Clarification on Prokka annotation within metaphor

[KatharinaHoff]

Dear developers of metaphor,

I find myself in confusion. I read your publication on metaphor, and from that publication, I am under the impression that metaphor would annotate MAGs with Prokka. Also, it is possible to activate Prokka when calling metaphor. But in our results, I fail to find the output of Prokka. Also, I do not see Prokka mentioned in https://metaphor-workflow.readthedocs.io/en/latest/ . I looked at the metaphor source code but I also don't quite understand how to proceed from this:

if config["prokka"]["activate"]:
        msg += " Please rerun it if you would like to annotate the genome bins."

What does this mean? Should we run Prokka outside or metaphor, or should metaphor somehow be relaunched?

I would appreciate a clarification :-)

Best wishes,

Katharina

[vinisalazar]

Dear @KatharinaHoff,

Firstly, thank you for your interest in using Metaphor.

To activate Prokka, edit your metaphor_settings.yaml file, which should be in your run directory, and set Prokka to be activated, like so:

prokka:
  activate: True
  args: "--quiet --force"

After you've done this, re-run Metaphor in the directory with your completed analysis. It should then start running Prokka for the filtered bins generated by DAS Tool.

Let me know how it goes.

Best, Vini

[s-junguy]

Hi, thank you for your suggestion. Unfortunately, we already ran Metaphor with Prokka activated and I also re-ran it after you suggested it but it still did not run. I noticed that Prokka also did not run in the metaphor test and that the necessary software for Prokka is not there.

Best, Julia

[vinisalazar]

Hello @s-junguy, thank you for reporting that.

I will look into this and try to submit a patch by next week.

Best, Vini

[vinisalazar]

Hello @KatharinaHoff and @s-junguy,

I just pushed a new release v1.7.11 which should fix the problems that you are facing. It should be available from Bioconda within a few hours, otherwise it's possible to install Metaphor from GitHub (clone the repo, activate the Metaphor conda environment and run pip install . in the directory).

Please update and let me know how it goes. Thanks again for reporting this problem.

Best, Vini

[s-junguy]

Hi @vinisalazar, sorry I totally forgot to give you an update. Prokka worked in the new version. Thanks!

Best, Julia