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java.lang.NullPointerException using BaseRecalibrator

I became this error and wonder what could be the reason for it:

ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate.keyForRepeat(RepeatCovariate.java:225)
at org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate.recordValues(RepeatCovariate.java:100)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.computeCovariates(RecalUtils.java:921)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.computeCovariates(RecalUtils.java:901)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:263)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:132)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-01-31-gc6765ad):
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: Code exception (see stack trace for error itself)

Comments

  • droazendroazen Cambridge, MAMember, Broadie, Dev

    I notice that you're using a nightly build of the GATK from January -- could you please try again with the official GATK 3.1 release and see if the error persists?

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