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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

DPP and FunctionEdge


when I'm running the DPP I get an error. I think it is because the command '.exec5886755893230759761' is removed from the temp folder while it is being used. I have tried with the '-keepIntermediates' option but the command is still being deleted.

Any suggestions to avoid it?

Thank you in advance,


The error (I have the complete output if needed):

DEBUG 15:42:19,212 FunctionEdge - Starting: /user > 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '' '-cp' '/My-programs/QueueLite-2.3-9-gdcdccbb/QueueLite.jar' 'net.sf.picard.sam.RevertSam' 'INPUT=/My-programs/QueueLite-2.3-9-gdcdccbb/resources/exampleBAM.bam' 'TMP_DIR=/temp' 'OUTPUT=/user/exampleBAM.reverted.bam' 'VALIDATION_STRINGENCY=SILENT' 'SO=queryname' 'CREATE_INDEX=true'

INFO 15:42:19,212 FunctionEdge - Output written to /user/exampleBAM.reverted.bam.out

DEBUG 15:42:19,214 IOUtils - Deleted /user/exampleBAM.reverted.bam.out

DEBUG 15:42:19,260 IOUtils - Deleted /temp/.exec5886755893230759761

ERROR 15:42:19,277 FunctionEdge - Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '' '-cp' '/My-programs/QueueLite-2.3-9-gdcdccbb/QueueLite.jar' 'net.sf.picard.sam.RevertSam' 'INPUT=/My-programs/QueueLite-2.3-9-gdcdccbb/resources/exampleBAM.bam' 'TMP_DIR=/temp' 'OUTPUT=/user/exampleBAM.reverted.bam' 'VALIDATION_STRINGENCY=SILENT' 'SO=queryname' 'CREATE_INDEX=true'
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to start command: sh /lustre/scratch109/sanger/ec8/REDUCED_BAM_files/temp/.exec5886755893230759761
at org.broadinstitute.sting.utils.runtime.ProcessController.exec(
at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:83)
at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:433)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:169)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

INFO 15:42:19,280 QGraph - 12 Pend, 1 Run, 0 Fail, 0 Done
INFO 15:42:49,189 QGraph - Writing incremental jobs reports...
INFO 15:42:49,191 QGraph - 12 Pend, 0 Run, 1 Fail, 0 Done
INFO 15:42:49,194 QCommandLine - Script failed with 13 total jobs


Best Answers


  • Yes, I think so, I have shortened the locations of directories but everything is at lustre, visible by all farm nodes.

  • I think it wasn't the problem. There is a command I can use to not delete the files in temp folder?

  • YES, you were right!
    At farm FAQ: "each blade has a local /tmp directory. This filesystem is not visible from any other machine"
    Thank you very much,
    now it's running!!

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