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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)
The text was updated successfully, but these errors were encountered:
lbergelson
changed the title
Can't write bams to /dev/null/ with spark
Allow writing bams to /dev/null/ with spark
Jan 15, 2016
Trying to write bam to dev null using PrintReadsSpark results in:
The text was updated successfully, but these errors were encountered: