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Bug Fixes
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@rhshah
rhshah committed Feb 18, 2016
1 parent 83a9d87 commit bdd5699
Showing 1 changed file with 14 additions and 14 deletions.
28 changes: 14 additions & 14 deletions bin/RunIlluminaProcess.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -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 "$outdir/Notify.csh"`;
}
};
if ($@) {
Expand All @@ -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" );
}
}
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