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/tmp is failing... 

We should be using hptmp anyways.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1793 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-08 18:13:49 +00:00
parent 15bf014e0b
commit 8461cc3a22
2 changed files with 10 additions and 10 deletions
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8
perl/1kgScripts/runCallingPipeline.pl
View File

@ -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 -Djava.io.tmpdir=/broad/hptmp/ -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 -Djava.io.tmpdir=/broad/hptmp/ -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) {
@ -58,13 +58,13 @@ if ($snps) {
if ($wait) {
$bsub .= " -w \"ended($wait)\"";
}
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 0.0";
$command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 0.0";
execute("$bsub $command", $dry);
my $filterFile = "$outputHead.snps.filtered.calls";
my $vcfFile = "$outputHead.snps.vcf";
$bsub = "bsub -q $queue -o $filterFile.sdout -w \"ended($outputHead)\"";
$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T VariantFiltration -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -vcf $vcfFile -included $filterFile -sample $sample -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod,variant,Variants,$snpsFile,";
$command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T VariantFiltration -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -vcf $vcfFile -included $filterFile -sample $sample -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod,variant,Variants,$snpsFile,";
if ($badsnps) {
$command .= "cleaned,CleanedOutSNP,$badsnps,";
}

12
perl/1kgScripts/runCleaningPipeline.pl
View File

@ -31,7 +31,7 @@ GetOptions( "i=s" => \$inputBam,
usage() if ( !$inputBam || !$outputBam );
my $indelIntervals = "$outputBam.indels.intervals";
my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputBam.intervals -q $queue";
my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputBam.intervals -q $queue";
if ($dry) {
$command .= " -dry";
}
@ -41,7 +41,7 @@ if ($wait) {
system($command);
my $mismatchIntervals = "$outputBam.mismatches.intervals";
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputBam.intervals -q $queue";
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputBam.intervals -q $queue";
if ($dry) {
$command .= " -dry";
}
@ -51,7 +51,7 @@ if ($wait) {
system($command);
my $mergedIntervals = "$outputBam.merged.intervals";
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputBam.intervals -j $outputBam.merged -q $queue";
$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputBam.intervals -j $outputBam.merged -q $queue";
if ($dry) {
$command .= " -dry";
}
@ -63,7 +63,7 @@ if ($inject) {
} else {
$cleanedBam = "$outputBam";
}
$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";
$command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -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.cleaner.clean";
} else {
@ -81,7 +81,7 @@ my $snpsFile = $badsnps;
if (!$snpsFile) {
$snpsFile = "$outputBam.badsnps";
}
$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\"";
$command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
if ($inject) {
$command .= " -j $outputBam.cleaner.badsnps";
} else {
@ -101,7 +101,7 @@ if ($inject) {
if ($jobName) {
$command .= " -J $jobName";
}
$command .= " -w \"ended($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";
$command .= " -w \"ended($outputBam.cleaner.*)\" java -Djava.io.tmpdir=/broad/hptmp/ -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 {