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# java.lang.NullPointerException using BaseRecalibrator

GermanyPosts: 6Member

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)