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Could not find walker

bishwobishwo Posts: 30Member

Am i just stupid or there is something wrong going on ?

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Could not find walker with name: RealignerTargetCreator
##### ERROR ------------------------------------------------------------------------------------------

$ java -jar GenomeAnalysisTK.jar -T IndelRealigner 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Could not find walker with name: IndelRealigner
##### ERROR ------------------------------------------------------------------------------------------

$ java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Could not find walker with name: UnifiedGenotyper
##### ERROR ------------------------------------------------------------------------------------------

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,468Administrator, Dev admin

    We had a few issues with the release system overnight, looks like you got a bad package. Please download the latest version -- you'll get the new v 2.2 in the bargain.

    Geraldine Van der Auwera, PhD

  • bishwobishwo Posts: 30Member

    I spotted the cause of this problem. It was because of '+' that was in the directory name 'SNP+Indels' inside which GATK jar file and other data files were located. When i renamed the directory removing '+' it worked.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,468Administrator, Dev admin

    Ah, that makes sense -- a path name with funny characters is nobody's friend. Glad to hear your problem's solved.

    Geraldine Van der Auwera, PhD

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