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Allow writing bams to /dev/null/ with spark #1436

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lbergelson opened this issue Jan 15, 2016 · 0 comments
Open

Allow writing bams to /dev/null/ with spark #1436

lbergelson opened this issue Jan 15, 2016 · 0 comments
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@lbergelson
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Trying to write bam to dev null using PrintReadsSpark results in:

org.broadinstitute.hellbender.exceptions.GATKException: unable to write bam: org.apache.hadoop.fs.ParentNotDirectoryException: Parent path is not a directory: file:/dev/null
    at org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark.runTool(PrintReadsSpark.java:50)
    at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:257)
    at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
    at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66)
    at org.broadinstitute.hellbender.Main.main(Main.java:81)
@lbergelson lbergelson changed the title Can't write bams to /dev/null/ with spark Allow writing bams to /dev/null/ with spark Jan 15, 2016
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