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

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer admin
edited March 2013 in Announcements

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.

Update: it seems the cases in the different tools aren't directly related. The PrintReads and HaplotypeCaller cases are now solved; still waiting on test files for the UG case.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Comments

  • nicolasnicolas Posts: 1

    New error in haplotypeCaller after arrayindexoutofboundsexception is fixed :

    ERROR ------------------------------------------------------------------------------------------
    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 ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
    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: START (3942) > (39) STOP -- this should never happen -- call Mauricio!
    ERROR ------------------------------------------------------------------------------------------

    What is the phone number of Mauricio?

  • yhoangyhoang Posts: 1Member

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

    ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 100
    ERROR A GATK RUNTIME ERROR has occurred (version 2.4-7-g5e89f01):
    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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • aeonsimaeonsim Posts: 64Member ✭✭

    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 ------------------------------------------------------------------------------------------
    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 ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
    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 ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • aeonsimaeonsim Posts: 64Member ✭✭

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

  • pascalgpascalg 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 ------------------------------------------------------------------------------------------
    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 ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
    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: 100
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • pascalgpascalg 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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • Martin1Martin1 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?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • gathreygathrey 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 ------------------------------------------------------------------------------------------
    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 ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-gf57256b):
    ERROR
    ERROR Please check the documentation guide 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: -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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • gathreygathrey Posts: 4Member

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

  • gathreygathrey 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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • gathreygathrey 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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • BiocybermanBiocyberman Posts: 9Member
    edited May 29

    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
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

  • BiocybermanBiocyberman Posts: 9Member

    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$TraverseReadsMap.apply(TraverseReadsNano.java:228)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.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 ------------------------------------------------------------------------------------------
    
  • BiocybermanBiocyberman Posts: 9Member
    edited May 30

    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
  • SheilaSheila Broad InstitutePosts: 624Member, GATK Developer, Broadie, Moderator admin

    @Biocyberman

    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

  • BiocybermanBiocyberman Posts: 9Member
    edited June 2

    @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
  • BiocybermanBiocyberman Posts: 9Member

    @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:

    text
    @‌name 
    T22.1
    +
    ;?!8@
    The correct one should be:
    text
    @‌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.
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer admin

    Ah, that would absolutely explain the error. Let us know if you can confirm.

    Geraldine Van der Auwera, PhD

  • BiocybermanBiocyberman Posts: 9Member

    @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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,629Administrator, GATK Developer 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

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