Problem with BaseRecalibrator in v2.2-8-gec077cd
Posted in Ask the team | Last updated on


Comments (3)

Hello dear GATK People,

I'm failing with BaseRecalibrator from the new GATK version - my pipeline worked with the 2.1-11, below is my error message. Any quick fix or should I stick to the old version?

Ania

ERROR stack trace

java.lang.IllegalArgumentException: fromIndex(402) > toIndex(101) at java.util.Arrays.rangeCheck(Unknown Source) at java.util.Arrays.fill(Unknown Source) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateKnownSites(BaseRecalibrator.java:280) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:259) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:239) 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.executeSingleThreaded(NanoScheduler.java:287) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) 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:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-8-gec077cd):

.....

ERROR MESSAGE: fromIndex(402) > toIndex(101)
ERROR ------------------------------------------------------------------------------------------

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