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error message: -3

edited January 2013 in Ask the GATK team

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

Post edited by Geraldine_VdAuwera on

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