htsjdk.samtools.util.RuntimeIOException: java.util.zip.DataFormatException: invalid distance too far back

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via broadinstitute.org by Unknown author, 1 year ago
java.util.zip.DataFormatException: invalid distance too far back
via broadinstitute.org by Unknown author, 1 year ago
via GitHub by jacarey
, 1 year ago
java.util.zip.DataFormatException: invalid block type
via GitHub by akiezun
, 1 year ago
java.util.zip.DataFormatException: invalid distance too far back
htsjdk.samtools.util.RuntimeIOException: java.util.zip.DataFormatException: invalid distance too far back
at java.util.zip.Inflater.inflateBytes(Native Method)
at java.util.zip.Inflater.inflate(Inflater.java:259)
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:402)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:384)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
at java.io.DataInputStream.read(DataInputStream.java:149)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
at htsjdk.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:490)
at htsjdk.samtools.util.BinaryCodec.readInt(BinaryCodec.java:501)
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:177)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:661)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:635)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:629)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:599)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545)
at org.broadinstitute.sv.util.gatk.SVBaseReadWalker.simulateTraversal(SVBaseReadWalker.java:231)
at org.broadinstitute.sv.util.gatk.SVBaseReadWalker.onTraversalDone(SVBaseReadWalker.java:202)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:59)
at org.broadinstitute.sv.metadata.isize.ComputeInsertSizeHistogramsWalker.onTraversalDone(ComputeInsertSizeHistogramsWalker.java:30)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:133)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:87)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:63)

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