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[ROCKY] - VariantAnnotator GATK castor bean

haojamhaojam Member

Dear Concern,

I have a query regarding VariantAnnotator available at GATK for castor bean _(Ricinus communis). The castor bean genome assembly fasta file available at JCVI http://castorbean.jcvi.org/downloads.php has been download and when I run the command there was error. I would be glad and highly appreciate for your support.



java -Xmx2g -jar GenomeAnalysisTK.jar -T VariantAnnotator -I /gsf-9_rmdup_rg.bam -R /ricinus_communis_val.fa -V /gsf-9_SNP.vcf -o /gsf-9_anno.txt



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    What was the error message?

  • haojamhaojam Member

    This is the error message when I run GATK VariantAnnotator -

    [[email protected] GenomeAnalysisTK-1.4-30-gf2ef8d1]$ java -Xmx2g -jar GenomeAnalysisTK.jar -R /state/partition1/results2/castor_bean/new_analysis/ricinus_communis_val.fa -T VariantAnnotator -I /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_rmdup_rg.bam -o /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_output.vcf --variant /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_SNP_flt.vcf -L /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_SNP_flt.vcf
    INFO 09:59:09,946 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 09:59:09,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-30-gf2ef8d1, Compiled 2012/02/17 20:18:04
    INFO 09:59:09,949 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 09:59:09,949 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
    INFO 09:59:09,950 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
    INFO 09:59:09,951 HelpFormatter - Program Args: -R /state/partition1/results2/castor_bean/new_analysis/ricinus_communis_val.fa -T VariantAnnotator -I /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_rmdup_rg.bam -o /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_output.vcf --variant /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_SNP_flt.vcf -L /state/partition1/results2/castor_bean/rocky_analysis/gsf-10_SNP_flt.vcf
    INFO 09:59:09,951 HelpFormatter - Date/Time: 2013/07/22 09:59:09
    INFO 09:59:09,951 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 09:59:09,952 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 09:59:13,460 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 1.4-30-gf2ef8d1):
    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 See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
    ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
    ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
    ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
    ERROR Name FeatureType Documentation
    ERROR VCF VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
    ERROR VCF3 VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
    ERROR ------------------------------------------------------------------------------------------
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