net.sf.samtools.util.RuntimeIOException

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    • net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: stdout at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199) at net.sf.samtools.util.BinaryCodec.writeByteBuffer(BinaryCodec.java:165) at net.sf.samtools.util.BinaryCodec.writeByte(BinaryCodec.java:176) at net.sf.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:262) at net.sf.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:239) at net.sf.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:146) at java.io.DataOutputStream.write(DataOutputStream.java:107) at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197) at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189) at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:120) at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:101) at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:155) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150) at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) Caused by: java.io.IOException: Broken pipe at java.io.FileOutputStream.writeBytes(Native Method) at java.io.FileOutputStream.write(FileOutputStream.java:297) at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197) ... 14 more

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