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VariantRecalibrator Usage Error -- Hard Time Understanding What's Wrong with Command

ekofmanekofman Member, Broadie

Hi,

I'm trying to rerun a command that I think I successfully ran previously, but now (maybe due to a new version of GATK) seems to be incorrectly specified. Based on looking at the parameter requirements I think I'm specifying them correctly, so maybe these error messages are side effects stemming from something entirely different.

This is the command I'm running:
java -jar $gatk -T VariantRecalibrator -nt 8 -R references/mm10.fa -input GATK_recalibrated_D4M3A_1.vcf -resource:mgpv5snps,known=true,training=true,truth=true,prior=12.0 references/mgp.v5.merged.snps_all.dbSNP142.with_chr.sorted.vcf -an QD -an FS -an MQ -an DP -mode SNP -recalFile vqsr.recal -tranchesFile vqsr.tranches

ERROR MESSAGE: Argument with name '--resource' (-resource) is missing.
ERROR Argument with name '--mode' (-mode) is missing.
ERROR Argument with name '--tranches_file' (-tranchesFile) is missing.
ERROR Argument with name '--use_annotation' (-an) is missing.
ERROR Argument with name '--recal_file' (-recalFile) is missing.
ERROR ------------------------------------------------------------------------------------------

/var/spool/sge/uger-c071/job_scripts/2031112: line 28: -resource:mgpv5indels,known=true,training=true,truth=true,prior=12.0: command not found

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.8-8-gea82f19):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Argument with name '--recal_file' (-recalFile) is missing.
ERROR ------------------------------------------------------------------------------------------

/var/spool/sge/uger-c071/job_scripts/2031112: line 31: -mode: command not found

Any idea what I might be doing wrong? Thank for the guidance.

Best Answer

Answers

  • ekofmanekofman Member, Broadie

    The same thing happened with version 3.6

    ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions https://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Argument with name '--resource' (-resource) is missing.
    ERROR Argument with name '--mode' (-mode) is missing.
    ERROR Argument with name '--tranches_file' (-tranchesFile) is missing.
    ERROR Argument with name '--use_annotation' (-an) is missing.
    ERROR Argument with name '--recal_file' (-recalFile) is missing.
    ERROR ------------------------------------------------------------------------------------------

    /var/spool/sge/uger-c085/job_scripts/2066663: line 26: -resource:mgpv5indels,known=true,training=true,truth=true,prior=12.0: command not found

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions https://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Argument with name '--recal_file' (-recalFile) is missing.
    ERROR ------------------------------------------------------------------------------------------

    /var/spool/sge/uger-c085/job_scripts/2066663: line 29: -mode: command not found
    (END)

  • SheilaSheila Broad InstituteMember, Broadie admin

    @ekofman
    Hi,

    It looks like the command is not being read properly. Sometimes \ is misread, or an extra space could be throwing things off. Are you copying and pasting the command from somewhere else?

    -Sheila

  • ekofmanekofman Member, Broadie
    Accepted Answer

    I originally pasted it from a google doc so maybe that's it. I'll try writing it out from scratch and see what happens.

  • ekofmanekofman Member, Broadie
    edited April 2018

    @Sheila
    Writing it from scratch produced the same error actually. I'm still scratching my head and not seeing anything obviously wrong with the way I have written the command.

    Post edited by ekofman on
  • SheilaSheila Broad InstituteMember, Broadie admin

    @ekofman
    Hi,

    Hmm. Is this happening with the last release of GATK3 as well? Is it on the Broad server?

    Thanks,
    Sheila

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