drmaa, host is neither submit nor admin host

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭
edited April 2016 in GenomeSTRiP


I'm trying to run the CNV pipeline on an SGE active login, on just one major chromosome (200 inds). I notice that the unmapped scaffolds are still incorporated at least in the initial stages of analysis. The script fails in stage 1, at one of the unmapped scaffolds, seq_chrUn_DS484773v1. Does anyone have any idea what's causing this.


INFO  09:59:53,495 HelpFormatter - Program Args: \
-S /cm/shared/apps/svtoolkit/2.0.1602//qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S /cm/shared/apps/svtoolkit/2.0.1602//qscript/SVQScript.q \
-jobRunner Drmaa -gatkJobRunner Drmaa -jobNative -V -pe openmp 10 -q bioinf.q \
-cp /cm/shared/apps/svtoolkit/2.0.1602//lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602//lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602//lib/gatk/Queue.jar \
-gatk /cm/shared/apps/svtoolkit/2.0.1602//lib/gatk/GenomeAnalysisTK.jar \
-configFile reference_data/params_dm6_gstrip.txt \
-R reference_data/dm6.fa -I reference_data/lhm_RG_bams.list \
-genderMapFile reference_data/gstrip_lhm_rg_gender.map \
-md preprocessing_metadata -runDirectory chr2L_cnvs -jobLogDir chr2L_cnvs/logs \
-genomeMaskFile reference_data/dm6.svmask.fasta -readDepthMaskFile reference_data/dm6.rdmask.bed \
-ploidyMapFile reference_data/ploidy_dm6.map \
-L chr2L \
-tempDir ./tmpdir \
-disableGATKTraversal -minimumRefinedLength 500 \
-tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 \
-debug true \
--verbose true -run 

Errors start with:

INFO  10:02:15,446 QCommandLine - Scripting CNVDiscoveryStage1 
INFO  10:02:15,732 QCommandLine - Added 2 functions 
INFO  10:02:15,733 QGraph - Generating graph. 
INFO  10:02:15,747 QGraph - Running jobs. 
ERROR 10:02:15,822 QGraph - Uncaught error running jobs. 
org.ggf.drmaa.DrmCommunicationException: denied: host "node053.cm.cluster" is neither submit nor admin host

Issue · Github
by Sheila

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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Will, I moved this to the GenomeStrip section as we (GATK support) can't help with this problem.

  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    Ta, could've sworn I put this in genomestrip.

  • cwhelancwhelan Cambridge, MAMember, Broadie, Dev

    Never mind on that last point, I see that you've already discussed this in prior questions.

  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    @cwhelan Thanks Chris, very informative. I guess the problem with trying to use -intervalList was due to not having a reference bundle, or only having custom masking and parameters files for the whole genome rather than for each chromosome .. but that doesn't matter now anyway hopefully if I can just use -L like with the deletion pipeline.

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