java.lang.OutOfMemoryError: GC overhead limit exceeded

usegalaxy.org | 8 months ago
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  1. 0

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

    usegalaxy.org | 8 months ago
    java.lang.OutOfMemoryError: GC overhead limit exceeded

    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      GC overhead limit exceeded

      at org.broad.tribble.index.linear.LinearIndexCreator.addFeature()
    2. picard
      IndexFactory.createIndex
      1. org.broad.tribble.index.linear.LinearIndexCreator.addFeature(LinearIndexCreator.java:58)
      2. org.broad.tribble.index.DynamicIndexCreator.addFeature(DynamicIndexCreator.java:159)
      3. org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:136)
      4. org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:123)
      4 frames
    3. 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