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# ArrayIndexOutOfBoundsException: -1, -2, -4, -5, -15 during BaseRecalibrator

Posts: 1Member
edited February 2013

Hi there,
I have a set of data I'm trying to process through GATK for SNP and Indel calling. When these files get to the BaseRecalibrator I get an error as follows.

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -1
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.executeSingleThreaded(NanoScheduler.java:248)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
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:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR ------------------------------------------------------------------------------------------

Each file has a different error number with -1, -2, -4, -5, or -15. The only other thing different in the outputs is line 4, at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) , in which the 246 is occasionally 225.

The same scripts I am using for these runs have successfully completed about 40+ other runs to date, so I'm at a bit of a loss here. I am running Java version 1.7.0_13 on Ubuntu 12.04. Any help resolving this would be appreciated.

Post edited by ramma on
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## Answers

• Posts: 7,776Administrator, GATK Dev admin

This is a bug that we believe we've fixed in our internal development version. You'll need to wait for version 2.4, which we hope to release next week.

Geraldine Van der Auwera, PhD

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