -299 5 -300 5 -301 9 -302 3 -303 5 -304 8 -305 3 -306 4 -307 4 -308 2 -309 2 -310 3 -311 2 -312 6 -313 9 -314 6 -315 2 -316 3 -317 5 -318 4 -319 5 -320 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1 -461 1 -462 1 -463 2 -464 1 -466 1 -468 3 -469 2 -471 2 -472 1 -473 1 -478 1 -481 1 -505 1 -507 1 -512 1 -525 1 -538 1 -540 1 -543 1 -601 51 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index d2ab7d6..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -7.688e-03 1.228e-03 -6.261 8.82e-10 *** -r 2.037e-02 3.805e-05 535.409 < 2e-16 *** -kmercov 1.320e+01 7.988e-03 1652.642 < 2e-16 *** -bias 6.980e-01 5.305e-03 131.580 < 2e-16 *** -length 4.540e+06 3.773e+03 1203.400 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 598.6 on 459 degrees of freedom - -Number of iterations to convergence: 7 -Achieved convergence tolerance: 4.689e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e16c57f..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 978e906..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index f83f8f8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 296002273.284434 -round 1 trimming to 9 trying 4peak model... converged. score: 204292656.015539 -round 2 trimming to 14 trying 4peak model... converged. score: 530923003.735615 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index aa1f737..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br1_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.02968% 2.0449% -Genome Haploid Length 4,608,621 bp 4,619,789 bp -Genome Repeat Length 43,707 bp 43,813 bp -Genome Unique Length 4,564,914 bp 4,575,976 bp -Model Fit 98.3049% 98.5889% -Read Error Rate 1.99151% 1.99151% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index 26d35ef..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,581 +0,0 @@ -1 3790314 -2 29505 -3 7629 -4 12939 -5 20896 -6 31549 -7 42510 -8 56115 -9 71356 -10 88818 -11 105565 -12 120380 -13 136351 -14 151894 -15 161782 -16 171773 -17 180182 -18 182494 -19 182535 -20 183157 -21 181178 -22 176801 -23 172798 -24 167252 -25 162480 -26 157634 -27 152441 -28 148954 -29 147406 -30 143122 -31 142207 -32 140036 -33 137341 -34 132694 -35 133378 -36 128328 -37 125701 -38 123221 -39 118646 -40 114516 -41 110601 -42 105327 -43 99295 -44 95160 -45 89181 -46 82860 -47 76989 -48 71443 -49 65210 -50 60065 -51 54328 -52 48637 -53 44055 -54 39205 -55 34379 -56 30953 -57 26961 -58 23445 -59 20515 -60 18204 -61 15828 -62 13621 -63 11623 -64 9826 -65 8453 -66 7008 -67 6081 -68 4990 -69 4284 -70 3619 -71 3214 -72 2783 -73 2203 -74 1929 -75 1679 -76 1541 -77 1213 -78 1118 -79 987 -80 786 -81 683 -82 571 -83 557 -84 464 -85 401 -86 401 -87 354 -88 316 -89 327 -90 348 -91 260 -92 290 -93 275 -94 256 -95 214 -96 226 -97 229 -98 199 -99 166 -100 193 -101 198 -102 180 -103 182 -104 163 -105 169 -106 179 -107 151 -108 113 -109 137 -110 155 -111 135 -112 121 -113 133 -114 109 -115 120 -116 116 -117 128 -118 129 -119 142 -120 149 -121 122 -122 124 -123 113 -124 103 -125 99 -126 83 -127 82 -128 66 -129 78 -130 95 -131 88 -132 83 -133 77 -134 62 -135 91 -136 61 -137 74 -138 73 -139 74 -140 83 -141 70 -142 43 -143 69 -144 66 -145 66 -146 75 -147 62 -148 59 -149 62 -150 63 -151 55 -152 74 -153 67 -154 66 -155 79 -156 69 -157 73 -158 84 -159 51 -160 64 -161 69 -162 63 -163 77 -164 73 -165 59 -166 57 -167 67 -168 70 -169 42 -170 67 -171 65 -172 64 -173 78 -174 68 -175 49 -176 61 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3 -452 2 -455 1 -456 4 -457 1 -458 3 -459 2 -460 4 -461 1 -463 3 -465 3 -466 1 -467 3 -468 2 -470 2 -471 2 -472 1 -473 1 -474 2 -475 3 -476 1 -477 2 -478 2 -479 3 -480 6 -481 2 -482 3 -483 4 -484 3 -485 4 -486 9 -487 3 -488 7 -489 3 -490 8 -491 5 -492 3 -493 5 -494 5 -495 1 -496 4 -497 2 -498 8 -499 4 -500 5 -501 8 -502 8 -503 6 -504 7 -505 3 -506 5 -507 4 -508 9 -509 13 -510 6 -511 5 -512 7 -513 7 -514 10 -515 8 -516 3 -517 6 -518 7 -519 7 -520 15 -521 16 -522 12 -523 9 -524 8 -525 9 -526 7 -527 10 -528 8 -529 6 -530 8 -531 8 -532 13 -533 10 -534 9 -535 9 -536 10 -537 7 -538 7 -539 6 -540 9 -541 8 -542 8 -543 8 -544 10 -545 11 -546 7 -547 12 -548 8 -549 3 -550 12 -551 4 -552 13 -553 11 -554 5 -555 12 -556 15 -557 11 -558 5 -559 11 -560 7 -561 10 -562 12 -563 9 -564 13 -565 11 -566 7 -567 12 -568 14 -569 14 -570 19 -571 8 -572 7 -573 16 -574 11 -575 9 -576 9 -577 9 -578 13 -579 12 -580 10 -581 10 -582 6 -583 7 -584 10 -585 5 -586 9 -587 5 -588 5 -589 4 -590 11 -591 7 -592 6 -593 7 -594 9 -595 7 -596 5 -597 3 -598 5 -599 8 -600 3 -601 232 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt deleted file mode 100644 index 9c06d7a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.451e-02 1.675e-03 -8.662 <2e-16 *** -r 2.093e-02 5.752e-05 363.884 <2e-16 *** -kmercov 1.999e+01 1.883e-02 1061.499 <2e-16 *** -bias 2.010e+00 1.435e-02 140.050 <2e-16 *** -length 4.493e+06 4.784e+03 939.118 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 567.5 on 563 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 2.47e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 36e3b21..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index bd03d0a..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 1cb390a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 242645247.667647 -round 1 trimming to 8 trying 4peak model... converged. score: 205436889.189976 -round 2 trimming to 13 trying 4peak model... converged. score: 203364330.259489 -round 3 trimming to 18 trying 4peak model... converged. score: 412721609.432808 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 05b77f1..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.08161% 2.10462% -Genome Haploid Length 4,534,391 bp 4,551,510 bp -Genome Repeat Length -7,070 bp -7,097 bp -Genome Unique Length 4,541,461 bp 4,558,607 bp -Model Fit 97.9323% 98.273% -Read Error Rate 0.105136% 0.105136% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 6e82bc8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,567 +0,0 @@ -1 31978049 -2 1450210 -3 87808 -4 35525 -5 43663 -6 61715 -7 81828 -8 104225 -9 129293 -10 151415 -11 170735 -12 188861 -13 201983 -14 209732 -15 214230 -16 217656 -17 215390 -18 212218 -19 207099 -20 201327 -21 195453 -22 189724 -23 183484 -24 177821 -25 172775 -26 168704 -27 164790 -28 160406 -29 156124 -30 152047 -31 148138 -32 143129 -33 136597 -34 130431 -35 124390 -36 116709 -37 108274 -38 99865 -39 91986 -40 83101 -41 74748 -42 67852 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2 -584 2 -587 1 -591 1 -601 58 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index af25191..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.674e-02 1.660e-03 -10.09 <2e-16 *** -r 2.096e-02 5.952e-05 352.23 <2e-16 *** -kmercov 1.656e+01 1.595e-02 1038.21 <2e-16 *** -bias 1.670e+00 1.167e-02 143.13 <2e-16 *** -length 4.496e+06 4.299e+03 1045.84 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 574.9 on 553 degrees of freedom - -Number of iterations to convergence: 9 -Achieved convergence tolerance: 2.765e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 876faa2..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index a1c74da..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 5f3775e..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 243424738.822145 -round 1 trimming to 9 trying 4peak model... converged. score: 182764868.631926 -round 2 trimming to 14 trying 4peak model... converged. score: 285077150.495965 -round 3 trimming to 19 trying 4peak model... converged. score: 825660364.686767 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 8446d7a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.0845% 2.1083% -Genome Haploid Length 4,534,156 bp 4,551,659 bp -Genome Repeat Length -18,358 bp -18,429 bp -Genome Unique Length 4,552,514 bp 4,570,088 bp -Model Fit 98.0481% 98.4081% -Read Error Rate 0.997796% 0.997796% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 614940d..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,475 +0,0 @@ -1 55915146 -2 3539079 -3 290694 -4 88069 -5 93799 -6 120547 -7 152491 -8 185319 -9 212535 -10 235561 -11 252423 -12 259370 -13 261878 -14 261133 -15 256458 -16 248986 -17 241216 -18 233195 -19 224663 -20 217357 -21 209961 -22 202838 -23 194794 -24 186932 -25 180211 -26 170829 -27 161419 -28 151570 -29 140832 -30 129217 -31 116863 -32 106196 -33 93842 -34 82649 -35 72672 -36 63225 -37 54373 -38 45725 -39 38322 -40 31768 -41 26347 -42 20946 -43 17000 -44 13678 -45 11472 -46 9081 -47 7189 -48 5845 -49 4498 -50 3568 -51 2758 -52 2079 -53 1692 -54 1464 -55 1112 -56 873 -57 673 -58 647 -59 548 -60 516 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4 -453 4 -454 3 -456 2 -457 2 -458 3 -459 2 -460 3 -461 2 -462 8 -463 2 -464 2 -468 1 -470 2 -471 2 -472 1 -474 1 -475 1 -478 1 -479 1 -489 1 -511 1 -519 1 -577 1 -601 46 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index f22a37e..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.643e-02 1.930e-03 -8.513 2.41e-16 *** -r 2.078e-02 7.291e-05 285.025 < 2e-16 *** -kmercov 1.333e+01 1.648e-02 809.047 < 2e-16 *** -bias 1.393e+00 1.519e-02 91.706 < 2e-16 *** -length 4.529e+06 5.597e+03 809.230 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 658.4 on 461 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 5.028e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index f2689a6..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index 0411f2e..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index afa73f9..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 505200184.472985 -round 1 trimming to 9 trying 4peak model... converged. score: 255414325.678173 -round 2 trimming to 14 trying 4peak model... converged. score: 708864571.643659 -round 3 trimming to 19 trying 4peak model... unconverged -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index dad2667..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br2_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.06343% 2.09259% -Genome Haploid Length 4,560,469 bp 4,583,072 bp -Genome Repeat Length -22,640 bp -22,752 bp -Genome Unique Length 4,583,108 bp 4,605,824 bp -Model Fit 98.1469% 98.4826% -Read Error Rate 1.98967% 1.98967% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist deleted file mode 100644 index abb4961..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist +++ /dev/null @@ -1,596 +0,0 @@ -1 3798681 -2 37110 -3 20304 -4 27209 -5 36139 -6 49583 -7 60295 -8 75264 -9 87591 -10 103244 -11 114071 -12 125137 -13 137783 -14 147864 -15 152251 -16 160162 -17 164521 -18 167180 -19 166490 -20 169161 -21 168987 -22 168385 -23 165696 -24 164446 -25 158641 -26 155081 -27 154757 -28 150569 -29 145544 -30 142063 -31 137770 -32 135080 -33 132300 -34 128591 -35 124581 -36 120039 -37 117306 -38 114255 -39 108253 -40 104715 -41 101921 -42 95928 -43 92633 -44 87452 -45 83285 -46 78316 -47 73156 -48 68061 -49 64389 -50 59469 -51 54745 -52 50961 -53 46658 -54 42879 -55 38450 -56 34408 -57 32673 -58 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- (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -2.742e-02 2.910e-03 -9.422 <2e-16 *** -r 2.127e-02 1.193e-04 178.269 <2e-16 *** -kmercov 2.024e+01 4.022e-02 503.156 <2e-16 *** -bias 3.114e+00 2.636e-02 118.111 <2e-16 *** -length 4.479e+06 6.378e+03 702.229 <2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 700.8 on 583 degrees of freedom - -Number of iterations to convergence: 10 -Achieved convergence tolerance: 8.031e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index 3ed1c87..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png deleted file mode 100644 index d49af32..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt deleted file mode 100644 index afa2098..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 3 trying 4peak model... converged. score: 359705667.169757 -round 1 trimming to 8 trying 4peak model... converged. score: 270868146.958791 -round 2 trimming to 13 trying 4peak model... converged. score: 276037583.990446 -round 3 trimming to 18 trying 4peak model... converged. score: 575750259.011437 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt deleted file mode 100644 index 116fc7a..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.001_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.10311% 2.15083% -Genome Haploid Length 4,466,642 bp 4,502,293 bp -Genome Repeat Length -100,535 bp -101,337 bp -Genome Unique Length 4,567,177 bp 4,603,630 bp -Model Fit 97.6577% 98.0429% -Read Error Rate 0.106307% 0.106307% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist deleted file mode 100644 index 9a18f81..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist +++ /dev/null @@ -1,573 +0,0 @@ -1 31945029 -2 1503203 -3 107463 -4 54399 -5 64744 -6 81504 -7 98692 -8 119173 -9 136413 -10 153035 -11 165957 -12 178779 -13 188667 -14 197088 -15 200216 -16 202090 -17 202050 -18 201234 -19 197349 -20 196101 -21 189970 -22 186065 -23 180384 -24 175894 -25 169869 -26 165262 -27 160822 -28 156713 -29 150122 -30 145042 -31 137688 -32 132680 -33 125829 -34 119912 -35 113695 -36 108848 -37 100500 -38 93062 -39 86820 -40 80697 -41 74428 -42 67605 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-578 1 -580 1 -581 1 -584 1 -586 1 -587 1 -588 1 -591 2 -594 2 -598 1 -601 56 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt deleted file mode 100644 index a20fd4e..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.675e-02 2.670e-03 -6.273 7.1e-10 *** -r 2.099e-02 1.062e-04 197.565 < 2e-16 *** -kmercov 1.668e+01 2.982e-02 559.510 < 2e-16 *** -bias 2.350e+00 2.534e-02 92.755 < 2e-16 *** -length 4.459e+06 6.472e+03 688.902 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 693.7 on 559 degrees of freedom - -Number of iterations to convergence: 13 -Achieved convergence tolerance: 4.524e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index e877060..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png deleted file mode 100644 index d7f1c2f..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt deleted file mode 100644 index 4ad2ff4..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 424378529.459464 -round 1 trimming to 9 trying 4peak model... converged. score: 269014361.645302 -round 2 trimming to 14 trying 4peak model... converged. score: 718176408.374216 -round 3 trimming to 19 trying 4peak model... converged. score: 1029847285.36042 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt deleted file mode 100644 index f25254e..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.01_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.07763% 2.12013% -Genome Haploid Length 4,488,351 bp 4,520,554 bp -Genome Repeat Length -19,289 bp -19,427 bp -Genome Unique Length 4,507,640 bp 4,539,981 bp -Model Fit 97.8567% 98.2333% -Read Error Rate 1.00433% 1.00433% diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist deleted file mode 100644 index 570e368..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist +++ /dev/null @@ -1,485 +0,0 @@ -1 55767786 -2 3645429 -3 322070 -4 113260 -5 115232 -6 137445 -7 162760 -8 188195 -9 206403 -10 221743 -11 236183 -12 243357 -13 246359 -14 247254 -15 242965 -16 240527 -17 232641 -18 226295 -19 219062 -20 211925 -21 204876 -22 196686 -23 189000 -24 178801 -25 169819 -26 160338 -27 150364 -28 141382 -29 131506 -30 121210 -31 110808 -32 102107 -33 92631 -34 82893 -35 74138 -36 64971 -37 58015 -38 50369 -39 44032 -40 37781 -41 32724 -42 27291 -43 23096 -44 19103 -45 16093 -46 13448 -47 11230 -48 9122 -49 7696 -50 6359 -51 5129 -52 4269 -53 3490 -54 2787 -55 2386 -56 1891 -57 1574 -58 1323 -59 1085 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2 -465 4 -467 1 -468 1 -469 1 -470 1 -471 2 -472 2 -473 1 -475 1 -476 3 -477 1 -485 1 -490 2 -491 2 -492 1 -496 1 -498 2 -499 2 -500 1 -502 1 -504 1 -505 2 -506 1 -507 3 -509 1 -511 1 -513 1 -514 1 -527 1 -531 1 -549 1 -564 1 -574 1 -601 50 diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt deleted file mode 100644 index 524ef38..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/model.txt +++ /dev/null @@ -1,25 +0,0 @@ - -Formula: y ~ (((2 * (1 - d) * (1 - (1 - r)^k)) + (2 * d * (1 - (1 - r)^k)^2) + - (2 * d * ((1 - r)^k) * (1 - (1 - r)^k))) * dnbinom(x, size = kmercov/bias, - mu = kmercov) * length + (((1 - d) * ((1 - r)^k)) + (d * - (1 - (1 - r)^k)^2)) * dnbinom(x, size = kmercov * 2/bias, - mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * - 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * - 4/bias, mu = kmercov * 4) * length) - -Parameters: - Estimate Std. Error t value Pr(>|t|) -d -1.335e-02 3.049e-03 -4.377 1.48e-05 *** -r 2.032e-02 1.208e-04 168.292 < 2e-16 *** -kmercov 1.334e+01 2.800e-02 476.189 < 2e-16 *** -bias 1.963e+00 3.417e-02 57.435 < 2e-16 *** -length 4.516e+06 9.825e+03 459.644 < 2e-16 *** ---- -Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 - -Residual standard error: 763.7 on 471 degrees of freedom - -Number of iterations to convergence: 15 -Achieved convergence tolerance: 9.796e-06 - diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png deleted file mode 100644 index cbb7612..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.log.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png deleted file mode 100644 index c32b864..0000000 Binary files a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/plot.png and /dev/null differ diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt deleted file mode 100644 index d4b4be8..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/progress.txt +++ /dev/null @@ -1,6 +0,0 @@ -starting -round 0 trimming to 4 trying 4peak model... converged. score: 771891175.868985 -round 1 trimming to 9 trying 4peak model... converged. score: 320588925.460595 -round 2 trimming to 14 trying 4peak model... converged. score: 1031803090.43026 -round 3 trimming to 19 trying 4peak model... converged. score: 2198339769.42663 -done diff --git a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt b/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt deleted file mode 100644 index e332d56..0000000 --- a/analysis/simulation_results_50x/Escherichia_coli_str_k_12_substr_w3110.GCA_000010245.1.26.dna.toplevel.fa_het0.02_br3_rl100_cov50_err0.02_reads.fa21.hist_results/summary.txt +++ /dev/null @@ -1,10 +0,0 @@ -GenomeScope version 1.0 -k = 21 - -property min max -Heterozygosity 2.0081% 2.05641% -Genome Haploid Length 4,545,568 bp 4,583,912 bp -Genome Repeat Length -4,408 bp -4,445 bp -Genome Unique Length 4,549,975 bp 4,588,356 bp -Model Fit 98.0931% 98.4409% -Read Error Rate 1.99473% 1.99473% diff --git a/analysis/summarize_field.sh b/analysis/summarize_field.sh deleted file mode 100755 index 4d76fc2..0000000 --- a/analysis/summarize_field.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/sh - -grep "Genome Haploid Length" */summary.txt | column -t | less -grep "Genome Unique Length" */summary.txt | column -t | less -grep "Genome Repeat Length" */summary.txt | column -t | less -grep Heterozygosity */summary.txt | rev | sort -t '_' -k7,7 -k8,8 | rev | column -t | less -grep Error */summary.txt | rev | sort -t '_' -k3,3 -k8,8 | rev | column -t | less -grep Duplication */summary.txt | rev | sort -t '_' -k6,6 -k8,8 | rev | column -t | less -grep 'Percent Kmers Modeled (All Kmers)' */summary.txt | column -t | less diff --git a/check_progress.php b/check_progress.php index abc8cdc..1b0a011 100755 --- a/check_progress.php +++ b/check_progress.php @@ -8,7 +8,7 @@ echo json_encode($progress_stats); } else { - $progress_stats = "file " + $filename + " doesn't exist"; + $progress_stats = array("File " . $filename . " doesn't exist."); echo json_encode($progress_stats); } diff --git a/genomescope.R b/genomescope.R index 058f900..df66407 100755 --- a/genomescope.R +++ b/genomescope.R @@ -1,9 +1,15 @@ #!/usr/bin/env Rscript ## GenomeScope: Fast Genome Analysis from Unassembled Short Reads -## -## This is the automated script for computing genome characteristics -## from a kmer histogram file, k-mer size, and readlength +## This is the automated script for computing genome characteristics +## from a kmer histogram file, k-mer size, and ploidy + +## Load libraries for non-linear least squares and argument parser +library('minpack.lm') +library('argparse') + +## Load the genomescope library +library('genomescope') ## Number of rounds before giving up NUM_ROUNDS=4 @@ -15,7 +21,7 @@ START_SHIFT=5 TYPICAL_ERROR = 15 ## Max rounds on NLS -MAX_ITERATIONS=20 +MAX_ITERATIONS=200 ## Overrule if two scores are within this percent (0.05 = 5%) but larger difference in het SCORE_CLOSE = 0.20 @@ -23,17 +29,14 @@ SCORE_CLOSE = 0.20 ## Overrule heterozygosity if there is a large difference in het rate SCORE_HET_FOLD_DIFFERENCE = 10 -## Print out VERBOSEging messages (0/1) -VERBOSE = 0 - ## Suppress the warnings if the modeling goes crazy, those are in try/catch blocks anyways options(warn=-1) ## Colors for plots COLOR_BGCOLOR = "light grey" COLOR_HIST = "#56B4E9" -COLOR_4PEAK = "black" -COLOR_2PEAK = "#F0E442" +COLOR_2pPEAK = "black" +COLOR_pPEAK = "#F0E442" COLOR_ERRORS = "#D55E00" COLOR_KMERPEAK = "black" COLOR_RESIDUAL = "purple" @@ -42,689 +45,187 @@ COLOR_COVTHRES = "red" ## Given mean +/- stderr, report min and max value within 2 SE ############################################################################### -min_max <- function(table){ - ##return (c( abs(table[1]) - 2*abs(table[2]) , abs(table[1])+ 2*abs(table[2]))) - return (c(table[1] - 2*table[2], table[1]+ 2*table[2])) +min_max <- function(table) { + return (c(max(0,table[1] - 2*table[2]), table[1]+ 2*table[2])) } +min_max1 <- function(table) { + return (c(max(0,table[1] - 2*table[2]), min(1, table[1]+ 2*table[2]))) +} - -## Use nls to fit 4 peak model +## Main program starts here ############################################################################### -nls_4peak<-function(x, y, k, estKmercov, estLength, max_iterations){ - model4 = NULL - - if (VERBOSE) { cat("trying nls_4peak standard algorithm\n") } - - try(model4 <- nls(y ~ (((2*(1-d)*(1-(1-r)^k)) + (2*d*(1-(1-r)^k)^2) + (2*d*((1-r)^k)*(1-(1-r)^k))) * dnbinom(x, size = kmercov / bias, mu = kmercov) * length + - (((1-d)*((1-r)^k)) + (d*(1-(1-r)^k)^2)) * dnbinom(x, size = kmercov*2 / bias, mu = kmercov * 2) * length + - (2*d*((1-r)^k)*(1-(1-r)^k)) * dnbinom(x, size = kmercov*3 / bias, mu = kmercov * 3) * length + - (d*(1-r)^(2*k)) * dnbinom(x, size = kmercov*4 / bias, mu = kmercov * 4) * length), - start = list(d=0, r=0, kmercov=estKmercov, bias = 0.5, length=estLength), - control = list(minFactor=1e-12, maxiter=max_iterations)), silent = TRUE) - - if(class(model4) == "try-error"){ - if (VERBOSE) { cat("retrying nls_4peak with port algorithm\n") } - - try(model4 <- nls(y ~ (((2*(1-d)*(1-(1-r)^k)) + (2*d*(1-(1-r)^k)^2) + (2*d*((1-r)^k)*(1-(1-r)^k))) * dnbinom(x, size = kmercov / bias, mu = kmercov) * length + - (((1-d)*((1-r)^k)) + (d*(1-(1-r)^k)^2)) * dnbinom(x, size = kmercov*2 / bias, mu = kmercov * 2) * length + - (2*d*((1-r)^k)*(1-(1-r)^k)) * dnbinom(x, size = kmercov*3 / bias, mu = kmercov * 3) * length + - (d*(1-r)^(2*k)) * dnbinom(x, size = kmercov*4 / bias, mu = kmercov * 4) * length), - start = list(d=0, r=0, kmercov=estKmercov, bias = 0.5, length=estLength), - algorithm="port", control = list(minFactor=1e-12, maxiter=max_iterations)), silent = TRUE) - } - - return(model4) +parser <- ArgumentParser() +parser$add_argument("-v", "--version", action="store_true", default=FALSE, help="print the version and exit") +parser$add_argument("-i", "--input", help = "input histogram file") +parser$add_argument("-o", "--output", help = "output directory name") +parser$add_argument("-p", "--ploidy", type = "integer", default = 2, help = "ploidy (1, 2, 3, 4, 5, or 6) for model to use [default 2]") +parser$add_argument("-k", "--kmer_length", type = "integer", default = 21, help = "kmer length used to calculate kmer spectra [default 21]") +parser$add_argument("-n", "--name_prefix", default = "", help = "optional name_prefix for output files") +parser$add_argument("-l", "--lambda", "--kcov", "--kmercov", type = "integer", default=-1, help = "optional initial kmercov estimate for model to use") +parser$add_argument("-m", "--max_kmercov", type = "integer", default=-1, help = "optional maximum kmer coverage threshold (kmers with coverage greater than max_kmercov are ignored by the model)") +parser$add_argument("--verbose", action="store_true", default=FALSE, help = "optional flag to print messages during execution") +parser$add_argument("--no_unique_sequence", action="store_true", default=FALSE, help = "optional flag to turn off yellow unique sequence line in plots") +parser$add_argument("-t", "--topology", type = "integer", default = 0, help = "ADVANCED: flag for topology for model to use") +parser$add_argument("--initial_repetitiveness", type="character", default = -1, help = "ADVANCED: flag to set initial value for repetitiveness") +parser$add_argument("--initial_heterozygosities", type="character", default = -1, help = "ADVANCED: flag to set initial values for nucleotide heterozygosity rates") +parser$add_argument("--transform_exp", type="integer", default=1, help = "ADVANCED: parameter for the exponent when fitting a transformed (x**transform_exp*y vs. x) kmer histogram [default 1]") +parser$add_argument("--testing", action="store_true", default=FALSE, help = "ADVANCED: flag to create testing.tsv file with model parameters") +parser$add_argument("--true_params", type="character", default = -1, help = "ADVANCED: flag to state true simulated parameters for testing mode") +parser$add_argument("--trace_flag", action="store_true", default=FALSE, help = "ADVANCED: flag to turn on printing of iteration progress of nlsLM function") +parser$add_argument("--num_rounds", type = "integer", default = 4, help = "ADVANCED: parameter for the number of optimization rounds") +parser$add_argument("--fitted_hist", action="store_true", default=FALSE, help = "ADVANCED: generates a fitted histogram for kmer multiplicity 0-4 and a lookup table of probabilities") + +arguments <- parser$parse_args() +version_message <- "GenomeScope 2.0\n" + +if (arguments$version) { + cat(version_message) + quit() } +if (is.null(arguments$input) | is.null(arguments$output)) { + cat("USAGE: genomescope.R -i input_histogram_file -o output_dir -p ploidy -k kmer_length\n") + cat("OPTIONAL PARAMETERS: -n 'name_prefix' -l lambda -m max_kmercov --verbose --no_unique_sequence\n") + cat("ADVANCED PARAMETERS: -t topology --initial_repetitiveness init_d --initial_heterozygosities init_r1,init_r2,...,init_rx --transform_exp t_exp --testing --true_params --trace_flag --num_rounds --fitted_hist\n") + cat("HELP: genomescope.R --help\n") +} else { + + ## Load the arguments from the user + histfile <- arguments$input + foldername <- arguments$output + p <- arguments$ploidy + k <- arguments$kmer_length + if (arguments$name_prefix != "") { + arguments$name_prefix = paste0(arguments$name_prefix,"_") + } + estKmercov <- arguments$lambda + max_kmercov <- arguments$max_kmercov + VERBOSE <- arguments$verbose + NO_UNIQUE_SEQUENCE <- arguments$no_unique_sequence + topology <- arguments$topology + d_init <- arguments$initial_repetitiveness + r_inits <- arguments$initial_heterozygosities + transform_exp <- arguments$transform_exp + TESTING <- arguments$testing + TRUE_PARAMS <- arguments$true_params + TRACE_FLAG <- arguments$trace_flag + NUM_ROUNDS <- arguments$num_rounds + FITTED_HIST <- arguments$fitted_hist + + cat(paste("GenomeScope analyzing ", histfile, " p=", p, " k=", k, " outdir=", foldername, "\n", sep="")) + + dir.create(foldername, showWarnings=FALSE) + + ## Initialize the status + progressFilename <- paste(foldername,"/", arguments$name_prefix, "progress.txt",sep="") + cat("starting", file=progressFilename, sep="\n") + + kmer_prof <- read.csv(file=histfile,sep="", header=FALSE,colClasses=c("numeric","numeric")) + + minkmerx = 1; + if (kmer_prof[1,1] == 0) { + if (VERBOSE) {cat("Histogram starts with zero, reseting minkmerx\n")} + minkmerx = 2; + } -## score model by number and percent of residual errors after excluding sequencing errors -######################################################################################### - -score_model<-function(kmer_hist_orig, nls, round, foldername){ - x = kmer_hist_orig[[1]] - y = kmer_hist_orig[[2]] - - pred=predict(nls, newdata=data.frame(x)) - model_sum=summary(nls) - kcovfloor = floor(min_max(model_sum$coefficients['kmercov',])[[1]]) - - ## Compute error rate, by counting kmers unexplained by model through first peak - ## truncate errors as soon as it goes to zero, dont allow it to go back up - error_xcutoff = kcovfloor - error_xcutoff_ind = which(x==error_xcutoff) + kmer_prof <- kmer_prof[c(minkmerx:(length(kmer_prof[,2])-1)),] #get rid of the last position + kmer_prof_orig <- kmer_prof - error_kmers = y[1:error_xcutoff_ind] - pred[1:error_xcutoff_ind] + ## try to find the local minimum between errors and the first (heterozygous) peak + kmer_trans = as.numeric(kmer_prof[,1])**transform_exp*as.numeric(kmer_prof[,2]) + start <- tail(which(kmer_trans[1:TYPICAL_ERROR]==min(kmer_trans[1:TYPICAL_ERROR])),n=1) + start_max <- start + which(kmer_trans[start:length(kmer_trans)]==max(kmer_trans[start:length(kmer_trans)])) - 1 - first_zero = -1 + maxCovIndex = -1 - for (i in 1:error_xcutoff_ind) - { - if (first_zero == -1) - { - if (error_kmers[i] < 1.0) - { - first_zero = i - if (VERBOSE) { cat(paste("Truncating errors at", i, "\n")) } - } - } - else - { - error_kmers[i] = 0 - } + ## Figure out which kmers to exclude, if any + if(max_kmercov == -1) { + maxCovIndex <- length(kmer_prof[,1]) + max_kmercov <- kmer_prof[maxCovIndex,1] } - - if (first_zero == -1) - { - first_zero = error_xcutoff_ind + else { + ## Figure out the index we should use for this coverage length + x <- kmer_prof[,1] + maxCovIndex <- length(x[x<=max_kmercov]) } - ## The fit is residual sum of square error, excluding sequencing errors - model_fit_all = c(sum(as.numeric(y[first_zero:length(y)] - pred[first_zero:length(y)]) ** 2), first_zero, x[length(y)]) - model_fit_full = c(sum(as.numeric(y[first_zero:(5*kcovfloor)] - pred[first_zero:(5*kcovfloor)]) ** 2), first_zero, (5*kcovfloor)) - model_fit_unique = c(sum(as.numeric(y[first_zero:(3*kcovfloor)] - pred[first_zero:(3*kcovfloor)]) ** 2), first_zero, (3*kcovfloor)) + if (VERBOSE) {cat(paste("using max_kmercov:", max_kmercov, " with index:", maxCovIndex, "\n"))} - ## The score is the percentage of unexplained kmers, excluding sequencing errors - model_fit_allscore = c(1-sum(abs(as.numeric(y[first_zero:length(y)] - pred[first_zero:length(y)]))) / sum(as.numeric(y[first_zero:length(y)])), first_zero, x[length(y)]) - model_fit_fullscore = c(1-sum(abs(as.numeric(y[first_zero:(5*kcovfloor)] - pred[first_zero:(5*kcovfloor)]))) / sum(as.numeric(y[first_zero:(5*kcovfloor)])), first_zero, (5*kcovfloor)) - model_fit_uniquescore = c(1-sum(abs(as.numeric(y[first_zero:(3*kcovfloor)] - pred[first_zero:(3*kcovfloor)]))) / sum(as.numeric(y[first_zero:(3*kcovfloor)])), first_zero, (3*kcovfloor)) + # terminate after NUM_ROUND iterations, store best result so far in container + round <- 0 + best_container <- list(NULL,0) - fit = data.frame(all = model_fit_all, allscore = model_fit_allscore, - full = model_fit_full, fullscore = model_fit_fullscore, - unique = model_fit_unique, uniquescore = model_fit_uniquescore) + while(round < NUM_ROUNDS) { + cat(paste("round", round, "trimming to", start, "trying 2p peak model... "), file=progressFilename, sep="", append=TRUE) + if (VERBOSE) {cat(paste("round", round, "trimming to", start, "trying 2p peak model... \n"))} - return (fit) -} + ## Reset the input trimming off low frequency error kmers + kmer_prof=kmer_prof_orig[1:maxCovIndex,] + x <- kmer_prof[start:maxCovIndex,1] + y <- kmer_prof[start:maxCovIndex,2] + model_peaks <- estimate_Genome_peakp(kmer_prof, x, y, k, p, topology, estKmercov, round, foldername, arguments) -## Pick between the two model forms, resolves ambiguity between which is the homozygous and which is the heterozygous peak -############################################################################### - -eval_model<-function(kmer_hist_orig, nls1, nls2, round, foldername){ - nls1score = -1 - nls2score = -1 - - ## Evaluate the score the nls1 - if (!is.null(nls1)) - { - nls1score = score_model(kmer_hist_orig, nls1, round+0.1, foldername) - - if(VERBOSE){ cat(paste("nls1score$all:\t", nls1score$all[[1]], "\n"))} + if (!is.null(model_peaks[[1]])) { + cat(paste("converged. score: ", model_peaks[[2]]$all[[1]]), file=progressFilename, sep="\n", append=TRUE) - if (VERBOSE) - { - mdir = paste(foldername, "/round", round, ".1", sep="") + if (VERBOSE) { + mdir = paste(foldername, "/round", round, sep="") dir.create(mdir, showWarnings=FALSE) - report_results(kmer_prof_orig,kmer_prof_orig, k, (list(nls1, nls1score)) , mdir) + report_results(kmer_prof,kmer_prof_orig, k, p, model_peaks, mdir, arguments, TRUE) } } - else - { - if (VERBOSE) { cat("nls1score failed to converge\n") } + else { + cat(paste("unconverged"), file=progressFilename, sep="\n", append=TRUE) } - - ## Evaluate the score of nls2 - if (!is.null(nls2)) - { - nls2score = score_model(kmer_hist_orig, nls2, round+0.2, foldername) - - if(VERBOSE){ cat(paste("nls2score$all:\t", nls2score$all[[1]], "\n"))} - - if (VERBOSE) - { - mdir = paste(foldername, "/round", round, ".2", sep="") - dir.create(mdir, showWarnings=FALSE) - report_results(kmer_prof_orig, kmer_prof_orig, k, (list(nls2, nls2score)) , mdir) + #check if this result is better than previous + if (!is.null(model_peaks[[1]])) { + if (is.null(best_container[[1]])) { + if (VERBOSE) {cat("no previous best, updating best\n")} + best_container = model_peaks } - } - else - { - if (VERBOSE) { cat("nls2score failed to converge\n") } - } - - ## Return the better of the scores - if (!is.null(nls1)) - { - if (!is.null(nls2)) - { - pdiff = abs(nls1score$all[[1]] - nls2score$all[[1]]) / max(nls1score$all[[1]], nls2score$all[[1]]) - - if (pdiff < SCORE_CLOSE) - { - het1 = summary(nls1)$coefficients['r',][[1]] - het2 = summary(nls2)$coefficients['r',][[1]] - - if (het2 * SCORE_HET_FOLD_DIFFERENCE < het1) - { - if (VERBOSE) { cat(paste("returning nls1, similar score, higher het\n")) } - return (list(nls1, nls1score)) + else { + best_container_score = best_container[[1]]$m$deviance() + model_peaks_score = model_peaks[[1]]$m$deviance() + pdiff = abs(model_peaks_score - best_container_score) / max(model_peaks_score, best_container_score) + + if (pdiff < SCORE_CLOSE) { + hetm = model_peaks[[1]]$ahet + hetb = best_container[[1]]$ahet + + #if (hetb * SCORE_HET_FOLD_DIFFERENCE < hetm) { + if (hetb + 0.01 < hetm) { + if (VERBOSE) {cat("model has significantly higher heterozygosity but similar score, overruling\n")} } - else if (het1 * SCORE_HET_FOLD_DIFFERENCE < het2) - { - if (VERBOSE) { cat(paste("returning nls2, similar score, higher het\n")) } - return (list(nls2, nls2score)) + #else if (hetm * SCORE_HET_FOLD_DIFFERENCE < hetb) { + else if (hetm + 0.01 < hetb) { + if (VERBOSE) {cat("previous best has significantly higher heterozygosity and similar score, keeping\n")} + best_container = model_peaks + } + else if (model_peaks_score < best_container_score) { + if (VERBOSE) {cat("score is marginally better but het rate is not extremely different, updating\n")} + best_container = model_peaks } } - - if (nls1score$all[[1]] < nls2score$all[[1]]) - { - if (VERBOSE) { cat(paste("returning nls1, better score\n")) } - return (list(nls1, nls1score)) - } - else - { - if (VERBOSE) { cat(paste("returning nls2, better score\n")) } - return (list(nls2, nls2score)) + else if (model_peaks_score < best_container_score) { + if (VERBOSE) {cat("score is significantly better, updating\n")} + best_container = model_peaks } } - else - { - if (VERBOSE) { cat(paste("returning nls1, nls2 fail\n")) } - return (list(nls1, nls1score)) - } } - if (VERBOSE) { cat(paste("returning nls2 by default\n")) } - return (list(nls2, nls2score)) -} - - -## Wrapper function to try fitting 4 peak model with 2 forms -############################################################################### - -estimate_Genome_4peak2<-function(kmer_hist_orig, x, y, k, readlength, round, foldername){ - ## First we see what happens when the max peak is the kmercoverage (typically the homozygous peak) for the plot - numofReads = sum(as.numeric(x*y))/(readlength-k+1) - estKmercov1 = x[which(y==max(y))][1] - estCoverage1 = estKmercov1*readlength/(readlength-k) - estLength1 = numofReads*readlength/estCoverage1 - - if (VERBOSE) { cat(paste("trying with kmercov: ", estKmercov1, "\n")) } - nls1 = nls_4peak(x, y, k, estKmercov1, estLength1, MAX_ITERATIONS) - if (VERBOSE) { print(summary(nls1)) } - - ## Second we half the max kmercoverage (typically the heterozygous peak) - estKmercov2 = estKmercov1 / 2 ##2.5 - estCoverage2 = estKmercov2*readlength/(readlength-k) - estLength2 = numofReads*readlength/estCoverage2 - - if (VERBOSE) { cat(paste("trying with kmercov: ", estKmercov2, "\n")) } - nls2 = nls_4peak(x, y, k, estKmercov2, estLength2, MAX_ITERATIONS) - if (VERBOSE) { print(summary(nls2)) } - - return(eval_model(kmer_hist_orig, nls1, nls2, round, foldername)) -} - - -## Format numbers -############################################################################### -bp_format<-function(num) { - paste(formatC(round(num),format="f",big.mark=",", digits=0), "bp",sep=" ") -} - -percentage_format<-function(num) { - paste(signif(num,6)*100,"%",sep="") -} -X_format<-function(num) { - paste(signif(num,4),"X",sep="") -} - - -## Report results and make plots -############################################################################### - -report_results<-function(kmer_hist,kmer_hist_orig, k, container, foldername) -{ - x=kmer_hist_orig[[1]] - y=kmer_hist_orig[[2]] - - #automatically zoom into the relevant regions of the plot, ignore first 15 positions - xmax=length(x) - start=which(y == min(y[1:TYPICAL_ERROR])) - zoomx=x[start:(xmax-1)] - zoomy=y[start:(xmax-1)] - - ## allow for a little space above max value past the noise - y_limit = max(zoomy[start:length(zoomy)])*1.1 - - x_limit = which(y == max(y[start:length(zoomx)])) * 3 - - if (min(zoomy) > zoomy[1]){ - x_limit=max(which(zoomy= 5)) { - maxCovGenomeLen = as.numeric(args[[5]]) - } - - if ((length(args) == 6) && (as.numeric(args[[6]] == 1))) { VERBOSE = 1 } - - ## values for testing - #histfile <- "~/build/genomescope/simulation/simulation_results/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist" - #k <- 21 - #readlength <- 100 - #foldername <- "~/build/genomescope/simulation/simulation_analysis/Arabidopsis_thaliana.TAIR10.26.dna_sm.toplevel.fa_het0.01_br1_rl100_cov100_err0.01_reads.fa21.hist" - - if (k > readlength) { stop("K cannot be greater than readlength") } - - cat(paste("GenomeScope analyzing ", histfile, " k=", k, " readlen=", readlength, " outdir=", foldername, "\n", sep="")) - - dir.create(foldername, showWarnings=FALSE) - - kmer_prof <- read.csv(file=histfile,sep=" ", header=FALSE) - - minkmerx = 1; - if (kmer_prof[1,1] == 0) { - if (VERBOSE) { cat("Histogram starts with zero, reseting minkmerx\n"); } - minkmerx = 2; - } - - kmer_prof <- kmer_prof[c(minkmerx:(length(kmer_prof[,2])-1)),] #get rid of the last position - kmer_prof_orig <- kmer_prof - - ## Initialize the status - progressFilename <- paste(foldername,"/progress.txt",sep="") - cat("starting", file=progressFilename, sep="\n") - - ## try to find the local minimum between errors and the first (heterozygous) peak - start <- which(kmer_prof[,2]==min(kmer_prof[1:TYPICAL_ERROR,2])) - - maxCovIndex = -1 - - ## Figure out which kmers to exclude, if any - if(maxCovGenomeLen == -1){ - maxCovIndex <- length(kmer_prof[,1]) - } - else - { - ## Figure out the index we should use for this coverage length - x <- kmer_prof[,1] - maxCovIndex <- length(x[x<=maxCovGenomeLen]) - } - - if (VERBOSE) { cat(paste("using maxCovGenomeLen:", maxCovGenomeLen, " with index:", maxCovIndex, "trying 4peak model... \n")) } - - ## terminate after NUM_ROUND iterations, store best result so far in container - round <- 0 - best_container <- list(NULL,0) - - while(round < NUM_ROUNDS) - { - cat(paste("round", round, "trimming to", start, "trying 4peak model... "), file=progressFilename, sep="", append=TRUE) - if (VERBOSE) { cat(paste("round", round, "trimming to", start, "trying 4peak model... \n")) } - - ## Reset the input trimming off low frequency error kmers - kmer_prof=kmer_prof_orig[1:maxCovIndex,] - x <- kmer_prof[start:maxCovIndex,1] - y <- kmer_prof[start:maxCovIndex,2] - - model_4peaks <- estimate_Genome_4peak2(kmer_prof, x, y, k, readlength, round, foldername) - - if (!is.null(model_4peaks[[1]])) { - cat(paste("converged. score: ", model_4peaks[[2]]$all[[1]]), file=progressFilename, sep="\n", append=TRUE) - - if (VERBOSE) - { - mdir = paste(foldername, "/round", round, sep="") - dir.create(mdir, showWarnings=FALSE) - report_results(kmer_prof,kmer_prof_orig, k, model_4peaks, mdir) - } - } else { - cat(paste("unconverged"), file=progressFilename, sep="\n", append=TRUE) - } - - #check if this result is better than previous - if (!is.null(model_4peaks[[1]])) - { - if (is.null(best_container[[1]])) - { - if (VERBOSE) { cat(paste("no previous best, updating best")) } - best_container = model_4peaks - } - else - { - pdiff = abs(model_4peaks[[2]]$all[[1]] - best_container[[2]]$all[[1]]) / max(model_4peaks[[2]]$all[[1]], best_container[[2]]$all[[1]]) - - if (pdiff < SCORE_CLOSE) - { - hetm = summary(model_4peaks[[1]])$coefficients['r',][[1]] - hetb = summary(best_container[[1]])$coefficients['r',][[1]] - - if (hetb * SCORE_HET_FOLD_DIFFERENCE < hetm) - { - if (VERBOSE) { cat(paste("model has significantly higher heterozygosity but similar score, overruling")) } - best_container = model_4peaks - } - else if (hetm * SCORE_HET_FOLD_DIFFERENCE < hetb) - { - if (VERBOSE) { cat(paste("previous best has significantly higher heterozygosity and similar score, keeping")) } - } - else if (model_4peaks[[2]]$all[[1]] < best_container[[2]]$all[[1]]) - { - if (VERBOSE) { cat(paste("score is marginally better but het rate is not extremely different, upating")) } - best_container = model_4peaks - } - } - else if (model_4peaks[[2]]$all[[1]] < best_container[[2]]$all[[1]]) - { - if (VERBOSE) { cat(paste("score is significantly better, upating")) } - best_container = model_4peaks - } - } - } - - ## Ignore a larger number of kmers as errors - start <- start + START_SHIFT - round <- round + 1 - } - ## Report the results, note using the original full profile - report_results(kmer_prof,kmer_prof_orig, k, best_container, foldername) + ## Ignore a larger number of kmers as errors + start <- start + START_SHIFT + round <- round + 1 + } + ## Report the results, note using the original full profile + report_results(kmer_prof,kmer_prof_orig, k, p, best_container, foldername, arguments, FALSE) +# if (!is.null(best_container[[1]])) { +# print('model score') +# print(best_container[[2]]$all[[1]]) +# print(best_container[[1]]$m$deviance()) +# } } diff --git a/header.html b/header.html index 4bd3c65..7df25af 100755 --- a/header.html +++ b/header.html @@ -72,6 +72,11 @@
  • Bird
  • Drosophila
  • Arabidopsis F1
    • +
  • Coastal Redwood
    • +
  • Cotton
    • +
  • Root-knot Nematode
    • +
  • Potato
    • +
  • Wheat
    • @@ -130,4 +135,4 @@ - \ No newline at end of file + diff --git a/index.php b/index.php index f342175..117ae4e 100755 --- a/index.php +++ b/index.php @@ -32,20 +32,26 @@ class="dropzone"

    - Kmer length + K-mer length

    - Read length - + Ploidy +

    - Max kmer coverage - + Max k-mer coverage + +
    +

    +

    +

    + Average k-mer coverage for polyploid genome +

    @@ -64,20 +70,35 @@ class="dropzone"

    Instructions

    -

    Upload results from running Jellyfish. Example: inputk21.hist

    Instructions for running Jellyfish:

    1. Download and install jellyfish from: +

      Upload results from running Jellyfish or KMC. Example: inputk21.hist

      Instructions for running Jellyfish:

      1. Download and install jellyfish from: http://www.genome.umd.edu/jellyfish.html#Release
        2. -
      2. Count kmers using jellyfish: +
      3. Count k-mers using jellyfish: 

        $ jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf

        - Note you should adjust the memory (-s) and threads (-t) parameter according to your server. This example will use 10 threads and 1GB of RAM. The kmer length (-m) may need to be scaled if you have low coverage or a high error rate. You should always use "canonical kmers" (-C) + Note you should adjust the memory (-s) and threads (-t) parameters according to your server. This example will use 10 threads and 1GB of RAM. The k-mer length (-m) may need to be scaled if you have low coverage or a high error rate. You should always use "canonical k-mers" (-C).

        4. -
      4. Export the kmer count histogram +
      5. Export the k-mer count histogram 

        $ jellyfish histo -t 10 reads.jf > reads.histo

        Again the thread count (-t) should be scaled according to your server.

      6. Upload reads.histo to GenomeScope
      - Note: High copy-number DNA such as chloroplasts can confuse the model. Set a max kmer coverage to avoid this. Default is -1 meaning no filter. + Instructions for running KMC:
      1. Download and install KMC from: + http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=download
        2. +
      2. Count k-mers using KMC: + 

        $ mkdir tmp

        + 

        $ ls *.fastq > FILES

        + 

        $ kmc -k21 -t10 -m64 -ci1 -cs10000 @FILES reads tmp/

        +

        + Note you should adjust the memory (-m) and threads (-t) parameters according to your server. This example will use 10 threads and 64GB of RAM. The k-mer length (-k) may need to be scaled if you have low coverage or a high error rate. The lower (-ci) and upper (-cs) bounds exclude k-mers with counts outside these boundaries. FILES is a file with a list of input files. +

        3. +
      3. Export the k-mer count histogram + 

        $ kmc_tools transform reads histogram reads.histo -cx10000

        +

        The upper bound (-cx) gives the cutoff for the histogram.

        4. +
      4. Upload reads.histo to GenomeScope
        5. +
      + + Note: High copy-number DNA such as chloroplasts can confuse the model. Set a max k-mer coverage to avoid this. Default is -1 meaning no filter.

    diff --git a/info.php b/info.php index 0e6cd3a..669ce0b 100755 --- a/info.php +++ b/info.php @@ -12,14 +12,15 @@

    Information

    -

    The code is open source on Github: github.com/schatzlab/genomescope

    +

    The code is open source on Github: github.com/tbenavi1/genomescope2.0


    -

    Statistical work by Gregory Vurture and Fritz Sedlazeck

    +

    Statistical work by Gregory Vurture and Fritz Sedlazeck

    +

    Polyploid 2.0 model by T. Rhyker Ranallo-Benavidez

    Web application by Maria Nattestad

    -

    Principal investigator / The Boss: Mike Schatz

    +

    Principal investigator / The Boss: Mike Schatz


    -

    For questions about the science, email: Mike Schatz at mschatz@cshl.edu

    -

    For questions about the web application, email: Maria Nattestad at mnattest@cshl.edu

    +

    For questions about the science, email: Mike Schatz at mschatz@cs.jhu.edu

    +

    For questions about the web application, email: T. Rhyker Ranallo-Benavidez at tbenavi1@jhu.edu

    @@ -31,4 +32,4 @@ - \ No newline at end of file + diff --git a/input_validation.php b/input_validation.php index fc44dbe..4cbb031 100755 --- a/input_validation.php +++ b/input_validation.php @@ -11,15 +11,17 @@ if( !isset($_POST['code']) ) { $aResult['error'] = 'ERROR: No code passed to input_validation.php';} $code=$_POST["code"]; if( !isset($_POST['kmer_length']) ) { echo shell_exec('echo ERROR: No kmer_length passed to input_validation.php >> user_data/$code/input_validation.log');} - if( !isset($_POST['read_length']) ) { echo shell_exec('echo ERROR: No read_length passed to input_validation.php >> user_data/$code/input_validation.log');} + if( !isset($_POST['ploidy']) ) { echo shell_exec('echo ERROR: No ploidy passed to input_validation.php >> user_data/$code/input_validation.log');} if( !isset($_POST['description']) ) { echo shell_exec('echo ERROR: No description passed to input_validation.php >> user_data/$code/input_validation.log');} if( !isset($_POST['max_kmer_cov']) ) { echo shell_exec('echo ERROR: No max_kmer_cov passed to input_validation.php >> user_data/$code/input_validation.log');} + if( !isset($_POST['lambda']) ) { echo shell_exec("echo ERROR: No lambda passed to run_now.php >> user_data/$code/input_validation.log");} $description = $_POST["description"]; $kmer_length = $_POST["kmer_length"]; - $read_length = $_POST["read_length"]; + $ploidy = $_POST["ploidy"]; $max_kmer_cov = $_POST["max_kmer_cov"]; + $lambda = $_POST["lambda"]; $url="analysis.php?code=$code"; @@ -29,7 +31,7 @@ $back_button= "
    "; //$continue_button= "
    "; - $continue_button= "
    "; + $continue_button= "
    "; if (!file_exists ($filename)) { @@ -44,18 +46,21 @@ $num_columns=0; $bin_history=array(); $consistent=true; + $dobreak = ""; + + //echo "scanning file... "; while(!feof($myfile)) { $bin_counter=0; $line=fgets($myfile); - // $line =trim(preg_replace( '/\s+/', ' ', $line )); + $line =trim(preg_replace( '/\s+/', ' ', $line )); if ($line=="" or $line==" ") { continue; } $array=array_map("trim",explode(' ',$line)); //var_dump($array); $bin_counter=count($array); - //echo $bin_counter . "
    "; - //echo $num_columns. "
    "; + // echo "
    " . $bin_counter . "
    "; + // echo $num_columns. "
    "; if ($num_columns != 0 and $num_columns != $bin_counter) { $consistent=false; @@ -65,12 +70,19 @@ $num_columns=$bin_counter; $line_counter=$line_counter+1; $bin_history[]=$bin_counter; + if ($line_counter > 100000) { + $dobreak=">"; + break; + } } fclose($myfile); + + //echo "
    "; + //echo "finished checking file
    "; if ($consistent) { if ($line_counter >= 50 and $num_columns == 2) { - echo "
    Great! File was uploaded and has acceptable dimensions: $line_counter rows by $num_columns columns
    "; + echo "
    Great! File was uploaded and has acceptable dimensions: $dobreak$line_counter rows by $num_columns columns
    "; echo "
    "; echo "$back_button"; echo "
    "; @@ -78,7 +90,7 @@ echo "
    "; } else { if ($num_columns != 2) { - echo "
    File was uploaded but it has $num_columns column(s). The file must have 2 columns separated by a single space, which is the default in Jellyfish
    "; + echo "
    File was uploaded but it has $num_columns column(s). The file must have 2 columns separated by a single space, which is the default in Jellyfish, or by a single tab, which is the default in KMC
    "; } if ($line_counter < 50) { echo "
    File was uploaded but it only has $line_counter rows, are you sure this is the right file?
    "; @@ -87,7 +99,7 @@ } } else { - echo "
    All lines in file must have the same number of elements (separated by single spaces). This file had the following numbers of elements per line: "; + echo "
    All lines in file must have the same number of elements (separated by a single space or by a single tab). This file had the following numbers of elements per line: "; foreach ($bin_history as $num) echo $num . ", "; echo "
    "; diff --git a/install.R b/install.R new file mode 100644 index 0000000..dd98a42 --- /dev/null +++ b/install.R @@ -0,0 +1,5 @@ +local_lib_path = "~/R_libs/" + +install.packages('minpack.lm', lib=local_lib_path, repos = "http://cran.us.r-project.org") +install.packages('argparse', lib=local_lib_path, repos = "http://cran.us.r-project.org") +install.packages('.', repos=NULL, type="source", lib=local_lib_path) diff --git a/js/analysis_page_script.js b/js/analysis_page_script.js index 00354b3..1dddb70 100755 --- a/js/analysis_page_script.js +++ b/js/analysis_page_script.js @@ -86,14 +86,24 @@ function getUrlVars() { // var content_width = $( window ).width(); - +function doesFileExist(urlToFile) { + var xhr = new XMLHttpRequest(); + xhr.open('HEAD', urlToFile, false); + xhr.send(); + + if (xhr.status == "404") { + return false; + } else { + return true; + } +} function check_plot_exists(counter,bool_succeeded) { var run_id_code=getUrlVars()["code"]; var file_url_prefix="user_data/"+run_id_code + "/"; - var file_to_check_for=file_url_prefix + "plot.png"; + var file_to_check_for=file_url_prefix + "summary.txt"; if (counter>100) { alert("Taking too long to find "+ file_to_check_for + " counter: " + counter); @@ -110,12 +120,19 @@ function check_plot_exists(counter,bool_succeeded) { // alert("inside success"); // document.getElementById("landing_for_plot1").innerHTML=''; // width="750" height="500" // style="max-height:100%; max-width:100%;" // document.getElementById("landing_for_plot1_details").innerHTML=''; - - document.getElementById("landing_for_plot1").innerHTML=''; - document.getElementById("landing_for_plot2").innerHTML=''; + var result = doesFileExist(file_url_prefix + "plot.png"); + if (result == true) { + document.getElementById("landing_for_plot1").innerHTML=''; + document.getElementById("landing_for_plot2").innerHTML=''; + } else { + document.getElementById("landing_for_plot1").innerHTML=''; + document.getElementById("landing_for_plot2").innerHTML=''; + document.getElementById("landing_for_plot3").innerHTML=''; + document.getElementById("landing_for_plot4").innerHTML=''; + } if (bool_succeeded) { - document.getElementById("landing_for_text1").innerHTML=''; + document.getElementById("landing_for_text1").innerHTML=''; document.getElementById("landing_for_text2").innerHTML=''; } else { document.getElementById("landing_for_text1").innerHTML='Model did not converge'; @@ -207,4 +224,4 @@ $(document).ready(function() { // for (i=0; i"; + document.getElementById("code").innerHTML = "Return to view your results at any time: "; document.getElementById("analysis_form").innerHTML = ''; document.getElementById("myAwesomeDropzone").innerHTML = ''; } diff --git a/man/estimate_Genome_peakp.Rd b/man/estimate_Genome_peakp.Rd new file mode 100644 index 0000000..9da7a68 --- /dev/null +++ b/man/estimate_Genome_peakp.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/estimate_genome_peak.R +\name{estimate_Genome_peakp} +\alias{estimate_Genome_peakp} +\title{Function to fit 2p peak model, with p forms} +\usage{ +estimate_Genome_peakp(kmer_hist_orig, x, y, k, p, topology, estKmercov, + round, foldername, arguments) +} +\arguments{ +\item{kmer_hist_orig}{A data frame of the original histogram data (starting at 1 and with last position removed).} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} + +\item{y}{A numeric vector of the y-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} + +\item{k}{An integer corresponding to the kmer length.} + +\item{p}{An integer corresponding to the ploidy.} + +\item{topology}{An integer corresponding to the topology to use.} + +\item{estKmercov}{An integer corresponding to the estimated kmer coverage of the polyploid genome. +Set to -1 if not specified by user.} + +\item{round}{An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process.} + +\item{foldername}{A character vector corresponding to the name of the output directory.} + +\item{arguments}{A data frame of the user-specified inputs.} +} +\value{ +A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms). +} +\description{ +Function to fit 2p peak model, with p forms +} diff --git a/man/eval_model.Rd b/man/eval_model.Rd new file mode 100644 index 0000000..c757841 --- /dev/null +++ b/man/eval_model.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/eval_model.R +\name{eval_model} +\alias{eval_model} +\title{Evaluate distinct model forms, in order to resolve ambiguity of which peak is the homozygous peak} +\usage{ +eval_model(kmer_hist_orig, nls0, nls1, p, round, foldername, arguments) +} +\arguments{ +\item{kmer_hist_orig}{A data frame of the original histogram data (starting at 1 and with last position removed).} + +\item{nls0, nls1}{The nlsLM model objects to evaluate and compare.} + +\item{p}{An integer corresponding to the ploidy.} + +\item{round}{An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process.} + +\item{foldername}{A character vector corresponding to the name of the output directory.} + +\item{arguments}{A data frame of the user-specified inputs.} +} +\value{ +A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms). +} +\description{ +Evaluate distinct model forms, in order to resolve ambiguity of which peak is the homozygous peak +} diff --git a/man/nls_peak.Rd b/man/nls_peak.Rd new file mode 100644 index 0000000..80ff98d --- /dev/null +++ b/man/nls_peak.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/nls_peak.R +\name{nls_peak} +\alias{nls_peak} +\title{Uses nlsLM to fit 2p peak model} +\usage{ +nls_peak(x, y, k, p, top, estKmercov, estLength, max_iterations) +} +\arguments{ +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} + +\item{y}{A numeric vector of the y-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} + +\item{k}{An integer corresponding to the kmer length.} + +\item{p}{An integer corresponding to the ploidy.} + +\item{top}{An integer corresponding to the topology.} + +\item{estKmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{estLength}{A numeric corresponding to the estimated polyploid genome length.} + +\item{max_iterations}{An integer corresponding to the maximum number iterations to use for nlsLM.} +} +\value{ +An nlsLM model object with some additional components. +} +\description{ +Uses nlsLM to fit 2p peak model +} diff --git a/man/predict1_0.Rd b/man/predict1_0.Rd new file mode 100644 index 0000000..0f951b3 --- /dev/null +++ b/man/predict1_0.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict1_0} +\alias{predict1_0} +\title{Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict1_0(k, d, kmercov, bias, x) +} +\arguments{ +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict1_0_unique.Rd b/man/predict1_0_unique.Rd new file mode 100644 index 0000000..efefc97 --- /dev/null +++ b/man/predict1_0_unique.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict1_0_unique} +\alias{predict1_0_unique} +\title{Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict1_0_unique(k, d, kmercov, bias, x) +} +\arguments{ +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict1_1.Rd b/man/predict1_1.Rd new file mode 100644 index 0000000..c98d299 --- /dev/null +++ b/man/predict1_1.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict1_1} +\alias{predict1_1} +\title{Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict1_1(k, d, kmercov, bias, x) +} +\arguments{ +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict1_1_unique.Rd b/man/predict1_1_unique.Rd new file mode 100644 index 0000000..a791a83 --- /dev/null +++ b/man/predict1_1_unique.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict1_1_unique} +\alias{predict1_1_unique} +\title{Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict1_1_unique(k, d, kmercov, bias, x) +} +\arguments{ +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict2_0.Rd b/man/predict2_0.Rd new file mode 100644 index 0000000..744fe64 --- /dev/null +++ b/man/predict2_0.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict2_0} +\alias{predict2_0} +\title{Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict2_0(r1, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1}{A numeric corresponding to the nucleotide heterozygosity ab.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict2_0_unique.Rd b/man/predict2_0_unique.Rd new file mode 100644 index 0000000..51513dc --- /dev/null +++ b/man/predict2_0_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict2_0_unique} +\alias{predict2_0_unique} +\title{Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict2_0_unique(r1, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1}{A numeric corresponding to the nucleotide heterozygosity ab.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict2_1.Rd b/man/predict2_1.Rd new file mode 100644 index 0000000..5551dcc --- /dev/null +++ b/man/predict2_1.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict2_1} +\alias{predict2_1} +\title{Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict2_1(r1, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1}{A numeric corresponding to the nucleotide heterozygosity ab.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict2_1_unique.Rd b/man/predict2_1_unique.Rd new file mode 100644 index 0000000..8b7b3f9 --- /dev/null +++ b/man/predict2_1_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict2_1_unique} +\alias{predict2_1_unique} +\title{Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict2_1_unique(r1, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1}{A numeric corresponding to the nucleotide heterozygosity ab.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict3_0.Rd b/man/predict3_0.Rd new file mode 100644 index 0000000..d9e9354 --- /dev/null +++ b/man/predict3_0.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict3_0} +\alias{predict3_0} +\title{Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict3_0(r1, r2, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1, r2}{Numerics corresponding to the nucleotide heterozygosities aab and abc respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict3_0_unique.Rd b/man/predict3_0_unique.Rd new file mode 100644 index 0000000..bdf6584 --- /dev/null +++ b/man/predict3_0_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict3_0_unique} +\alias{predict3_0_unique} +\title{Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict3_0_unique(r1, r2, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1, r2}{Numerics corresponding to the nucleotide heterozygosities aab and abc respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict3_1.Rd b/man/predict3_1.Rd new file mode 100644 index 0000000..f41b498 --- /dev/null +++ b/man/predict3_1.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict3_1} +\alias{predict3_1} +\title{Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict3_1(r1, r2, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1, r2}{Numerics corresponding to the nucleotide heterozygosities aab and abc respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict3_1_unique.Rd b/man/predict3_1_unique.Rd new file mode 100644 index 0000000..9e493e0 --- /dev/null +++ b/man/predict3_1_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict3_1_unique} +\alias{predict3_1_unique} +\title{Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict3_1_unique(r1, r2, k, d, kmercov, bias, x) +} +\arguments{ +\item{r1, r2}{Numerics corresponding to the nucleotide heterozygosities aab and abc respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_0.Rd b/man/predict4_0.Rd new file mode 100644 index 0000000..51b5e2e --- /dev/null +++ b/man/predict4_0.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_0} +\alias{predict4_0} +\title{Produce model estimated (p=4, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_0(raaab, raabb, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaab, raabb, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aaab, aabb, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_0_unique.Rd b/man/predict4_0_unique.Rd new file mode 100644 index 0000000..08a7135 --- /dev/null +++ b/man/predict4_0_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_0_unique} +\alias{predict4_0_unique} +\title{Produce model estimated (p=4, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_0_unique(raaab, raabb, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaab, raabb, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aaab, aabb, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_1.Rd b/man/predict4_1.Rd new file mode 100644 index 0000000..39ef6ac --- /dev/null +++ b/man/predict4_1.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_1} +\alias{predict4_1} +\title{Produce model estimated (p=4, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_1(raaab, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaab, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aaab, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_1_unique.Rd b/man/predict4_1_unique.Rd new file mode 100644 index 0000000..bb073cb --- /dev/null +++ b/man/predict4_1_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_1_unique} +\alias{predict4_1_unique} +\title{Produce model estimated (p=4, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_1_unique(raaab, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaab, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aaab, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_2.Rd b/man/predict4_2.Rd new file mode 100644 index 0000000..9f416b6 --- /dev/null +++ b/man/predict4_2.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_2} +\alias{predict4_2} +\title{Produce model estimated (p=4, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_2(raabb, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raabb, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aabb, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict4_2_unique.Rd b/man/predict4_2_unique.Rd new file mode 100644 index 0000000..dc2e98b --- /dev/null +++ b/man/predict4_2_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict4_2_unique} +\alias{predict4_2_unique} +\title{Produce model estimated (p=4, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict4_2_unique(raabb, raabc, rabcd, k, d, kmercov, bias, x) +} +\arguments{ +\item{raabb, raabc, rabcd}{Numerics corresponding to the nucleotide heterozygosities aabb, aabc, and abcd respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=4, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_0.Rd b/man/predict5_0.Rd new file mode 100644 index 0000000..5bf0eff --- /dev/null +++ b/man/predict5_0.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_0} +\alias{predict5_0} +\title{Produce model estimated (p=5, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_0(raaaab, raaabb, raaabc, raabbc, raabcd, rabcde, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaab, raaabb, raaabc, raabbc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_0_unique.Rd b/man/predict5_0_unique.Rd new file mode 100644 index 0000000..68bd1d5 --- /dev/null +++ b/man/predict5_0_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_0_unique} +\alias{predict5_0_unique} +\title{Produce model estimated (p=5, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_0_unique(raaaab, raaabb, raaabc, raabbc, raabcd, rabcde, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaab, raaabb, raaabc, raabbc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_1.Rd b/man/predict5_1.Rd new file mode 100644 index 0000000..6303e56 --- /dev/null +++ b/man/predict5_1.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_1} +\alias{predict5_1} +\title{Produce model estimated (p=5, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_1(raaaab, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaab, raaabc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaaab, aaabc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_1_unique.Rd b/man/predict5_1_unique.Rd new file mode 100644 index 0000000..256d2d2 --- /dev/null +++ b/man/predict5_1_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_1_unique} +\alias{predict5_1_unique} +\title{Produce model estimated (p=5, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_1_unique(raaaab, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaab, raaabc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaaab, aaabc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_2.Rd b/man/predict5_2.Rd new file mode 100644 index 0000000..9114c3b --- /dev/null +++ b/man/predict5_2.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_2} +\alias{predict5_2} +\title{Produce model estimated (p=5, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_2(raaaab, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaab, raabbc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaaab, aabbc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_2_unique.Rd b/man/predict5_2_unique.Rd new file mode 100644 index 0000000..ddd5a48 --- /dev/null +++ b/man/predict5_2_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_2_unique} +\alias{predict5_2_unique} +\title{Produce model estimated (p=5, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_2_unique(raaaab, raabbc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaab, raabbc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaaab, aabbc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_3.Rd b/man/predict5_3.Rd new file mode 100644 index 0000000..b3dc0d4 --- /dev/null +++ b/man/predict5_3.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_3} +\alias{predict5_3} +\title{Produce model estimated (p=5, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_3(raaabb, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raaabc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aaabc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_3_unique.Rd b/man/predict5_3_unique.Rd new file mode 100644 index 0000000..2dff14f --- /dev/null +++ b/man/predict5_3_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_3_unique} +\alias{predict5_3_unique} +\title{Produce model estimated (p=5, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_3_unique(raaabb, raaabc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raaabc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aaabc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_4.Rd b/man/predict5_4.Rd new file mode 100644 index 0000000..2426dcf --- /dev/null +++ b/man/predict5_4.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_4} +\alias{predict5_4} +\title{Produce model estimated (p=5, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_4(raaabb, raabcc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raabcc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_4_unique.Rd b/man/predict5_4_unique.Rd new file mode 100644 index 0000000..917120c --- /dev/null +++ b/man/predict5_4_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_4_unique} +\alias{predict5_4_unique} +\title{Produce model estimated (p=5, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_4_unique(raaabb, raabcc, raabcd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raabcc, raabcd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, aabcd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_5.Rd b/man/predict5_5.Rd new file mode 100644 index 0000000..3a445e7 --- /dev/null +++ b/man/predict5_5.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_5} +\alias{predict5_5} +\title{Produce model estimated (p=5, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_5(raaabb, raabcc, rabcdd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raabcc, rabcdd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, abcdd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict5_5_unique.Rd b/man/predict5_5_unique.Rd new file mode 100644 index 0000000..f1048aa --- /dev/null +++ b/man/predict5_5_unique.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict5_5_unique} +\alias{predict5_5_unique} +\title{Produce model estimated (p=5, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict5_5_unique(raaabb, raabcc, rabcdd, rabcde, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaabb, raabcc, rabcdd, rabcde}{Numerics corresponding to the nucleotide heterozygosities aaabb, aabcc, abcdd, and abcde respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=5, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_0.Rd b/man/predict6_0.Rd new file mode 100644 index 0000000..e20a916 --- /dev/null +++ b/man/predict6_0.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_0} +\alias{predict6_0} +\title{Produce model estimated (p=6, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_0(raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, raaabcd, + raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, raaabcd, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_0_unique.Rd b/man/predict6_0_unique.Rd new file mode 100644 index 0000000..ab77000 --- /dev/null +++ b/man/predict6_0_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_0_unique} +\alias{predict6_0_unique} +\title{Produce model estimated (p=6, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_0_unique(raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, + raaabcd, raabbcd, raabcde, rabcdef, k, d, kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaaabb, raaabbb, raaaabc, raaabbc, raabbcc, raaabcd, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_1.Rd b/man/predict6_1.Rd new file mode 100644 index 0000000..ed1b6f8 --- /dev/null +++ b/man/predict6_1.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_1} +\alias{predict6_1} +\title{Produce model estimated (p=6, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_1(raaaaab, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaaab, raaaabc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_10.Rd b/man/predict6_10.Rd new file mode 100644 index 0000000..8ab39a6 --- /dev/null +++ b/man/predict6_10.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_10} +\alias{predict6_10} +\title{Produce model estimated (p=6, topology=10) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_10(raaaabb, raaabcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raabcdd, rabcdee, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, abcdee, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=10) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_10_unique.Rd b/man/predict6_10_unique.Rd new file mode 100644 index 0000000..c059789 --- /dev/null +++ b/man/predict6_10_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_10_unique} +\alias{predict6_10_unique} +\title{Produce model estimated (p=6, topology=10, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_10_unique(raaaabb, raaabcc, raabcdd, rabcdee, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raabcdd, rabcdee, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, abcdee, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=10, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_11.Rd b/man/predict6_11.Rd new file mode 100644 index 0000000..26b66b8 --- /dev/null +++ b/man/predict6_11.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_11} +\alias{predict6_11} +\title{Produce model estimated (p=6, topology=11) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_11(raaaabb, raabbcc, raabbcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=11) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_11_unique.Rd b/man/predict6_11_unique.Rd new file mode 100644 index 0000000..188e6bf --- /dev/null +++ b/man/predict6_11_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_11_unique} +\alias{predict6_11_unique} +\title{Produce model estimated (p=6, topology=11, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_11_unique(raaaabb, raabbcc, raabbcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=11, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_12.Rd b/man/predict6_12.Rd new file mode 100644 index 0000000..55a4882 --- /dev/null +++ b/man/predict6_12.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_12} +\alias{predict6_12} +\title{Produce model estimated (p=6, topology=12) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_12(raaaabb, raabbcc, raabcdd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabcdd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=12) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_12_unique.Rd b/man/predict6_12_unique.Rd new file mode 100644 index 0000000..b0d9106 --- /dev/null +++ b/man/predict6_12_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_12_unique} +\alias{predict6_12_unique} +\title{Produce model estimated (p=6, topology=12, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_12_unique(raaaabb, raabbcc, raabcdd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabcdd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=12, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_13.Rd b/man/predict6_13.Rd new file mode 100644 index 0000000..c600f97 --- /dev/null +++ b/man/predict6_13.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_13} +\alias{predict6_13} +\title{Produce model estimated (p=6, topology=13) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_13(raaaabb, raabbcc, raabcdd, rabcdee, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabcdd, rabcdee, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, abcdee, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=13) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_13_unique.Rd b/man/predict6_13_unique.Rd new file mode 100644 index 0000000..c914cd8 --- /dev/null +++ b/man/predict6_13_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_13_unique} +\alias{predict6_13_unique} +\title{Produce model estimated (p=6, topology=13, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_13_unique(raaaabb, raabbcc, raabcdd, rabcdee, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raabbcc, raabcdd, rabcdee, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aabbcc, aabcdd, abcdee, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=13, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_14.Rd b/man/predict6_14.Rd new file mode 100644 index 0000000..9328ec9 --- /dev/null +++ b/man/predict6_14.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_14} +\alias{predict6_14} +\title{Produce model estimated (p=6, topology=14) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_14(raaabbb, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=14) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_14_unique.Rd b/man/predict6_14_unique.Rd new file mode 100644 index 0000000..d77cfd7 --- /dev/null +++ b/man/predict6_14_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_14_unique} +\alias{predict6_14_unique} +\title{Produce model estimated (p=6, topology=14, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_14_unique(raaabbb, raaabbc, raaabcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=14, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_15.Rd b/man/predict6_15.Rd new file mode 100644 index 0000000..81a3450 --- /dev/null +++ b/man/predict6_15.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_15} +\alias{predict6_15} +\title{Produce model estimated (p=6, topology=15) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_15(raaabbb, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raabccd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=15) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_15_unique.Rd b/man/predict6_15_unique.Rd new file mode 100644 index 0000000..40300a6 --- /dev/null +++ b/man/predict6_15_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_15_unique} +\alias{predict6_15_unique} +\title{Produce model estimated (p=6, topology=15, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_15_unique(raaabbb, raaabbc, raabccd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raabccd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=15, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_16.Rd b/man/predict6_16.Rd new file mode 100644 index 0000000..9d8fe07 --- /dev/null +++ b/man/predict6_16.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_16} +\alias{predict6_16} +\title{Produce model estimated (p=6, topology=16) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_16(raaabbb, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raabccd, rabcdde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, abcdde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=16) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_16_unique.Rd b/man/predict6_16_unique.Rd new file mode 100644 index 0000000..5f9cbe5 --- /dev/null +++ b/man/predict6_16_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_16_unique} +\alias{predict6_16_unique} +\title{Produce model estimated (p=6, topology=16, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_16_unique(raaabbb, raaabbc, raabccd, rabcdde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaabbb, raaabbc, raabccd, rabcdde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaabbb, aaabbc, aabccd, abcdde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=16, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_1_unique.Rd b/man/predict6_1_unique.Rd new file mode 100644 index 0000000..bed32c0 --- /dev/null +++ b/man/predict6_1_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_1_unique} +\alias{predict6_1_unique} +\title{Produce model estimated (p=6, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_1_unique(raaaaab, raaaabc, raaabcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaaabc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_2.Rd b/man/predict6_2.Rd new file mode 100644 index 0000000..2a8ad19 --- /dev/null +++ b/man/predict6_2.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_2} +\alias{predict6_2} +\title{Produce model estimated (p=6, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_2(raaaaab, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaaab, raaaabc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_2_unique.Rd b/man/predict6_2_unique.Rd new file mode 100644 index 0000000..85c9801 --- /dev/null +++ b/man/predict6_2_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_2_unique} +\alias{predict6_2_unique} +\title{Produce model estimated (p=6, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_2_unique(raaaaab, raaaabc, raabbcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaaabc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaaabc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_3.Rd b/man/predict6_3.Rd new file mode 100644 index 0000000..b4cab77 --- /dev/null +++ b/man/predict6_3.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_3} +\alias{predict6_3} +\title{Produce model estimated (p=6, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_3(raaaaab, raaabbc, raaabcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_3_unique.Rd b/man/predict6_3_unique.Rd new file mode 100644 index 0000000..d43d224 --- /dev/null +++ b/man/predict6_3_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_3_unique} +\alias{predict6_3_unique} +\title{Produce model estimated (p=6, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_3_unique(raaaaab, raaabbc, raaabcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_4.Rd b/man/predict6_4.Rd new file mode 100644 index 0000000..cefab14 --- /dev/null +++ b/man/predict6_4.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_4} +\alias{predict6_4} +\title{Produce model estimated (p=6, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_4(raaaaab, raaabbc, raabccd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raabccd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_4_unique.Rd b/man/predict6_4_unique.Rd new file mode 100644 index 0000000..2de1ed9 --- /dev/null +++ b/man/predict6_4_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_4_unique} +\alias{predict6_4_unique} +\title{Produce model estimated (p=6, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_4_unique(raaaaab, raaabbc, raabccd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raabccd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_5.Rd b/man/predict6_5.Rd new file mode 100644 index 0000000..fb0f1d4 --- /dev/null +++ b/man/predict6_5.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_5} +\alias{predict6_5} +\title{Produce model estimated (p=6, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_5(raaaaab, raaabbc, raabccd, rabcdde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raabccd, rabcdde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, abcdde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_5_unique.Rd b/man/predict6_5_unique.Rd new file mode 100644 index 0000000..67c4b4e --- /dev/null +++ b/man/predict6_5_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_5_unique} +\alias{predict6_5_unique} +\title{Produce model estimated (p=6, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_5_unique(raaaaab, raaabbc, raabccd, rabcdde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaaab, raaabbc, raabccd, rabcdde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaaab, aaabbc, aabccd, abcdde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_6.Rd b/man/predict6_6.Rd new file mode 100644 index 0000000..45d4e62 --- /dev/null +++ b/man/predict6_6.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_6} +\alias{predict6_6} +\title{Produce model estimated (p=6, topology=6) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_6(raaaabb, raaaabc, raaabcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raaaabc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=6) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_6_unique.Rd b/man/predict6_6_unique.Rd new file mode 100644 index 0000000..24ed1ca --- /dev/null +++ b/man/predict6_6_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_6_unique} +\alias{predict6_6_unique} +\title{Produce model estimated (p=6, topology=6, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_6_unique(raaaabb, raaaabc, raaabcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raaaabc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=6, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_7.Rd b/man/predict6_7.Rd new file mode 100644 index 0000000..95c11dd --- /dev/null +++ b/man/predict6_7.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_7} +\alias{predict6_7} +\title{Produce model estimated (p=6, topology=7) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_7(raaaabb, raaaabc, raabbcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raaaabc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=7) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_7_unique.Rd b/man/predict6_7_unique.Rd new file mode 100644 index 0000000..5f8a823 --- /dev/null +++ b/man/predict6_7_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_7_unique} +\alias{predict6_7_unique} +\title{Produce model estimated (p=6, topology=7, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_7_unique(raaaabb, raaaabc, raabbcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raaaabc, raabbcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaaabc, aabbcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=7, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_8.Rd b/man/predict6_8.Rd new file mode 100644 index 0000000..a507069 --- /dev/null +++ b/man/predict6_8.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_8} +\alias{predict6_8} +\title{Produce model estimated (p=6, topology=8) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_8(raaaabb, raaabcc, raaabcd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=8) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_8_unique.Rd b/man/predict6_8_unique.Rd new file mode 100644 index 0000000..49d6cbd --- /dev/null +++ b/man/predict6_8_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_8_unique} +\alias{predict6_8_unique} +\title{Produce model estimated (p=6, topology=8, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_8_unique(raaaabb, raaabcc, raaabcd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raaabcd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aaabcd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=8, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_9.Rd b/man/predict6_9.Rd new file mode 100644 index 0000000..ad17515 --- /dev/null +++ b/man/predict6_9.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_9} +\alias{predict6_9} +\title{Produce model estimated (p=6, topology=9) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_9(raaaabb, raaabcc, raabcdd, raabcde, rabcdef, k, d, kmercov, + bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raabcdd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=9) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/predict6_9_unique.Rd b/man/predict6_9_unique.Rd new file mode 100644 index 0000000..da53f69 --- /dev/null +++ b/man/predict6_9_unique.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model_functions.R +\name{predict6_9_unique} +\alias{predict6_9_unique} +\title{Produce model estimated (p=6, topology=9, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra.} +\usage{ +predict6_9_unique(raaaabb, raaabcc, raabcdd, raabcde, rabcdef, k, d, + kmercov, bias, x) +} +\arguments{ +\item{raaaabb, raaabcc, raabcdd, raabcde, rabcdef}{Numerics corresponding to the nucleotide heterozygosities aaaabb, aaabcc, aabcdd, aabcde, and abcdef respectively.} + +\item{k}{An integer corresponding to the kmer length.} + +\item{d}{A numeric corresponding to the repetitiveness.} + +\item{kmercov}{A numeric corresponding to the estimated average kmer coverage of the polyploid genome.} + +\item{bias}{A numeric corresponding to the overdispersion of the negative binomial distribution.} + +\item{x}{An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).} +} +\value{ +A numeric vector of the model estimated y-coordinates of the kmer spectra. +} +\description{ +Produce model estimated (p=6, topology=9, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. +} diff --git a/man/report_results.Rd b/man/report_results.Rd new file mode 100644 index 0000000..7c7517a --- /dev/null +++ b/man/report_results.Rd @@ -0,0 +1,30 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/report_results.R +\name{report_results} +\alias{report_results} +\title{Report results and make plots} +\usage{ +report_results(kmer_hist, kmer_hist_orig, k, p, container, foldername, + arguments, IN_VERBOSE) +} +\arguments{ +\item{kmer_hist}{A data frame of the original histogram data (starting at 1 and going up to the max kmer coverage threshold).} + +\item{kmer_hist_orig}{A data frame of the original histogram data (starting at 1 and with last position removed).} + +\item{k}{An integer corresponding to the kmer length.} + +\item{p}{An integer corresponding to the ploidy.} + +\item{container}{A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) +and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms).} + +\item{foldername}{A character vector corresponding to the name of the output directory.} + +\item{arguments}{A data frame of the user-specified inputs.} + +\item{IN_VERBOSE}{A boolean flag to designate whether report_results is being called in a VERBOSE block.} +} +\description{ +Report results and make plots +} diff --git a/man/score_model.Rd b/man/score_model.Rd new file mode 100644 index 0000000..0d77c60 --- /dev/null +++ b/man/score_model.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/score_model.R +\name{score_model} +\alias{score_model} +\title{Score nlsLM model by number and percent of residual errors after excluding sequencing errors} +\usage{ +score_model(kmer_hist_orig, nls, round, foldername) +} +\arguments{ +\item{kmer_hist_orig}{A data frame of the original histogram data (starting at 1 and with last position removed).} + +\item{nls}{An nlsLM model object.} + +\item{round}{An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process.} + +\item{foldername}{A character vector corresponding to the name of the output directory.} +} +\value{ +A data frame where the variables "all", "full", and "unique" correspond to the model residual sum of square error (excluding sequencing error) +including x-values up to the end of kmer_hist_orig, up to (2p+1)*lambda, and up to (p+1)*lambda respectively. +Additionally, the variables "allscore", "fullscore", and "uniquescore" are the +corresponding percentage of kmers that are correctly modeled. +} +\description{ +Score nlsLM model by number and percent of residual errors after excluding sequencing errors +} diff --git a/run_now.php b/run_now.php index d67b550..4b6e3ed 100755 --- a/run_now.php +++ b/run_now.php @@ -1,22 +1,24 @@ - - + > user_data/ERRORS/input_validation.log');} $code=$_POST["code"]; - mkdir("user_data/$code"); + if (!file_exists("user_data/$code")) { + mkdir("user_data/$code"); + } if( !isset($_POST['kmer_length']) ) { echo shell_exec("echo ERROR: No kmer_length passed to run_now.php >> user_data/$code/input_validation.log");} - if( !isset($_POST['read_length']) ) { echo shell_exec("echo ERROR: No read_length passed to run_now.php >> user_data/$code/input_validation.log");} + if( !isset($_POST['ploidy']) ) { echo shell_exec("echo ERROR: No ploidy passed to run_now.php >> user_data/$code/input_validation.log");} if( !isset($_POST['max_kmer_cov']) ) { echo shell_exec("echo ERROR: No max_kmer_cov passed to run_now.php >> user_data/$code/input_validation.log");} + if( !isset($_POST['lambda']) ) { echo shell_exec("echo ERROR: No lambda passed to run_now.php >> user_data/$code/input_validation.log");} if( !isset($_POST['description']) ) { echo shell_exec("echo ERROR: No description passed to run_now.php >> user_data/$code/input_validation.log");} echo shell_exec("echo user_data/$code/input_validation.log >> user_data/$code/input_validation.log"); $kmer_length = escapeshellarg($_POST["kmer_length"]); - $read_length = escapeshellarg($_POST["read_length"]); + $ploidy = escapeshellarg($_POST["ploidy"]); $max_kmer_cov = escapeshellarg($_POST["max_kmer_cov"]); + $lambda = escapeshellarg($_POST["lambda"]); $description = escapeshellarg($_POST["description"]); echo shell_exec("echo $description > user_data/$code/description.txt"); @@ -31,7 +33,11 @@ // For new version: // genomescope.R histogram_file k-mer_length read_length output_dir - echo shell_exec("Rscript genomescope.R $filename $kmer_length $read_length user_data/$code $max_kmer_cov &> user_data/$code/run.log &"); + // echo shell_exec("Rscript genomescope.R $filename $kmer_length $read_length user_data/$code $max_kmer_cov &> user_data/$code/run.log &"); + + // For 2.0: + // genomescope.R -i histogram_file -k k-mer_length -p ploidy -o output_dir + echo shell_exec("./genomescope.R -i $filename -k $kmer_length -p $ploidy -l $lambda -m $max_kmer_cov -o user_data/$code >user_data/$code/run.log 2>&1 &"); $new_dataset = array( "date"=>time(), "codename"=>$code, "description"=> $description ); @@ -43,12 +49,9 @@ // echo "cookie not set, creating new one"; } array_push($my_datasets, $new_dataset); - setcookie("results", json_encode($my_datasets)); - - header('Location: '.$url); + setcookie("results", json_encode($my_datasets)); ?> - diff --git a/user_data/example10/description.txt b/user_data/example10/description.txt new file mode 100644 index 0000000..00dc33f --- /dev/null +++ b/user_data/example10/description.txt @@ -0,0 +1 @@ +Potato (Solanum tuberosum) diff --git a/user_data/example10/linear_plot.png b/user_data/example10/linear_plot.png new file mode 100644 index 0000000..1417a70 Binary files /dev/null and b/user_data/example10/linear_plot.png differ diff --git a/user_data/example10/log_plot.png b/user_data/example10/log_plot.png new file mode 100644 index 0000000..d768be3 Binary files /dev/null and b/user_data/example10/log_plot.png differ diff --git a/user_data/example10/model.txt b/user_data/example10/model.txt new file mode 100644 index 0000000..f92bf5b --- /dev/null +++ b/user_data/example10/model.txt @@ -0,0 +1,22 @@ + +Formula: y_transform ~ x^transform_exp * length * predict4_0(r1, + r2, r3, r4, k, d, kmercov, bias, x) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +d 1.330e-01 2.903e-04 457.966 <2e-16 *** +r1 4.531e-02 3.134e-05 1445.708 <2e-16 *** +r2 2.173e-02 2.048e-04 106.085 <2e-16 *** +r3 1.000e-05 3.063e-04 0.033 0.974 +r4 2.119e-03 9.728e-05 21.787 <2e-16 *** +kmercov 2.426e+01 4.017e-03 6039.897 <2e-16 *** +bias 1.139e+00 1.393e-03 817.501 <2e-16 *** +length 3.731e+08 1.070e+05 3487.071 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 424800 on 999971 degrees of freedom + +Number of iterations to convergence: 24 +Achieved convergence tolerance: 1.49e-08 + diff --git a/user_data/example10/progress.txt b/user_data/example10/progress.txt new file mode 100644 index 0000000..2e6a0eb --- /dev/null +++ b/user_data/example10/progress.txt @@ -0,0 +1,6 @@ +starting +round 0 trimming to 6 trying 2p peak model... converged. score: 198630610233765280 +round 1 trimming to 11 trying 2p peak model... converged. score: 196035062284482592 +round 2 trimming to 16 trying 2p peak model... converged. score: 187940943959353760 +round 3 trimming to 21 trying 2p peak model... converged. score: 177023847393578464 +done diff --git a/user_data/example10/summary.txt b/user_data/example10/summary.txt new file mode 100644 index 0000000..e051f28 --- /dev/null +++ b/user_data/example10/summary.txt @@ -0,0 +1,18 @@ +GenomeScope version 2.0 +p = 4 +k = 21 +initial kmercov estimate = 23 +NO_UNIQUE_SEQUENCE set to TRUE + +property min max +Homozygous (aaaa) 92.9548% 93.1504% +Heterozygous (not aaaa) 6.84956% 7.0452% +aaab 4.52507% 4.53761% +aabb 2.132% 2.21394% +aabc 0% 0.0622612% +abcd 0.192484% 0.231395% +Genome Haploid Length 751,908,823 bp 752,406,949 bp +Genome Repeat Length 428,529,485 bp 428,813,378 bp +Genome Unique Length 323,379,338 bp 323,593,571 bp +Model Fit 51.8623% 95.3911% +Read Error Rate 0.308181% 0.308181% diff --git a/user_data/example10/transformed_linear_plot.png b/user_data/example10/transformed_linear_plot.png new file mode 100644 index 0000000..ced53be Binary files /dev/null and b/user_data/example10/transformed_linear_plot.png differ diff --git a/user_data/example10/transformed_log_plot.png b/user_data/example10/transformed_log_plot.png new file mode 100644 index 0000000..6901880 Binary files /dev/null and b/user_data/example10/transformed_log_plot.png differ diff --git a/user_data/example11/description.txt b/user_data/example11/description.txt new file mode 100644 index 0000000..118d5cd --- /dev/null +++ b/user_data/example11/description.txt @@ -0,0 +1 @@ +Wheat (Triticum aestivum) diff --git a/user_data/example11/linear_plot.png b/user_data/example11/linear_plot.png new file mode 100644 index 0000000..6d348d5 Binary files /dev/null and b/user_data/example11/linear_plot.png differ diff --git a/user_data/example11/log_plot.png b/user_data/example11/log_plot.png new file mode 100644 index 0000000..9d99f5c Binary files /dev/null and b/user_data/example11/log_plot.png differ diff --git a/user_data/example11/model.txt b/user_data/example11/model.txt new file mode 100644 index 0000000..4331f1f --- /dev/null +++ b/user_data/example11/model.txt @@ -0,0 +1,29 @@ + +Formula: y_transform ~ x^transform_exp * length * predict6_0(r1, + r2, r3, r4, r5, r6, r7, r8, r9, r10, k, d, kmercov, bias, + x) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +d 6.239e-01 1.557e-03 400.795 <2e-16 *** +r1 1.000e-05 3.438e-04 0.029 0.977 +r2 3.311e-03 1.531e+01 0.000 1.000 +r3 1.889e-02 8.856e-05 213.258 <2e-16 *** +r4 7.698e-04 1.531e+01 0.000 1.000 +r5 2.727e-02 1.753e-01 0.156 0.876 +r6 2.522e-02 2.124e+01 0.001 0.999 +r7 1.000e-05 1.752e-01 0.000 1.000 +r8 2.199e-03 3.576e+01 0.000 1.000 +r9 1.440e-03 1.736e+01 0.000 1.000 +r10 2.161e-02 7.262e-05 297.607 <2e-16 *** +kmercov 5.257e+01 1.628e-03 32289.245 <2e-16 *** +bias 8.362e-01 5.696e-04 1467.981 <2e-16 *** +length 5.002e+08 5.022e+05 996.033 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 2544000 on 999956 degrees of freedom + +Number of iterations to convergence: 66 +Achieved convergence tolerance: 1.49e-08 + diff --git a/user_data/example11/progress.txt b/user_data/example11/progress.txt new file mode 100644 index 0000000..b51fd46 --- /dev/null +++ b/user_data/example11/progress.txt @@ -0,0 +1,6 @@ +starting +round 0 trimming to 15 trying 2p peak model... converged. score: 6295284274002482176 +round 1 trimming to 20 trying 2p peak model... converged. score: 6293966612129074176 +round 2 trimming to 25 trying 2p peak model... converged. score: 6289477665936505856 +round 3 trimming to 30 trying 2p peak model... converged. score: 6272593770753348608 +done diff --git a/user_data/example11/summary.txt b/user_data/example11/summary.txt new file mode 100644 index 0000000..7a74106 --- /dev/null +++ b/user_data/example11/summary.txt @@ -0,0 +1,14 @@ +GenomeScope version 2.0 +p = 6 +k = 21 +initial kmercov estimate = 51 +NO_UNIQUE_SEQUENCE set to TRUE + +property min max +Homozygous (aaaaaa) 89.9276% +Heterozygous (not aaaaaa) 10.0724% +Genome Haploid Length 2,351,570,838 bp 2,351,862,170 bp +Genome Repeat Length 2,163,467,601 bp 2,163,735,628 bp +Genome Unique Length 188,103,238 bp 188,126,541 bp +Model Fit 32.179% 90.5483% +Read Error Rate 0.506403% 0.506403% diff --git a/user_data/example11/transformed_linear_plot.png b/user_data/example11/transformed_linear_plot.png new file mode 100644 index 0000000..73de2f2 Binary files /dev/null and b/user_data/example11/transformed_linear_plot.png differ diff --git a/user_data/example11/transformed_log_plot.png b/user_data/example11/transformed_log_plot.png new file mode 100644 index 0000000..c1a8ce8 Binary files /dev/null and b/user_data/example11/transformed_log_plot.png differ diff --git a/user_data/example7/description.txt b/user_data/example7/description.txt new file mode 100644 index 0000000..8da585f --- /dev/null +++ b/user_data/example7/description.txt @@ -0,0 +1 @@ +Coastal Redwood (Sequoia sempervirens) diff --git a/user_data/example7/linear_plot.png b/user_data/example7/linear_plot.png new file mode 100644 index 0000000..9c6ce04 Binary files /dev/null and b/user_data/example7/linear_plot.png differ diff --git a/user_data/example7/log_plot.png b/user_data/example7/log_plot.png new file mode 100644 index 0000000..59975db Binary files /dev/null and b/user_data/example7/log_plot.png differ diff --git a/user_data/example7/model.txt b/user_data/example7/model.txt new file mode 100644 index 0000000..d06f4b7 --- /dev/null +++ b/user_data/example7/model.txt @@ -0,0 +1,20 @@ + +Formula: y_transform ~ x^transform_exp * length * predict3_0(r1, + r2, k, d, kmercov, bias, x) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +d 1.354e-01 1.360e-04 995.4 <2e-16 *** +r1 3.355e-02 1.538e-05 2182.5 <2e-16 *** +r2 1.029e-02 5.512e-06 1866.4 <2e-16 *** +kmercov 2.787e+01 3.057e-03 9117.5 <2e-16 *** +bias 1.108e+00 9.652e-04 1147.4 <2e-16 *** +length 4.810e+09 9.411e+05 5110.6 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 5346000 on 999969 degrees of freedom + +Number of iterations to convergence: 6 +Achieved convergence tolerance: 1.49e-08 + diff --git a/user_data/example7/progress.txt b/user_data/example7/progress.txt new file mode 100644 index 0000000..fb8a816 --- /dev/null +++ b/user_data/example7/progress.txt @@ -0,0 +1,6 @@ +starting +round 0 trimming to 10 trying 2p peak model... converged. score: 29100840861034582016 +round 1 trimming to 15 trying 2p peak model... converged. score: 29000332708657721344 +round 2 trimming to 20 trying 2p peak model... converged. score: 28781942559245672448 +round 3 trimming to 25 trying 2p peak model... converged. score: 28501936939239657472 +done diff --git a/user_data/example7/summary.txt b/user_data/example7/summary.txt new file mode 100644 index 0000000..7c8cf82 --- /dev/null +++ b/user_data/example7/summary.txt @@ -0,0 +1,16 @@ +GenomeScope version 2.0 +p = 3 +k = 31 +initial kmercov estimate = 27 +NO_UNIQUE_SEQUENCE set to TRUE + +property min max +Homozygous (aaa) 95.6115% 95.6198% +Heterozygous (not aaa) 4.38016% 4.38852% +aab 3.35241% 3.35856% +abc 1.02775% 1.02996% +Genome Haploid Length 8,949,767,894 bp 8,953,695,151 bp +Genome Repeat Length 4,792,368,862 bp 4,794,471,807 bp +Genome Unique Length 4,157,399,031 bp 4,159,223,344 bp +Model Fit 56.0498% 96.7787% +Read Error Rate 0.285544% 0.285544% diff --git a/user_data/example7/transformed_linear_plot.png b/user_data/example7/transformed_linear_plot.png new file mode 100644 index 0000000..d819454 Binary files /dev/null and b/user_data/example7/transformed_linear_plot.png differ diff --git a/user_data/example7/transformed_log_plot.png b/user_data/example7/transformed_log_plot.png new file mode 100644 index 0000000..fa60fde Binary files /dev/null and b/user_data/example7/transformed_log_plot.png differ diff --git a/user_data/example8/description.txt b/user_data/example8/description.txt new file mode 100644 index 0000000..97396c3 --- /dev/null +++ b/user_data/example8/description.txt @@ -0,0 +1 @@ +Cotton (Gossypium barbadense) diff --git a/user_data/example8/linear_plot.png b/user_data/example8/linear_plot.png new file mode 100644 index 0000000..a2f3fc9 Binary files /dev/null and b/user_data/example8/linear_plot.png differ diff --git a/user_data/example8/log_plot.png b/user_data/example8/log_plot.png new file mode 100644 index 0000000..172474c Binary files /dev/null and b/user_data/example8/log_plot.png differ diff --git a/user_data/example8/model.txt b/user_data/example8/model.txt new file mode 100644 index 0000000..73e35cd --- /dev/null +++ b/user_data/example8/model.txt @@ -0,0 +1,22 @@ + +Formula: y_transform ~ x^transform_exp * length * predict4_0(r1, + r2, r3, r4, k, d, kmercov, bias, x) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +d 4.143e-01 6.258e-04 662.126 <2e-16 *** +r1 1.000e-05 2.713e-04 0.037 0.971 +r2 5.421e-02 1.029e-04 527.062 <2e-16 *** +r3 6.688e-03 3.281e-04 20.381 <2e-16 *** +r4 5.467e-02 7.576e-05 721.594 <2e-16 *** +kmercov 8.264e+01 1.578e-03 52357.386 <2e-16 *** +bias 1.661e+00 5.402e-04 3075.388 <2e-16 *** +length 2.366e+08 1.070e+05 2211.405 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 738400 on 999962 degrees of freedom + +Number of iterations to convergence: 30 +Achieved convergence tolerance: 1.49e-08 + diff --git a/user_data/example8/progress.txt b/user_data/example8/progress.txt new file mode 100644 index 0000000..b3f910b --- /dev/null +++ b/user_data/example8/progress.txt @@ -0,0 +1,6 @@ +starting +round 0 trimming to 15 trying 2p peak model... converged. score: 532349517611601920 +round 1 trimming to 20 trying 2p peak model... converged. score: 532364099932201728 +round 2 trimming to 25 trying 2p peak model... converged. score: 532486792683885760 +round 3 trimming to 30 trying 2p peak model... converged. score: 532432031845827712 +done diff --git a/user_data/example8/summary.txt b/user_data/example8/summary.txt new file mode 100644 index 0000000..0eff801 --- /dev/null +++ b/user_data/example8/summary.txt @@ -0,0 +1,18 @@ +GenomeScope version 2.0 +p = 4 +k = 21 +initial kmercov estimate = 79 +NO_UNIQUE_SEQUENCE set to TRUE + +property min max +Homozygous (aaaa) 88.2864% 88.5444% +Heterozygous (not aaaa) 11.4556% 11.7136% +aaab 0% 0.05526% +aabb 5.40059% 5.44174% +aabc 0.603173% 0.73443% +abcd 5.45188% 5.48219% +Genome Haploid Length 572,729,399 bp 572,773,156 bp +Genome Repeat Length 434,169,479 bp 434,202,649 bp +Genome Unique Length 138,559,920 bp 138,570,507 bp +Model Fit 54.6064% 90.0372% +Read Error Rate 0.196664% 0.196664% diff --git a/user_data/example8/transformed_linear_plot.png b/user_data/example8/transformed_linear_plot.png new file mode 100644 index 0000000..bbebf95 Binary files /dev/null and b/user_data/example8/transformed_linear_plot.png differ diff --git a/user_data/example8/transformed_log_plot.png b/user_data/example8/transformed_log_plot.png new file mode 100644 index 0000000..e83ce2e Binary files /dev/null and b/user_data/example8/transformed_log_plot.png differ diff --git a/user_data/example9/description.txt b/user_data/example9/description.txt new file mode 100644 index 0000000..85d9aa1 --- /dev/null +++ b/user_data/example9/description.txt @@ -0,0 +1 @@ +Root-knot Nematode (Meloidogyne enterolobii) diff --git a/user_data/example9/linear_plot.png b/user_data/example9/linear_plot.png new file mode 100644 index 0000000..c38fa66 Binary files /dev/null and b/user_data/example9/linear_plot.png differ diff --git a/user_data/example9/log_plot.png b/user_data/example9/log_plot.png new file mode 100644 index 0000000..5b4dbf4 Binary files /dev/null and b/user_data/example9/log_plot.png differ diff --git a/user_data/example9/model.txt b/user_data/example9/model.txt new file mode 100644 index 0000000..60f3d7e --- /dev/null +++ b/user_data/example9/model.txt @@ -0,0 +1,20 @@ + +Formula: y_transform ~ x^transform_exp * length * predict3_0(r1, + r2, k, d, kmercov, bias, x) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +d 1.407e-01 9.327e-04 150.8 <2e-16 *** +r1 5.152e-02 1.267e-04 406.7 <2e-16 *** +r2 9.354e-03 4.702e-05 199.0 <2e-16 *** +kmercov 1.511e+02 4.047e-02 3734.3 <2e-16 *** +bias 4.088e+00 1.409e-02 290.1 <2e-16 *** +length 6.447e+07 8.591e+04 750.4 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 1696000 on 9964 degrees of freedom + +Number of iterations to convergence: 8 +Achieved convergence tolerance: 1.49e-08 + diff --git a/user_data/example9/progress.txt b/user_data/example9/progress.txt new file mode 100644 index 0000000..946dc63 --- /dev/null +++ b/user_data/example9/progress.txt @@ -0,0 +1,6 @@ +starting +round 0 trimming to 15 trying 2p peak model... converged. score: 26487003968702944 +round 1 trimming to 20 trying 2p peak model... converged. score: 26487003963949460 +round 2 trimming to 25 trying 2p peak model... converged. score: 26487003948433368 +round 3 trimming to 30 trying 2p peak model... converged. score: 26487003944705224 +done diff --git a/user_data/example9/summary.txt b/user_data/example9/summary.txt new file mode 100644 index 0000000..f78facd --- /dev/null +++ b/user_data/example9/summary.txt @@ -0,0 +1,16 @@ +GenomeScope version 2.0 +p = 3 +k = 21 +initial kmercov estimate = 149 +NO_UNIQUE_SEQUENCE set to TRUE + +property min max +Homozygous (aaa) 93.8776% 93.9471% +Heterozygous (not aaa) 6.05295% 6.12243% +aab 5.12693% 5.17761% +abc 0.926018% 0.944825% +Genome Haploid Length 89,427,077 bp 89,522,919 bp +Genome Repeat Length 34,059,252 bp 34,095,755 bp +Genome Unique Length 55,367,825 bp 55,427,164 bp +Model Fit 76.0449% 91.0869% +Read Error Rate 0.743148% 0.743148% diff --git a/user_data/example9/transformed_linear_plot.png b/user_data/example9/transformed_linear_plot.png new file mode 100644 index 0000000..fb0431f Binary files /dev/null and b/user_data/example9/transformed_linear_plot.png differ diff --git a/user_data/example9/transformed_log_plot.png b/user_data/example9/transformed_log_plot.png new file mode 100644 index 0000000..85e2a4e Binary files /dev/null and b/user_data/example9/transformed_log_plot.png differ