tweaking sort parameters for SLURM. Adding mode in-situ

libraryName="HiC_library"

## Read arguments                                                     

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n                 [-a about] [-S stage] [-p chrom.sizes path] [-C chunk size]\n                 [-y restriction site file] [-z reference genome file]\n                 [-D Juicer scripts parent dir] [-Q queue time limit]\n                 [-L long queue time limit] [-b ligation] [-t threads]\n                 [-T threadsHic] [-A account] [-i sample] [-k library] [-w wobble]\n                 [-e] [-h] [-f] [-j] [-u] [-m] [--assembly] [--cleanup] [--qc_apa] [--qc]"

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n                 [-a about] [-S stage] [-p chrom.sizes path] [-C chunk size]\n                 [-y restriction site file] [-z reference genome file]\n                 [-D Juicer scripts parent dir] [-Q queue time limit]\n                 [-L long queue time limit] [-b ligation] [-t threads]\n                 [-T threadsHic] [-A account] [-i sample] [-k library] [-w wobble]\n                 [-e] [-h] [-f] [-j] [-u] [-m] [--assembly] [--cleanup] [--qc_apa] [--qc] [--in-situ]"

genomeHelp="* [genomeID] must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \n  \"$genomeID\"); alternatively, it can be defined using the -z command"

dirHelp="* [topDir] is the top level directory (default\n  \"$topDir\")\n     [topDir]/fastq must contain the fastq files\n     [topDir]/splits will be created to contain the temporary split files\n     [topDir]/aligned will be created for the final alignment"

queueHelp="* [queue] is the queue for running alignments (default \"$queue\")"

assemblyHelp="* --assembly: For use before 3D-DNA; early exit and create old style merged_nodups"

cleanupHelp="* --cleanup: Automatically clean up files if pipeline successfully completes"

qcapaHelp="* --qc_apa: Run QC APA"

qcHelp="* --qc: Only build map down to 1000bp" 

qcHelp="* --qc: Only build map down to 1000bp, no feature annotation" 

insituHelp="* --in-situ: Only build map down to 1000bp"

helpHelp="* -h, --help: print this help and exit"

printHelpAndExit() {

    echo -e "$cleanupHelp"

    echo -e "$qcapaHelp"

    echo -e "$qcHelp"

    echo -e "$insituHelp"

    echo "$helpHelp"

    exit "$1"

}

	    qc_apa)   qc_apa=1 ;;

	    qc) qc=1 ;;

	    "help")   printHelpAndExit 0;;

	    in-situ) insitu=1 ;;

	    *) echo "Unknown argument --${OPTARG}"; 

	       printHelpAndExit 1;;

           esac;;

    if [ $isRice -eq 1 ]

    then

	threads=8

	sortthreads=8

	threadstring="-t $threads"

	sthreadstring="-@ $threads"

    elif [ $isBCM -eq 1 ]

    elif [ $isVoltron -eq 1 ]

    then

	threads=1

	threadstring="-t $threads"

	sthreadstring="-@ $threads"

    else

	threads=8 # VOLTRON; may need to make this separate and specific for Voltron

	threads=8 

	## On voltron with 8 thread per core Power8 CPU bwa can use more threads

	threadstring="-t \$SLURM_JOB_CPUS_PER_NODE"

	sthreadstring="-@ \$SLURM_JOB_CPUS_PER_NODE"

	sortthreads=8

    else

	# only one thread if undefined; also if isBCM

	threads=1

	sortthreads=1

	threadstring="-t $threads"

	sthreadstring="-@ $threads"

    fi

else

    if [ $isVoltron -eq 1 ]

    then

	threadstring="-t \$SLURM_JOB_CPUS_PER_NODE"

	sthreadstring="-@ \$SLURM_JOB_CPUS_PER_NODE"

	sortthreads=8

    else

	threadstring="-t $threads"

	sthreadstring="-@ $threads"

	sortthreads=$threads

    fi

fi

    userstring="#SBATCH -A $user"

fi

# Add header containing command executed and timestamp:

# Add header containing command executed and timestamp

if [ "$methylation" = 1 ]

then

    queuestring="#SBATCH -p weka"

else

    queuestring="#SBATCH -p $queue"

fi

jid=`sbatch <<- HEADER | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l 

        $userstring

	#SBATCH -p $queue

	$queuestring

	#SBATCH -t 2

	#SBATCH -c 1

	#SBATCH -o $debugdir/head-%j.out

	# Get version numbers of all software

	echo -ne "Juicer version $juicer_version;" 

	bwa 2>&1 | awk '\\\$1=="Version:"{printf(" BWA %s; ", \\\$2)}'

	if [ "$methylation" -eq 1 ]

	if [ "$methylation" = 1 ]

	then

		activate conda

		$call_bwameth --version 2>&1 | awk '{printf("%s; ", \\\$0)}'

	fi

	echo -ne "$threads threads; "

	    # align fastqs

	    jid=`sbatch <<- ALGNR1 | egrep -o -e "\b[0-9]+$"

		#!/bin/bash -l

		#SBATCH -p $queue

		$queuestring

		#SBATCH -o $debugdir/align1-%j.out

		#SBATCH -e $debugdir/align1-%j.err

		#SBATCH -t $queue_time

		dependalign="afterok:$jid"

	    fi

	fi

	jid2=`sbatch <<- MRGALL2 | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p $long_queue

#SBATCH -o $debugdir/mergesort-%j.out

#SBATCH -e $debugdir/mergesort-%j.err

#SBATCH --mem=64G

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

#SBATCH -t $long_queue_time

#SBATCH -c $threads

#SBATCH -c $sortthreads

#SBATCH --ntasks=1

#SBATCH -d $dependalign 

#SBATCH -J "${groupname}_mergesort_${jname}"

$userstring

${load_samtools}

#we should probably set the -m based on memory / num of threads

if time samtools sort -t cb -n -O SAM $sthreadstring -l 0 -m 2G $name$ext.sam3 >  ${name}${ext}.sam

if time samtools sort -t cb -n -O SAM -@ $sortthreads -l 0 -m 2G $name$ext.sam3 >  ${name}${ext}.sam

then

   rm -f $name$ext.sam2 $name$ext.sam3

   touch $touchfile

	  time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged1.txt 500000 > ${outputdir}/merged1_index.txt

	fi

	if [ "$qc" = 1 ]

	if [ "$qc" = 1 ] || [ "$insitu" = 1 ]

	then

	  if [ "$nofrag" -eq 1 ]

	  then 

	  time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged30.txt 500000 > ${outputdir}/merged30_index.txt

	fi

	if [ "$qc" = 1 ]

	if [ "$qc" = 1 ] || [ "$insitu" = 1 ]

	then

          if [ "$nofrag" -eq 1 ]

          then