From 86305a5dcfc058a8a31bb27aaefe2576c993a3aa Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 21 Oct 2011 17:41:52 -0400 Subject: [PATCH] Adjusting the memory limits of the MDCP Indel caller needs more than 3G for large datasets. --- .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index 88c1bd2c8..da02c8ac5 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -205,7 +205,6 @@ class MethodsDevelopmentCallingPipeline extends QScript { // 1.) Unified Genotyper Base class GenotyperBase (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS { - this.memoryLimit = 3 this.reference_sequence = t.reference this.intervalsString ++= List(t.intervals) this.scatterCount = 140 @@ -232,6 +231,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { // 1b.) Call Indels with UG class indelCall (t: Target) extends GenotyperBase(t) { + this.memoryLimit = 6 this.out = t.rawIndelVCF this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF @@ -259,7 +259,6 @@ class MethodsDevelopmentCallingPipeline extends QScript { // 3.) Variant Quality Score Recalibration - Generate Recalibration table class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS { - this.memoryLimit = 4 this.nt = 2 this.reference_sequence = t.reference this.intervalsString ++= List(t.intervals)