Question: Realignertargetcreator --- Arrayindexoutofboundsexception
0
gravatar for sandeep.deverasetty
8.2 years ago by
sandeep.deverasetty60 wrote:
[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 ------------------------------------------------------------------------------------------
gatk next-gen calling variant • 2.3k views
ADD COMMENTlink modified 6.8 years ago by Biostar ♦♦ 20 • written 8.2 years ago by sandeep.deverasetty60
3

worst bug report ever...

ADD REPLYlink written 8.2 years ago by Michael Dondrup47k
1

Yes. In future can you (1) take the time to format your post so it is readable (or consider pasting long output elsewhere on the web and linking to it) and (2) ask a proper question, rather than simply posting the content of your terminal.

ADD REPLYlink written 8.2 years ago by Neilfws48k
0
gravatar for Michael Dondrup
8.2 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Read:

 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>
ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Michael Dondrup47k

i did post this over there but didnt get proper response. so i reposted over here..

ADD REPLYlink written 8.2 years ago by sandeep.deverasetty60
1

If your post there was the same as the one here, I'm not surprised they did not respond.

ADD REPLYlink written 8.2 years ago by Neilfws48k
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