Error running CombineGVCFs with Queue

HI GATK team/users,

We're doing a targeted sequencing project with ~1500 samples so I'm trying to make run-level files with batches of 36 samples with CombineGVCFs. I've written a super simple Qscript in the past that worked well. However we've moved to a new server since that use slurm instead of SGE.
I've installed slurm-drmaa and that seems to be working well, but now I can't specify the list of vcf files correctly and I don't know enough about scala syntax to know what I'm doing wrong. Any help on this would be very appreciated. I've spent too many hours trying to figure this out with no success!
I've tried submitted a list of vcfs or individual file names. Both give me the same error.

**Here is the scala script.
// Import classes
package org.broadinstitute.sting.queue.qscripts.examples

import collection.JavaConversions._
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk._

class RunCombineGVCFs extends QScript {

@Input(fullName="variant", shortName = "V", doc="List of input gVCF files", required=true)
var gvcfFile: List[File] = Nil
@Argument(doc="Name of output merged GVCF file.", shortName="o")
var output: File = _

var stupiderror: Boolean = true
def script() {
val combineGVCFs = new CombineGVCFs
combineGVCFs.reference_sequence = new File("hs37d5.fa")
combineGVCFs.variant = gvcfFile
combineGVCFs.disable_auto_index_creation_and_locking_when_reading_rods = stupiderror
combineGVCFs.out = output
combineGVCFs.scatterCount=26
add(combineGVCFs)
}
}

Submission variables
java -Xmx5G -jar Queue.jar \
-S RunCombineGVCFs.test.scala \
-qsub \
--memory_limit 10 \
--run_name VCFFILE \
-o ../RunVCF/VCFFILE \
--variant SampleFR.79707.GATGAATC.g.vcf \
--variant SampleCADB.79202.GACAGTGC.g.vcf \
--variant SampleNFBC.1183222.CGGATTGC.g.vcf \
--variant SampleFR.57509.AGTCACTA.g.vcf \
-startFromScratch \
-run

Error message
INFO 10:41:14,300 QScriptManager - Compiling 1 QScript
INFO 10:41:26,173 QScriptManager - Compilation complete
INFO 10:41:26,246 HelpFormatter - ----------------------------------------------------------------------
INFO 10:41:26,246 HelpFormatter - Queue v3.4-46-gbc02625, Compiled 2015/07/09 17:37:55
INFO 10:41:26,246 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 10:41:26,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:41:26,247 HelpFormatter - Program Args: -S /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/RunCombineGVCFs.test.scala -qsub --memory_limit 10 --run_name VCFFILE -o ../RunVCF/VCFFILE --variant SampleFR.79707.GATGAATC.g.vcf --variant SampleCADB.79202.GACAGTGC.g.vcf --variant SampleNFBC.1183222.CGGATTGC.g.vcf --variant SampleFR.57509.AGTCACTA.g.vcf -startFromScratch -run
INFO 10:41:26,248 HelpFormatter - Executing as fashar1@jhu.edu@login-node04 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_85-mockbuild_2015_07_15_12_57-b00.
INFO 10:41:26,248 HelpFormatter - Date/Time: 2015/10/01 10:41:26
INFO 10:41:26,248 HelpFormatter - ----------------------------------------------------------------------
INFO 10:41:26,248 HelpFormatter - ----------------------------------------------------------------------
INFO 10:41:26,253 QCommandLine - Scripting RunCombineGVCFs
INFO 10:41:26,300 QCommandLine - Added 1 functions
INFO 10:41:26,300 QGraph - Generating graph.
INFO 10:41:26,312 QGraph - Generating scatter gather jobs.
INFO 10:41:26,341 QGraph - Removing original jobs.
INFO 10:41:26,342 QGraph - Adding scatter gather jobs.
INFO 10:41:26,475 QGraph - Regenerating graph.
INFO 10:41:26,523 QGraph - Running jobs.
INFO 10:41:26,555 QGraph - Removing outputs from previous runs.
INFO 10:41:26,629 FunctionEdge - Starting: LocusScatterFunction: List(/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/hs37d5.fa, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf) > List(/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_02_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_03_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_04_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_05_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_06_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_07_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_08_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_09_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_10_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_11_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_12_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_13_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_14_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_15_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_16_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_17_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_18_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_19_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_20_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_21_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_22_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_23_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_24_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_25_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_26_of_26/scatter.intervals)
INFO 10:41:26,629 FunctionEdge - Output written to /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/scatter/scatter.out
INFO 10:41:26,747 QGraph - 28 Pend, 1 Run, 0 Fail, 0 Done
INFO 10:41:56,651 FunctionEdge - Done: LocusScatterFunction: List(/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf.idx, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/hs37d5.fa, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf) > List(/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_02_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_03_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_04_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_05_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_06_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_07_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_08_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_09_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_10_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_11_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_12_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_13_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_14_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_15_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_16_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_17_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_18_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_19_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_20_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_21_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_22_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_23_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_24_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_25_of_26/scatter.intervals, /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_26_of_26/scatter.intervals)
INFO 10:41:56,652 QGraph - Writing incremental jobs reports...
INFO 10:41:56,652 QJobsReporter - Writing JobLogging GATKReport to file /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/VCFFILE.jobreport.txt
INFO 10:41:56,686 FunctionEdge - Starting: 'java' '-Xmx10240m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/tmp' '-cp' '/work-zfs/darking1/software/src/gatk/Queue.jar' 'org.broadinstitute.gatk.engine.CommandLineGATK' '-T' 'CombineGVCFs' '-L' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/scatter.intervals' '-R' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/hs37d5.fa' '-disable_auto_index_creation_and_locking_when_reading_rods' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf' '-o' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/VCFFILE'
INFO 10:41:56,686 FunctionEdge - Output written to /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/VCFFILE.out
INFO 10:41:56,707 GridEngineJobRunner - Native spec is: -V -l h_rss=12288M
ERROR 10:41:56,709 Retry - Caught error during attempt 1 of 4.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I'm confused -- why do you think this is a problem in how you specify the list of VCFs? That looks fine to me. Looks more like a problem submitting jobs to the scheduler afaict.

  • Sorry! I truncated the error file at the wrong point. The "Unsupported option -V" made me think it was about the VCF list. Am I wrong about this?

    INFO 10:41:56,652 QGraph - Writing incremental jobs reports...
    INFO 10:41:56,652 QJobsReporter - Writing JobLogging GATKReport to file /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/VCFFILE.jobreport.txt
    INFO 10:41:56,686 FunctionEdge - Starting: 'java' '-Xmx10240m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/tmp' '-cp' '/work-zfs/darking1/software/src/gatk/Queue.jar' 'org.broadinstitute.gatk.engine.CommandLineGATK' '-T' 'CombineGVCFs' '-L' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/scatter.intervals' '-R' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/hs37d5.fa' '-disable_auto_index_creation_and_locking_when_reading_rods' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.79707.GATGAATC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleCADB.79202.GACAGTGC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleNFBC.1183222.CGGATTGC.g.vcf' '-V' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/SampleFR.57509.AGTCACTA.g.vcf' '-o' '/work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/VCFFILE'
    INFO 10:41:56,686 FunctionEdge - Output written to /work-zfs/darking1/active/projects/BAZ2B/SureSelect/Sequencing/variant.calling/SampleVCF/.queue/scatterGather/VCFFILE-1-sg/temp_01_of_26/VCFFILE.out
    INFO 10:41:56,707 GridEngineJobRunner - Native spec is: -V -l h_rss=12288M
    ERROR 10:41:56,709 Retry - Caught error during attempt 1 of 4.
    org.broadinstitute.gatk.queue.QException: Unable to submit job: Invalid native specification: -V -l h_rss=12288M (Unsupported option: -V)
    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:440)
    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:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, I see. Well, there are three sets of arguments that get sent around when you run your command. The set you specify on the command line goes to Queue, which then creates two more sets. One goes to GATK based on what you put in your script, and the other goes to your job scheduler to tell it to execute the GATK commands.

    There's not any cross-over between the job scheduler set and the GATK set, so considering the GATK commands look fine in the log output, I think you're fine on that front. In any case if there was anything wrong in how you specified arguments in your script, Queue would throw a script compilation error.

    So there must be something that's going wrong with the set getting sent to the job scheduler. It seems the default settings for the DRMAA jobrunner include an option that your platform doesn't recognize -- that's where that -V in the error is coming from, and why the output tells you something about the native spec (= the default configuration):

    INFO 10:41:56,707 GridEngineJobRunner - Native spec is: -V -l h_rss=12288M
    

    I can't help you resolve this; you probably need to find out from your sysadmin what the proper configuration should be.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    edited October 2015

    Oh I should add -- once you know what you need to pass to the jobrunner, you'll do it by using the jobNative argument in your Queue command line. The argument definition is this:

      @Argument(fullName="job_native_arg", shortName="jobNative", doc="Native arguments to pass to the job runner.", required=false)
      var jobNativeArgs: Seq[String] = Nil
    

    as listed in https://github.com/broadgsa/gatk/blob/master/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala

  • This is very helpful! I at least know which part I need to work on now. Thanks Geraldine!

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