java.lang.OutOfMemoryError: Requested array size exceeds VM limit

GitHub | cacampbell | 6 months ago
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Root Cause Analysis

  1. java.lang.OutOfMemoryError

    Requested array size exceeds VM limit

    at java.util.Arrays.copyOf()
  2. Java RT
    StringBuilder.append
    1. java.util.Arrays.copyOf(Arrays.java:3332)
    2. java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
    3. java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121)
    4. java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:421)
    5. java.lang.StringBuilder.append(StringBuilder.java:136)
    5 frames
  3. HTS JDK
    SamReaderFactory$SamReaderFactoryImpl.open
    1. htsjdk.samtools.SAMTextHeaderCodec.advanceLine(SAMTextHeaderCodec.java:131)
    2. htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:86)
    3. htsjdk.samtools.SAMTextReader.readHeader(SAMTextReader.java:200)
    4. htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:63)
    5. htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:73)
    6. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:319)
    7. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145)
    7 frames
  4. picard.sam
    CleanSam.doWork
    1. picard.sam.CleanSam.doWork(CleanSam.java:81)
    1 frame
  5. picard.cmdline
    PicardCommandLine.main
    1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
    2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
    3 frames