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via by Unknown author, 1 year ago
Write error; BinaryCodec in writemode; file: stdout
via Google Groups by Hong Hur, 1 year ago
Write error; BinaryCodec in writemode; streamed file (filename not available)
net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: stdout at net.sf.samtools.util.BinaryCodec.writeBytes( at net.sf.samtools.util.BinaryCodec.writeByteBuffer( at net.sf.samtools.util.BinaryCodec.writeByte( at net.sf.samtools.util.BlockCompressedOutputStream.writeGzipBlock( at net.sf.samtools.util.BlockCompressedOutputStream.deflateBlock( at net.sf.samtools.util.BlockCompressedOutputStream.write( at at net.sf.samtools.util.BinaryCodec.writeBytes( at net.sf.samtools.util.BinaryCodec.writeBytes( at net.sf.samtools.BAMRecordCodec.encode( at net.sf.samtools.BAMFileWriter.writeAlignment( at net.sf.samtools.SAMFileWriterImpl.addAlignment( at net.sf.picard.sam.MarkDuplicates.doWork( at net.sf.picard.cmdline.CommandLineProgram.instanceMain( at net.sf.picard.sam.MarkDuplicates.main( by: Broken pipe at Method) at at net.sf.samtools.util.BinaryCodec.writeBytes( ... 14 more