RealignerTargetCreator --- ArrayIndexOutOfBoundsException

sandeepsandeep Member
edited July 2012 in Ask the GATK team
[[email protected] 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.
  • sandeepsandeep Member
    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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