htsjdk.samtools.FileTruncatedException

Premature end of file

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  • Stack trace

    • htsjdk.samtools.FileTruncatedException: Premature end of file at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:382) 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.readBytes(BinaryCodec.java:366) at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:199) at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:660) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:634) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:527) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:501) at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:287) at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:271) at picard.sam.BuildBamIndex.doWork(BuildBamIndex.java:138) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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