[svtoolkit-help] genome strip error

[Can A. <ca...@gm...>]

Hi Bob

I'm running the latest version of GenomeSTRiP, and after preprocessing, the
discovery step exited with an exception. I copied the stack below.  I
didn't do anything fancy, just edited the discovery.sh file. here are the
cmd lines:


java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/SVPreprocess.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    --disableJobReport \
    -cp ${classpath} \
    -configFile genstrip_installtest_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
    -genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
    -copyNumberMaskFile $BUNDLE_DIR/human_g1k_hs37d5.gcmask.fasta \
    -genderMapFile gender.map \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -disableGATKTraversal \
    -useMultiStep \
    -reduceInsertSizeDistributions false \
    -computeGCProfiles true \
    -computeReadCounts true \
    -jobLogDir ${runDir}/logs \
    -I ${bam} \
    -run \
    || exit 1

# Run discovery.
java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/SVDiscovery.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    --disableJobReport \
    -cp ${classpath} \
    -configFile genstrip_installtest_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R $BUNDLE_DIR/human_g1k_hs37d5.fasta \
    -genomeMaskFile $BUNDLE_DIR/human_g1k_hs37d5.svmask.fasta \
    -genderMapFile gender.map \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -disableGATKTraversal \
    -jobLogDir ${runDir}/logs \
    -minimumSize 100 \
    -maximumSize 1000000 \
    -suppressVCFCommandLines \
    -I ${bam} \
    -O $runDir/${sites} \
    -run \
    || exit 1


the error stack:


##### ERROR stack trace
java.lang.IllegalArgumentException: Invalid reference index -1
    at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    at
htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:473)
    at
htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryContained(SamReader.java:356)
    at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runTraversal(DeletionDiscoveryAlgorithm.java:141)
    at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:107)
    at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
    at
org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
    at
org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
    at
org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
    at
org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
    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.sv.main.SVCommandLine.main(SVCommandLine.java:78)
    at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the
GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid reference index -1
##### ERROR
------------------------------------------------------------------------------------------