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A USER ERROR has occurred: TMP_DIR is not a recognized option

WeichiWeichi Member
edited September 12 in Ask the GATK team

After upgrade the GATK4 version to 4.1.3.0
I saw this error when running BaseRecalibrator and HaplotypeCaller.

A USER ERROR has occurred: TMP_DIR is not a recognized option

I found that Optional Common Arguments was changed from --TMP_DIR to --tmp-dir.
After change --TMP_DIR into --tmp-dir, the problem was solved.
But some function like MarkDuplicates, the Temp directory argument still --TMP_DIR.

I'm just curious to know why to do this small change?
May I possibly suggest to unify it?

Post edited by Weichi on

Best Answer

  • SkyWarriorSkyWarrior Turkey ✭✭✭
    edited September 12 Accepted Answer

    Some parts of the gatk package comes from picard which uses a seperate command line argument consensus still compared to original gatk tools. You may need to bear with it for a while until complete merging and alignment is done I guess.

    Other than that you may try to symlink the tmp folder before you run your actual gatk argument without tmp_dir change and therefore you will not be messing with multiple argument styles but this approach is also not very convenient from a system wide perspective.

Answers

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited September 12 Accepted Answer

    Some parts of the gatk package comes from picard which uses a seperate command line argument consensus still compared to original gatk tools. You may need to bear with it for a while until complete merging and alignment is done I guess.

    Other than that you may try to symlink the tmp folder before you run your actual gatk argument without tmp_dir change and therefore you will not be messing with multiple argument styles but this approach is also not very convenient from a system wide perspective.

  • WeichiWeichi Member

    I see.
    Thanks for your explanation.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Thank you for your input @SkyWarrior. We appreciate your contribution to the community!

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