org.broadinstitute.hellbender.exceptions.UserException: A USER ERROR has occurred: Failed to read bam header from gs://sv-data-dsde-dev/test_data/smallCram.cram Caused by:null

GitHub | SHuang-Broad | 2 months ago
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  1. 0

    null message

    GitHub | 4 months ago | eddiebroad
    java.lang.RuntimeException: org.broadinstitute.hellbender.exceptions.UserException$MissingReferenceDictFile
  2. 0

    blowup on direct runner with hdfs

    GitHub | 1 year ago | akiezun
    java.lang.IllegalArgumentException: Wrong FS: hdfs:/user/akiezun/data/HCC1143_BL.bam, expected: file:///
  3. 0

    PrintReadsSpark throws error "Invalid splitting BAM index" on writing BAM

    GitHub | 5 months ago | mwalker174
    org.broadinstitute.hellbender.exceptions.GATKException: unable to write bam: java.io.IOException: Invalid splitting BAM index: should contain at least 1 offset and the file size
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  5. 0

    `ReadsSparkSource` cannot (seem to) read cram file on hdfs or gcs.

    GitHub | 2 months ago | SHuang-Broad
    org.broadinstitute.hellbender.exceptions.UserException$MissingReference: A USER ERROR has occurred: The specified fasta file (gs://sv-data-dsde-dev/reference/Homo_sapiens_assembly38.fasta) does not exist.
  6. 0

    Allow writing bams to /dev/null/ with spark

    GitHub | 1 year ago | lbergelson
    org.broadinstitute.hellbender.exceptions.GATKException: unable to write bam: org.apache.hadoop.fs.ParentNotDirectoryException: Parent path is not a directory: file:/dev/null

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Root Cause Analysis

  1. java.lang.NullPointerException

    No message provided

    at java.io.ByteArrayInputStream.<init>()
  2. Java RT
    ByteArrayInputStream.<init>
    1. java.io.ByteArrayInputStream.<init>(ByteArrayInputStream.java:106)
    1 frame
  3. org.broadinstitute.hellbender
    Main.main
    1. org.broadinstitute.hellbender.engine.AuthHolder.getOfflineAuth(AuthHolder.java:79)
    2. org.broadinstitute.hellbender.engine.AuthHolder.makeStorageClient(AuthHolder.java:94)
    3. org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getHeader(ReadsSparkSource.java:177)
    4. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReads(GATKSparkTool.java:381)
    5. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:361)
    6. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:351)
    7. org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
    8. org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:112)
    9. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170)
    10. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189)
    11. org.broadinstitute.hellbender.Main.instanceMain(Main.java:96)
    12. org.broadinstitute.hellbender.Main.instanceMain(Main.java:103)
    13. org.broadinstitute.hellbender.Main.mainEntry(Main.java:116)
    14. org.broadinstitute.hellbender.Main.main(Main.java:158)
    14 frames
  4. 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
  5. Spark
    SparkSubmit.main
    1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
    2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)
    3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)
    4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)
    5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
    5 frames