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SURPI.sh
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SURPI.sh
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#!/bin/bash
#
# SURPI.sh
#
# This is the main driver script for the SURPI pipeline.
# Chiu Laboratory
# University of California, San Francisco
#
#
# Copyright (C) 2014 Samia N Naccache, Scot Federman, and Charles Y Chiu - All Rights Reserved
# SURPI has been released under a modified BSD license.
# Please see license file for details.
#
SURPI_version="1.0.22"
optspec=":f:hvz:"
bold=$(tput bold)
normal=$(tput sgr0)
green='\e[0;32m'
red='\e[0;31m'
endColor='\e[0m'
host=$(hostname)
scriptname=${0##*/}
while getopts "$optspec" option; do
case "${option}" in
f) config_file=${OPTARG};; # get parameters from config file if specified
h) HELP=1;;
v) VERIFICATION=1;;
z) create_config_file=${OPTARG}
configprefix=${create_config_file%.fastq}
;;
:) echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
if [[ $HELP -eq 1 || $# -lt 1 ]]
then
cat <<USAGE
${bold}SURPI version ${SURPI_version}${normal}
This program will run the SURPI pipeline with the parameters supplied by the config file.
${bold}Command Line Switches:${normal}
-h Show this help & ignore all other switches
-f Specify config file
This switch is used to initiate a SURPI run using a specified config file. Verification (see -v switch) will occur at the beginning of the run.
The pipeline will cease if SURPI fails to find a software dependency or necessary reference data.
-v Verification mode
When using verification mode, SURPI will verify necessary dependencies, but will
stop after verification. This same verification is also done
before each SURPI run.
• software dependencies
SURPI will check for the presence of all software dependencies.
• reference data specified in config file
SURPI does a cursory check for the presence of reference data. This check is
not a comprehensive test of the reference data.
• taxonomy lookup functionality
SURPI verifies the functionality of the taxonomy lookup.
• FASTQ file (if requested in config file)
SURPI uses fastQValidator to check the integrity of the FASTQ file.
-z Create default config file and go file. [optional] (specify fastq filename)
This option will create a standard .config file, and go file.
${bold}Usage:${normal}
Create default config and go file.
$scriptname -z test.fastq
Run SURPI pipeline in verification mode:
$scriptname -f config -v
Run SURPI pipeline with the config file:
$scriptname -f config
USAGE
exit
fi
if [[ $create_config_file ]]
then
echo "PATH=/usr/local/bin/surpi:/usr/local/bin:/usr/bin/:/bin" > go_$configprefix
echo "nohup $scriptname -f $configprefix.config > SURPI.$configprefix.log 2> SURPI.$configprefix.err" >> go_$configprefix
chmod +x go_$configprefix
#------------------------------------------------------------------------------------------------
(
cat <<EOF
# This is the config file used by SURPI. It contains mandatory parameters,
# optional parameters, and server related constants.
# Do not change the config_file_version - it is auto-generated.
# and used to ensure that the config file used matches the version of the SURPI pipeline run.
config_file_version="$SURPI_version"
##########################
# Input file
##########################
#To create this file, concatenate the entirety of a sequencing run into one FASTQ file.
#SURPI currently does not have paired-end functionality, we routinely concatenate Read 1 and Read 2 into the unified input file.
#For SURPI to provide proper readcount statistics, all read headers in a single SURPI input dataset should share a
#common 3 letter string (eg: M00, HWI, HIS, SCS, SRR for example). SURPI currently selects the string from the first and last reads only.
inputfile="$create_config_file"
#input filetype. [FASTA/FASTQ]
inputtype="FASTQ"
#FASTQ quality score type: [Sanger/Illumina]
#Sanger = Sanger score (ASCII-33)
#Illumina = Illumina score (ASCII-64)
#Counterintuitively, the Sanger quality format is likely the method your data is encoded in if you are generating data on an Illumina machine after early 2011.
#Selecting Illumina quality on Sanger data will likely lead to improper preprocessing, resulting in preprocessed files of 0 length.
quality="Sanger"
#Adapter set used. [Truseq/Nextera/NexSolB/NexSolTruseq]
#Truseq = trims truseq adaptors
#Nextera = trims Nextera adaptors
adapter_set="Truseq"
#Verify FASTQ quality
# 0 = skip validation
# 1 [default] = run validation, don't check for unique names, quit on failure
# 2 = run validation, check for unique names, quit on failure (helpful with newer MiSeq output that has same name for read1 and read2 due to spacing)
# 3 = run validation, check for unique names, do not quit on failure
VERIFY_FASTQ=1
##########################
# Run Mode
##########################
#Run mode to use. [Comprehensive/Fast]
#Comprehensive mode allows SNAP to NT -> denovo contig assembly -> RAPSearch to Viral proteins or NR
#Fast mode allows SNAP to curated FAST databases
run_mode="Comprehensive"
#Below options are to skip specific steps.
#Uncomment preprocess parameter to skip preprocessing
#(useful for large data sets that have already undergone preprocessing step)
# If skipping preprocessing, be sure these files exist in the working directory.
# $basef.cutadapt.fastq
# $basef.preprocessed.fastq
#preprocess="skip"
##########################
# Preprocessing
##########################
#length_cutoff: after quality and adaptor trimming, any sequence with length smaller than length_cutoff will be discarded
length_cutoff="50"
#Cropping values. Highly recommended default = 10,75
#Cropping quality trimmed reads prior to SNAP alignment
#snapt_nt = Where to start crop
#crop_length = how long to crop
start_nt=10
crop_length=75
#quality cutoff ( -q switch in cutadapt )
quality_cutoff=18
##########################
# SNAP
##########################
#SNAP executable
snap="/usr/local/bin/snap-dev"
#SNAP edit distance for Computational Subtraction of host genome [Highly recommended default: d_human=12]
#see Section 3.1.2 MaxDist description: http://snap.cs.berkeley.edu/downloads/snap-1.0beta-manual.pdf
d_human=12
#SNAP edit distance for alignment to NCBI nt DB [validated only at: d=12]
d_NT_alignment=12
#snap_nt iterator to use. [inline/end]
#inline : compares each SNAP iteration to the previous as they are completed
# Uses more disk space, and should be faster for larger input files.
# also allows for concurrent SNAP runs.
#end : compares all SNAP iterations once they have all completed.
#These two methods should give identical results, but may have different performance.
#Note: use inline for now (6/24/14), there is a bug with "end"
snap_integrator="inline"
#only used if snap_integrator=end
#if using this parameter, the SNAP databases should reside on separate disks in order to increase throughput.
#(Mechanism for doing this is not yet in place)
num_simultaneous_SNAP_runs=1
##########################
# RAPSEARCH
##########################
#RAPSearch database method to use. [Viral/NR]
#Viral database contains viral proteins derived from genbank
#NR contains all NR proteins
rapsearch_database="Viral"
#RAPSearch e_cutoffs
#E-value of 1e+1, 1e+0 1e-1 is represented by RAPSearch2 http://omics.informatics.indiana.edu/mg/RAPSearch2/ in log form (1,0,-1).
#Larger E-values are required to find highly divergent viral sequences.
ecutoff_Vir="1"
ecutoff_NR="1"
#This parameter sets whether RAPSearch will be run in its fast mode or its normal mode.
# see RAPSearch -a option for details
# T will give (10~30 fold) speed improvement, at the cost of sensitivity at high e-values
# [T: perform fast search, F: perform normal search]
RAPSearch_NR_fast_mode="T"
##########################
# de novo Assembly
##########################
#kmer value for ABySS in DeBruijn portion of denovo contig assembly. Highly recommended default=34
abysskmer=34
#Set ignore_barcodes_for_de_novo=N [default] to deNovo assemble for each barcode independently.
#Set ignore_barcodes_for_de_novo=Y to assemble all barcodes together into a single assembly.
ignore_barcodes_for_de_novo=N
#e value for BLASTn used in coverage map generation
eBLASTn="1e-15"
##########################
# Reference Data
##########################
# SNAP-indexed database of host genome (for subtraction phase)
# SURPI will subtract all SNAP databases found in this directory from the input sequence
# Useful if you want to subtract multiple genomes (without combining SNAP databases)
# or, if you need to split a db if it is larger than available RAM.
SNAP_subtraction_folder="/reference/hg19"
# directory for SNAP-indexed databases of NCBI NT (for mapping phase in comprehensive mode)
# directory must ONLY contain snap indexed databases
SNAP_COMPREHENSIVE_db_dir="/reference/COMP_SNAP"
# directory for SNAP-indexed databases for mapping phase in FAST mode
# directory must ONLY contain snap indexed databases
SNAP_FAST_db_dir="/reference/FAST_SNAP"
#Taxonomy Reference data directory
#This folder should contain the 3 SQLite files created by the script "create_taxonomy_db.sh"
#gi_taxid_nucl.db - nucleotide db of gi/taxonid
#gi_taxid_prot.db - protein db of gi/taxonid
#names_nodes_scientific.db - db of taxonid/taxonomy
taxonomy_db_directory="/reference/taxonomy"
#RAPSearch viral database name: indexed protein dataset (all of Viruses)
#make sure that directory also includes the .info file
RAPSearch_VIRUS_db="/reference/RAPSearch/rapsearch_viral_db"
#RAPSearch nr database name: indexed protein dataset (all of NR)
#make sure that directory also includes the .info file
RAPSearch_NR_db="/reference/RAPSearch/rapsearch_nr_db"
ribo_snap_bac_euk_directory="/reference/RiboClean_SNAP"
##########################
# Server related values
##########################
#Number of cores to use. Will use all cores on machine if unspecified.
#Uncomment the parameter to set explicitly.
#cores=64
#specify a location for storage of temporary files.
#Space needed may be up to 10x the size of the input file.
#This folder will not be created by SURPI, so be sure it already exists with proper permissions.
temporary_files_directory="/tmp/"
#This parameter controls whether dropcache is used throughout the pipeline. If free RAM is less than cache_reset,
# then dropcache. If cache_reset=0, then dropcache will never be used.
cache_reset="0"
##########################
# AWS related values
##########################
# AWS_master_slave will start up a slave instance on AWS for each division of the nt database
# It will be more costly, but should run significantly faster than the solo method, which
# runs each NT division through SNAP serially on a single machine.
# If using the "AWS_master_slave" option, be sure that all parameters in the AWS section below are
# set properly.
# These values are only used if the "AWS_master_slave" option is set below.
# Note: this method is currently incomplete and experimental.
#Which method to use for SNAP to nt [AWS_master_slave/solo]
# AWS_master_slave will start up a slave instance on AWS for each division of the nt database
# It will be more costly, but should run significantly faster than the solo method, which
# runs each NT division through SNAP serially on a single machine.
# If using the "AWS_master_slave" option, be sure that all parameters in the AWS section below are
# set properly.
#6/24/14 AWS_master_slave option is currently experimental and incomplete. Please use "solo" for the time being.
snap_nt_procedure="solo"
#ami-b93264d0 = Ubuntu 12.04 HVM 64-bit
#ami-5ef61936 = custom AMI (ami-b93264d0 + SNAP setup)
ami_id="ami-5ef61936"
#Number of slave instances will not exceed this value. Useful for testing, in order to restrict instance count.
#Otherwise, number of instances should be equal to number of SNAP-NT database divisions. This value is
#automatically calculated by SURPI.
max_slave_instances=29
instance_type="c3.8xlarge"
#this parameter is currently tied to the $keypair used during slave_setup.sh. should be cleaned up prior to release
pemkey="/home/ubuntu/.ssh/surpi.pem"
keypair="surpi"
security_group="SURPI"
availability_zone="us-east-1d"
placement_group="surpi"
#specify directory for incoming data from slaves
#this directory will not be created by SURPI - it should pre-exist.
#There must be sufficient space in this directory to contain all returning compressed SAM files
incoming_dir="/ssd4/incoming"
EOF
) > $configprefix.config
#------------------------------------------------------------------------------------------------
echo "$configprefix.config generated. Please edit it to contain the proper parameters for your analysis."
echo "go_$configprefix generated. Initiate the pipeline by running this program. (./go_$configprefix)"
echo
exit
fi
if [[ -r $config_file ]]
then
source "$config_file"
#verify that config file version matches SURPI version
if [ "$config_file_version" != "$SURPI_version" ]
then
echo "The config file $config_file was created with SURPI $config_file_version."
echo "The current version of SURPI running is $SURPI_version."
echo "Please generate a new config file with SURPI $SURPI_version in order to run SURPI."
exit 65
fi
else
echo "The config file specified: $config_file is not present."
exit 65
fi
#check that $inputfile is a FASTQ file, and has a FASTQ suffix.
# convert from FASTA if necessary, add FASTQ suffix if necessary.
if [ $inputtype = "FASTQ" ]
then
if [ ${inputfile##*.} != "fastq" ]
then
ln -s $inputfile $inputfile.fastq
FASTQ_file=$inputfile.fastq
else
FASTQ_file=$inputfile
fi
elif [ $inputtype = "FASTA" ]
then
echo "Converting $inputfile to FASTQ format..."
FASTQ_file="$inputfile.fastq"
fasta_to_fastq $inputfile > $FASTQ_file
fi
#set cores. if none specified, use all cores present on machine
if [ ! $cores ]
then
total_cores=$(grep processor /proc/cpuinfo | wc -l)
cores=${cores:-$total_cores}
fi
if [ ! $run_mode ]
then
run_mode="Comprehensive"
fi
if [ "$run_mode" != "Comprehensive" -a "$run_mode" != "Fast" ]
then
echo "${bold}$run_mode${normal} is not a valid run mode - must be Comprehensive or Fast."
echo "Please specify a valid run mode using the -u switch."
exit 65
fi
#set cache_reset. if none specified:
# >500GB -> 200GB
# >200GB -> 150GB
# otherwise -> 50GB
# note: this may cause problems on a machine with <50GB RAM
if [ ! $cache_reset ]
then
total_ram=$(grep MemTotal /proc/meminfo | awk '{print $2}')
if [ "$total_ram" -gt "500000000" ] #500GiB
then
cache_reset=200 # This is 200GB
elif [ "$total_ram" -gt "200000000" ] #200 GiB
then
cache_reset=150
else
cache_reset=50
fi
fi
#these 2 parameters are for cropping prior to snap in the preprocessing stage
if [ ! $start_nt ]
then
start_nt=10
fi
if [ ! $crop_length ]
then
crop_length=75
fi
if [ "$adapter_set" != "Truseq" -a "$adapter_set" != "Nextera" -a "$adapter_set" != "NexSolB" -a "$adapter_set" != "NexSolTruseq" ]
then
echo "${bold}$adapter_set${normal} is not a valid adapter_set - must be Truseq, Nextera, NexSolTruseq, or NexSolB."
echo "Please specify a valid adapter set using the -a switch."
exit 65
fi
if [ "$quality" != "Sanger" -a "$quality" != "Illumina" ]
then
echo "${bold}$quality${normal} is not a valid quality - must be Sanger or Illumina."
echo "Please specify a valid quality using the -q switch."
exit 65
fi
if [ $quality = "Sanger" ]
then
quality="S"
else
quality="I"
fi
#RAPSearch e_cutoffs
if [ ! $ecutoff_Vir ]
then
ecutoff_Vir="1"
fi
if [ ! $ecutoff_NR ]
then
ecutoff_NR="0"
fi
if [ ! $d_human ]
then
d_human=12
fi
if [ ! $length_cutoff ]
then
echo "${bold}length_cutoff${normal} was not specified."
echo "Please specify a valid length_cutoff using the -x switch."
exit 65
fi
if [ "$rapsearch_database" != "Viral" -a "$rapsearch_database" != "NR" ]
then
echo "${bold}$rapsearch_database${normal} is not a valid RAPSearch database - must be Viral or NR."
echo "Please specify a valid rapsearch_database using the -r switch, or place one of the above options in your config file."
exit 65
fi
nopathf=${FASTQ_file##*/} # remove the path to file
basef=${nopathf%.fastq}
#verify that all software dependencies are properly installed
declare -a dependency_list=("gt" "seqtk" "fastq" "fqextract" "cutadapt" "prinseq-lite.pl" "dropcache" "$snap" "rapsearch" "fastQValidator" "abyss-pe" "ABYSS-P" "Minimo")
echo "-----------------------------------------------------------------------------------------"
echo "DEPENDENCY VERIFICATION"
echo "-----------------------------------------------------------------------------------------"
for command in "${dependency_list[@]}"
do
if hash $command 2>/dev/null; then
echo -e "$command: ${green}OK${endColor}"
else
echo
echo -e "$command: ${red}BAD${endColor}"
echo "$command does not appear to be installed properly."
echo "Please verify your SURPI installation and \$PATH, then restart the pipeline"
echo
dependency_check="FAIL"
fi
done
echo "-----------------------------------------------------------------------------------------"
echo "SOFTWARE VERSION INFORMATION"
echo "-----------------------------------------------------------------------------------------"
gt_version=$(gt -version | head -1 | awk '{print $3}')
seqtk_version=$(seqtk 2>&1 | head -3 | tail -1 | awk '{print $2}')
cutadapt_version=$(cutadapt --version)
prinseqlite_version=$(prinseq-lite.pl --version 2>&1 | awk '{print $2}')
snap_version=$(snap 2>&1 | grep version | awk '{print $5}')
snap_dev_version=$(snap-dev 2>&1 | grep version | awk '{print $5}')
rapsearch_version=$(rapsearch 2>&1 | head -2 | tail -1 | awk '{print $2}')
abyss_pe_version=$(abyss-pe version | head -2 | tail -1 | awk '{print $3}')
ABYSS_P_version=$(ABYSS-P --version | head -1 | awk '{print $3}')
Minimo_version=$(Minimo -h | tail -2 | awk '{print $2}')
echo -e "SURPI version: $SURPI_version"
echo -e "config file version: $config_file_version"
echo -e "gt: $gt_version"
echo -e "seqtk: $seqtk_version"
echo -e "cutadapt: $cutadapt_version"
echo -e "prinseq-lite: $prinseqlite_version${endColor}"
echo -e "snap: $snap_version${endColor}"
echo -e "snap-dev: $snap_dev_version${endColor}"
echo -e "RAPSearch: $rapsearch_version"
echo -e "abyss-pe: $abyss_pe_version"
echo -e "ABYSS-P: $ABYSS_P_version"
echo -e "Minimo: $Minimo_version"
echo "-----------------------------------------------------------------------------------------"
echo "REFERENCE DATA VERIFICATION"
echo "-----------------------------------------------------------------------------------------"
echo -e "SNAP subtraction db"
for f in $SNAP_subtraction_folder/*
do
if [ -f $f/Genome ]
then
echo -e "\t$f: ${green}OK${endColor}"
else
echo -e "\t$f: ${red}BAD${endColor}"
reference_check="FAIL"
fi
done
echo -e "SNAP Comprehensive Mode database"
for f in $SNAP_COMPREHENSIVE_db_dir/*
do
if [ -f $f/Genome ]
then
echo -e "\t$f: ${green}OK${endColor}"
else
echo -e "\t$f: ${red}BAD${endColor}"
if [ "$run_mode" = "Comprehensive" ]
then
reference_check="FAIL"
fi
fi
done
echo -e "SNAP FAST Mode database"
for f in $SNAP_FAST_db_dir/*
do
if [ -f $f/Genome ]
then
echo -e "\t$f: ${green}OK${endColor}"
else
echo -e "\t$f: ${red}BAD${endColor}"
if [ "$run_mode" = "Fast" ]
then
reference_check="FAIL"
fi
fi
done
#verify taxonomy is functioning properly
result=$( taxonomy_lookup_embedded.pl -d nucl -q $taxonomy_db_directory 149408158 )
if [ $result = "149408158" ]
then
echo -e "taxonomy: ${green}OK${endColor}"
else
echo -e "taxonomy: ${red}BAD${endColor}"
echo "taxonomy appears to be malfunctioning. Please check logs and config file to verify proper taxonomy functionality."
reference_check="FAIL"
fi
echo -e "RAPSearch viral database"
if [ -f $RAPSearch_VIRUS_db ]
then
echo -e "\t$RAPSearch_VIRUS_db: ${green}OK${endColor}"
else
echo -e "\t$RAPSearch_VIRUS_db: ${red}BAD${endColor}"
echo
reference_check="FAIL"
fi
if [ -f $RAPSearch_VIRUS_db.info ]
then
echo -e "\t$RAPSearch_VIRUS_db.info: ${green}OK${endColor}"
else
echo -e "\t$RAPSearch_VIRUS_db.info: ${red}BAD${endColor}"
echo
reference_check="FAIL"
fi
echo -e "RAPSearch NR database"
if [ -f $RAPSearch_NR_db ]
then
echo -e "\t$RAPSearch_NR_db: ${green}OK${endColor}"
else
echo -e "\t$RAPSearch_NR_db: ${red}BAD${endColor}"
echo
reference_check="FAIL"
fi
if [ -f $RAPSearch_NR_db.info ]
then
echo -e "\t$RAPSearch_NR_db.info: ${green}OK${endColor}"
else
echo -e "\t$RAPSearch_NR_db.info: ${red}BAD${endColor}"
echo
reference_check="FAIL"
fi
if [[ ($dependency_check = "FAIL" || $reference_check = "FAIL") ]]
then
echo -e "${red}There is an issue with one of the dependencies or reference databases above.${endColor}"
exit 65
else
echo -e "${green}All necessary dependencies and reference data pass.${endColor}"
fi
actual_slave_instances=$(ls -1 "$SNAP_COMPREHENSIVE_db_dir" | wc -l)
if [ $max_slave_instances -lt $actual_slave_instances ]
then
actual_slave_instances=$max_slave_instances
fi
length=$( expr length $( head -n2 $FASTQ_file | tail -1 ) ) # get length of 1st sequence in FASTQ file
contigcutoff=$(perl -le "print int(1.75 * $length)")
echo "-----------------------------------------------------------------------------------------"
echo "INPUT PARAMETERS"
echo "-----------------------------------------------------------------------------------------"
echo "Command Line Usage: $scriptname $@"
echo "SURPI version: $SURPI_version"
echo "config_file: $config_file"
echo "config file version: $config_file_version"
echo "Server: $host"
echo "Working directory: $( pwd )"
echo "run_mode: $run_mode"
echo "inputfile: $inputfile"
echo "inputtype: $inputtype"
echo "FASTQ_file: $FASTQ_file"
echo "cores used: $cores"
echo "Raw Read quality: $quality"
echo "Quality cutoff: $quality_cutoff"
echo "Read length_cutoff for preprocessing under which reads are thrown away: $length_cutoff"
echo "temporary files location: $temporary_files_directory"
echo "SNAP_db_directory housing the reference databases for Subtraction: $SNAP_subtraction_folder"
echo "SNAP_db_directory housing the reference databases for Comprehensive Mode: $SNAP_COMPREHENSIVE_db_dir"
echo "SNAP_db_directory housing the reference databases for Fast Mode: $SNAP_FAST_db_dir"
echo "snap_integrator: $snap_integrator"
echo "SNAP edit distance for SNAP to Human: d_human: $d_human"
echo "SNAP edit distance for SNAP to NT: d_NT_alignment: $d_NT_alignment"
echo "rapsearch_database: $rapsearch_database"
echo "RAPSearch indexed viral db used: $RAPSearch_VIRUS_db"
echo "RAPSearch indexed NR db used: $RAPSearch_NR_db"
echo "taxonomy database directory: $taxonomy_db_directory"
echo "adapter_set: $adapter_set"
echo "Raw Read length: $length"
echo "contigcutoff for abyss assembly unitigs: $contigcutoff"
echo "abysskmer length: $abysskmer"
echo "Ignore barcodes for assembly? $ignore_barcodes_for_de_novo"
echo "cache_reset (if 0, then dropcache will never be used): $cache_reset"
echo "start_nt: $start_nt"
echo "crop_length: $crop_length"
echo "e value for BLASTn used in coverage map generation: $eBLASTn"
if [ $snap_nt_procedure = "AWS_master_slave" ]
then
echo "---------------------------------------------"
echo "Cluster settings"
echo "snap_nt_procedure: $snap_nt_procedure"
echo "ami_id: $ami_id"
echo "max_slave_instances: $max_slave_instances"
echo "actual_slave_instances: $actual_slave_instances"
echo "instance_type: $instance_type"
echo "keypair: $keypair"
echo "security_group: $security_group"
echo "placement_group: $placement_group"
echo "availability_zone: $availability_zone"
echo "incoming_dir: $incoming_dir"
echo "---------------------------------------------"
fi
echo "-----------------------------------------------------------------------------------------"
if [ "$VERIFY_FASTQ" = 1 ]
then
fastQValidator --file $FASTQ_file --printBaseComp --avgQual --disableSeqIDCheck > quality.$basef.log
if [ $? -eq 0 ]
then
echo -e "${green}$FASTQ_file appears to be a valid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
else
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}"
exit 65
fi
elif [ "$VERIFY_FASTQ" = 2 ]
then
fastQValidator --file $FASTQ_file --printBaseComp --avgQual > quality.$basef.log
if [ $? -eq 0 ]
then
echo -e "${green}$FASTQ_file appears to be a valid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
else
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}"
exit 65
fi
elif [ "$VERIFY_FASTQ" = 3 ]
then
fastQValidator --file $FASTQ_file --printBaseComp --avgQual > quality.$basef.log
fi
if [[ $VERIFICATION -eq 1 ]] #stop pipeline if using verification mode
then
exit
fi
###########################################################
echo -e "$(date)\t$scriptname\t########## STARTING SURPI PIPELINE ##########"
START_PIPELINE=$(date +%s)
echo -e "$(date)\t$scriptname\tFound file $FASTQ_file"
echo -e "$(date)\t$scriptname\tAfter removing path: $nopathf"
############ Start up AWS slave machines ##################
file_with_slave_ips="slave_list.txt"
if [ "$snap_nt_procedure" = "AWS_master_slave" ]
then
# start the slaves as a background process. They should be ready to run at the SNAP to NT step in the pipeline.
start_slaves.sh $ami_id $actual_slave_instances $instance_type $keypair $security_group $availability_zone $file_with_slave_ips $placement_group & # > $basef.AWS.log 2>&1
fi
############ PREPROCESSING ##################
if [ "$preprocess" != "skip" ]
then
echo -e "$(date)\t$scriptname\t############### PREPROCESSING ###############"
echo -e "$(date)\t$scriptname\tStarting: preprocessing using $cores cores "
START_PREPROC=$(date +%s)
echo -e "$(date)\t$scriptname\tParameters: preprocess_ncores.sh $basef.fastq $quality N $length_cutoff $cores Y N $adapter_set $start_nt $crop_length $temporary_files_directory >& $basef.preprocess.log"
preprocess_ncores.sh $basef.fastq $quality N $length_cutoff $cores $cache_reset N $adapter_set $start_nt $crop_length $temporary_files_directory $quality_cutoff >& $basef.preprocess.log
echo -e "$(date)\t$scriptname\tDone: preprocessing "
END_PREPROC=$(date +%s)
diff_PREPROC=$(( END_PREPROC - START_PREPROC ))
echo -e "$(date)\t$scriptname\tPreprocessing took $diff_PREPROC seconds" | tee timing.$basef.log
fi
# verify preprocessing step
if [ ! -s $basef.cutadapt.fastq ] || [ ! -s $basef.preprocessed.fastq ]
then
echo -e "$(date)\t$scriptname\t${red}Preprocessing appears to have failed. One of the following files does not exist, or is of 0 size:${endColor}"
echo "$basef.cutadapt.fastq"
echo "$basef.preprocessed.fastq"
exit
fi
############# BEGIN SNAP PIPELINE #################
freemem=$(free -g | awk '{print $4}' | head -n 2 | tail -1)
echo -e "$(date)\t$scriptname\tThere is $freemem GB available free memory...[cutoff=$cache_reset GB]"
if [[ $dropcache == "Y" ]]
then
if [ "$freemem" -lt "$cache_reset" ]
then
echo -e "$(date)\t$scriptname\tClearing cache..."
dropcache
fi
fi
############# HUMAN MAPPING #################
if [ "$human_mapping" != "skip" ]
then
echo -e "$(date)\t$scriptname\t############### SNAP TO HUMAN ###############"
basef_h=${nopathf%.fastq}.preprocessed.s20.h250n25d${d_human}xfu # remove fastq extension
echo -e "$(date)\t$scriptname\tBase file: $basef_h"
echo -e "$(date)\t$scriptname\tStarting: $basef_h human mapping"
file_to_subtract="$basef.preprocessed.fastq"
subtracted_output_file="$basef_h.human.snap.unmatched.sam"
SUBTRACTION_COUNTER=0
START_SUBTRACTION=$(date +%s)
for SNAP_subtraction_db in $SNAP_subtraction_folder/*; do
SUBTRACTION_COUNTER=$[$SUBTRACTION_COUNTER +1]
# check if SNAP db is cached in RAM, use optimal parameters depending on result
SNAP_db_cached=$(vmtouch -m500G -f "$SNAP_subtraction_db" | grep 'Resident Pages' | awk '{print $5}')
if [[ "$SNAP_db_cached" == "100%" ]]
then
echo -e "$(date)\t$scriptname\tSNAP database is cached ($SNAP_db_cached)."
SNAP_cache_option=" -map "
else
echo -e "$(date)\t$scriptname\tSNAP database is not cached ($SNAP_db_cached)."
SNAP_cache_option=" -pre -map "
fi
echo -e "$(date)\t$scriptname\tParameters: snap-dev single $SNAP_subtraction_db $file_to_subtract -o -sam $subtracted_output_file.$SUBTRACTION_COUNTER.sam -t $cores -x -f -h 250 -d ${d_human} -n 25 -F u $SNAP_cache_option"
START_SUBTRACTION_STEP=$(date +%s)
snap-dev single "$SNAP_subtraction_db" "$file_to_subtract" -o -sam "$subtracted_output_file.$SUBTRACTION_COUNTER.sam" -t $cores -x -f -h 250 -d ${d_human} -n 25 -F u $SNAP_cache_option
END_SUBTRACTION_STEP=$(date +%s)
echo -e "$(date)\t$scriptname\tDone: SNAP to human"
diff_SUBTRACTION_STEP=$(( END_SUBTRACTION_STEP - START_SUBTRACTION_STEP ))
echo -e "$(date)\t$scriptname\tSubtraction step: $SUBTRACTION_COUNTER took $diff_SUBTRACTION_STEP seconds"
file_to_subtract="$subtracted_output_file.$SUBTRACTION_COUNTER.sam"
done
egrep -v "^@" "$subtracted_output_file.$SUBTRACTION_COUNTER.sam" | awk '{if($3 == "*") print "@"$1"\n"$10"\n""+"$1"\n"$11}' > $(echo "$basef_h".human.snap.unmatched.sam | sed 's/\(.*\)\..*/\1/').fastq
END_SUBTRACTION=$(date +%s)
diff_SUBTRACTION=$(( END_SUBTRACTION - START_SUBTRACTION ))
rm $subtracted_output_file.*.sam
echo -e "$(date)\t$scriptname\tSubtraction took $diff_SUBTRACTION seconds" | tee -a timing.$basef.log
fi
######dropcache?#############
freemem=$(free -g | awk '{print $4}' | head -n 2 | tail -1)
echo -e "$(date)\t$scriptname\tThere is $freemem GB available free memory...[cutoff=$cache_reset GB]"
if [[ $dropcache == "Y" ]]
then
if [ "$freemem" -lt "$cache_reset" ]
then
echo -e "$(date)\t$scriptname\tClearing cache..."
dropcache
fi
fi
############################# SNAP TO NT ##############################
if [ "$alignment" != "skip" ]
then
if [ ! -f $basef.NT.snap.sam ]
then
echo -e "$(date)\t$scriptname\t####### SNAP UNMATCHED SEQUENCES TO NT ######"
echo -e -n "$(date)\t$scriptname\tCalculating number of sequences to analyze using SNAP to NT: "
echo $(awk 'NR%4==1' "$basef_h".human.snap.unmatched.fastq | wc -l)
echo -e "$(date)\t$scriptname\tStarting: Mapping by SNAP to NT from $basef_h.human.snap.unmatched.fastq"
START_SNAPNT=$(date +%s)
# SNAP to NT for unmatched reads (d value threshold cutoff = 12)
if [ $run_mode = "Comprehensive" ]
then
if [ $snap_integrator = "inline" ]
then
echo -e "$(date)\t$scriptname\tParameters: snap_nt.sh $basef_h.human.snap.unmatched.fastq ${SNAP_COMPREHENSIVE_db_dir} $cores $cache_reset $d_NT_alignment $snap"
snap_nt.sh "$basef_h.human.snap.unmatched.fastq" "${SNAP_COMPREHENSIVE_db_dir}" "$cores" "$cache_reset" "$d_NT_alignment" "$snap"
elif [ $snap_integrator = "end" ]
then
if [ "$snap_nt_procedure" = "AWS_master_slave" ]
then
# transfer data to slave, start SNAP on each slave, and wait for results
#check if slave_setup is running before progressing to snap_on_slave.sh
#slave_setup should be responsible for verifying that all slaves are properly running.
echo -n -e "$(date)\t$scriptname\tWaiting for slave_setup to complete."
while [ ! -f $file_with_slave_ips ]
do
echo -n "."
sleep 2
done
echo
echo -e "$(date)\t$scriptname\tParameters: snap_on_slave.sh $basef_h.human.snap.unmatched.fastq $pemkey $file_with_slave_ips $incoming_dir ${basef}.NT.snap.sam $d_NT_alignment"
snap_on_slave.sh "$basef_h.human.snap.unmatched.fastq" "$pemkey" "$file_with_slave_ips" "$incoming_dir" "${basef}.NT.snap.sam" "$d_human"> "$basef.AWS.log" 2>&1
elif [ "$snap_nt_procedure" = "solo" ]
then
echo -e "$(date)\t$scriptname\tParameters: snap_nt_combine.sh $basef_h.human.snap.unmatched.fastq ${SNAP_COMPREHENSIVE_db_dir} $cores $cache_reset $d_NT_alignment $num_simultaneous_SNAP_runs"
snap_nt_combine.sh "$basef_h.human.snap.unmatched.fastq" "${SNAP_COMPREHENSIVE_db_dir}" "$cores" "$cache_reset" "$d_NT_alignment" "$num_simultaneous_SNAP_runs"
fi
fi
elif [ $run_mode = "Fast" ]
then
echo -e "$(date)\t$scriptname\tParameters: snap_nt.sh $basef_h.human.snap.unmatched.fastq ${SNAP_FAST_db_dir} $cores $cache_reset $d_NT_alignment $snap"
snap_nt.sh "$basef_h.human.snap.unmatched.fastq" "${SNAP_FAST_db_dir}" "$cores" "$cache_reset" "$d_NT_alignment" "$snap"
fi
echo -e "$(date)\t$scriptname\tDone: SNAP to NT"
END_SNAPNT=$(date +%s)
diff_SNAPNT=$(( END_SNAPNT - START_SNAPNT ))
echo -e "$(date)\t$scriptname\tSNAP to NT took $diff_SNAPNT seconds." | tee -a timing.$basef.log
mv -f "$basef_h.human.snap.unmatched.NT.sam" "$basef.NT.snap.sam"
fi
echo -e "$(date)\t$scriptname\tStarting: parsing $basef.NT.snap.sam"
echo -e "$(date)\t$scriptname\textract matched/unmatched $basef.NT.snap.sam"
egrep -v "^@" $basef.NT.snap.sam | awk '{if($3 != "*") print }' > $basef.NT.snap.matched.sam
egrep -v "^@" $basef.NT.snap.sam | awk '{if($3 == "*") print }' > $basef.NT.snap.unmatched.sam
echo -e "$(date)\t$scriptname\tconvert sam to fastq from $basef.NT.snap.sam"
echo -e "$(date)\t$scriptname\tDone: parsing $basef.NT.snap.unmatched.sam"
if [ ! -f "$basef.NT.snap.matched.all.annotated" ]
then
## convert to FASTQ and retrieve full-length sequences
echo -e "$(date)\t$scriptname\tconvert to FASTQ and retrieve full-length sequences for SNAP NT matched hits"
echo -e "$(date)\t$scriptname\tParameters: extractHeaderFromFastq_ncores.sh $cores $basef.cutadapt.fastq $basef.NT.snap.matched.sam $basef.NT.snap.matched.fulllength.fastq $basef.NT.snap.unmatched.sam $basef.NT.snap.unmatched.fulllength.fastq"
extractHeaderFromFastq_ncores.sh "$cores" "$basef.cutadapt.fastq" "$basef.NT.snap.matched.sam" "$basef.NT.snap.matched.fulllength.fastq" "$basef.NT.snap.unmatched.sam" "$basef.NT.snap.unmatched.fulllength.fastq" #SNN140507
sort -k1,1 "$basef.NT.snap.matched.sam" > "$basef.NT.snap.matched.sorted.sam"
cut -f1-9 "$basef.NT.snap.matched.sorted.sam" > "$basef.NT.snap.matched.sorted.sam.tmp1"
cut -f12- "$basef.NT.snap.matched.sorted.sam" > "$basef.NT.snap.matched.sorted.sam.tmp2" #SNN140507 -f11 -> -f12
awk '(NR%4==1) {printf("%s\t",$0)} (NR%4==2) {printf("%s\t", $0)} (NR%4==0) {printf("%s\n",$0)}' "$basef.NT.snap.matched.fulllength.fastq" | sort -k1,1 | awk '{print $2 "\t" $3}' > "$basef.NT.snap.matched.fulllength.sequence.txt" #SNN140507 change this to bring in quality lines as well
paste "$basef.NT.snap.matched.sorted.sam.tmp1" "$basef.NT.snap.matched.fulllength.sequence.txt" "$basef.NT.snap.matched.sorted.sam.tmp2" > "$basef.NT.snap.matched.fulllength.sam"
###retrieve taxonomy matched to NT ###
echo -e "$(date)\t$scriptname\ttaxonomy retrieval for $basef.NT.snap.matched.fulllength.sam"
echo -e "$(date)\t$scriptname\tParameters: taxonomy_lookup.pl $basef.NT.snap.matched.fulllength.sam sam nucl $cores $taxonomy_db_directory"
taxonomy_lookup.pl "$basef.NT.snap.matched.fulllength.sam" sam nucl $cores $taxonomy_db_directory
sort -k 13.7n "$basef.NT.snap.matched.fulllength.all.annotated" > "$basef.NT.snap.matched.fulllength.all.annotated.sorted" # sam format is no longer disturbed
rm -f "$basef.NT.snap.matched.fulllength.gi" "$basef.NT.snap.matched.fullength.gi.taxonomy"
fi
# adjust filenames for FAST mode
grep "Viruses;" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" > "$basef.NT.snap.matched.fl.Viruses.annotated"
grep "Bacteria;" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" > "$basef.NT.snap.matched.fl.Bacteria.annotated"
##SNN140507 cleanup bacterial reads
echo -e "$(date)\t$scriptname\tParameters: ribo_snap_bac_euk.sh $basef.NT.snap.matched.fl.Bacteria.annotated BAC $cores $ribo_snap_bac_euk_directory"
ribo_snap_bac_euk.sh $basef.NT.snap.matched.fl.Bacteria.annotated BAC $cores $ribo_snap_bac_euk_directory #SNN140507
if [ $run_mode = "Comprehensive" ]
then
grep "Primates;" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" > "$basef.NT.snap.matched.fl.Primates.annotated"
grep -v "Primates" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" | grep "Mammalia" > "$basef.NT.snap.matched.fl.nonPrimMammal.annotated"
grep -v "Mammalia" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" | grep "Chordata" > "$basef.NT.snap.matched.fl.nonMammalChordat.annotated"
grep -v "Chordata" "$basef.NT.snap.matched.fulllength.all.annotated.sorted" | grep "Eukaryota" > "$basef.NT.snap.matched.fl.nonChordatEuk.annotated"
ribo_snap_bac_euk.sh $basef.NT.snap.matched.fl.nonChordatEuk.annotated EUK $cores $ribo_snap_bac_euk_directory
fi
echo -e "$(date)\t$scriptname\tDone taxonomy retrieval"
echo -e "$(date)\t$scriptname\tParameters: table_generator.sh $basef.NT.snap.matched.fl.Viruses.annotated SNAP Y Y Y Y>& $basef.table_generator_snap.matched.fl.log"
table_generator.sh "$basef.NT.snap.matched.fl.Viruses.annotated" SNAP Y Y Y Y>& "$basef.table_generator_snap.matched.fl.log"
if [ $run_mode = "Comprehensive" ]
then
### convert to FASTQ and retrieve full-length sequences to add to unmatched SNAP for viral RAPSearch###
egrep -v "^@" "$basef.NT.snap.matched.fl.Viruses.annotated" | awk '{if($3 != "*") print "@"$1"\n"$10"\n""+"$1"\n"$11}' > $(echo "$basef.NT.snap.matched.fl.Viruses.annotated" | sed 's/\(.*\)\..*/\1/').fastq
echo -e "$(date)\t$scriptname\tDone: convert to FASTQ and retrieve full-length sequences for SNAP NT hits "
fi
echo -e "$(date)\t$scriptname\t############# SORTING unmatched to NT BY LENGTH AND UNIQ AND LOOKUP ORIGINAL SEQUENCES #################"
if [ $run_mode = "Comprehensive" ]
then
#SNN 140507 extractHeaderFromFastq.csh "$basef.NT.snap.unmatched.fastq" FASTQ "$basef.cutadapt.fastq" "$basef.NT.snap.unmatched.fulllength.fastq"
sed "n;n;n;d" "$basef.NT.snap.unmatched.fulllength.fastq" | sed "n;n;d" | sed "s/^@/>/g" > "$basef.NT.snap.unmatched.fulllength.fasta"
fi
cat "$basef.NT.snap.unmatched.fulllength.fasta" | perl -e 'while (<>) {$h=$_; $s=<>; $seqs{$h}=$s;} foreach $header (reverse sort {length($seqs{$a}) <=> length($seqs{$b})} keys %seqs) {print $header.$seqs{$header}}' > $basef.NT.snap.unmatched.fulllength.sorted.fasta
if [ $run_mode = "Comprehensive" ]
then
echo -e "$(date)\t$scriptname\twe will be using 50 as the length of the cropped read for removing unique and low-complexity reads"
echo -e "$(date)\t$scriptname\tParameters: crop_reads.csh $basef.NT.snap.unmatched.fulllength.sorted.fasta 25 50 > $basef.NT.snap.unmatched.fulllength.sorted.cropped.fasta"
crop_reads.csh "$basef.NT.snap.unmatched.fulllength.sorted.fasta" 25 50 > "$basef.NT.snap.unmatched.fulllength.sorted.cropped.fasta"
echo -e "$(date)\t$scriptname\t*** reads cropped ***"
echo -e "$(date)\t$scriptname\tParameters: gt sequniq -seqit -force -o $basef.NT.snap.unmatched.fulllength.sorted.cropped.uniq.fasta $basef.NT.snap.unmatched.fulllength.sorted.cropped.fasta"
gt sequniq -seqit -force -o "$basef.NT.snap.unmatched.fulllength.sorted.cropped.uniq.fasta" "$basef.NT.snap.unmatched.fulllength.sorted.cropped.fasta"
echo -e "$(date)\t$scriptname\tParameters: extractAlltoFast.sh $basef.NT.snap.unmatched.fulllength.sorted.cropped.uniq.fasta FASTA $basef.NT.snap.unmatched.fulllength.fasta FASTA $basef.NT.snap.unmatched.uniq.fl.fasta FASTA"
extractAlltoFast.sh "$basef.NT.snap.unmatched.fulllength.sorted.cropped.uniq.fasta" FASTA "$basef.NT.snap.unmatched.fulllength.fasta" FASTA "$basef.NT.snap.unmatched.uniq.fl.fasta" FASTA #SNN140507
fi
echo -e "$(date)\t$scriptname\tDone uniquing full length sequences of unmatched to NT"
fi
####################### DENOVO CONTIG ASSEMBLY #####
if [ $run_mode = "Comprehensive" ]
then
echo -e "$(date)\t$scriptname\t######### Running ABYSS and Minimus #########"
START_deNovo=$(date +%s)
echo -e "$(date)\t$scriptname\tAdding matched viruses to NT unmatched"
sed "n;n;n;d" "$basef.NT.snap.matched.fl.Viruses.fastq" | sed "n;n;d" | sed "s/^@/>/g" | sed 's/>/>Vir/g' > "$basef.NT.snap.matched.fl.Viruses.fasta"
gt sequniq -seqit -force -o "$basef.NT.snap.matched.fl.Viruses.uniq.fasta" "$basef.NT.snap.matched.fl.Viruses.fasta"
cat "$basef.NT.snap.unmatched.uniq.fl.fasta" "$basef.NT.snap.matched.fl.Viruses.uniq.fasta" > "$basef.NT.snap.unmatched_addVir_uniq.fasta"
echo -e "$(date)\t$scriptname\tStarting deNovo assembly"
echo -e "$(date)\t$scriptname\tParameters: abyss_minimus.sh $basef.NT.snap.unmatched_addVir_uniq.fasta $length $contigcutoff $cores $abysskmer $ignore_barcodes_for_de_novo"
abyss_minimus.sh "$basef.NT.snap.unmatched_addVir_uniq.fasta" "$length" "$contigcutoff" "$cores" "$abysskmer" "$ignore_barcodes_for_de_novo"
echo -e "$(date)\t$scriptname\tCompleted deNovo assembly: generated all.$basef.NT.snap.unmatched_addVir_uniq.fasta.unitigs.cut${length}.${contigcutoff}-mini.fa"
END_deNovo=$(date +%s)
diff_deNovo=$(( END_deNovo - START_deNovo ))
echo -e "$(date)\t$scriptname\tdeNovo Assembly took $diff_deNovo seconds." | tee -a timing.$basef.log
fi
#######RAPSearch#####
#################### RAPSearch to Vir ###########
if [ $run_mode = "Comprehensive" ]
then
if [ "$rapsearch_database" == "Viral" ]
then
if [ -f "$basef.NT.snap.unmatched.uniq.fl.fasta" ]
then
echo -e "$(date)\t$scriptname\t############# RAPSearch to ${RAPSearch_VIRUS_db} ON NT-UNMATCHED SEQUENCES #################"
if [[ $dropcache == "Y" ]]
then
dropcache
fi
echo -e "$(date)\t$scriptname\tStarting: RAPSearch $basef.NT.snap.unmatched.uniq.fl.fasta "
START14=$(date +%s)
echo -e "$(date)\t$scriptname\tParameters: rapsearch -q $basef.NT.snap.unmatched.uniq.fl.fasta -d $RAPSearch_VIRUS_db -o $basef.$rapsearch_database.RAPSearch.e1 -z $cores -e $ecutoff_Vir -v 1 -b 1 -t N >& $basef.$rapsearch_database.RAPSearch.log"
rapsearch -q "$basef.NT.snap.unmatched.uniq.fl.fasta" -d $RAPSearch_VIRUS_db -o $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir} -z "$cores" -e "$ecutoff_Vir" -v 1 -b 1 -t N >& $basef.$rapsearch_database.RAPSearch.log
echo -e "$(date)\t$scriptname\tDone RAPSearch"
END14=$(date +%s)
diff=$(( END14 - START14 ))
echo -e "$(date)\t$scriptname\tRAPSearch to Vir Took $diff seconds"
echo -e "$(date)\t$scriptname\tStarting: add FASTA sequences to RAPSearch m8 output file "
START15=$(date +%s)
sed -i '/^#/d' $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir}.m8
seqtk subseq $basef.NT.snap.unmatched.uniq.fl.fasta $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir}.m8 > $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir}.m8.fasta
sed '/>/d' $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir}.m8.fasta > $basef.$rapsearch_database.RAPSearch.e${ecutoff_Vir}.m8.fasta.seq