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upping mem limit since something was unhappy with the lower limit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4427 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-10-05 02:38:17 +00:00
parent bb44044ce0
commit e340be34d8
1 changed files with 4 additions and 4 deletions
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8
scala/qscript/fullCallingPipeline.q
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@ -61,7 +61,7 @@ class fullCallingPipeline extends QScript {
this.intervals = qscript.pipeline.getProject.getIntervalList this.intervals = qscript.pipeline.getProject.getIntervalList
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.pipeline.getProject.getReferenceFile this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
this.memoryLimit = Some(4) this.memoryLimit = Some(6)
} }
@ -131,7 +131,7 @@ class fullCallingPipeline extends QScript {
realigner.scatterClass = classOf[ContigScatterFunction] realigner.scatterClass = classOf[ContigScatterFunction]
realigner.setupGatherFunction = { realigner.setupGatherFunction = {
case (gather: BamGatherFunction, _) => case (gather: BamGatherFunction, _) =>
gather.memoryLimit = Some(4) gather.memoryLimit = Some(6)
gather.jarFile = qscript.picardFixMatesJar gather.jarFile = qscript.picardFixMatesJar
// Don't pass this AS=true to fix mates! // Don't pass this AS=true to fix mates!
gather.assumeSorted = None gather.assumeSorted = None
@ -141,7 +141,7 @@ class fullCallingPipeline extends QScript {
// Explicitly run fix mates if the function won't be scattered. // Explicitly run fix mates if the function won't be scattered.
fixMates.memoryLimit = Some(4) fixMates.memoryLimit = Some(6)
fixMates.jarFile = qscript.picardFixMatesJar fixMates.jarFile = qscript.picardFixMatesJar
fixMates.unfixed = realigner.out fixMates.unfixed = realigner.out
fixMates.fixed = cleaned_bam fixMates.fixed = cleaned_bam
@ -279,7 +279,7 @@ class fullCallingPipeline extends QScript {
clusters.DBSNP = qscript.pipeline.getProject.getDbsnpFile clusters.DBSNP = qscript.pipeline.getProject.getDbsnpFile
val clusters_clusterFile = swapExt(new File(snps.out.getAbsolutePath),".vcf",".cluster") val clusters_clusterFile = swapExt(new File(snps.out.getAbsolutePath),".vcf",".cluster")
clusters.clusterFile = clusters_clusterFile clusters.clusterFile = clusters_clusterFile
clusters.memoryLimit = Some(4) clusters.memoryLimit = Some(6)
clusters.jobQueue = "gsa" clusters.jobQueue = "gsa"
clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")