htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device

broadinstitute.org | 8 months ago
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  1. 0

    GATK | GATK | Tagged #markduplicates

    broadinstitute.org | 11 months ago
    htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
  2. 0

    picard-tools MarkDuplicates - spilling to disk — GATK-Forum

    broadinstitute.org | 8 months ago
    htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
  3. 0

    picard-tools MarkDuplicates - spilling to disk — GATK-Forum

    broadinstitute.org | 1 month ago
    htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
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  5. 0

    Realtime task with lost segment reported as SUCCESS

    GitHub | 2 years ago | tisonet
    java.io.IOException: No space left on device
  6. 0

    temporary directory?

    Google Groups | 9 years ago | shlomo....@gmail.com
    java.io.IOException: No space left on device

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    Root Cause Analysis

    1. java.io.IOException

      No space left on device

      at java.io.FileOutputStream.writeBytes()
    2. Java RT
      BufferedOutputStream.write
      1. java.io.FileOutputStream.writeBytes(Native Method)
      2. java.io.FileOutputStream.write(FileOutputStream.java:318)
      3. java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
      4. java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
      4 frames
    3. snappy-java
      SnappyOutputStream.close
      1. org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:127)
      2. org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100)
      3. org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137)
      3 frames
    4. HTS JDK
      SortingCollection.add
      1. htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:236)
      2. htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:165)
      2 frames
    5. picard.sam.markduplicates
      MarkDuplicates.doWork
      1. picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:281)
      2. picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114)
      2 frames
    6. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames