org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.

broadinstitute.org | 4 months ago
  1. 0

    GATK_UnifiedGenotyper_Unable to merge temporary Tribble output file - GATK-Forum

    broadinstitute.org | 2 years ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
  2. 0

    GATK_UnifiedGenotyper_Unable to merge temporary Tribble output file — GATK-Forum

    broadinstitute.org | 4 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
  3. 0

    ArcGISCompactCacheTest fails in path with spaces

    GitHub | 3 years ago | bencaradocdavies
    java.io.FileNotFoundException: /home/car605/geoserver/src%20with%20spaces/geowebcache/geowebcache/arcgiscache/target/test-classes/compactcache/_alllayers/L05/R0000C0000.bundlx (No such file or directory)
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  5. 0

    RFE: sbt should not try to parse every file that ends with .sbt

    GitHub | 4 years ago | harrah
    java.io.FileNotFoundException: /<snip>/.#props.sbt (No such file or directory)
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    New index fails with java.lang.NullPointerException

    GitHub | 4 years ago | fluential
    java.io.FileNotFoundException: /data/zookeeper/data/version-2/exhibitor-1361546755727 (Is a directory)

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Root Cause Analysis

  1. java.io.FileNotFoundException

    /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)

    at java.io.FileInputStream.open()
  2. Java RT
    FileInputStream.<init>
    1. java.io.FileInputStream.open(Native Method)
    2. java.io.FileInputStream.<init>(FileInputStream.java:120)
    2 frames
  3. picard
    AbstractFeatureReader.getFeatureReader
    1. org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:56)
    2. org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:96)
    3. org.broad.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:58)
    4. org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)
    4 frames
  4. org.broadinstitute.sting
    CommandLineGATK.main
    1. org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:182)
    2. org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:52)
    3. org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)
    4. org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)
    5. org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
    6. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
    7. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    8. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    9. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    10. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    10 frames