htsjdk.samtools.util.RuntimeIOException

java.util.zip.DataFormatException: invalid distance too far back

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    • htsjdk.samtools.util.RuntimeIOException: java.util.zip.DataFormatException: invalid distance too far back at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112) at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:410) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:392) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:260) 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$BAMFileIterator.getNextRecord(BAMFileReader.java:682) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:656) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:650) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:620) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:519) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:409) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:193) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Caused by: 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) ... 21 more

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