Error when associating TFs to TREs and genes (mapTF / get.proximal.genes) #1
Comments
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Thank you for the feedback. Could you show the first 10 lines of your
$ANNOTATION_BED ? I suspect this might be a MAC-specific issue. Did you try
any linux system?
Best,
Tinyi
…On Wed, May 22, 2019 at 12:24 AM mattgalbraith ***@***.***> wrote:
When running tfTarget via run_tfTarget.bsh with the following command:
bash run_tfTarget.bsh \ -query $TREATMENT_SAMPLES \ -control
$CONTROL_SAMPLES \ -bigWig.path $BIGWIG_PATH \ -prefix gencode_test \
-TRE.path $TRE_MERGED_BED \ -gene.path $ANNOTATION_BED \ -2bit.path
$HG19_2BIT \ -pval.up 0.1 \ -pval.down 0.1 \ -ncores 3 \ -dist 50000 \
-closest.N 2 \ -pval.gene 0.1
I am getting the following error:
[1] "associating TFs to TREs and genes"
awk: syntax error at source line 1
context is
BEGIN{OFS=" "} {print >>> $1,$6== <<<
awk: illegal statement at source line 1
awk: illegal statement at source line 1
Error in $<-.data.frame(*tmp*, "closest.N", value = c(1L, 2L, 1L, :
replacement has 36 rows, data has 37
Calls: mapTF -> get.proximal.genes -> $<- -> $<-.data.frame
Execution halted
This appears to be related to the awk command at lines 18-20 or 43-45 of
mapTF.R
R session info with tfTarget loaded:
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.4
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tfTarget_1.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.54.0 rtfbsdb_0.4.5
[4] bit64_0.9-7 RColorBrewer_1.1-2 GenomeInfoDb_1.18.1
[7] tools_3.5.1 backports_1.1.3 R6_2.3.0
[10] KernSmooth_2.23-15 rpart_4.1-13 sm_2.2-5.4
[13] Hmisc_4.1-1 DBI_1.0.0 lazyeval_0.2.1
[16] BiocGenerics_0.28.0 colorspace_1.3-2 nnet_7.3-12
[19] tidyselect_0.2.5 gridExtra_2.3 DESeq2_1.22.1
[22] bit_1.1-14 compiler_3.5.1 Biobase_2.42.0
[25] htmlTable_1.12 DelayedArray_0.8.0 rphast_1.6.9
[28] caTools_1.17.1.1 scales_1.0.0 checkmate_1.8.5
[31] genefilter_1.64.0 stringr_1.3.1 apcluster_1.4.7
[34] digest_0.6.18 foreign_0.8-71 XVector_0.22.0
[37] vioplot_0.3.0 base64enc_0.1-3 pkgconfig_2.0.2
[40] htmltools_0.3.6 htmlwidgets_1.3 rlang_0.3.0.1
[43] rstudioapi_0.8 RSQLite_2.1.1 bindr_0.1.1
[46] zoo_1.8-5 BiocParallel_1.16.5 bigWig_0.2-9
[49] gtools_3.8.1 acepack_1.4.1 dplyr_0.7.8
[52] RCurl_1.95-4.11 magrittr_1.5 GenomeInfoDbData_1.2.0
[55] Formula_1.2-3 Matrix_1.2-15 Rcpp_1.0.0
[58] munsell_0.5.0 S4Vectors_0.20.1 stringi_1.2.4
[61] yaml_2.2.0 rtfbs_0.3.9 SummarizedExperiment_1.12.0
[64] zlibbioc_1.28.0 gplots_3.0.1 plyr_1.8.4
[67] grid_3.5.1 blob_1.1.1 gdata_2.18.0
[70] parallel_3.5.1 crayon_1.3.4 lattice_0.20-38
[73] splines_3.5.1 annotate_1.60.0 locfit_1.5-9.1
[76] knitr_1.21 pillar_1.3.0 GenomicRanges_1.34.0
[79] geneplotter_1.60.0 stats4_3.5.1 XML_3.98-1.16
[82] glue_1.3.0 latticeExtra_0.6-28 data.table_1.11.8
[85] gtable_0.2.0 purrr_0.2.5 assertthat_0.2.0
[88] ggplot2_3.1.0 xfun_0.4 xtable_1.8-3
[91] survival_2.43-3 tibble_1.4.2 AnnotationDbi_1.44.0
[94] memoise_1.1.0 IRanges_2.16.0 bindrcpp_0.2.2
[97] cluster_2.0.7-1
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I was unable to successfully get all the R dependencies installed on our linux system, hence using the Mac. |
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I have now managed to get tfTarget and all dependencies running on linux and no longer get the awk error. However, I am now getting a new error:
From looking into the mapTF function, it appears that
I will try running the R commands manually to see if I can track this down any further... |
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For reference: |
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Thank you for your feedback. I guess this is caused by the lack of
statistical power (determined by DESeq2) where fewer than 2 replicates were
used for each condition.
…On Tue, May 28, 2019 at 12:42 PM mattgalbraith ***@***.***> wrote:
For reference:
The last error was caused by an empty TF.TRE.gene.tab object due to the
stringency of settings used.
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I am having the same issue. I wonder if your manual solution did work. Best regards |
When running tfTarget via run_tfTarget.bsh with the following command:
bash run_tfTarget.bsh \ -query $TREATMENT_SAMPLES \ -control $CONTROL_SAMPLES \ -bigWig.path $BIGWIG_PATH \ -prefix gencode_test \ -TRE.path $TRE_MERGED_BED \ -gene.path $ANNOTATION_BED \ -2bit.path $HG19_2BIT \ -pval.up 0.1 \ -pval.down 0.1 \ -ncores 3 \ -dist 50000 \ -closest.N 2 \ -pval.gene 0.1I am getting the following error:
This appears to be related to the awk command at lines 18-20 or 43-45 of mapTF.R
R session info with tfTarget loaded:
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