java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back

sourceforge.net | 6 months ago
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    SAM tools / Mailing Lists

    sourceforge.net | 6 months ago
    java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back
  2. 0

    “java.lang.NegativeArraySizeException” when I run gatk_AddorReplaceReadgroups - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -667232877
  3. 0

    “java.lang.NegativeArraySizeException” when I run picard_AddorReplaceReadgroups [Archive] - SEQanswers

    seqanswers.com | 4 months ago
    java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -667232877
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    Root Cause Analysis

    1. java.lang.RuntimeException

      java.util.zip.DataFormatException: invalid distance too far back

      at net.sf.samtools.util.BlockGunzipper.unzipBlock()
    2. picard
      BlockCompressedInputStream.read
      1. net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112)
      2. net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:320)
      3. net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:302)
      4. net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:106)
      5. net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:175)
      5 frames
    3. Java RT
      DataInputStream.read
      1. java.io.DataInputStream.read(DataInputStream.java:149)
      1 frame
    4. picard
      AddOrReplaceReadGroups.main
      1. net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
      2. net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
      3. net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
      4. net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
      5. net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:159)
      6. net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:486)
      7. net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460)
      8. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
      9. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
      10. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
      11. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
      12. net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:91)
      13. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:169)
      14. net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
      15. net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
      15 frames