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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

DPP and FunctionEdge

ecuencaecuenca Member Posts: 24

Hi,

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,
Best,

Ester

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' '-Djava.io.tmpdir=/temp' '-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' '-Djava.io.tmpdir=/temp' '-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(ProcessController.java:168)
at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:69)
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.engine.QGraph.run(QGraph.scala:155)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:169)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
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

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Best Answers

Answers

  • ecuencaecuenca Member Posts: 24

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

  • ecuencaecuenca Member Posts: 24

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

  • ecuencaecuenca Member Posts: 24

    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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