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Error of BaseRecalibrator, i have confirm all database and software are ok.

INFO 12:31:08,666 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 12:31:08,666 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:31:08,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:31:08,669 HelpFormatter - Program Args: -T BaseRecalibrator -R /media/Analysis/gatk_resource/ucsc.hg19.fasta -I aCGH5875.rmdup.bam -knownSites /media/Analysis/gatk_resource/dbsnp_138.hg19.vcf -knownSites /media/Analysis/gatk_resource/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites /media/Analysis/gatk_resource/1000G_phase1.indels.hg19.sites.vcf -o ./BaseRecal.grp
INFO 12:31:08,679 HelpFormatter -
INFO 12:31:08,679 HelpFormatter - Date/Time: 2014/11/14 12:31:08
INFO 12:31:08,679 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:31:08,679 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:31:09,102 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:31:09,388 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 12:31:09,395 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:31:09,424 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 12:31:09,765 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 12:31:09,769 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:31:09,769 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:31:09,770 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:31:09,770 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 12:31:09,881 BaseRecalibrator - The covariates being used here:
INFO 12:31:09,881 BaseRecalibrator - ReadGroupCovariate
INFO 12:31:09,881 BaseRecalibrator - QualityScoreCovariate
INFO 12:31:09,881 BaseRecalibrator - ContextCovariate
INFO 12:31:09,882 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 12:31:09,882 BaseRecalibrator - CycleCovariate
INFO 12:31:09,884 ReadShardBalancer$1 - Loading BAM index data
INFO 12:31:09,884 ReadShardBalancer$1 - Done loading BAM index data
INFO 12:31:13,174 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: -25
at org.broadinstitute.gatk.utils.baq.BAQ.calcEpsilon(BAQ.java:185)
at org.broadinstitute.gatk.utils.baq.BAQ.hmm_glocal(BAQ.java:272)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:553)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:610)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:536)
at org.broadinstitute.gatk.utils.baq.BAQ.baqRead(BAQ.java:680)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:481)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:257)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:130)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
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.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
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:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR
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
ERROR MESSAGE: -25
ERROR ------------------------------------------------------------------------------------------

Answers

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