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rename some jobnames so that LSF doesn't complain 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1657 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-18 19:02:15 +00:00
parent 83e6e5a3e4
commit d9ee515a9b
5 changed files with 14 additions and 14 deletions
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4
perl/1kgScripts/runCallingPipeline.pl
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@ -41,7 +41,7 @@ my $bsub = "bsub -q $queue -o $indelsHigh.sdout";
if ($wait) {
$bsub .= " -w \"ended($wait)\"";
}
my $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -o $indelsHigh";
my $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -O $indelsHigh";
execute("$bsub $command", $dry);
my $indelsLow = "$outputHead.indels.low.calls";
@ -49,7 +49,7 @@ $bsub = "bsub -q $queue -o $indelsLow.sdout -J $outputHead";
if ($wait) {
$bsub .= " -w \"ended($wait)\"";
}
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -o $indelsLow";
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -O $indelsLow";
execute("$bsub $command", $dry);
if ($snps) {

6
perl/1kgScripts/runCleaningPipeline.pl
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@ -65,7 +65,7 @@ if ($inject) {
}
$command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
if ($inject) {
$command .= " -cleanedOnly\" -j $outputBam.cleaned";
$command .= " -cleanedOnly\" -j $outputBam.cleaner.clean";
} else {
$command .= "\" -j $jobName";
}
@ -83,7 +83,7 @@ if (!$snpsFile) {
}
$command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
if ($inject) {
$command .= " -j $outputBam.cleaned";
$command .= " -j $outputBam.cleaner.badsnps";
} else {
$command .= " -j $jobName";
}
@ -101,7 +101,7 @@ if ($inject) {
if ($jobName) {
$command .= " -J $jobName";
}
$command .= " -w \"ended($outputBam.cleaned)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
$command .= " -w \"ended($outputBam.cleaner.*)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
if ($dry) {
print "$command\n";
} else {

4
perl/1kgScripts/runPilot1Pipeline.pl
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@ -31,7 +31,7 @@ foreach my $sample (@samples) {
my $outputBam = "$outputHead.bam";
my $badsnps = "$outputBam.badsnps";
clean($inputBam, $outputBam, $queue, $sting, $dry, $badsnps);
call("-I $outputBam", $outputHead, $queue, $sting, $dry, "$inputBam.cleaningpipeline", $sample, $badsnps);
call("-I $outputBam", $outputHead, $queue, $sting, $dry, "$inputBam.cleaner.*", $sample, $badsnps);
}
sub clean {
@ -43,7 +43,7 @@ sub clean {
my $dry = $_[4];
my $badsnps = $_[5];
my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -j $outputBam.cleaningpipeline -sting $sting -badsnps $badsnps";
my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -j $outputBam.cleaner.pipeline -sting $sting -badsnps $badsnps";
if ($dry) {
$cmd .= " -dry";
}

10
perl/1kgScripts/runPilot2Pipeline.pl
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@ -46,7 +46,7 @@ foreach my $sample (@samples) {
my $outputBamSLX = "$outputHeadSLX.bam";
my $badsnpsSLX = "$outputBamSLX.badsnps";
clean($inputBamSLX, $outputBamSLX, $queue, $sting, $dry, $badsnpsSLX);
call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$inputBamSLX.cleaningpipeline", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$outputBamSLX.cleaner.*", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
if ($sample eq "NA12878" || $sample eq "NA19240") {
my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
@ -54,17 +54,17 @@ foreach my $sample (@samples) {
my $outputBamSOLID = "$outputHeadSOLID.bam";
my $badsnpsSOLID = "$outputBamSOLID.badsnps";
clean($inputBamSOLID, $outputBamSOLID, $queue, $sting, $dry, $badsnpsSOLID);
call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$inputBamSOLID.cleaningpipeline", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});
call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});
my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
my $outputHead454 = "$outputDir/$sample.454";
call("-I $inputBam454", $outputHead454, $queue, $sting, $dry, undef, $sample, $badsnpsSLX, $DoC_454{$sample}, $MQ_hash{"454"});
my $outputHead = "$outputDir/$sample.SOLID_454";
call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$inputBamSOLID.cleaningpipeline", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});
call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});
$outputHead = "$outputDir/$sample.allTechs";
call("-I $outputBamSLX -I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "*.cleaningpipeline", $sample, $badsnpsSLX, $DoC_all{$sample}, $MQ_hash{"ALL"});
call("-I $outputBamSLX -I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "*.cleaner.*", $sample, $badsnpsSLX, $DoC_all{$sample}, $MQ_hash{"ALL"});
}
}
@ -77,7 +77,7 @@ sub clean {
my $dry = $_[4];
my $badsnps = $_[5];
my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -inject -j $outputBam.cleaningpipeline -sting $sting -badsnps $badsnps";
my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -inject -j $outputBam.cleaner.pipeline -sting $sting -badsnps $badsnps";
if ($dry) {
$cmd .= " -dry";
}

4
perl/splitAndEnqueueGATKjobs.pl
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@ -128,11 +128,11 @@ sub mergeResults {
$cmd .= "$output.$i.bam ";
}
} else {
$cmd .= " cat ";
$cmd .= " \"cat ";
for (my $i = 1; $i <= $intervalcount; $i++) {
$cmd .= "$output.$i ";
}
$cmd .= "> $output";
$cmd .= "> $output\"";
}
execute($cmd, $dry);