htsjdk.samtools.FileTruncatedException: Premature end of file

broadinstitute.org | 5 months ago
  1. 0

    GATK | GATK | Tagged #indelrealigner

    broadinstitute.org | 6 months ago
    htsjdk.samtools.FileTruncatedException: Premature end of file
  2. 0

    erroneous bam file from indel realigner — GATK-Forum

    broadinstitute.org | 5 months ago
    htsjdk.samtools.FileTruncatedException: Premature end of file
  3. 0

    vcf corrupt

    GitHub | 1 year ago | dwaggott
    htsjdk.samtools.FileTruncatedException: Premature end of file
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    Root Cause Analysis

    1. htsjdk.samtools.FileTruncatedException

      Premature end of file

      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock()
    2. HTS JDK
      BlockCompressedInputStream.read
      1. htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:382)
      2. htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
      3. htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
      3 frames
    3. Java RT
      DataInputStream.read
      1. java.io.DataInputStream.read(DataInputStream.java:149)
      1 frame
    4. HTS JDK
      BAMIndexer.createIndex
      1. htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
      2. htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
      3. htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366)
      4. htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:199)
      5. htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:660)
      6. htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:634)
      7. htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628)
      8. htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598)
      9. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:527)
      10. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:501)
      11. htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:287)
      12. htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:271)
      12 frames
    5. picard.sam
      BuildBamIndex.doWork
      1. picard.sam.BuildBamIndex.doWork(BuildBamIndex.java:138)
      1 frame
    6. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames