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"GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" running out of memory

jjiaojjiao Member, Broadie

Some of my samples on Firehose running the task "GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" failed due to what seems like memory errors. An example error log is below:

Picked up JAVA_TOOL_OPTIONS: -Xmx1g -DR_HOME=/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_2.10.1
[October 12, 2016 2:24:51 PM EDT] --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta --normal /seq/picard_aggregation/RP-945/Exome/115WB_2-11-15/v2/115WB_2-11-15.bam --tumor /seq/picard_aggregation/RP-945/Exome/115A_3-18-14/v1/115A_3-18-14.bam --snpIntervals /xchip/tcga/Tools/gatk4cnv/allchr.1kg.phase3.v5a.snp.maf10.biallelic.recode.fixed.prune5.interval_list --normalHets 115T-TP-NB-SM-A2WOM-SM-A3PYW.normal.hets.tsv --tumorHets 115T-TP-NB-SM-A2WOM-SM-A3PYW.tumor.hets.tsv --readDepthThreshold 15 --minimumMappingQuality 30 --minimumBaseQuality 20 --hetCallingStringency 30.0 --minimumAbnormalFraction 0.8 --maximumAbnormalFraction 0.9 --maximumCopyNumber 2 --quadratureOrder 200 --errorAdjustmentFactor 1.0 --VALIDATION_STRINGENCY SILENT --help false --version false --verbosity INFO --QUIET false
[October 12, 2016 2:24:51 PM EDT] Executing as [email protected] on Linux 2.6.32-573.18.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14; Version: Version:version-unknown-SNAPSHOT
[October 12, 2016 9:27:09 PM EDT] done. Elapsed time: 422.31 minutes.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(
at java.util.ArrayList.grow(
at java.util.ArrayList.ensureExplicitCapacity(
at java.util.ArrayList.ensureCapacityInternal(
at java.util.ArrayList.addAll(
at htsjdk.samtools.BAMFileSpan.merge(
at htsjdk.samtools.BAMFileReader.createIndexIterator(
at htsjdk.samtools.BAMFileReader.query(
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(
at htsjdk.samtools.util.SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(
at htsjdk.samtools.util.SamLocusIterator.iterator(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.instanceMain(
at org.broadinstitute.hellbender.Main.main(

"Reserved Disk Space" doesn't seem to be a field I can modify. Is there a task config somewhere where I can modify the amount of memory reserved for this task?

I looked at the task author and it says "gatkforums". Please let me know if I should be posting this elsewhere. Thanks!



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