bash: gatk: command not found

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Jeremy Sutherland

• December 01, 2021 19:20

a) GATK version used: gatk-4.2.3.0
b) Exact command used:  gatk
c) Entire error log: bash: gatk: command not found

 

Hello,

I'm trying to run gatk on my university's cluster. I do not have root privileges. Therefore, I need to use conda. 

I created the gatk env and installed the package following the instructions here: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

After activating the environment and running 'gatk' (or 'gatk --help', or 'gatk you-name-it'), I get this error: 'bash: gatk: command not found'

 

If I test whether the new variant filtering tool (CNNScoreVariants) is working using 'python -c "import vqsr_cnn"' I get the correct output: 'Using TensorFlow backend'. But I cannot get gatk to run anything in my env.

 

Any ideas what might be happening?

Jeremy

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  Jeremy Sutherland

  • December 01, 2021 19:33

  Additionally, when I run 'conda list', 'gatkpythonpackages' is listed.

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  Genevieve Brandt (she/her)

  • January 05, 2022 02:26

  Hi Jeremy Sutherland,

  Are you in the directory where you have stored the GATK jar files?

  Best,

  Genevieve

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