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Error when running CNVDiscoveryPipeline using the latest version(SVToolkit version 2.00 (build 1747)

zzqzzq ChinaMember
edited August 2017 in GenomeSTRiP

Dear @bhandsaker

I have finished running the deletion discovery pipeline, but when running CNVDiscoveryPipeline using following command, it gave me an error. It is difficult for me to figure it out. Hope your help. Thanks.


java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -tempDir ${SV_TMPDIR}/tmp \
    -configFile /home/conf/genstrip_parameters.txt \
    -R  /home/conf/merge.fa \
    -genderMapFile  /home/conf/gender \
    -runDirectory ${runDir} \
    -md  /home/CNV/$1/metadata/ \
    -jobLogDir ${runDir}/logs \
    -I  /home/conf/bam.list \
    -intervalList  /home/conf/$1.list \
    -ploidyMapFile  /home/conf/ploidymap.txt \
    -jobRunner Shell -gatkJobRunner Shell -tilingWindowSize 5000 \
    -tilingWindowOverlap 2500 -maximumReferenceGapLength 2500 -boundaryPrecision 200 -minimumRefinedLength 2500 -run \
    || exit 1

Error information

Error: Exception processing cnp: null
CNP: CNV_1_35000000_35005000 1:35000001-35005000
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
        at org.broadinstitute.sv.common.ReadCountDiskCache.getReadCounts(ReadCountDiskCache.java:103)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:283)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:240)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getReadCounts(GenotypingDepthModule.java:225)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getCnpReadCounts(GenotypingDepthModule.java:212)

Best wishes


  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I am pretty sure this error is due to a bug that occurs when you are not using any mask files. A workaround should be to create a dummy mask file that does not mask any portions of the reference genome and pass that explicitly as a mask file, e.g. using -genomeMaskFile.

    This problem has since been fixed in the code base, so as soon as we make a new release the workaround should not be necessary.

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