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via broadinstitute.org by Unknown author, 2 years ago
java.lang.ArrayIndexOutOfBoundsException: -4	at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)	at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)	at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)	at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)	at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)	at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)	at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)	at java.util.concurrent.FutureTask.run(FutureTask.java:166)	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)	at java.lang.Thread.run(Thread.java:679)