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Array index out of bounds exception in RealignerTargetCreator

jpfeiljpfeil capote23Member

INFO 01:05:48,346 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-ge91472d, Compiled 2016/03/18 09:18:48
INFO 01:05:48,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 01:05:48,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 01:05:48,352 HelpFormatter - Program Args: -T RealignerTargetCreator -R ucsc.hg19.fasta -I input.bam -known 1000G_phase1.indels.hg19.sites.vcf -known Mills_and_1000G_gold_standard.indels.hg19.sites.vcf --downsampling_type NONE
-o sample.intervals
INFO 01:05:48,358 HelpFormatter - Executing as [email protected] on Linux 4.4.0-34-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_72-intern$
l-b15.
INFO 01:05:48,358 HelpFormatter - Date/Time: 2016/11/17 01:05:48
INFO 01:05:48,358 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,358 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,460 GenomeAnalysisEngine - Strictness is SILENT
INFO 01:05:49,083 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 01:05:49,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 01:05:49,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
INFO 01:06:13,929 RMDTrackBuilder - Writing Tribble index to disk for file 1000G_phase1.indels.hg19.sites.vcf.idx
INFO 01:06:29,320 RMDTrackBuilder - Writing Tribble index to disk for file Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx
INFO 01:06:31,411 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 01:06:32,089 GenomeAnalysisEngine - Done preparing for traversal
INFO 01:06:32,089 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 01:06:32,090 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 01:06:32,090 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 01:06:33,501 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: -94
at org.broadinstitute.gatk.utils.BaseUtils.convertIUPACtoN(BaseUtils.java:215)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:347)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:163)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:139)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
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-ge91472d):
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: -94
ERROR ------------------------------------------------------------------------------------------

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