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# Bug in various tools, 2.4-7 : "ArrayIndexOutOfBoundsException"

Posts: 8,043Administrator, GATK Dev admin
edited December 2014

As reported here:

If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread to let us know you have also had the same problem. Tell us what version of the GATK you were using and post your command line.

Thank you for your patience while we work to fix this issue.

### Latest update: we found that the three tools (PrintRead, HaplotypeCaller and UnifiedGenotyper) had different issues that only produced the same symptom (the ArrayIndexOutOfBoundsException error). The underlying issues have all been fixed in version 2.5. If you encounter an ArrayIndexOutOfBoundsException in later versions, it is certainly caused by a different problem, so please open a new thread to report the issue.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Tagged:

## Comments

• Posts: 1

New error in haplotypeCaller after arrayindexoutofboundsexception is fixed :

##### ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (3942) > (39) STOP -- this should never happen -- call Mauricio!
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:537)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipBothEndsByReferenceCoordinates(ReadClipper.java:235)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipBothEndsByReferenceCoordinates(ReadClipper.java:246)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipToRegion(ReadClipper.java:355)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.finalizeActiveRegion(HaplotypeCaller.java:585)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:477)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:69)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR ------------------------------------------------------------------------------------------

What is the phone number of Mauricio?

• Posts: 1Member

Hi, I am getting this problem for every sample I have

##### ERROR MESSAGE: 100

java -Xmx85g -jar /tools/gatk/2.4-7/gatk/GenomeAnalysisTK.jar \
-T BaseRecalibrator\
-R /refs/b37/human_g1k_v37.fasta \
-I bwamem.rmd.realigned.bam \
--knownSites /refs/b37/dbsnp_135.b37.vcf \
--knownSites /refs/b37/1000G_omni2.5.b37.sites.vcf\
-o bwamem_recal_data.grp

And also, I got another problem:
even after using --fix_misencoded_quality_scores in RealignerTargetCreator, there are some samples where I need to do the following step IndelRealigner with -allowPotentiallyMisencodedQuals, but with an older version (2.1.) I do not need to fix anything at all. What is the problem right here?

Thanks

Yen

• Posts: 8,043Administrator, GATK Dev admin

Hi @nicolas,

I will tell Mauricio that I'm going to post his phone number on the forum if he doesn't fix the bug quickly

More seriously, can you post the command line that led to this error?

Geraldine Van der Auwera, PhD

• Posts: 8,043Administrator, GATK Dev admin

Hi Yen,

Could you please try again with the latest version (2.4-9) and let me know if the first error still occurs?

Regarding the second problem, older versions of gatk did not check base quality encoding. So you could have already had that problem but without knowing it.

Geraldine Van der Auwera, PhD

• Posts: 65Member ✭✭

Hi
Looks like I'm still getting the ArrayIndexOutOfBoundsException: -1 with the 2.4.9 version of the HaplotypeCaller:

java -Xmx6G -jar GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -R bosTau6.fasta -T HaplotypeCaller -I odd.list -L chr13 -A LowMQ -stand_call_conf 50 -D /home/genmol2/chad/VCFs/Bos_taurus.dbsnp.137.ulg.vcf.gz -stand_emit_conf 10 -o HC-Trio-pMara.chr13.vcf -rf BadCigar -rf MaxInsertSize --maxInsertSize 1000

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -1
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.generateVCsFromAlignment(GenotypingEngine.java:675)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:140)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:500)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:69)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR ------------------------------------------------------------------------------------------
• Posts: 8,043Administrator, GATK Dev admin

Hi @aeonsim,

i believe that's the second error case that we found using your data -- the fix for that problem is in our development version, but it was too complex to patch onto 2.4, so it will only be released in 2.5. That said the fix is in the nightly build of our dev tree, so you can try the latest nightly to confirm whether this is indeed fixed for you.

Geraldine Van der Auwera, PhD

• Posts: 65Member ✭✭

@Geraldine_VdAuwera Thanks I've had a go with the nightly version and I am no longer getting the error.

• Posts: 2Member

Hi,

I have the same error as Yen as shown below. I tried the current version (v2.4-9-g532efad) and the nightly (nightly-2013-04-03-g231698f).

Thanks,

Pascal

java -Xmx14g -jar GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-I realigned.bam \
-R rn5.fa \
-S LENIENT \
--log_to_file BR.log \
-o realigned.recal.bam \
--plot_pdf_file recal.pdf \
--intermediate_csv_file recal.csv \
--knownSites dbSNP136.vcf

INFO 19:19:14,020 ProgressMeter - chr14:32233412 9.07e+07 5.3 h 3.5 m 24.1% 22.1 h 16.8 h
INFO 19:20:06,316 GATKRunReport - Uploaded run statistics report to AWS S3

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 100
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsIndel(BaseRecalibrator.java:387)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131)
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.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:109)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR ------------------------------------------------------------------------------------------
• Posts: 8,043Administrator, GATK Dev admin

Hi Pascal,

Could you please validate your input files? I see you're running with lenient validation, which may be letting through malformed data.

Geraldine Van der Auwera, PhD

• Posts: 2Member

Thanks Geraldine, you are right, I should not run it in lenient mode.
I checked the file by ValidateSamFile (and the vcf file by vcf-validator), but the same error occurs.

• Posts: 8,043Administrator, GATK Dev admin

I see. Can you please try again with our very latest nightly build (see Downloads page)? I think we have a fix for this now.

If that still doesn't work I'll need you to upload a snippet of your bam file to our server. Detailed instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

Geraldine Van der Auwera, PhD

• Posts: 6Member

Hello, I have the same error for version 2.5.2. I my case it happens with the BaseRecalibrator:

INFO 15:58:09,019 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:58:09,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
INFO 15:58:09,023 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:58:09,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:58:09,031 HelpFormatter - Program Args: -T BaseRecalibrator -nct 4 -R /data/common/Genomes/H.Sapiens/hg19_sorted/gatk/ucsc.hg19.fasta -knownSites /data/common/gatk_bundle_2.3/d
bsnp_137.hg19.vcf -knownSites /data/common/gatk_bundle_2.3/1000G_omni2.5.hg19.vcf -knownSites /data/common/gatk_bundle_2.3/hapmap_3.3.hg19.vcf -I 5073.realign.bam -cov ReadGroupCovariat
e -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o 5073.recal_data.grp
INFO 15:58:09,031 HelpFormatter - Date/Time: 2013/05/02 15:58:09

and the stack trace:

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 100
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsIndel(BaseRecalibrator.java:387)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131)
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)

Is this the same error?

• Posts: 8,043Administrator, GATK Dev admin

Hi Martin,

I think this is different from the others in this thread, but it might be the same as a similar case I'm currently looking into for someone else here: http://gatkforums.broadinstitute.org/discussion/2551/error-stack-trace

Can you tell me if your file passes validation?

Geraldine Van der Auwera, PhD

• Posts: 4Member

Hello!

I seem to be having simiar errors to the ones posted above but only while running HaplotypeCaller. Has this bug been fixed?

I did not have any trouble with Unifiedgenotyper. I got the same error using multiple bam files or a single merged_bam file. I am running GATK version 2.52 on ubuntu.

here is the stack trace:

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -50
at org.broadinstitute.sting.utils.BaseUtils.convertIUPACtoN(BaseUtils.java:172)
at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:272)
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:221)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:70)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR MESSAGE: -50

My bam file is deduplicated-merged-realigned. I am running a very stripped down command as I am still scoping out what works trying to understand how this works. But here is the code:

java -jar ~/Bioinformatics/GATK2/GenomeAnalysisTK.jar -T HaplotypeCaller -R ~/Bioinformatics/Aligned/agamp318.fa -I merged_realigned.bam -o ~/Bioinformatics/gatk_haplotypes/merged_bam.raw.snps.indels.vcf -debug

thanks for the help!
GA

• Posts: 8,043Administrator, GATK Dev admin

Can you please try running this again with the latest nightly build (see Downloads page)? The nightlies are built from the latest internal development version; they are not supported for general use but that will tell us if the bug is still present or not.

Geraldine Van der Auwera, PhD

• Posts: 4Member

Sure. I'll try that and get back to you

• Posts: 4Member

I have not been able to run the nightly build because I am getting 'unsupported major.minor version 51.0' errors for java. I am running the latest java version and I am getting the same error on both linux and mac. I went all the way back to the oldest nightly build available, but I have the same error. So unable to figure this out but will keep trying.

• Posts: 8,043Administrator, GATK Dev admin

I see -- @gathrey, when you say latest java version, which one do you mean exactly? We have been working on migrating from Java 6 to 7 so we're interested in the details if there are any version incompatibilities.

Geraldine Van der Auwera, PhD

• Posts: 4Member

@Geraldine: I am running Java Version 7 update 21 (build 1.7.0_21_b12)

here is the full text of the error I am getting when I try to initiate GenomeAnalysisTK.jar

Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) Hope this is useful and thanks for helping! GA • Posts: 8,043Administrator, GATK Dev admin Hmm, that's strange. Could you please run java -version and javac -version, and post the complete output of each? Geraldine Van der Auwera, PhD • Posts: 25Member edited May 2014 Hello, I have been search around about this problem and decided to post my report here. This seems to be a known bug, but I don't know if my case has anything special because of my colorspace data. uname -a Linux localhost 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux java -version java version "1.7.0_55" Java(TM) SE Runtime Environment (build 1.7.0_55-b13) Java HotSpot(TM) 64-Bit Server VM (build 24.55-b03, mixed mode) picard-tools ValidateSamFile I=/home/user/test/sample6.sorted.bam R=/home/user/test/genomes/GRCh37wd.fa INFO 2014-05-30 12:05:17 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 66s. Last read position: 8:75,928,866 INFO 2014-05-30 12:06:19 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:02:08s. Time for last 10,000,000: 61s. Last read position: 22:16,686,966 No errors found gatk -T BaseRecalibrator -o /home/user/test/sample6.sorted.grp \ > -I /home/user/test/sample6.sorted.bam \ > -R /home/user/test/genomes/GRCh37wd.fa --solid_nocall_strategy PURGE_READ \ > --solid_recal_mode SET_Q_ZERO_BASE_N \ > --knownSites /home/user/test/genomes/variation/dbsnp_138.vcf \ > -L /home/user/test/bed/S04380110_Covered_editted.bed INFO 00:43:38,786 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:43:38,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 00:43:38,788 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 00:43:38,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 00:43:38,792 HelpFormatter - Program Args: -T BaseRecalibrator -o /home/user/test/sample6.sorted.grp -I /home/user/test/sample6.sorted.bam -R /home/user/test/genomes/GRCh37wd.fa --solid_nocall_strategy PURGE_READ --solid_recal_mode SET_Q_ZERO_BASE_N --knownSites /home/user/test/genomes/variation/dbsnp_138.vcf -L /home/user/test/bed/S04380110_Covered_editted.bed INFO 00:43:38,794 HelpFormatter - Executing as user@localhost on Linux 3.5.0-45-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13. INFO 00:43:38,794 HelpFormatter - Date/Time: 2014/05/30 00:43:38 INFO 00:43:38,795 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:43:38,795 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:43:39,312 GenomeAnalysisEngine - Strictness is SILENT INFO 00:43:39,540 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 00:43:39,558 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  00:43:39,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 INFO 00:43:40,342 IntervalUtils - Processing 50390601 bp from intervals INFO 00:43:40,395 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 00:43:40,659 GenomeAnalysisEngine - Done preparing for traversal INFO 00:43:40,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 00:43:40,660 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 00:43:40,702 BaseRecalibrator - The covariates being used here: INFO 00:43:40,703 BaseRecalibrator - ReadGroupCovariate INFO 00:43:40,704 BaseRecalibrator - QualityScoreCovariate INFO 00:43:40,704 BaseRecalibrator - ContextCovariate INFO 00:43:40,705 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 00:43:40,705 BaseRecalibrator - CycleCovariate INFO 00:43:40,710 ReadShardBalancer$1 - Loading BAM index data
INFO  00:43:41,458 ReadShardBalancer$1 - Done loading BAM index data INFO 00:43:49,148 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 58 at org.broadinstitute.sting.utils.recalibration.RecalUtils.isColorSpaceConsistent(RecalUtils.java:793) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:130) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8): ##### 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: 58 ##### ERROR ------------------------------------------------------------------------------------------  Post edited by Biocyberman on • Posts: 8,043Administrator, GATK Dev admin Hi @Biocyberman, could you try using the latest nightly build (see Downloads) and let me know if the issue persists? Geraldine Van der Auwera, PhD • Posts: 25Member Hi Geraldine, I have just tried with the latest nightly build: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 58 at org.broadinstitute.gatk.utils.recalibration.RecalUtils.isColorSpaceConsistent(RecalUtils.java:821) at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246) at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:130) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNanoTraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) 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 nightly-2014-05-29-g33cdc45): ##### 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: 58 ##### ERROR ------------------------------------------------------------------------------------------  • Posts: 25Member edited May 2014 Update: I tested with first 2000 records of my bam file. It worked fine. So I think there is something in my BAM file that BaseRecalibrator is not prepared to deal with. I can send my bam file (3GB) if it can be any help for the debug process. Or is there a way to identify the problematic BAM record(s)? Post edited by Biocyberman on • Broad InstitutePosts: 1,409Member, GATK Dev, Broadie, Moderator, DSDE Dev admin Hi, Please narrow down the file to a small snippet where the error occurs and send it to us. Directions on how to upload are here: http://gatkforums.broadinstitute.org/discussion/1894/how-do-i-submit-a-detailed-bug-report#latest -Sheila • Posts: 25Member edited June 2014 @Sheila‌ Thanks for the instructions. I did not know about the -L option and the PrintReads tool. I already uploaded the BAM snipet to gsapubftp@ftp.broadinstitute.org this file: biocbyerman.exception58.tar.gz. I usedGRCh37 with decoy reference genome. The BAM snipet contains 53 records. I am wondering if it has something to do with the way novoalignCS calculates quality score of aligned bases which may result in unusually high score between 80 and 90. And GATK does not expect this. Post edited by Biocyberman on • Posts: 25Member @Sheila‌ and @Geraldine_VdAuwera‌: If this could be any help. It is rather my mistake actually. I had a bug in the read trimming program which produce malformed colorspace reads like this: @‌name T22.1 + ;?!8@  The correct one should be: @‌name T22.1 + ;?!8  Where the qualities line should be one char less than the bases line. I am regenerating the BAM file and will try again. • Posts: 8,043Administrator, GATK Dev admin Ah, that would absolutely explain the error. Let us know if you can confirm. Geraldine Van der Auwera, PhD • Posts: 25Member @Geraldine_VdAuwera‌ : It took me some time to get back to the work and got it right. I want to confirm that the malformed CSFATQ entries to be blamed (That's a nicer way to tell my all mistake :-) ). But I think if Picard/GATK can do some check about this, it will be less confusing for similar case. However, I understand that too much fool-proof will slow down the program. • Posts: 8,043Administrator, GATK Dev admin Thanks for confirming, @Biocyberman‌. As you guessed, it is difficult to check for every possible source of error. But that might be something that can be checked by Picard ValidateSAMFile. Geraldine Van der Auwera, PhD • AustriaPosts: 22Member Hi, I've looked around where to post my question, and didn't find any more appropriate place than here. Please redirect me if I've chosen wrongly or I missed the relevant post. I'm using GATKv3.3 to run the protocol of HC followed by CombineGVCFs in six batches of ~190 individuals each and finally GenotypeGVCFs of these six gVCFs. My failed command is below followed by the error message. In addition, I can tell you that my output file (1135g_.vcf) is empty even when it crashed after more than two hours of running time. Kindly, Alberto java -Djava.io.tmpdir=mytmp -Xmx232g -jar $EBROOTGATK/GenomeAnalysisTK.jar -R$ref -T GenotypeGVCFs -nt 40 -o 1135g_.vcf -V 1135g_listof.list

**##### ERROR ------------------------------------------------------------------------------------------

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 10000
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL(ReferenceConfidenceVariantContextMerger.java:357)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.jav
a:331)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:134)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:200)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:119)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
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 ------------------------------------------------------------------------------------------**
• Posts: 8,043Administrator, GATK Dev admin

Hi @Fer,

This must be a different problem, albeit with the same symptom (see my update to the original post above, which I added to clarify). Please check if this issue reproduces without the -nt argument and if it does, post it as a new thread (using the "Ask a question" button) in the "Ask the GATK team" category.

Geraldine Van der Auwera, PhD

• Posts: 4Member

Hi,

I wonder what is the status of the bug reported by @Fer? I run into the exactly the same error when using v3.3.0 but without -nt.

Best,
Daniel

Error trace:
java.lang.ArrayIndexOutOfBoundsException: 10000
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL(ReferenceConfidenceVariantContextMerger.java:357)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:331)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:134)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:200)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:119)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
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)

• Broad InstitutePosts: 1,409Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

@dtaliun
Hi Daniel,

Can you post the exact command you used?

Thanks,
Sheila

• Posts: 4Member

Hi Sheila,

The command line:
java -jar -Xmx8g GenomeAnalysisTK.jar -T GenotypeGVCFs -R hs37d5.fa --variant 16_7000001_8000000.vcf.gz -o 16_7000001_8000000.genotypes.vcf.gz

Best,
Daniel

• Broad InstitutePosts: 1,409Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

@dtaliun
Hi Daniel,

I have already submitted a bug report for this. It just has not been fixed yet. You can follow this thread for updates: http://gatkforums.broadinstitute.org/discussion/4898/java-lang-arrayindexoutofboundsexception-in-genotypegvcfs-when-multi-threading

-Sheila

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