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RealignerTargetCreator --- ArrayIndexOutOfBoundsException

sandeepsandeep Member
edited July 2012 in Ask the GATK team
[sandeep@login2 chr16]$ java -Xmx2G -jar /u/home/sandeep/Tools/GATK/GenomeAnalysisTK.jar -R /u/home/sandeep/Files/hg19/ucsc/ucsc.hg19.fasta -I gatk/Genomic.alignment.recalibrated.bam -T RealignerTargetCreator --known /u/home/sandeep/Files/dbSNP/dbsnp132.ucsc.hg19.vcf -L ./Genomic.alignment.merged.bed -o gatk/Genomic.alignment.forRealigner.intervals
INFO 17:36:03,903 RodBindingArgumentTypeDescriptor - Dynamically determined type of ./Genomic.alignment.merged.bed to be BED
INFO 17:36:03,936 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:36:03,936 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 17:36:03,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:36:03,936 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 17:36:03,937 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 17:36:03,937 HelpFormatter - Program Args: -R /u/home/eeskin/sandeep1/Files/hg19/ucsc/ucsc.hg19.fasta -I gatk/Genomic.alignment.recalibrated.bam -T RealignerTargetCreator --known /u/home/eeskin/sandeep1/Files/dbSNP/dbsnp132.ucsc.hg19.vcf -L ./Genomic.alignment.merged.bed -o gatk/Genomic.alignment.forRealigner.intervals
INFO 17:36:03,938 HelpFormatter - Date/Time: 2012/07/19 17:36:03
INFO 17:36:03,938 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:36:03,938 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:36:04,184 RodBindingArgumentTypeDescriptor - Dynamically determined type of /u/home/eeskin/sandeep1/Files/dbSNP/dbsnp132.ucsc.hg19.vcf to be VCF
INFO 17:36:04,188 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:36:04,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:36:05,528 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.78
INFO 17:36:06,296 RMDTrackBuilder - Loading Tribble index from disk for file /u/home/eeskin/sandeep1/Files/dbSNP/dbsnp132.ucsc.hg19.vcf
INFO 17:36:11,811 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 17:36:11,812 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 17:36:40,000 TraversalEngine - chr16:107592 2.07e+05 30.0 s 2.4 m 0.1% 13.8 h 13.8 h
INFO 17:37:42,170 TraversalEngine - chr16:446167 1.49e+06 92.2 s 61.9 s 0.5% 5.3 h 5.2 h
INFO 17:38:14,287 TraversalEngine - chr16:495321 1.65e+06 2.1 m 75.1 s 0.5% 6.3 h 6.3 h
INFO 17:38:44,411 TraversalEngine - chr16:532611 1.75e+06 2.6 m 88.1 s 0.6% 7.2 h 7.2 h
INFO 17:39:17,426 TraversalEngine - chr16:1062765 4.32e+06 3.1 m 43.4 s 1.3% 4.1 h 4.1 h
INFO 17:39:50,883 TraversalEngine - chr16:1091633 4.50e+06 3.7 m 49.1 s 1.3% 4.7 h 4.7 h
INFO 17:40:20,886 TraversalEngine - chr16:1882443 7.94e+06 4.2 m 31.6 s 2.3% 3.1 h 3.0 h
INFO 17:40:50,887 TraversalEngine - chr16:5697324 2.16e+07 4.7 m 13.0 s 7.1% 65.8 m 61.1 m
INFO 17:41:21,924 TraversalEngine - chr16:10443051 3.69e+07 5.2 m 8.5 s 13.1% 39.8 m 34.6 m
INFO 17:41:52,000 TraversalEngine - chr16:14695587 5.07e+07 5.7 m 6.7 s 18.5% 30.9 m 25.2 m
INFO 17:42:23,773 TraversalEngine - chr16:19665973 7.06e+07 6.2 m 5.3 s 24.8% 25.2 m 18.9 m
INFO 17:42:53,939 TraversalEngine - chr16:25567366 8.95e+07 6.7 m 4.5 s 32.2% 20.9 m 14.1 m
INFO 17:43:24,401 TraversalEngine - chr16:31598034 1.11e+08 7.2 m 3.9 s 39.9% 18.1 m 10.9 m
INFO 17:43:54,402 TraversalEngine - chr16:47359030 1.26e+08 7.7 m 3.7 s 45.6% 17.0 m 9.2 m
INFO 17:44:24,405 TraversalEngine - chr16:52405336 1.43e+08 8.2 m 3.4 s 52.0% 15.8 m 7.6 m
INFO 17:44:54,408 TraversalEngine - chr16:57671927 1.63e+08 8.7 m 3.2 s 58.7% 14.9 m 6.1 m
INFO 17:45:24,897 TraversalEngine - chr16:61755189 1.80e+08 9.2 m 3.1 s 63.9% 14.5 m 5.2 m
INFO 17:45:55,616 TraversalEngine - chr16:67010814 2.02e+08 9.8 m 2.9 s 70.5% 13.8 m 4.1 m
INFO 17:46:25,714 TraversalEngine - chr16:70784003 2.15e+08 10.3 m 2.9 s 75.3% 13.6 m 3.4 m
INFO 17:46:55,716 TraversalEngine - chr16:73385026 2.24e+08 10.8 m 2.9 s 78.6% 13.7 m 2.9 m
INFO 17:47:25,738 TraversalEngine - chr16:77603999 2.41e+08 11.3 m 2.8 s 84.0% 13.4 m 2.1 m
INFO 17:48:01,486 TraversalEngine - chr16:83445383 2.61e+08 11.9 m 2.7 s 91.4% 13.0 m 67.0 s
INFO 17:48:31,489 TraversalEngine - chr16:87090384 2.73e+08 12.4 m 2.7 s 96.0% 12.9 m 30.7 s
INFO 17:49:12,905 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 1
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBase(ReferenceContext.java:180)
at org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:192)
at org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:97)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:248)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.6-13-g91f02df):
##### 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 GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: 1
##### ERROR ------------------------------------------------------------------------------------------

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev
    My guess is that something is wrong with your reference fasta file. You can get the UCSC hg19 reference from our resource bundle, so I'd recommend using that one instead.
  • i did try with hg 19 reference fasta file from your resource bundle and i still get same error. I'm getting this error only when using RealignerTargetCreator and its not crashing for all the chromosomes.
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