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

Member Posts: 1
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.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)

##### 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.