java.lang.RuntimeException

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  • Deflater / Inflater problem, code incl.
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    • java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112) 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 net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619) at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:33) at org.broadinstitute.sting.gatk.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:14) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$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) Caused by: 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) ... 55 more

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