From 6e9b8559d8b733fb32f6cda7d8865151ad70cb2c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 12 Mar 2012 23:20:00 -0400 Subject: [PATCH] Unfortunately need to bump up memory needed for liftover to get Omni file sorted --- .../sting/queue/qscripts/GATKResourcesBundle.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index 804e50421..236516786 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -320,7 +320,7 @@ class GATKResourcesBundle extends QScript { } class LiftOverPerl(@Input val in: File, @Output val out: File, @Input val chain: File, oldRef: Reference, newRef: Reference) extends CommandLineFunction { - this.memoryLimit = 8 + this.memoryLimit = 12 def commandLine = ("%s -vcf %s -chain %s -out %s " + "-gatk ./ -newRef %s -oldRef %s -tmp %s").format(liftOverPerl, in.getAbsolutePath, chain, out.getAbsolutePath, newRef.file.replace(".fasta", ""),