IndelRealigner Stack Trace Error
Posted in Ask the GATK team | Last updated on 2012-10-19 18:17:30


Comments (7)

Hi everyone,

I'm using IndelRealigner to do a local realignment in the standard GATK workflow. I have used this pipeline before with success, but am now met with this error. I could not find any other examples of this, so I am posting as per the instructions in the error.

Cheers,

A.B.

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException 
at org.broadinstitute.sting.utils.sam.AlignmentUtils.createIndelString(AlignmentUtils.java:710) 
at org.broadinstitute.sting.utils.sam.AlignmentUtils.leftAlignIndel(AlignmentUtils.java:603) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.determineReadsThatNeedCleaning(IndelRealigner.java:912) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.clean(IndelRealigner.java:681) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.cleanAndCallMap(IndelRealigner.java:547) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:519) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:114) 
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:104) 
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:52) 
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:71) 
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265) 
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 2.1-11-g13c0244):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

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