net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: stdout

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  1. davidvanlaatum 8 times, last 5 days ago
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Root Cause Analysis

  1. java.io.IOException

    Broken pipe

    at java.io.FileOutputStream.writeBytes()
  2. Java RT
    FileOutputStream.write
    1. java.io.FileOutputStream.writeBytes(Native Method)
    2. java.io.FileOutputStream.write(FileOutputStream.java:297)
    2 frames
  3. picard
    BlockCompressedOutputStream.write
    1. net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
    2. net.sf.samtools.util.BinaryCodec.writeByteBuffer(BinaryCodec.java:165)
    3. net.sf.samtools.util.BinaryCodec.writeByte(BinaryCodec.java:176)
    4. net.sf.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:262)
    5. net.sf.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:239)
    6. net.sf.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:146)
    6 frames
  4. Java RT
    DataOutputStream.write
    1. java.io.DataOutputStream.write(DataOutputStream.java:107)
    1 frame
  5. picard
    MarkDuplicates.main
    1. net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
    2. net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
    3. net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:120)
    4. net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:101)
    5. net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:155)
    6. net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
    7. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
    8. net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
    8 frames