Re: [svtoolkit-help] genome strip error

[Bob H. <han...@br...>]

Hi, Can,

My first guess is that you have an incompatible version of htsjdk on 
your classpath.
GS comes bundled with its own copy of the GATK (usually somewhat out of 
date) that the software is compatible with.

If that isn't it, it will require more investigation.
 From the stack trace, this is blowing up inside of htsjdk trying to 
read one of your bam files.

-Bob

On 9/16/15 8:04 AM, Can Alkan wrote:
> 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 
> ------------------------------------------------------------------------------------------ 
>
>
>
>
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