This is a template script written by Scott Hunicke-Smith to illustrate how to run exome analysis much faster on lonestar. It only requires two fastq files (paired files) and two parameters. It is NOT optimized, not highly robust, etc. It relies on many sub-scripts both within Scott's home directory and the BioITeam corral directories.
This bash script needs to be run on a head node somewhere where it won't be killed:
...
- Create one job on one node which splits the two input fastq files into files with
$splitSize lines per file each using split.sge and split.script. Wait for job to finish. - Create as many subdirectories as needed for the split output files to be mapped
$batchSize per directory. Lonestar nodes have two sockets with 12 processors per socket, so a good choice here is to make $batchSize two so that the mapping step can use 6 threads. - Create
$batchSize * originalFileSize % $splitSize lines in map.script and submit map.sge to do the mapping. Note that the embedded mapping script bwaexome_mapPairstep1.sh splits the mapping output into chromosome-specific files during the bwa sampe step. This mapping script is also where multi-threading for bwa is set. It should be parameterized of course. - Merge all the chromosome-specific files from these subdirectories back to the run directory using
merge.sge and merge.script - Run GATK on sets of these chromosome-specific files, with 2 GATK's per node (hardcoded in script right now) using
variants.sge and variants.script; since chromosomes are usually named based on their size (i.e. chr1 < chr2 < chr3, etc.), randomize the list so that we don't wind up with all the big chromosomes on one node. - Merge the final GATK chromosome-specific variant calls - both the BAM files and the VCF files - using
merge2.sge and merge2.script.
...
Benchmark analysis on ~40 million read pairs from a single human exome experiment show that this script takes about 2 hours vs. about 15 hours if all these same processes are run on only 1 node.
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| Expand here to see example split.sge and split.script |
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| Expand here to see example split.sge and split.script |
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#!/bin/csh
#
# Simple SGE script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
#
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory. Then, edit the CONTROL_FILE to specify
# each executable per process.
#-------------------------------------------------------
#-------------------------------------------------------
#
# <------ Setup Parameters ------>
#
#$ -N split
#$ -pe 12way 12
#$ -q normal
#$ -o split.o$JOB_ID
#$ -l h_rt=1:00:00
#$ -V
#$ -cwd
# <------ You MUST Specify a Project String ----->
#$ -A DNAdenovo
#------------------------------------------------------
#
# Usage:
# #$ -pe <parallel environment> <number of slots>
# #$ -l h_rt=hours:minutes:seconds to specify run time limit
# #$ -N <job name>
# #$ -q <queue name>
# #$ -o <job output file>
# NOTE: The env variable $JOB_ID contains the job id.
#
module load launcher
setenv EXECUTABLE $TACC_LAUNCHER_DIR/init_launcher
setenv CONTROL_FILE split.script
setenv WORKDIR .
#
# Variable description:
#
# EXECUTABLE = full path to the job launcher executable
# CONTROL_FILE = text input file which specifies
# executable for each process
# (should be located in WORKDIR)
# WORKDIR = location of working directory
#
# <------ End Setup Parameters ------>
#--------------------------------------------------------
#--------------------------------------------------------
#----------------
# Error Checking
#----------------
if ( ! -e $WORKDIR ) then
echo " "
echo "Error: unable to change to working directory."
echo " $WORKDIR"
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $EXECUTABLE ) then
echo " "
echo "Error: unable to find launcher executable $EXECUTABLE."
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $WORKDIR/$CONTROL_FILE ) then
echo " "
echo "Error: unable to find input control file $CONTROL_FILE."
echo " "
echo "Job not submitted."
exit
endif
#----------------
# Job Submission
#----------------
cd $WORKDIR/
echo " WORKING DIR: $WORKDIR/"
$TACC_LAUNCHER_DIR/paramrun $EXECUTABLE $CONTROL_FILE
echo " "
echo " Parameteric Job Complete"
echo " "
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split -d -l 1500000 Sample_5_L003_R1.cat.fastq r1.
split -d -l 1500000 Sample_5_L003_R2.cat.fastq r2.
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| Expand here to see example merge.sge and merge.script |
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| Expand here to see example merge.sge and merge.script |
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#!/bin/csh
#
# Simple SGE script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
#
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory. Then, edit the CONTROL_FILE to specify
# each executable per process.
#-------------------------------------------------------
#-------------------------------------------------------
#
# <------ Setup Parameters ------>
#
#$ -N merge
#$ -pe 4way 72
#$ -q normal
#$ -o merge.o$JOB_ID
#$ -l h_rt=1:00:00
#$ -V
#$ -cwd
# <------ You MUST Specify a Project String ----->
#$ -A DNAdenovo
#------------------------------------------------------
#
# Usage:
# #$ -pe <parallel environment> <number of slots>
# #$ -l h_rt=hours:minutes:seconds to specify run time limit
# #$ -N <job name>
# #$ -q <queue name>
# #$ -o <job output file>
# NOTE: The env variable $JOB_ID contains the job id.
#
module load launcher
setenv EXECUTABLE $TACC_LAUNCHER_DIR/init_launcher
setenv CONTROL_FILE merge.script
setenv WORKDIR .
#
# Variable description:
#
# EXECUTABLE = full path to the job launcher executable
# CONTROL_FILE = text input file which specifies
# executable for each process
# (should be located in WORKDIR)
# WORKDIR = location of working directory
#
# <------ End Setup Parameters ------>
#--------------------------------------------------------
#--------------------------------------------------------
#----------------
# Error Checking
#----------------
if ( ! -e $WORKDIR ) then
echo " "
echo "Error: unable to change to working directory."
echo " $WORKDIR"
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $EXECUTABLE ) then
echo " "
echo "Error: unable to find launcher executable $EXECUTABLE."
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $WORKDIR/$CONTROL_FILE ) then
echo " "
echo "Error: unable to find input control file $CONTROL_FILE."
echo " "
echo "Job not submitted."
exit
endif
#----------------
# Job Submission
#----------------
cd $WORKDIR/
echo " WORKING DIR: $WORKDIR/"
$TACC_LAUNCHER_DIR/paramrun $EXECUTABLE $CONTROL_FILE
echo " "
echo " Parameteric Job Complete"
echo " "
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samtools merge -f chr6.sorted.bam b.*/chr6.mapped.*.sorted.bam; samtools index chr6.sorted.bam
samtools merge -f chrX.sorted.bam b.*/chrX.mapped.*.sorted.bam; samtools index chrX.sorted.bam
samtools merge -f chr17.sorted.bam b.*/chr17.mapped.*.sorted.bam; samtools index chr17.sorted.bam
samtools merge -f chr21.sorted.bam b.*/chr21.mapped.*.sorted.bam; samtools index chr21.sorted.bam
samtools merge -f chr5.sorted.bam b.*/chr5.mapped.*.sorted.bam; samtools index chr5.sorted.bam
samtools merge -f chrY.sorted.bam b.*/chrY.mapped.*.sorted.bam; samtools index chrY.sorted.bam
samtools merge -f chr4.sorted.bam b.*/chr4.mapped.*.sorted.bam; samtools index chr4.sorted.bam
samtools merge -f chr19.sorted.bam b.*/chr19.mapped.*.sorted.bam; samtools index chr19.sorted.bam
samtools merge -f chr13.sorted.bam b.*/chr13.mapped.*.sorted.bam; samtools index chr13.sorted.bam
samtools merge -f chr16.sorted.bam b.*/chr16.mapped.*.sorted.bam; samtools index chr16.sorted.bam
samtools merge -f chr7.sorted.bam b.*/chr7.mapped.*.sorted.bam; samtools index chr7.sorted.bam
samtools merge -f chr9.sorted.bam b.*/chr9.mapped.*.sorted.bam; samtools index chr9.sorted.bam
samtools merge -f chr14.sorted.bam b.*/chr14.mapped.*.sorted.bam; samtools index chr14.sorted.bam
samtools merge -f chr11.sorted.bam b.*/chr11.mapped.*.sorted.bam; samtools index chr11.sorted.bam
samtools merge -f chr22.sorted.bam b.*/chr22.mapped.*.sorted.bam; samtools index chr22.sorted.bam
samtools merge -f chr1.sorted.bam b.*/chr1.mapped.*.sorted.bam; samtools index chr1.sorted.bam
samtools merge -f chr10.sorted.bam b.*/chr10.mapped.*.sorted.bam; samtools index chr10.sorted.bam
samtools merge -f chr15.sorted.bam b.*/chr15.mapped.*.sorted.bam; samtools index chr15.sorted.bam
samtools merge -f chr18.sorted.bam b.*/chr18.mapped.*.sorted.bam; samtools index chr18.sorted.bam
samtools merge -f chr3.sorted.bam b.*/chr3.mapped.*.sorted.bam; samtools index chr3.sorted.bam
samtools merge -f chr20.sorted.bam b.*/chr20.mapped.*.sorted.bam; samtools index chr20.sorted.bam
samtools merge -f chr8.sorted.bam b.*/chr8.mapped.*.sorted.bam; samtools index chr8.sorted.bam
samtools merge -f chr2.sorted.bam b.*/chr2.mapped.*.sorted.bam; samtools index chr2.sorted.bam
samtools merge -f chr12.sorted.bam b.*/chr12.mapped.*.sorted.bam; samtools index chr12.sorted.bam
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| Expand here to see example map.sge and map.script; note that the fastExon.sh script creates this within subdirectories. |
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| Expand here to see example map.sge and map.script; note that the fastExon.sh script creates this within subdirectories. |
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#!/bin/csh
#
# Simple SGE script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
#
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory. Then, edit the CONTROL_FILE to specify
# each executable per process.
#-------------------------------------------------------
#-------------------------------------------------------
#
# <------ Setup Parameters ------>
#
#$ -N map.b.1
#$ -pe 2way 12
#$ -q normal
#$ -o map.b.1.o$JOB_ID
#$ -l h_rt=1:00:00
#$ -V
#$ -cwd
# <------ You MUST Specify a Project String ----->
#$ -A DNAdenovo
#------------------------------------------------------
#
# Usage:
# #$ -pe <parallel environment> <number of slots>
# #$ -l h_rt=hours:minutes:seconds to specify run time limit
# #$ -N <job name>
# #$ -q <queue name>
# #$ -o <job output file>
# NOTE: The env variable $JOB_ID contains the job id.
#
module load launcher
setenv EXECUTABLE $TACC_LAUNCHER_DIR/init_launcher
setenv CONTROL_FILE map.script
setenv WORKDIR .
#
# Variable description:
#
# EXECUTABLE = full path to the job launcher executable
# CONTROL_FILE = text input file which specifies
# executable for each process
# (should be located in WORKDIR)
# WORKDIR = location of working directory
#
# <------ End Setup Parameters ------>
#--------------------------------------------------------
#--------------------------------------------------------
#----------------
# Error Checking
#----------------
if ( ! -e $WORKDIR ) then
echo " "
echo "Error: unable to change to working directory."
echo " $WORKDIR"
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $EXECUTABLE ) then
echo " "
echo "Error: unable to find launcher executable $EXECUTABLE."
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $WORKDIR/$CONTROL_FILE ) then
echo " "
echo "Error: unable to find input control file $CONTROL_FILE."
echo " "
echo "Job not submitted."
exit
endif
#----------------
# Job Submission
#----------------
cd $WORKDIR/
echo " WORKING DIR: $WORKDIR/"
$TACC_LAUNCHER_DIR/paramrun $EXECUTABLE $CONTROL_FILE
echo " "
echo " Parameteric Job Complete"
echo " "
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/home1/01057/sphsmith/local/bin/exome_step1.bash r1.00 r2.00 /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta mapped.00 >& mapped.00.log
/home1/01057/sphsmith/local/bin/exome_step1.bash r1.01 r2.01 /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta mapped.01 >& mapped.01.log
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| Expand here to see example variants.sge and variants.script |
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#!/bin/csh
#
# Simple SGE script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
#
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory. Then, edit the CONTROL_FILE to specify
# each executable per process.
#-------------------------------------------------------
#-------------------------------------------------------
#
# <------ Setup Parameters ------>
#
#$ -N variants
#$ -pe 2way 144
#$ -q normal
#$ -o variants.o$JOB_ID
#$ -l h_rt=4:00:00
#$ -V
#$ -cwd
# <------ You MUST Specify a Project String ----->
#$ -A DNAdenovo
#------------------------------------------------------
#
# Usage:
# #$ -pe <parallel environment> <number of slots>
# #$ -l h_rt=hours:minutes:seconds to specify run time limit
# #$ -N <job name>
# #$ -q <queue name>
# #$ -o <job output file>
# NOTE: The env variable $JOB_ID contains the job id.
#
module load launcher
module load java64
module load samtools
setenv EXECUTABLE $TACC_LAUNCHER_DIR/init_launcher
setenv CONTROL_FILE variants.script
setenv WORKDIR .
#
# Variable description:
#
# EXECUTABLE = full path to the job launcher executable
# CONTROL_FILE = text input file which specifies
# executable for each process
# (should be located in WORKDIR)
# WORKDIR = location of working directory
#
# <------ End Setup Parameters ------>
#--------------------------------------------------------
#--------------------------------------------------------
#----------------
# Error Checking
#----------------
if ( ! -e $WORKDIR ) then
echo " "
echo "Error: unable to change to working directory."
echo " $WORKDIR"
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $EXECUTABLE ) then
echo " "
echo "Error: unable to find launcher executable $EXECUTABLE."
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $WORKDIR/$CONTROL_FILE ) then
echo " "
echo "Error: unable to find input control file $CONTROL_FILE."
echo " "
echo "Job not submitted."
exit
endif
#----------------
# Job Submission
#----------------
cd $WORKDIR/
echo " WORKING DIR: $WORKDIR/"
$TACC_LAUNCHER_DIR/paramrun $EXECUTABLE $CONTROL_FILE
echo " "
echo " Parameteric Job Complete"
echo " "
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/home1/01057/sphsmith/local/bin/exome_step2.bash chrY.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chrY >& variants.chrY.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr22.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr22 >& variants.chr22.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr9.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr9 >& variants.chr9.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr3.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr3 >& variants.chr3.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr21.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr21 >& variants.chr21.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr5.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr5 >& variants.chr5.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr16.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr16 >& variants.chr16.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr19.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr19 >& variants.chr19.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr18.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr18 >& variants.chr18.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr4.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr4 >& variants.chr4.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr12.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr12 >& variants.chr12.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr15.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr15 >& variants.chr15.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr14.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr14 >& variants.chr14.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chrX.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chrX >& variants.chrX.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr6.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr6 >& variants.chr6.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr13.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr13 >& variants.chr13.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr8.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr8 >& variants.chr8.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr7.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr7 >& variants.chr7.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr11.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr11 >& variants.chr11.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr20.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr20 >& variants.chr20.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr10.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr10 >& variants.chr10.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr1.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr1 >& variants.chr1.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr2.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr2 >& variants.chr2.log
/home1/01057/sphsmith/local/bin/exome_step2.bash chr17.sorted.bam /scratch/01057/sphsmith/hg19/Homo_sapiens.GRCh37.60.dna.fasta /work/01057/sphsmith/dbsnp/dbsnp_132.hg19.vcf chr17 >& variants.chr17.log
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| Expand here to see example merge2.sge and merge2.script |
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| Expand here to see example merge2.sge and merge2.script |
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#!/bin/csh
#
# Simple SGE script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
#
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory. Then, edit the CONTROL_FILE to specify
# each executable per process.
#-------------------------------------------------------
#-------------------------------------------------------
#
# <------ Setup Parameters ------>
#
#$ -N merge2
#$ -pe 4way 12
#$ -q normal
#$ -o merge2.o$JOB_ID
#$ -l h_rt=1:00:00
#$ -V
#$ -cwd
# <------ You MUST Specify a Project String ----->
#$ -A DNAdenovo
#------------------------------------------------------
#
# Usage:
# #$ -pe <parallel environment> <number of slots>
# #$ -l h_rt=hours:minutes:seconds to specify run time limit
# #$ -N <job name>
# #$ -q <queue name>
# #$ -o <job output file>
# NOTE: The env variable $JOB_ID contains the job id.
#
module load launcher
setenv EXECUTABLE $TACC_LAUNCHER_DIR/init_launcher
setenv CONTROL_FILE merge2.script
setenv WORKDIR .
#
# Variable description:
#
# EXECUTABLE = full path to the job launcher executable
# CONTROL_FILE = text input file which specifies
# executable for each process
# (should be located in WORKDIR)
# WORKDIR = location of working directory
#
# <------ End Setup Parameters ------>
#--------------------------------------------------------
#--------------------------------------------------------
#----------------
# Error Checking
#----------------
if ( ! -e $WORKDIR ) then
echo " "
echo "Error: unable to change to working directory."
echo " $WORKDIR"
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $EXECUTABLE ) then
echo " "
echo "Error: unable to find launcher executable $EXECUTABLE."
echo " "
echo "Job not submitted."
exit
endif
if ( ! -f $WORKDIR/$CONTROL_FILE ) then
echo " "
echo "Error: unable to find input control file $CONTROL_FILE."
echo " "
echo "Job not submitted."
exit
endif
#----------------
# Job Submission
#----------------
cd $WORKDIR/
echo " WORKING DIR: $WORKDIR/"
$TACC_LAUNCHER_DIR/paramrun $EXECUTABLE $CONTROL_FILE
echo " "
echo " Parameteric Job Complete"
echo " "
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samtools merge -f Sample_5_L003_R1.cat.fastq.sorted.bam *.sorted.bam
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