Commit 90e05b27 authored by nchernia's avatar nchernia
Browse files

Adding in options to mega script; updating memory requirements

parent 809943d3

SLURM/scripts/mega.sh

+23 −18
Changes for SLURM/scripts/mega.sh: 23 added lines, 18 removed lines.
Original line number Diff line number Diff line
@@ -94,7 +94,7 @@ site="MboI" 
genomeID="hg19"



## Read arguments                                                     

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-h]"

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-S stage] [-q queue] [-l long queue] [-Q queue time] [-L long queue time] [-x] [-h]"

genomeHelp="   genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"

dirHelp="   [topDir] is the top level directory (default \"$topDir\") and must contain links to all merged_nodups files underneath it"

siteHelp="   [site] must be defined in the script, e.g.  \"HindIII\" or \"MboI\" (default \"$site\"); alternatively, this can be the restriction site file"
@@ -113,7 +113,7 @@ printHelpAndExit() { 
    exit "$1"

}



while getopts "d:g:hxs:S:" opt; do

while getopts "d:g:hxs:S:l:L:q:Q:" opt; do

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;
@@ -121,6 +121,10 @@ while getopts "d:g:hxs:S:" opt; do 
	s) site=$OPTARG ;;

	x) exclude=1 ;;

	S) stage=$OPTARG ;;

	l) long_queue=$OPTARG ;;

	L) long_queue_time=$OPTARG ;;

	q) queue=$OPTARG ;;

	Q) queue_time=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done
@@ -233,7 +237,7 @@ then 
#SBATCH -o $logdir/topstats-%j.out

#SBATCH -e $logdir/topstats-%j.err

#SBATCH -J "${groupname}_topstats"

#SBATCH --mem-per-cpu=32G 

#SBATCH --mem-per-cpu=4G 

export LC_COLLATE=C

if ! awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt

then
@@ -254,12 +258,11 @@ TOPSTATS` 
#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=16384

#SBATCH -o $logdir/merge-%j.out

#SBATCH -e $logdir/merge-%j.err

#SBATCH -J "${groupname}_merge"

#SBATCH -d "${dependtopstats}"

#SBATCH --mem-per-cpu=32G 

#SBATCH --mem-per-cpu=8G

if [ ! -f "${touchfile1}" ]

then

    echo "***! Top stats job failed, type \"scontrol show job $jid1\" to see what happened."
@@ -268,13 +271,13 @@ fi 


  if [ $isRice -eq 1 ]

  then

    if ! /poscratch/aidenlab/olga/sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

    if ! ${juiceDir}/scripts/sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

    then

      echo "***! Some problems occurred somewhere in creating sorted merged_nodups files."

      exit 1

    fi

  else

    if ! sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

    if ! sort --parallel=40 -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

    then 

      echo "***! Some problems occurred somewhere in creating sorted merged_nodups files."

      exit 1
@@ -303,7 +306,7 @@ then 
#SBATCH -o $logdir/inter0-%j.out

#SBATCH -e $logdir/inter0-%j.err

#SBATCH -J "${groupname}_inter0"

#SBATCH --mem-per-cpu=32G 

#SBATCH --mem-per-cpu=2G

${dependmerge}

if [ ! -f "${touchfile2}" ]

then
@@ -327,7 +330,7 @@ INTER0` 
#SBATCH -o $logdir/inter30-%j.out

#SBATCH -e $logdir/inter30-%j.err

#SBATCH -J "${groupname}_inter30"

#SBATCH --mem-per-cpu=32G 

#SBATCH --mem-per-cpu=2G 

${dependmerge}

if [ ! -f "${touchfile2}" ]

then
@@ -346,24 +349,25 @@ INTER30` 
#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH -c 8

#SBATCH --ntasks=1

#SBATCH -o $logdir/hic0-%j.out

#SBATCH -e $logdir/hic0-%j.err

#SBATCH -J "${groupname}_hic0"

#SBATCH -d "${dependinter0}"

#SBATCH --mem-per-cpu=32G

#SBATCH --mem=73G

#source $usePath

$load_java

export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"

if [ ! -f "${touchfile3}" ]

then

   echo "***! Statistics q=1 job failed."

   exit 1

fi

if [ -z "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

if [ -z "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools72g pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

then

   touch $touchfile5

elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools72g pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

then

   touch $touchfile5 

fi
@@ -381,18 +385,19 @@ HIC0` 
#SBATCH -e $logdir/hic30-%j.err

#SBATCH -J "${groupname}_hic30"

#SBATCH -d "${dependinter30}"

#SBATCH --mem-per-cpu=32G

#SBATCH --mem=73G

#source $usePath

$load_java	

export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"

if [ ! -f "${touchfile4}" ]

then

   echo "***! Statistics q=30 job failed."

   exit 1

fi

if [ -z "${exclude}" ] &&  ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

if [ -z "${exclude}" ] &&  ${juiceDir}/scripts/juicer_tools72g pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

then

   touch $touchfile6

elif [ -n "${exclude}" ] && ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

elif [ -n "${exclude}" ] && ${juiceDir}/scripts/juicer_tools72g pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

then

   touch $touchfile6

fi
@@ -434,7 +439,7 @@ then 
	   exit 1

	fi

	${load_gpu}

	${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

	${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools72g -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

	touch $touchfile7

	HICCUPS`

	dependhic30="${dependhic30}:$jid7"
@@ -461,7 +466,7 @@ then 
   echo "***! HIC maps q=30 job failed."

   exit 1

fi

${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic

${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools72g -i $outputdir/inter_30.hic

touch $touchfile8

ARROWHEAD`

    dependhic30="${dependhic0}:$jid8"

CRA Git | Maintained and supported by SUSTech CRA and CCSE