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PBS-DRMAA problems when I try execute Haplotyope-Caller

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Good Morning,

I'm trying to perform a parallel job using queue with a PBS scheduler but my script can't be executed. In particular, the script runs properly on a single node (so i won't attach the script for brevity) but when I try to run a batch job on more node using PBS I got an error.

Here's the file that launches the script:

export LD_LIBRARY_PATH=/path/drmaa/bin/lib
java -jar Queue.jar  \
    -S BaseHaplMerg.scala \
    -R genomePath/genome.fa \
    -I Input.bam \
    -knownSites knownSites.vcf \
    -L enriched.bed \
    --dbsnp dbsnp.vcf \
    --varindpar 128000 \
    -stand_emit_conf 10 \
    -stand_call_conf 30 \
    -o myOutput.vcf \
    -nct 8 \
    -jobRunner PbsEngine \
    -run

After the usual INFO (added 3 functions etc) i got this error:

ERROR 15:21:43,754 Retry - Caught error during attempt 1 of 4. 
org.broadinstitute.gatk.queue.QException: Unable to submit job: Illegal attribute or resource value: Illegal attribute or resource value 
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
    at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:453)
    at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
    at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 15:21:43,756 Retry - Retrying in 1.0 minute. 

And this Error is repeated for 4 times, as specified in DrmaaJobRunner.scala line 89.

I should point out that we installed DRMAA for PBS (http://apps.man.poznan.pl/trac/pbs-drmaa/wiki).

What sould I do?

Thank you for your attention

Best Reguards

Ilario Tagliaferri


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