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

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via biostars.org by Unknown author, 1 year ago
java.util.zip.DataFormatException: invalid stored block lengths
via sourceforge.net by Unknown author, 1 year ago
java.util.zip.DataFormatException: invalid distance too far back
java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths
at java.util.zip.Inflater.inflateBytes(Native Method)
at java.util.zip.Inflater.inflate(Inflater.java:238)
at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:379)
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at java.io.DataInputStream.read(DataInputStream.java:132)
at net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
at net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
at net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:176)
at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:519)
at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:626)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:493)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:483)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:449)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641)
at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:33)
at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:14)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.advance(SAMDataSource.java:1023)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:1004)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$IntervalOverlapFilteringIterator.next(SAMDataSource.java:936)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:126)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:921)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:887)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState$ReadStateManager.collectPendingReads(LocusIteratorByState.java:627)
at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:339)
at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.hasNext(LocusIteratorByState.java:309)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:70)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:156)
at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:125)
at org.broadinstitute.sting.gatk.datasources.providers.LocusView.advance(LocusView.java:151)
at org.broadinstitute.sting.gatk.datasources.providers.LocusView.hasNextLocus(LocusView.java:117)
at org.broadinstitute.sting.gatk.datasources.providers.CoveredLocusView.hasNext(CoveredLocusView.java:32)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:50)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)

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