Touchfile in chimeric needs to be set. Flags added to samtools sort -... (2e3e773f) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+4 −4

Changes for SLURM/scripts/juicer.sh: 4 added lines, 4 removed lines.
Original line number	Diff line number	Diff line
		@@ -735,7 +735,7 @@ SPLITEND`
		else
		rg="@RG\\tID:${jname%.fastq*}\\tSM:${sampleName}\\tPL:ILM\\tLB:${libraryName}"
		fi

		touchfile=${tmpdir}/${jname}
		if [ -z "$chimeric" ]
		then
		usegzip=0
		@@ -743,7 +743,6 @@ SPLITEND`
		then
		usegzip=1
		fi
		touchfile=${tmpdir}/${jname}

		# count ligations
		jid=`sbatch <<- CNTLIG \| egrep -o -e "\b[0-9]+$"
		@@ -939,7 +938,7 @@ MRGALL3`
		#SBATCH -p $long_queue
		#SBATCH -o $debugdir/mergesort-%j.out
		#SBATCH -e $debugdir/mergesort-%j.err
		#SBATCH --mem=50G
		#SBATCH --mem=64G
		#SBATCH -t $long_queue_time
		#SBATCH -c $threads
		#SBATCH --ntasks=1
		@@ -948,7 +947,8 @@ MRGALL3`
		#SBATCH --threads-per-core=1
		$userstring
		${load_samtools}
		if time samtools sort -t cb -n -O SAM $sthreadstring $name$ext.sam3 > ${name}${ext}.sam
		#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
		then
		rm -f $name$ext.sam2 $name$ext.sam3
		touch $touchfile