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CombineGVCFs (gatk- tool throwing java memory error despite high memory provided

AlvaAlva SwitzerlandMember ✭✭
edited July 22 in Ask the GATK team

Dear All,

I am runinng CombineGVCFs tool for combining 310 gvf files. Initially when I ran the command line as following (without java-options),

            export PATH=$PATH:/cluster/work/grlab/share/software/gatk-
            export PATH=/usr/bin:$PATH
            module load jdk
            gatk CombineGVCFs -R $reference $mergefiles -O ${outdir}/${outid}.g.vcf.gz > ${outdir}/${outid}.gatk.log 2>&1 && touch ${outdir}/${outid}.gvcf.done

It threw the following error message,

A fatal error has been detected by the Java Runtime Environment:
#  SIGSEGV (0xb) at pc=0x00002abde45fb02e, pid=50102, tid=0x00002abde30da280
# JRE version: Java(TM) SE Runtime Environment (8.0_172-b11) (build 1.8.0_172-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.172-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V  []  SR_handler(int, siginfo*, ucontext*)+0x3e
# Core dump written. Default location: /cluster/work/grlab/projects/tmp_alva/test_wxs_aml/scripts/core or core.50102
# An error report file with more information is saved as:
# /cluster/work/grlab/projects/tmp_alva/test_wxs_aml/scripts/hs_err_pid50102.log
# If you would like to submit a bug report, please visit:

Then in the second run, I tried with java-options as following,

gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC' CombineGVCFs -R $reference $mergefiles -O ${outdir}/${outid}.g.vcf.gz && touch ${outdir}/${outid}.gvcf.done

From the second run (above command) I am getting the following error,

10:21:44.374 INFO  CombineGVCFs - Shutting down engine
[July 22, 2019 10:21:48 AM CEST] done. Elapsed time: 2.30 minutes.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at htsjdk.tribble.readers.TabixReader.readIndex(
    at htsjdk.tribble.readers.TabixReader.readIndex(
    at htsjdk.tribble.readers.TabixReader.<init>(
    at htsjdk.tribble.readers.TabixReader.<init>(
    at htsjdk.tribble.TabixFeatureReader.<init>(
    at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(
    at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(
    at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(
    at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(
    at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$initializeDrivingVariants$0(
    at org.broadinstitute.hellbender.engine.MultiVariantWalker$$Lambda$58/1622066826.accept(Unknown Source)
    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(
    at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(
    at org.broadinstitute.hellbender.engine.GATKTool.onStartup(
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(
    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.runCommandLineProgram(
    at org.broadinstitute.hellbender.Main.mainEntry(
    at org.broadinstitute.hellbender.Main.main(

Any clue/ suggestions would help go forward with the step. Thank you!!

Best Answer


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