Tagged with #arrayindexoutofboundsexception
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Comments (9)

Hi,

I'm trying to apply my recalibrated quality values with the following command:

java -jar GenomeAnalysisTK.jar -T PrintReads -R genome_noHap.fa -I realigned.bam -BQSR realigned.recal_data.grp -o realigned.recal.bam -nct 25

And get the following error. I couldn't find it elsewhere. Would be happy if I could get some advice.

Let me know if you need more info.

Best,

Karl

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

java.lang.ArrayIndexOutOfBoundsException: 0 at org.broadinstitute.sting.utils.recalibration.BaseRecalibration.recalibrateRead(BaseRecalibration.java:151) at org.broadinstitute.sting.utils.recalibration.BQSRReadTransformer.apply(BQSRReadTransformer.java:93) at org.broadinstitute.sting.gatk.walkers.readutils.PrintReads.map(PrintReads.java:251) at org.broadinstitute.sting.gatk.walkers.readutils.PrintReads.map(PrintReads.java:98) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-3-g2a7af43):
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 website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: 0
ERROR ------------------------------------------------------------------------------------------
Comments (1)

Hi there, I have a set of data I'm trying to process through GATK for SNP and Indel calling. When these files get to the BaseRecalibrator I get an error as follows.

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

java.lang.ArrayIndexOutOfBoundsException: -1 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530) at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):
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 website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: -1
ERROR ------------------------------------------------------------------------------------------

Each file has a different error number with -1, -2, -4, -5, or -15. The only other thing different in the outputs is line 4, at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) , in which the 246 is occasionally 225.

The same scripts I am using for these runs have successfully completed about 40+ other runs to date, so I'm at a bit of a loss here. I am running Java version 1.7.0_13 on Ubuntu 12.04. Any help resolving this would be appreciated.

Comments (4)

Hi,

I did search on the site and seems several have had a similar problem but I couldn't fix mine based on those. I've managed to get to this point succesfully with creating a realigned bam file with IndelRealigner. I'm using a non-model organism with self created masking list from a VCF run done before the realignment (list in bed format). I've had to use the -fixMisencodedQuals so far through out my runs. I checked the masking file so that the ranges do not go over the ranges that are specified in my list of regions to cover (-L option).

Is there anything else I would need to check still?

Command line view:

sulyba@hippu4:/fs/lustre/wrk/sulyba/stickleback_capture> java -jar ./GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T BaseRecalibrator -R gasAcu_combinedbac_inv7.fa -I realigned_FF1_inv7c.bam -knownSites Sites_to_Mask.bed -L Capture_Target_Regions.intervals -o recalc_FF1_inv7c.grp -plots recal_FF1_plots.grp.pdf -fixMisencodedQuals

INFO  12:34:10,502 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,510 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14
INFO  12:34:10,510 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  12:34:10,510 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  12:34:10,516 HelpFormatter - Program Args: -T BaseRecalibrator -R gasAcu_combinedbac_inv7.fa -I realigned_FF1_inv7c.bam -knownSites Sites_to_Mask.bed -L Capture_Target_Regions.intervals -o recalc_FF1_inv7c.grp -plots recal_FF1_plots.grp.pdf -fixMisencodedQuals
INFO  12:34:10,516 HelpFormatter - Date/Time: 2013/02/01 12:34:10
INFO  12:34:10,517 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,517 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,551 ArgumentTypeDescriptor - Dynamically determined type of Sites_to_Mask.bed to be BED
INFO  12:34:10,563 GenomeAnalysisEngine - Strictness is SILENT
INFO  12:34:11,309 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO  12:34:11,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  12:34:11,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
INFO  12:34:11,416 RMDTrackBuilder - Loading Tribble index from disk for file Sites_to_Mask.bed
INFO  12:34:11,660 GenomeAnalysisEngine - Processing 20350670 bp from intervals
INFO  12:34:11,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  12:34:11,674 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining
INFO  12:34:11,946 BaseRecalibrator - The covariates being used here:
INFO  12:34:11,947 BaseRecalibrator -   ReadGroupCovariate
INFO  12:34:11,947 BaseRecalibrator -   QualityScoreCovariate
INFO  12:34:11,947 BaseRecalibrator -   ContextCovariate
INFO  12:34:11,947 ContextCovariate -           Context sizes: base substitution model 2, indel substitution model 3
INFO  12:34:11,947 BaseRecalibrator -   CycleCovariate
INFO  12:34:11,952 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3]
INFO  12:34:11,952 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,952 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3]
INFO  12:34:11,953 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3]
INFO  12:34:11,953 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3]
INFO  12:34:11,954 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,954 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:12,109 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO  12:34:12,120 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO  12:34:12,644 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO  12:34:12,645 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO  12:34:14,901 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -2
        at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
        at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
        at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
##### 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 website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: -2
##### ERROR ------------------------------------------------------------------------------------------
Comments (1)

hello I am a new user of GATK, until now I found the answer to my questions on your forum. Following is the command "java -jar ../GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -I 9485_realignedBam.fixed.bam -R hg19.fa -knownSites dbsnp_132_hg19.vcf -o recal_data.grp -filterMBQ" from wich I get this error message :

# # # # # ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -3
at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon (BAQ.java: 158)
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal (BAQ.java: 246)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM (BAQ.java: 542)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM (BAQ.java: 595)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM (BAQ.java: 530)
at org.broadinstitute.sting.utils.baq.BAQ.baqRead (BAQ.java: 663)
at
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map (BaseRecalibrator.java: 243)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map (BaseRecalibrator.java: 112)
at
at
at
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute (NanoScheduler.java: 219)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse (TraverseReadsNano.java: 91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse (TraverseReadsNano.java: 55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute (LinearMicroScheduler.java: 83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute (GenomeAnalysisEngine.java: 281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute (CommandLineExecutable.java: 113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start (CommandLineProgram.java: 237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start (CommandLineProgram.java: 147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main (CommandLineGATK.java: 91)
# # # # # ERROR -------------------------------------------- ----------------------------------------------
# # # # # ERROR A RUNTIME ERROR GATK has occurred (version 2.3-6-gebbba25)
# # # # # 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 forum GATK
# # # # # ERROR Visit our website and forum for extensive documentation and answers to
# # # # # ERROR Commonly asked questions http://www.broadinstitute.org/gatk
# # # # # ERROR
# # # # # ERROR MESSAGE: -3
# # # # # ERROR --------------------

I can not find it on a forum, can you explain it and help me

thank you

Comments (6)

Hello,

When I run countcovariates I get the following error message;

java.lang.ArrayIndexOutOfBoundsException: 0

I think this has to do with the bam output of an upstream stage of my pipeline because when I run CalculateHsMetrics with lenient validation stringency I get hundreds of errors like the following;


Ignoring SAM validation error: ERROR: Record 542418, Read name (null), Zero-length read without CS or CQ tag Ignoring SAM validation error: ERROR: Record 542419, Read name (null), Zero-length read without CS or CQ tag Ignoring SAM validation error: ERROR: Record 542420, Read name (null), Zero-length read without CS or CQ tag Ignoring SAM validation error: ERROR: Record 542421, Read name (null), Zero-length read without CS or CQ tag Ignoring SAM validation error: ERROR: Record 542422, Read name (null), Zero-length read without CS or CQ tag Ignoring SAM validation error: ERROR: Record 542423, Read name (null), Zero-length read without CS or CQ tag


When I examine some of these lines in the bam file I get the following...

samtools view 19542Js.bam | head -542420 | tail -5 (null) 73 11 67353661 25 0M = 67353661 0 * * RG:Z:HaloPilot-19542J XT:A:U NM:i:0 SM:i:25AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0 (null) 73 11 67353661 25 0M = 67353661 0 * * RG:Z:HaloPilot-19542J XT:A:U NM:i:0 SM:i:25AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0 (null) 97 11 67353661 25 0M 9 98215962 0 * * RG:Z:HaloPilot-19542J XT:A:U NM:i:0 SM:i:25AM:i:25 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0 (null) 99 11 67353661 17 0M = 67391488 37850 * * RG:Z:HaloPilot-19542J XT:A:U NM:i:0 SM:i:17AM:i:17 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0 (null) 97 11 67353661 25 0M 2 47378438 0 * * RG:Z:HaloPilot-19542J XT:A:U NM:i:0 SM:i:25AM:i:25 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0

Is there a problem with these reads? It looks like the reads aren't present. Is that causing the out of bounds error? How can I fix the bam file?

Any help would be greatly appreciated.

-Rob

Here is the rest of my output...


INFO 2012-12-04 14:29:58 SinglePassSamProgram Processed 1,000,000 records. INFO 2012-12-04 14:30:09 ProcessExecutor null device INFO 2012-12-04 14:30:09 ProcessExecutor 1 INFO 2012-12-04 14:31:20 ProcessExecutor null device INFO 2012-12-04 14:31:20 ProcessExecutor 1 INFO 2012-12-04 14:31:20 ProcessExecutor null device INFO 2012-12-04 14:31:20 ProcessExecutor 1 [Tue Dec 04 14:31:20 EST 2012] net.sf.picard.analysis.CollectMultipleMetrics done. Elapsed time: 2.26 minutes. Runtime.totalMemory()=2176253952 Run the recalibration INFO 14:31:28,081 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:31:28,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.5-32-g2761da9, Compiled 2012/04/26 15:31:17 INFO 14:31:28,084 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:31:28,084 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 14:31:28,084 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 14:31:28,085 HelpFormatter - Program Args: -T CountCovariates -l INFO -U ALLOW_UNSET_BAM_SORT_ORDER --default_platform illumina -R /proj/re2sqs/re2sq00/Resources/Bundle/human_g1k_v37.fasta --knownSites /proj/re2sqs/re2sq00/Resources/Bundle/dbsnp_132.b37.vcf -I 19542Js.bam --standard_covs -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile 19542JCovars.csv INFO 14:31:28,085 HelpFormatter - Date/Time: 2012/12/04 14:31:28 INFO 14:31:28,085 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:31:28,086 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:31:28,142 RodBindingArgumentTypeDescriptor - Dynamically determined type of /proj/re2sqs/re2sq00/Resources/Bundle/dbsnp_132.b37.vcf to be VCF INFO 14:31:28,155 GenomeAnalysisEngine - Strictness is SILENT INFO 14:31:28,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:31:28,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 INFO 14:31:28,459 RMDTrackBuilder - Loading Tribble index from disk for file /proj/re2sqs/re2sq00/Resources/Bundle/dbsnp_132.b37.vcf INFO 14:31:29,552 CountCovariatesWalker - The covariates being used here:
INFO 14:31:29,553 CountCovariatesWalker - ReadGroupCovariate INFO 14:31:29,553 CountCovariatesWalker - QualityScoreCovariate INFO 14:31:29,553 CountCovariatesWalker - CycleCovariate INFO 14:31:29,553 CountCovariatesWalker - DinucCovariate INFO 14:31:30,029 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] INFO 14:31:30,029 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 14:32:00,000 TraversalEngine - 3:20577904 2.34e+05 30.4 s 2.2 m 16.5% 3.1 m 2.6 m INFO 14:32:30,211 TraversalEngine - 5:113081909 4.36e+05 60.7 s 2.3 m 32.1% 3.2 m 2.1 m INFO 14:33:00,249 TraversalEngine - 7:5852794 7.07e+05 90.7 s 2.1 m 40.0% 3.8 m 2.3 m INFO 14:33:30,337 TraversalEngine - 9:78429646 9.62e+05 2.0 m 2.1 m 52.1% 3.9 m 110.8 s INFO 14:34:07,411 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: 0 at org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate.getValues(DinucCovariate.java:82) at org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager.computeCovariates(RecalDataManager.java:615) at org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesWalker.map(CountCovariatesWalker.java:381) at org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesWalker.map(CountCovariatesWalker.java:134) 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:246) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128) 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 1.5-32-g2761da9):
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: 0
ERROR ------------------------------------------------------------------------------------------
Comments (7)

Hi everyone,

I'm using IndelRealigner to do a local realignment in the standard GATK workflow. I have used this pipeline before with success, but am now met with this error. I could not find any other examples of this, so I am posting as per the instructions in the error.

Cheers,

A.B.

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException 
at org.broadinstitute.sting.utils.sam.AlignmentUtils.createIndelString(AlignmentUtils.java:710) 
at org.broadinstitute.sting.utils.sam.AlignmentUtils.leftAlignIndel(AlignmentUtils.java:603) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.determineReadsThatNeedCleaning(IndelRealigner.java:912) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.clean(IndelRealigner.java:681) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.cleanAndCallMap(IndelRealigner.java:547) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:519) 
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:114) 
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:104) 
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:52) 
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:71) 
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265) 
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:93)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.1-11-g13c0244):
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 website and forum for extensive documentation and answers to
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ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
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