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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

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

raneffraneff Member
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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