net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)

biosupport.se | 3 months ago
  1. 0

    AddOrReplaceReadGroups picard problem: Caused by: java.io.IOException: No space left on device

    biosupport.se | 3 months ago
    net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
  2. 0

    Read error; BinaryCodec in readmode; streamed file

    GitHub | 3 years ago | arahuja
    net.sf.samtools.util.RuntimeIOException: Read error; BinaryCodec in readmode; streamed file (filename not available)

    Root Cause Analysis

    1. net.sf.samtools.util.RuntimeIOException

      Write error; BinaryCodec in writemode; streamed file (filename not available)

      at net.sf.samtools.util.BinaryCodec.writeBytes()
    2. picard
      AddOrReplaceReadGroups.main
      1. net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
      2. net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
      3. net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:141)
      4. net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
      5. net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
      6. net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
      7. net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
      8. net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:93)
      9. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
      10. net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
      11. net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
      11 frames