java.lang.OutOfMemoryError: Java heap space

usegalaxy.org | 5 months ago
  1. 0

    Error java.lang.OutOfMemoryError: Java heap space on GATK Count Covariates

    usegalaxy.org | 5 months ago
    java.lang.OutOfMemoryError: Java heap space
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Root Cause Analysis

  1. java.lang.OutOfMemoryError

    Java heap space

    at java.util.Arrays.copyOf()
  2. Java RT
    ArrayList.add
    1. java.util.Arrays.copyOf(Unknown Source)
    2. java.util.ArrayList.grow(Unknown Source)
    3. java.util.ArrayList.ensureExplicitCapacity(Unknown Source)
    4. java.util.ArrayList.ensureCapacityInternal(Unknown Source)
    5. java.util.ArrayList.add(Unknown Source)
    5 frames
  3. picard
    IndexFactory.createIndex
    1. org.broad.tribble.index.linear.LinearIndex$ChrIndex.addBlock(LinearIndex.java:161)
    2. org.broad.tribble.index.linear.LinearIndexCreator.addFeature(LinearIndexCreator.java:46)
    3. org.broad.tribble.index.DynamicIndexCreator.addFeature(DynamicIndexCreator.java:159)
    4. org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:136)
    5. org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:123)
    5 frames
  4. org.broadinstitute.sting
    CommandLineGATK.main
    1. org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:361)
    2. org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:258)
    3. org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:199)
    4. org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:128)
    5. org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:205)
    6. org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:85)
    7. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:783)
    8. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:653)
    9. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:212)
    10. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
    11. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    12. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    13. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
    13 frames