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problem in launching prokka

Good morning,

I installed prokka in conda and when I run the application it gives an error that I didn't understand.

<< /Users/nfs/abdeljalil> prokka
Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /Users/nfs/abdeljalil/anaconda3/bin/../perl5 /Users/nfs/abdeljalil/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /Users/nfs/abdeljalil/anaconda3/lib/site_perl/5.26.2 /Users/nfs/abdeljalil/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /Users/nfs/abdeljalil/anaconda3/lib/5.26.2 .) at /Users/nfs/abdeljalil/anaconda3/bin/prokka line 32.
BEGIN failed--compilation aborted at /Users/nfs/abdeljalil/anaconda3/bin/prokka line 32. >>

thank you for explaining the error to me.

prokka next-gen-sequencing genome
• 6,917 views • link
updated by Ram Ram • written by AbdelAbdel • AbdelAbdel

It looks to be complaining about not having a perl module installed called: Bio::Root::Version . Could you please share your commands on how you installed via conda, and then your prokka command?

• 0 views • link
written by kapsakcj kapsakcj
  • line install anaconda3: bash Anaconda3-5.2.0-Linux-x86_64.sh
  • line install prokka: conda install -c bioconda prokka
• 0 views • link
written by AbdelAbdel • AbdelAbdel

Your last line might have missed anything installed via the conda-forge conda channel. Prokka has a few dependencies that should be pulled from the conda-forge channel.

Try this command to create a new conda environment, which uses the conda-forge and bioconda channels to install:

conda create -n prokka-env -c conda-forge -c bioconda -c defaults prokka

To avoid having to type out -c CHANNEL each time you install something, you can follow the directions here: https://bioconda.github.io/user/install.html#set-up-channels

EDIT: added "-c defaults" to conda command, just in case it's necessary.

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written by kapsakcj kapsakcj

How did you install prokka?

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written by Asaf Asaf

line install prokka: conda install -c bioconda prokka

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written by AbdelAbdel • AbdelAbdel

1 answer

Did you get the solution of the issue? I tried these all but prokka still shows the error.

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written by Kumar Kumar

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