VariantRecalibrator: ERROR stack trace
Posted in Ask the GATK team | Last updated on 2012-12-06 15:56:14


Comments (5)

Hi, I'm encountering this error running VariantRecalibrator with data from 3 samples (I'm testing): Maybe is the problem due to small sample size?

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NullPointerException
        at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantDataManager.selectWorstVariants(VariantDataManager.java:179)
        at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:306)
        at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:107)
        at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-16-g9f648cb):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, 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: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

Thanks


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