From bdd569945ea74c81e8178333dbf1c4e2e0092e4e Mon Sep 17 00:00:00 2001 From: Ronak H Shah Date: Thu, 18 Feb 2016 12:10:32 -0500 Subject: [PATCH] Bug Fixes --- bin/RunIlluminaProcess.pl | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/bin/RunIlluminaProcess.pl b/bin/RunIlluminaProcess.pl index 6231bbb..41e9d19 100644 --- a/bin/RunIlluminaProcess.pl +++ b/bin/RunIlluminaProcess.pl @@ -1907,35 +1907,35 @@ sub MergeDataFromDirectory { if ( $CLUSTER eq "SGE" ) { my $cmd = -"$QSUB -q $queue -V -wd $outdir -N MergeRead1.$newIndex.$sampleNum.$$ -e MergeRead1.$newIndex.$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y \"$ZCAT $read1ListName | gzip > $read1Name\""; +"$QSUB -q $queue -V -wd $outdir -N MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y \"$ZCAT $read1ListName | gzip > $read1Name\""; $logger->debug("COMMAND: $cmd"); #Read1 -`$QSUB -q $queue -V -wd $outdir -N MergeRead1.$newIndex.$sampleNum.$$ -e MergeRead1.$newIndex.$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$ZCAT $read1ListName | gzip > $read1Name"`; -`$QSUB -q $queue -V -wd $outdir -hold_jid MergeRead1.$newIndex.$sampleNum.$$ -N NotifyMR.Read1.$sampleNum.$$ -e NotifyMR.Read1.$sampleNum.$$.stderr -o NotifyMR.Read1.$sampleNum.$$.stat -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$outdir/Notify.csh"`; +`$QSUB -q $queue -V -wd $outdir -N MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$ZCAT $read1ListName | gzip > $read1Name"`; +`$QSUB -q $queue -V -wd $outdir -hold_jid MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -N NotifyMR.Read1.$sampleNum.$$ -e NotifyMR.Read1.$sampleNum.$$.stderr -o NotifyMR.Read1.$sampleNum.$$.stat -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$outdir/Notify.csh"`; $cmd = -"$QSUB -q $queue -V -wd $outdir -N MergeRead2.$newIndex.$sampleNum.$$ -e MergeRead2.$newIndex.$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y \"$ZCAT $read2ListName | gzip > $read2Name\""; +"$QSUB -q $queue -V -wd $outdir -N MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y \"$ZCAT $read2ListName | gzip > $read2Name\""; $logger->debug("COMMAND: $cmd"); #Read2 -`$QSUB -q $queue -V -wd $outdir -N MergeRead2.$newIndex.$sampleNum.$$ -e MergeRead2.$newIndex.$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$ZCAT $read2ListName | gzip > $read2Name"`; -`$QSUB -q $queue -V -wd $outdir -hold_jid MergeRead2.$newIndex.$sampleNum.$$ -N NotifyMR.Read2.$sampleNum.$$ -e NotifyMR.Read2.$sampleNum.$$.stderr -o NotifyMR.Read2.$sampleNum.$$.stat -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$outdir/Notify.csh"`; +`$QSUB -q $queue -V -wd $outdir -N MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -o /dev/null -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$ZCAT $read2ListName | gzip > $read2Name"`; +`$QSUB -q $queue -V -wd $outdir -hold_jid MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -N NotifyMR.Read2.$sampleNum.$$ -e NotifyMR.Read2.$sampleNum.$$.stderr -o NotifyMR.Read2.$sampleNum.$$.stat -l h_vmem=2G,virtual_free=2G -pe smp 1 -b y "$outdir/Notify.csh"`; } else { #Read1 my $cmd = -"$BSUB -q $queue -cwd $outdir -J MergeRead1.$newIndex.$sampleNum.$$ -e MergeRead1.$newIndex.$sampleNum.$$.stderr -R \"rusage[mem=2]\" -M 4 -n 1 \"$ZCAT $read1ListName | gzip > $read1Name\""; +"$BSUB -q $queue -cwd $outdir -J MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -R \"rusage[mem=2]\" -M 4 -n 1 \"$ZCAT $read1ListName | gzip > $read1Name\""; $logger->debug("COMMAND: $cmd"); -`$BSUB -q $queue -cwd $outdir -J MergeRead1.$newIndex.$sampleNum.$$ -e MergeRead1.$newIndex.$sampleNum.$$.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$ZCAT $read1ListName | gzip > $read1Name"`; -`$BSUB -q $queue -cwd $outdir -w "post_done(MergeRead1.$newIndex.$sampleNum.$$)" -J MergeRead1.$newIndex.$sampleNum.$$ -e NotifyMR.Read1.$sampleNum.$$.%J.stderr -o NotifyMR.Read1.$sampleNum.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh"`; +`$BSUB -q $queue -cwd $outdir -J MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$ZCAT $read1ListName | gzip > $read1Name"`; +`$BSUB -q $queue -cwd $outdir -w "post_done(MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$)" -J MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$ -e NotifyMR.Read1.$sampleNum.$$.%J.stderr -o NotifyMR.Read1.$sampleNum.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh"`; #Read2 $cmd = -"$BSUB -q $queue -cwd $outdir -J MergeRead2.$newIndex.$sampleNum.$$ -e MergeRead2.$newIndex.$sampleNum.$$.stderr -R \"rusage[mem=2]\" -M 4 -n 1 \"$ZCAT $read2ListName | gzip > $read2Name\""; +"$BSUB -q $queue -cwd $outdir -J MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -R \"rusage[mem=2]\" -M 4 -n 1 \"$ZCAT $read2ListName | gzip > $read2Name\""; $logger->debug("COMMAND: $cmd"); -`$BSUB -q $queue -cwd $outdir -J MergeRead2.$newIndex.$sampleNum.$$ -e MergeRead2.$newIndex.$sampleNum.$$.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$ZCAT $read2ListName | gzip > $read2Name"`; -`$BSUB -q $queue -cwd $outdir -w "post_done(MergeRead2.$newIndex.$sampleNum.$$)" -J MergeRead2.$newIndex.$sampleNum.$$ -e NotifyMR.Read2.$sampleNum.$$.%J.stderr -o NotifyMR.Read2.$sampleNum.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh"`; +`$BSUB -q $queue -cwd $outdir -J MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -e MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$.stderr -We 0:59 -R "rusage[mem=2]" -M 4 -n 1 "$ZCAT $read2ListName | gzip > $read2Name"`; +`$BSUB -q $queue -cwd $outdir -w "post_done(MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$)" -J MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$ -e NotifyMR.Read2.$sampleNum.$$.%J.stderr -o NotifyMR.Read2.$sampleNum.$$.stat -We 0:59 -R "rusage[mem=2]" -R "rusage[iounits=0]" -M 4 -n 1 "$outdir/Notify.csh"`; } }; if ($@) { @@ -1944,10 +1944,10 @@ sub MergeDataFromDirectory { } push( @notifyNames, "NotifyMR.Read1.$sampleNum.$$.stat" ); push( @checkErrorFiles, - "MergeRead1.$newIndex.$sampleNum.$$.err" ); + "MergeRead1.$titleBarcode[$sampleNum].$sampleNum.$$.err" ); push( @notifyNames, "NotifyMR.Read2.$sampleNum.$$.stat" ); push( @checkErrorFiles, - "MergeRead2.$newIndex.$sampleNum.$$.err" ); + "MergeRead2.$titleBarcode[$sampleNum].$sampleNum.$$.err" ); push( @parseFilenames, "$read1Name,$read2Name" ); } }