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DPP and FunctionEdge

ecuencaecuenca Posts: 24Member

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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