adjusting the ordering of the stats jobs to be correct; eliminating the stats on the dups (39ceb9f0) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+33 −12

Changes for SLURM/scripts/juicer.sh: 33 added lines, 12 removed lines.
Original line number	Diff line number	Diff line
		@@ -282,6 +282,7 @@ if [ -z "$ligation" ]; then
		DpnII) ligation="GATCGATC";;
		MboI) ligation="GATCGATC";;
		NcoI) ligation="CCATGCATGG";;
		MboI+HindIII) ligation="'(GATCGATC\|AAGCTAGCTT)'";;
		none) ligation="XXXX";;
		*) ligation="XXXX"
		echo "$site not listed as recognized enzyme. Using $site_file as site file"
		@@ -1076,6 +1077,33 @@ if [ -z $postproc ]
		date
		DUPCHECK`
		sbatch_wait="#SBATCH -d afterok:$jid"

		jid=`sbatch <<- PRESTATS \| egrep -o -e "\b[0-9]+$"
		#!/bin/bash -l
		#SBATCH -p $queue
		#SBATCH -o $debugdir/prestats-%j.out
		#SBATCH -e $debugdir/prestats-%j.err
		#SBATCH -t $queue_time
		#SBATCH -c 1
		#SBATCH --ntasks=1
		#SBATCH --mem-per-cpu=1G
		#SBATCH -J "${groupname}_prestats"
		${sbatch_wait}
		$userstring

		date
		${load_java}
		export IBM_JAVA_OPTIONS="-Xmx1024m -Xgcthreads1"
		export _JAVA_OPTIONS="-Xmx1024m -Xms1024m"

		tail -n1 $headfile \| awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt
		cat $splitdir/*.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt
		${juiceDir}/scripts/juicer_tools LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt
		cp $outputdir/inter.txt $outputdir/inter_30.txt
		date
		PRESTATS`

		sbatch_wait0="#SBATCH -d afterok:$jid"
		jid=`sbatch <<- STATS \| egrep -o -e "\b[0-9]+$"
		#!/bin/bash -l
		#SBATCH -p $long_queue
		@@ -1086,7 +1114,7 @@ DUPCHECK`
		#SBATCH --ntasks=1
		#SBATCH --mem=25G
		#SBATCH -J "${groupname}_stats"
		${sbatch_wait}
		${sbatch_wait0}
		$userstring

		date
		@@ -1095,20 +1123,12 @@ DUPCHECK`
		echo "***! Found errorfile. Exiting."
		exit 1
		fi
		${load_java}
		export IBM_JAVA_OPTIONS="-Xmx16384m -Xgcthreads1"
		export _JAVA_OPTIONS="-Xmx16384m -Xms16384m"
		tail -n1 $headfile \| awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt

		${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt
		cat $splitdir/*.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt
		${juiceDir}/scripts/juicer_tools LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt
		cp $outputdir/inter.txt $outputdir/inter_30.txt
		${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt

		date
		STATS`
		sbatch_wait1="#SBATCH -d afterok:$jid"

		dependstats="afterok:$jid"
		jid=`sbatch <<- STATS30 \| egrep -o -e "\b[0-9]+$"
		#!/bin/bash -l
		@@ -1120,7 +1140,7 @@ STATS`
		#SBATCH --ntasks=1
		#SBATCH --mem=25G
		#SBATCH -J "${groupname}_stats"
		${sbatch_wait}
		${sbatch_wait0}
		$userstring

		${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt
		@@ -1128,7 +1148,8 @@ STATS`
		STATS30`

		dependstats30="afterok:$jid"

		sbatch_wait1="${sbatch_wait1}:$jid"
		# This job is waiting on deduping, thus sbatch_wait (vs sbatch_wait0 or 1)
		jid=`sbatch <<- CONCATFILES \| egrep -o -e "\b[0-9]+$"
		#!/bin/bash -l
		#SBATCH -p $long_queue

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