Searched on Google with the first line of a JAVA stack trace?

We can recommend more relevant solutions and speed up debugging when you paste your entire stack trace with the exception message. Try a sample exception.

Recommended solutions based on your search

Solutions on the web

java.lang.ArrayIndexOutOfBoundsException: 83	at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow(CGAAlignmentUtils.java:135)	at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads(MuTect.java:787)	at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:511)	at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:79)	at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)	at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)	at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)	at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)	at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)	at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)	at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)