error message: -3

MUNIER_Patrick

hello I am a new user of GATK, until now I found the answer to my questions on your forum. Following is the command "java -jar ../GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -I 9485_realignedBam.fixed.bam -R hg19.fa -knownSites dbsnp_132_hg19.vcf -o recal_data.grp -filterMBQ" from wich I get this error message :

# # # # # ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -3
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
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
at
at
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 -------------------------------------------- ----------------------------------------------
# # # # # ERROR A RUNTIME ERROR GATK has occurred (version 2.3-6-gebbba25)
# # # # # 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 forum GATK
# # # # # ERROR Visit our website and forum for extensive documentation and answers to
# # # # # ERROR Commonly asked questions http://www.broadinstitute.org/gatk
# # # # # ERROR
# # # # # ERROR MESSAGE: -3
# # # # # ERROR --------------------

I can not find it on a forum, can you explain it and help me

thank you

Geraldine_VdAuwera

Hi Patrick,

Thanks for trying to find an answer on the forum before asking, we appreciate that.

Could you please try running this again with the latest version (currently 2.3-9)? If you still get the same error, we'll need you to submit a bug report as described here:

http://www.broadinstitute.org/gatk/guide/article?id=1894