[svtoolkit-help] problem using the slurm-drmaa bridge

[Sergiu N. <ser...@sc...>]

Greetings,


I am using the slurm-drmaa bridge, and the pipeline has trouble 
submitting jobs. Is there a way to see the actual cluster job submission 
and figure out what parameters are rejected by the SLURM system?

Submitting with:
java -Xmx4g -cp 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/SVToolkit.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/Queue.jar 
org.broadinstitute.gatk.queue.QCommandLine -S 
/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/qscript/SVPreprocess.q 
-S 
/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/qscript/SVQScript.q 
-gatk 
/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/GenomeAnalysisTK.jar 
-configFile 
/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/conf/genstrip_parameters.txt 
-R /sw/data/uppnex/GATK/2.8/b37/human_g1k_v37.fasta -I 
/proj/sens2016011/nobackup/melt/data/bam_links/00028292.sorted.bam -md 
meta -bamFilesAreDisjoint true -jobLogDir 
/proj/sens2016011/nobackup/genomestrip/tests/batch/logs -run -jobRunner 
Drmaa -gatkJobRunner Drmaa -jobNative -t 4:0:0 -jobNative -p node 
-jobNative -A sens2016011-bianca


Error goes like this:

$ cat logs/SVPreprocess-1.out
  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC' 
'-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50' 
'-XX:GCHeapFreeLimit=10' 
'-Djava.io.tmpdir=/castor/project/proj_nobackup/genomestrip/tests/batch/.queue/tmp' 
  '-cp' 
'/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/SVToolkit.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/Queue.jar' 
  'org.broadinstitute.sv.apps.CreateMetaDataDirectory'  '-md' 'meta' 
'-configFile' 
'/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/conf/genstrip_parameters.txt' 

org.broadinstitute.gatk.queue.util.RetryException: Gave up after 4 attempts.
	at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:67)
	at 
org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:91)
	at 
org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:101)
.........
	at 
org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.checkError(JnaSession.java:392)
	at 
org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.runJob(JnaSession.java:79)
	at 
org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.runJob(DrmaaJobRunner.scala:115)
	at 
org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:93)
	at 
org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:91)
	at 
org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:91)
	at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:50)
	... 10 more


Thanks!
-- 
---
Sergiu Netotea, PhD
Researcher at NBIS
(National Bioinformatics Infrastructure Sweden)
Department of Biology and Biological Engineering
Chalmers University of Technology
Kemivägen 10, SE-412 96 Göteborg
ser...@sc...
skype: sergiunetotea
+46 (0)70 28 36 306