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NullPointerException when trying to run UnifiedGenotyper with s/g-count >1 with qscript

Johan_DahlbergJohan_Dahlberg Member Posts: 96 ✭✭✭
edited November 2012 in Ask the GATK team

I'm building a variant calling qscript (it's available here), heavily based on the the MethodsDevelopmentCallingPipeline.scala. I cannot however run into trouble when setting the "this.scatterCount" of the GenotyperBase to more than 1 - in which case I get a NullPointerException (I include the full error message below).

I use the following command line:

java -jar dist/Queue.jar -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/NewVariantCalling.scala -i NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -R /bubo/nobackup/uppnex/reference/biodata/GATK/ -res /bubo/nobackup/uppnex/reference/biodata/GATK/ **-sg 2** -nt 8 -run -l DEBUG -startFromScratch

As you can see, I'm using the files from the gatk bundle, and I guess these should be alright for this purpose? Just to be clear I use the "-res" parameter to point to the directory where all the resource files are located, dbsnp, hapmap, etc. and the -sg parameter is what controls the scatter/gather count.

I've tried to search in the code for what might be causing this, and I can conclude that the org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc is called with str (its parameter) being an empty string, which is what causes contig to be null, which in turn creates the NullPointerException on line 408 when this line is executed:
stop = getContigInfo(contig).getSequenceLength();

This, I guess, is the obvious stuff, but this far I haven't been able to figure this out any further that this. I'm not sure if this is caused by a bug in my script, or by a bug in the GATK. Right now I'm thinking the latter of the two, since I have used the scatter/gather function in other scripts without any trouble.

Any ideas of where to continue from here, or confirmation that this is indeed something related to the GATK code would be much appreciated.


ERROR 16:22:50,781 FunctionEdge - Error: LocusScatterFunction: List(/bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam.bai, /bubo/nobackup/uppnex/reference/biodata/GATK/, /bubo/nobackup/uppnex/reference/biodata/GATK/, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bai, /bubo/nobackup/uppnex/reference/biodata/GATK/, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam) > List(/bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/.queue/scatterGather/.qlog/project.snpcall-sg/temp_1_of_2/scatter.intervals, /bubo/proj/a2009002/SnpSeqPipeline/SnpSeqPipeline/gatk/.queue/scatterGather/.qlog/project.snpcall-sg/temp_2_of_2/scatter.intervals) 
        at org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(
        at org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(
        at org.broadinstitute.sting.utils.interval.IntervalUtils.loadIntervals(
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalBindingsPair(
        at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalBindings(
        at org.broadinstitute.sting.queue.extensions.gatk.GATKIntervals.locs(GATKIntervals.scala:60)
        at org.broadinstitute.sting.queue.engine.InProcessRunner.start(InProcessRunner.scala:28)
        at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:83)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:432)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:145)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Hi Johan,

    Unfortunately we don't have the resources right now to provide troubleshooting support for qscripts. All I can say is that using the bundle files should be okay; just keep in mind that the bam file provided there only contains chromosome 20, so if you're scattering by contig that effectively creates only one job. For what it's worth I would recommend testing the MethodsDevelopmentCallingPipeline.scala on the same data to make sure that's not what's causing the problem. Good luck...

    Geraldine Van der Auwera, PhD

  • Johan_DahlbergJohan_Dahlberg Member Posts: 96 ✭✭✭

    I will keep looking into this when I have the time, and get back to you if I figure it out (or magically goes away as I'm hoping at the moment).

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