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