java.lang.NullPointerException

GitHub | droazen | 9 months ago
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    NPE when file missing

    GitHub | 1 year ago | akiezun
    java.lang.NullPointerException
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    FilterVcf blows up with NPE

    GitHub | 1 year ago | akiezun
    java.lang.NullPointerException

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    Root Cause Analysis

    1. java.lang.NullPointerException

      No message provided

      at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames()
    2. org.broadinstitute.hellbender
      Main.main
      1. org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(SequenceDictionaryUtils.java:464)
      2. org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(SequenceDictionaryUtils.java:458)
      3. org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(SequenceDictionaryUtils.java:234)
      4. org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:150)
      5. org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
      6. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.validateToolInputs(GATKSparkTool.java:402)
      7. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:312)
      8. org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
      9. org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
      10. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
      11. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
      12. org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
      13. org.broadinstitute.hellbender.Main.main(Main.java:92)
      13 frames
    3. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:498)
      4 frames
    4. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
      2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
      3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
      4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
      5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      5 frames