java.lang.OutOfMemoryError in RNAseq workspace

Hi,

I have been trying out the new RNAseq pipeline and got an error in one of my samples:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp
[Wed Oct 19 22:40:13 GMT 2016] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/cromwell_root/fc-e2421839-93d5-4ed5-8861-593f00364e54/Homo_sapiens_assembly19.fasta OUTPUT=/cromwell_root/fc-e2421839-93d5-4ed5-8861-593f00364e54/dict8317998367159823769.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Oct 19 22:40:13 GMT 2016] Executing as [email protected] on Linux 3.16.0-0.bpo.4-amd64 amd64; OpenJDK 64-Bit Server VM 1.7.0_95-b00; Picard version: null
[Wed Oct 19 22:40:28 GMT 2016] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.24 minutes.
Runtime.totalMemory()=1602224128
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:2550)
at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:287)
at org.broadinstitute.sting.gatk.datasources.providers.ReferenceView.getReferenceBases(ReferenceView.java:91)
at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView$Provider.getBases(ReadReferenceView.java:62)
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.fetchBasesFromProvider(ReferenceContext.java:145)
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBases(ReferenceContext.java:189)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.countMismatchedBases(CountReadMetricsWalker.java:252)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:155)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:38)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:213)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:220)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:59)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:211)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:162)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:133)

I think the problem might be in the "broadinstitute_gtex/rnaseq_fastq_star_rsem_rnaseqc_v1-0_BETA_cfg" WDL, specifically in the rnaseqc task, where in line 162 it specifies 6G of memory:

"/usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java -Xmx6g -jar /opt/RNA-SeQC_1.1.9/RNA-SeQC.jar -n 1000 \"

Is there any way to fix this myself or can you update the file?

Thank you,
Dan

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