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

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.

command

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
java.lang.NullPointerException
        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
Zhuqing