java.lang.OutOfMemoryError: GC overhead limit exceeded

broadinstitute.org | 2 months ago
  1. 0

    Picard SamToFastq problem : Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit - GATK-Forum

    broadinstitute.org | 11 months ago
    java.lang.OutOfMemoryError: GC overhead limit exceeded
  2. Speed up your debug routine!

    Automated exception search integrated into your IDE

  3. 0

    GitHub comment 572#246607309

    GitHub | 3 months ago | car2008
    java.lang.OutOfMemoryError: GC overhead limit exceeded

    Not finding the right solution?
    Take a tour to get the most out of Samebug.

    Tired of useless tips?

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      GC overhead limit exceeded

      at htsjdk.samtools.BinaryTagCodec.readNullTerminatedString()
    2. HTS JDK
      SAMRecord.getReadGroup
      1. htsjdk.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:414)
      2. htsjdk.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318)
      3. htsjdk.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282)
      4. htsjdk.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308)
      5. htsjdk.samtools.BAMRecord.getAttribute(BAMRecord.java:288)
      6. htsjdk.samtools.SAMRecord.getReadGroup(SAMRecord.java:691)
      6 frames
    3. picard.sam
      SamToFastq.doWork
      1. picard.sam.SamToFastq.doWork(SamToFastq.java:166)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames