Unable to load library 'lsf': liblsf.so: and Unable to submit job: denied(CNVdiscovery)

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termius

• July 19, 2020 14:40

Hello, I am trying to run CNVdiscovery pipeline by using data of human_b36_chr1.fasta, I got the following error ,and attach my script,

when i run it without -jobRunner Drmaa -gatkJobRunner Drmaa ,i got error
Unable to load library 'lsf': liblsf.so:

when i run it with -jobRunner Drmaa -gatkJobRunner Drmaa ,and export LD_LIBRARY_PATH=/opt/lib/linux-x64/:${LD_LIBRARY_PATH}(the path of libdrmaa.so ),i got error
Unable to submit job: denied: host "compute-0-1.local" is no submit host

i don't know how to do it next,Can you give me some advice.

 

################## my code
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
# Run preprocessing.
# For large scale use, you should use -reduceInsertSizeDistributions, but this is too slow for the installation test.
# The method employed by -computeGCProfiles requires a GC mask and is currently only supported for human genomes.

java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-jobRunner Drmaa \
-gatkJobRunner Drmaa \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-ploidyMapFile $mapfile \
-R $reference \
-I $inputfile \
-runDirectory ${runDir} \
-md ./test1/metadata \
-jobLogDir ${runDir}/logs \
-intervalList 1 \
-tilingWindowSize 5000 \
-tilingWindowOverlap 2500 \
-maximumReferenceGapLength 2500 \
-boundaryPrecision 200 \
-minimumRefinedLength 2500 \
-run

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#####results

ERROR 22:22:05,207 Retry - Caught error during attempt 1 of 4.
org.broadinstitute.gatk.queue.QException: Unable to submit job: denied: host "compute-0-1.local" is no submit host
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:96)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$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)
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.queue.engine.QGraph.startOneJob(QGraph.scala:646)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:507)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 22:22:05,209 Retry - Retrying in 1.0 minute.

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• 

  Genevieve Brandt (she/her)

  • July 20, 2020 20:23
  • Edited

  Bob Handsaker, could you look at this issue?

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  Bob Handsaker

  • July 21, 2020 11:28

  As to the question about liblsf.so, that makes sense, as if you don't supply the other arguments the historical default to assume LSF.

  As to the second question about "not a submit host", the answer depends a bit on whether this error is from the top-level Queue invocation or a sub-invocation. If it is for the top-level invocation, then you need to run Queue on a submit host for whatever cluster software you are running (you didn't say).

  The CNV discovery pipeline, unlike all of the other Genome STRiP pipelines, also recursively runs Queue to do scatter/gather at different stages and thus it requires the execution hosts to also be submit hosts. If you are getting this error on a sub-invocation (i.e. it's in one of the log files produced by a submitted job) then this is the problem. In this case, the first thing I would recommend is to ask your local system admin if they would kindly enable the execution hosts to also be submit hosts.

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  Bob Handsaker

  • July 29, 2020 15:33

  This is a separate question. Can you submit it as a separate question, please, not a comment on the question about LSF?

  Thanks.

   

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