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IndelRealigner Stack Trace Error

AlexanderBAlexanderB Member Posts: 17
edited October 2012 in Ask the GATK team

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
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

~

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Hi Alexander, can you please post your command line?

    Geraldine Van der Auwera, PhD

  • AlexanderBAlexanderB Member Posts: 17
    edited October 2012

    File names changed, but here it is:

    INFO  10:33:14,849 HelpFormatter - ---------------------------------------------------------------------------------
    INFO  10:33:14,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-11-g13c0244, Compiled 2012/09/29 06:03:05
    INFO  10:33:14,853 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  10:33:14,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  10:33:14,854 HelpFormatter - Program Args: -I my_bam.bam -R human_g1k_v37.fasta -T IndelRealigner -targetIntervals forIndelRealigner.intervals -o output_file.bam
    INFO  10:33:14,854 HelpFormatter - Date/Time: 2012/10/19 10:33:14
    INFO  10:33:14,854 HelpFormatter - ---------------------------------------------------------------------------------
    INFO  10:33:14,854 HelpFormatter - ---------------------------------------------------------------------------------
    INFO  10:33:15,033 GenomeAnalysisEngine - Strictness is SILENT
    INFO  10:33:15,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO  10:33:15,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
    INFO  10:33:16,698 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
    INFO  10:33:16,699 TraversalEngine -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining
    INFO  10:33:46,819 TraversalEngine -       1:1660422        7.12e+05   30.1 s       42.3 s      0.1%        15.6 h    15.6 h
    INFO  10:34:47,724 TraversalEngine -      1:12898530        1.84e+06   91.0 s       49.4 s      0.4%         6.1 h     6.1 h
    INFO  10:35:19,115 TraversalEngine -      1:16119587        2.40e+06    2.0 m       51.0 s      0.5%         6.5 h     6.5 h
    INFO  10:35:49,669 TraversalEngine -      1:16890144        2.60e+06    2.5 m       58.8 s      0.5%         7.8 h     7.8 h
    INFO  10:36:19,765 TraversalEngine -      1:16902822        2.69e+06    3.1 m       68.2 s      0.5%         9.3 h     9.3 h
    INFO  10:36:50,337 TraversalEngine -      1:17087279        2.92e+06    3.6 m       73.2 s      0.6%        10.8 h    10.7 h
    INFO  10:37:20,379 TraversalEngine -      1:21094109        3.37e+06    4.1 m       72.2 s      0.7%        10.0 h     9.9 h
    INFO  10:37:50,421 TraversalEngine -      1:24297176        3.79e+06    4.6 m       72.3 s      0.8%         9.7 h     9.6 h
    INFO  10:38:20,855 TraversalEngine -      1:27312193        4.19e+06    5.1 m       72.6 s      0.9%         9.6 h     9.5 h
    INFO  10:38:50,859 TraversalEngine -      1:31344075        4.54e+06    5.6 m       73.6 s      1.0%         9.2 h     9.1 h
    INFO  10:39:20,863 TraversalEngine -      1:36031790        5.07e+06    6.1 m       71.9 s      1.2%         8.7 h     8.6 h
    INFO  10:39:50,915 TraversalEngine -      1:40184398        5.56e+06    6.6 m       71.0 s      1.3%         8.5 h     8.3 h
    INFO  10:40:20,926 TraversalEngine -      1:44159689        6.03e+06    7.1 m       70.3 s      1.4%         8.3 h     8.2 h
    INFO  10:40:50,985 TraversalEngine -      1:46507637        6.37e+06    7.6 m       71.3 s      1.5%         8.4 h     8.3 h
    INFO  10:41:22,078 TraversalEngine -      1:52817990        6.78e+06    8.1 m       71.6 s      1.7%         7.9 h     7.8 h
    INFO  10:41:56,621 TraversalEngine -      1:58521993        7.19e+06    8.7 m       72.4 s      1.9%         7.7 h     7.5 h
    INFO  10:42:27,105 TraversalEngine -      1:65158040        7.43e+06    9.2 m       74.1 s      2.1%         7.3 h     7.1 h
    INFO  10:42:57,107 TraversalEngine -      1:74507435        7.77e+06    9.7 m       74.7 s      2.4%         6.7 h     6.6 h
    INFO  10:43:28,834 TraversalEngine -      1:79356901        8.06e+06   10.2 m       75.9 s      2.6%         6.6 h     6.5 h
    INFO  10:43:59,926 TraversalEngine -      1:89448664        8.43e+06   10.7 m       76.3 s      2.9%         6.2 h     6.0 h
    INFO  10:44:30,539 TraversalEngine -      1:93307376        8.71e+06   11.2 m       77.4 s      3.0%         6.2 h     6.0 h
    INFO  10:45:05,820 TraversalEngine -      1:98012118        8.92e+06   11.8 m       79.5 s      3.2%         6.2 h     6.0 h
    INFO  10:45:37,294 TraversalEngine -     1:102252090        9.11e+06   12.3 m       81.3 s      3.3%         6.2 h     6.0 h
    INFO  10:46:07,308 TraversalEngine -     1:109817173        9.54e+06   12.8 m       80.8 s      3.5%         6.0 h     5.8 h
    INFO  10:46:37,332 TraversalEngine -     1:111983550        9.87e+06   13.3 m       81.2 s      3.6%         6.2 h     5.9 h
    INFO  10:47:08,576 TraversalEngine -     1:114940358        1.01e+07   13.9 m       82.2 s      3.7%         6.2 h     6.0 h
    INFO  10:47:38,583 TraversalEngine -     1:118693138        1.05e+07   14.4 m       82.4 s      3.8%         6.3 h     6.0 h
    INFO  10:48:08,626 TraversalEngine -     1:142721975        1.08e+07   14.9 m       82.8 s      4.6%         5.4 h     5.1 h
    INFO  10:48:39,002 TraversalEngine -     1:142806681        1.08e+07   15.4 m       85.3 s      4.6%         5.6 h     5.3 h
    INFO  10:49:10,880 TraversalEngine -     1:143209661        1.09e+07   15.9 m       87.3 s      4.6%         5.7 h     5.5 h
    INFO  10:49:40,902 TraversalEngine -     1:144891029        1.14e+07   16.4 m       86.5 s      4.7%         5.9 h     5.6 h
    INFO  10:50:21,961 TraversalEngine -     1:145116491        1.14e+07   17.1 m       89.7 s      4.7%         6.1 h     5.8 h
    INFO  10:50:52,009 TraversalEngine -     1:145533412        1.18e+07   17.6 m       89.7 s      4.7%         6.2 h     6.0 h
    

    etc. etc. etc.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Thanks. Is your intervals file BED-formatted, by any chance?

    Geraldine Van der Auwera, PhD

  • AlexanderBAlexanderB Member Posts: 17
    edited October 2012

    I generated it using the RealignTargetCreator passing minimal inputs (input bam, reference). The .intervals file looks like:

    ...
    x:y \n
    x:y'-z'
    ...

    Where y, y', and z' are all integers. x can be an integer, or X/Y/MT. Separation is newline.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    OK, just checking it's not an 'off by one' error, we get a lot of those from people with BED files.

    Can you check with the latest version? We're on build 13, I believe. Try downloading that and running again on the interval where you encountered the error.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    If it's still not working with the latest release, please upload the BAM segment where the error occurs to our FTP server (see FAQs) and we'll take a closer look at it.

    Geraldine Van der Auwera, PhD

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