java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths

biostars.org | 3 months ago
  1. 0

    Gatk Error

    biostars.org | 3 months ago
    java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths
  2. 0

    SAM tools / Mailing Lists

    sourceforge.net | 4 months ago
    java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back
  3. 0

    Gzip.gunzip throws java.util.zip.DataFormatException: invalid stored block lengths

    GitHub | 2 years ago | Holmyara
    java.util.zip.DataFormatException: invalid stored block lengths
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  5. 0

    Netty throws exception when using SSL and a compression codec together

    Stack Overflow | 2 years ago
    io.netty.handler.codec.compression.DecompressionException: decompression failure
  6. 0

    Deflater / Inflater problem...

    Google Groups | 2 decades ago | Marek J Radacz
    java.util.zip.DataFormatException: invalid stored block lengths

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    Root Cause Analysis

    1. java.util.zip.DataFormatException

      invalid stored block lengths

      at java.util.zip.Inflater.inflateBytes()
    2. Java RT
      Inflater.inflate
      1. java.util.zip.Inflater.inflateBytes(Native Method)
      2. java.util.zip.Inflater.inflate(Inflater.java:238)
      2 frames
    3. picard
      BlockCompressedInputStream.read
      1. net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
      2. net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:379)
      3. net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
      4. net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
      5. net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
      5 frames
    4. Java RT
      DataInputStream.read
      1. java.io.DataInputStream.read(DataInputStream.java:132)
      1 frame
    5. picard
      SAMFileReader$AssertableIterator.next
      1. net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
      2. net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
      3. net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
      4. net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
      5. net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:176)
      6. net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:519)
      7. net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:626)
      8. net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:493)
      9. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:483)
      10. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:449)
      11. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641)
      12. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619)
      12 frames
    6. org.broadinstitute.sting
      SAMDataSource$IntervalOverlapFilteringIterator.next
      1. org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:33)
      2. org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:14)
      3. org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.advance(SAMDataSource.java:1023)
      4. org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:1004)
      5. org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:936)
      5 frames
    7. picard
      MergingSamRecordIterator.next
      1. net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
      2. net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
      3. net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:126)
      4. net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39)
      4 frames
    8. org.broadinstitute.sting
      PrivateStringSAMCloseableIterator.next
      1. org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
      2. org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
      3. org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:921)
      4. org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:887)
      5. org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105)
      6. org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81)
      7. org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41)
      8. org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
      9. org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
      9 frames
    9. picard
      PeekableIterator.next
      1. net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
      2. net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
      2 frames
    10. org.broadinstitute.sting
      LocusIteratorByState.hasNext
      1. org.broadinstitute.sting.gatk.iterators.LocusIteratorByState$ReadStateManager.collectPendingReads(LocusIteratorByState.java:627)
      2. org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:339)
      3. org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.hasNext(LocusIteratorByState.java:309)
      3 frames
    11. picard
      PeekableIterator.next
      1. net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:70)
      2. net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
      2 frames
    12. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:156)
      2. org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:125)
      3. org.broadinstitute.sting.gatk.datasources.providers.LocusView.advance(LocusView.java:151)
      4. org.broadinstitute.sting.gatk.datasources.providers.LocusView.hasNextLocus(LocusView.java:117)
      5. org.broadinstitute.sting.gatk.datasources.providers.CoveredLocusView.hasNext(CoveredLocusView.java:32)
      6. org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:50)
      7. org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
      8. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
      9. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233)
      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