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GATK RUNTIME ERROR in RealignerTargetCreator

ehoutgastehoutgast NetherlandsMember
edited March 2015 in Ask the GATK team

I am trying to reproduce running the GATK pipeline (best practices) on Power8, but during the RealignerTargetCreator phase, I run into the following problem:
INFO 06:05:39,926 HelpFormatter - --------------------------------------------------------------------------------
INFO 06:05:39,928 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 06:05:39,929 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 06:05:39,929 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 06:05:39,933 HelpFormatter - Program Args: -T RealignerTargetCreator -R genome/hg19.fasta -I results/out_sorted_dup.bam -o results/out_target_intervals.interval_list -known vcf/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -known vcf/1000G_phase1.indels.hg19.sites.vcf
INFO 06:05:39,941 HelpFormatter - Executing as admin@power8-2xl on Linux 3.14.17-100.fc19.ppc64p7 ppc64; OpenJDK 64-Bit Server VM 1.7.0_65-mockbuild_2014_07_26_03_56-b00.
INFO 06:05:39,942 HelpFormatter - Date/Time: 2015/03/09 06:05:39
INFO 06:05:39,942 HelpFormatter - --------------------------------------------------------------------------------
INFO 06:05:39,942 HelpFormatter - --------------------------------------------------------------------------------
INFO 06:05:40,016 GenomeAnalysisEngine - Strictness is SILENT
INFO 06:05:40,150 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 06:05:40,159 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 06:05:40,182 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 06:05:40,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 06:05:41,576 GenomeAnalysisEngine - Done preparing for traversal
INFO 06:05:41,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 06:05:41,578 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 06:05:41,578 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 06:05:43,206 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:216)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:288)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
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:319)
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 3.3-0-g37228af):
##### 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

This is the command I used:
java jar ~Xmx32g -jar ~/workspace/GATK/tools/GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R genome/hg19.fasta -I results/out_sorted_dup.bam -o results/out_target_intervals.interval_list -known vcf/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -known vcf/1000G_phase1.indels.hg19.sites.vcf

I tried to look for a similar problem on the forum, but could not find anything. Could you advise how to resolve this situation? The error message suggests this may be a bug..

Thanks in advance!

Answers

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