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drmaa, host is neither submit nor admin host
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