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Error when using SelectVariants (affects at least 1.6 - 2.1)

raneffraneff Posts: 1Member
edited September 2012 in Ask the GATK team
INFO  20:55:27,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-10-gdbc86ec, Compiled 2012/09/27 05:17:49 
INFO  20:55:27,109 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  20:55:27,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  20:55:27,109 HelpFormatter - Program Args: -R ../generated_consensus/ASW_woSNPsindelsdelsdupsinvsEUR.fa -T SelectVariants --variant:VCF /media/Data/raw_seq/ASW_allsamples_ASW_coords.vcf -o /media/Data/raw_seq/ASW_NA19914_ASW_coords.vcf -sn NA19914 
INFO  20:55:27,110 HelpFormatter - Date/Time: 2012/09/27 20:55:27 
INFO  20:55:27,110 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  20:55:27,110 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  20:55:27,132 GenomeAnalysisEngine - Strictness is SILENT 
INFO  20:55:27,208 RMDTrackBuilder - Creating Tribble index in memory for file /media/Data/raw_seq/ASW_allsamples_ASW_coords.vcf 
INFO  20:55:37,632 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.IllegalArgumentException: Start must be greater than 0!
    at org.broad.tribble.index.interval.MutableInterval.setStart(IntervalIndexCreator.java:134)
    at org.broad.tribble.index.interval.IntervalIndexCreator.addFeature(IntervalIndexCreator.java:72)
    at org.broad.tribble.index.DynamicIndexCreator.addFeature(DynamicIndexCreator.java:155)
    at org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:245)
    at org.broad.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:237)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:362)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:259)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:203)
    at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:132)
    at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:205)
    at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:85)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:852)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:713)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:244)
    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 2.1-10-gdbc86ec):
##### 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 must be greater than 0!
##### ERROR ------------------------------------------------------------------------------------------
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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin

    Could you try to isolate which record(s) are implicated in this error?

    Geraldine Van der Auwera, PhD

  • ebanksebanks Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin

    But first please confirm that your VCF adheres to the specification using the VCFTools validator.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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