diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 19cd311dc..ad8e8cdd0 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -109,11 +109,11 @@ class MethodsDevelopmentCallingPipeline extends QScript { "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass), "HiSeq19" -> new Target("NA12878.HiSeq19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"), - new File("/humgen/gsa-hpprojects/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"), + new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass), "GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"), - new File("/humgen/gsa-hpprojects/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), + new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass), "WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18_129, hapmap_hg18, "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask", @@ -122,7 +122,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, !lowPass), "WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), - new File("/humgen/gsa-hpprojects/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), + new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass), "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), diff --git a/scala/qscript/oneoffs/carneiro/dataProcessing.scala b/scala/qscript/oneoffs/carneiro/dataProcessing.scala index 4f1297534..37a7cc7fe 100755 --- a/scala/qscript/oneoffs/carneiro/dataProcessing.scala +++ b/scala/qscript/oneoffs/carneiro/dataProcessing.scala @@ -59,7 +59,7 @@ class dataProcessing extends QScript { trait CommandLineGATKArgs extends CommandLineGATK { this.jarFile = qscript.GATKjar this.reference_sequence = qscript.reference - this.memoryLimit = Some(4) + this.memoryLimit = Some(8) this.isIntermediate = true }