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Fix SLURM account specification: ensure $userstring is correctly parsed by SLURM #376

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Fix SLURM account specification: ensure $userstring is correctly parsed by SLURM #376

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2b40c7e
Fix: make heredoc recognize to pick up the correct account name
zapell Jun 6, 2025
59a5344
remove account header
zapell Jun 6, 2025
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48 changes: 24 additions & 24 deletions SLURM/scripts/juicer.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -587,7 +587,7 @@ else
fi
jid=`sbatch <<- HEADER | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
$userstring
$userstring
$queuestring
#SBATCH -t 2
#SBATCH -c 1
Expand Down Expand Up @@ -669,7 +669,7 @@ then
#SBATCH -o $debugdir/split-%j.out
#SBATCH -e $debugdir/split-%j.err
#SBATCH -J "${groupname}_split_${i}"
$userstring
$userstring
date
echo "Split file: $filename"
split -a 3 -l $splitsize -d --additional-suffix=.fastq $i $splitdir/$filename
Expand All @@ -685,7 +685,7 @@ SPLITEND`
#SBATCH -o $debugdir/split-%j.out
#SBATCH -e $debugdir/split-%j.err
#SBATCH -J "${groupname}_split_${i}"
$userstring
$userstring
date
echo "Split file: $filename"
zcat $i | split -a 3 -l $splitsize -d --additional-suffix=.fastq - $splitdir/$filename
Expand Down Expand Up @@ -769,7 +769,7 @@ SPLITEND`
#SBATCH -e $debugdir/count_ligation-%j.err
#SBATCH -J "${groupname}_${jname}_Count_Ligation"
#SBATCH --mem=5G
$userstring
$userstring

date
export usegzip=${usegzip}; export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation=${ligation}; export singleend=${singleend}; ${juiceDir}/scripts/countligations.sh
Expand All @@ -790,7 +790,7 @@ CNTLIG`
#SBATCH --mem=$alloc_mem
#SBATCH -J "${groupname}_align1_${jname}"
#SBATCH --threads-per-core=1
$userstring
$userstring

${load_bwa}
# Align reads
Expand Down Expand Up @@ -847,7 +847,7 @@ ALGNR1`
#SBATCH --mem=5G
${load_awk}
${load_samtools}
$userstring
$userstring

date
echo -ne "0 " > ${name}${ext}_norm.txt.res.txt
Expand All @@ -873,7 +873,7 @@ CNTLINE`
#SBATCH -d $dependalign
#SBATCH -J "${groupname}_merge_${jname}"
#SBATCH --threads-per-core=1
$userstring
$userstring
${load_awk}

date
Expand Down Expand Up @@ -901,7 +901,7 @@ MRGALL`
#SBATCH -d $dependalign
#SBATCH -J "${groupname}_merge_${jname}"
#SBATCH --threads-per-core=1
$userstring
$userstring
${load_awk}
#time awk -v maxcount=1000000 -f $juiceDir/scripts/calculate_insert_size.awk $name$ext.sam > $name$ext.insert_size
#will need to combine chimeric_sam and adjust_insert_size
Expand All @@ -921,7 +921,7 @@ MRGALL1`
#SBATCH -d $dependalign
#SBATCH -J "${groupname}_merge_${jname}"
#SBATCH --threads-per-core=1
$userstring
$userstring
${load_awk}
#time awk -v maxcount=1000000 -f $juiceDir/scripts/calculate_insert_size.awk $name$ext.sam > $name$ext.insert_size
#will need to combine chimeric_sam and adjust_insert_size
Expand All @@ -940,7 +940,7 @@ MRGALL1`
#SBATCH -d $dependalign
#SBATCH -J "${groupname}_merge_${jname}"
#SBATCH --threads-per-core=1
$userstring
$userstring
${load_awk}

time awk -v avgInsertFile=${name}${ext}_norm.txt.res.txt -f $juiceDir/scripts/adjust_insert_size.awk $name$ext.sam2 > $name$ext.sam3
Expand Down Expand Up @@ -997,7 +997,7 @@ MRGALL2`
#SBATCH -p $queue
#SBATCH -J "${groupname}_check"
#SBATCH -d $dependmerge
$userstring
$userstring

date
echo "Checking $f"
Expand Down Expand Up @@ -1050,7 +1050,7 @@ then
${sbatch_cpu_alloc}
#SBATCH -J "${groupname}_fragmerge"
${sbatch_wait}
$userstring
$userstring

date
if [ -f "${errorfile}" ]
Expand Down Expand Up @@ -1102,7 +1102,7 @@ then
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_dedup_guard"
${sbatch_wait}
$userstring
$userstring

date
DEDUPGUARD`
Expand All @@ -1121,7 +1121,7 @@ DEDUPGUARD`
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_dedup"
${sbatch_wait}
$userstring
$userstring

${load_awk}
date
Expand Down Expand Up @@ -1158,7 +1158,7 @@ DEDUP`
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_post_dedup"
#SBATCH -d ${dependguard}
$userstring
$userstring

date
rm -Rf $tmpdir;
Expand Down Expand Up @@ -1195,7 +1195,7 @@ if [ -z $postproc ] && [ -z $final ]
#SBATCH --mem-per-cpu=8G
#SBATCH -J "${groupname}_dupcheck"
${sbatch_wait}
$userstring
$userstring
${load_awk}
date
wc -l ${outputdir}/merged_sort.sam | awk '{printf("%s ", \\\$1)}' > $debugdir/dupcheck-${groupname}
Expand Down Expand Up @@ -1346,7 +1346,7 @@ METH`
#SBATCH --mem=25G
#SBATCH -J "${groupname}_stats"
${sbatch_wait000}
$userstring
$userstring

date
if [ -f "${errorfile}" ]
Expand Down Expand Up @@ -1416,7 +1416,7 @@ then
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_mnd"
${sbatch_wait1}
$userstring
$userstring
${load_samtools}
date

Expand All @@ -1438,7 +1438,7 @@ MND`
#SBATCH -J "${groupname}_prep_done"
#SBATCH --mail-type=END,FAIL
${sbatch_wait1}
$userstring
$userstring
date
export splitdir=${splitdir}; export outputdir=${outputdir}; export early=1;
if ${juiceDir}/scripts/check.sh
Expand Down Expand Up @@ -1478,7 +1478,7 @@ FINCLN1`
#SBATCH --mem=150G
#SBATCH -J "${groupname}_hic"
${sbatch_waitstats}
$userstring
$userstring

${load_java}
export IBM_JAVA_OPTIONS="-Xmx150000m -Xgcthreads1"
Expand Down Expand Up @@ -1516,7 +1516,7 @@ HIC`
#SBATCH --mem=150G
#SBATCH -J "${groupname}_hic30"
${sbatch_waitstats30}
$userstring
$userstring

${load_java}
export IBM_JAVA_OPTIONS="-Xmx150000m -Xgcthreads1"
Expand Down Expand Up @@ -1565,7 +1565,7 @@ then
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_hiccups_wrap"
${sbatch_wait}
$userstring
$userstring

${load_gpu}
echo "load: $load_gpu"
Expand Down Expand Up @@ -1598,7 +1598,7 @@ then
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_arrowhead_wrap"
${sbatch_wait}
$userstring
$userstring

${load_java}
date
Expand Down Expand Up @@ -1648,7 +1648,7 @@ jid=`sbatch <<- FINCLN1 | egrep -o -e "\b[0-9]+$"
#SBATCH --ntasks=1
#SBATCH -J "${groupname}_prep_done"
$dependarrows
$userstring
$userstring

date
export splitdir=${splitdir}
Expand Down