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ArrayIndexOutOfBoundsException: 1 in RealignerTargetCreator

alfredoalfredo londonMember

I am running the following command:
java -Xms4g -Xmx5g -jar /path/GenomeAnalysisTK.jar -nt 1 -T RealignerTargetCreator -R /path_to_reference/hg19.fasta -I /path_to_bam/LP6008118-DNA_A02_indexed.bam -U ALLOW_SEQ_DICT_INCOMPATIBILITY

and I get the following error:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 1
at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:237)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:142)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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 ------------------------------------------------------------------------------------------

Any ideas? do you think it can be due to some problems related to the input bam file?

Thanks a lot in advance for your help


  • SheilaSheila Broad InstituteMember, Broadie admin


    Can you please try validating your input BAM file with Picard's ValidateSamFile?


  • alfredoalfredo londonMember

    Hello Sheila!

    thanks for you answer, anyway I just tried and no errors were found


  • pdexheimerpdexheimer Member ✭✭✭✭

    I'm very concerned that you're running with the -U option, and even more concerned that you're specifically allowing incompatible sequence dictionaries. This is because the stack trace you posted indicates that the problem came in looking up the reference base at a particular position (second line, ReferenceContext.getBase()). My expectation is that your incompatible sequence dictionaries are actually meaningfully incompatible, and this is what's leading to the crash. Use a common reference everywhere, and I think this error goes away

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