Bakta exits with amrfinder error code 1 about bakta

[oschwengers]

it's online. I'll release a patch version soon.

[oschwengers]

Hi @naturepoker , thanks for trying Bakta and filing this issue!

Bakta internally takes advantage of AMRFinderPlus which in turn uses its own databases which must be setup once before the first execution. Seems like this is the case here.
Could you lease try amrfinder -u to update the internal AMRFinderPlus database?

If this is the case, I'll adopt the error message to help other users running into this.

[naturepoker]

Your solution worked perfectly

amrfinder -u

Above command updates the amrfinder database to version 2021-03-01.1 and the rest of the bakta process finished without any issues.

Thanks again!

[lauralwd]

Hi There, just confirming that I hit the same bug yesterday and that the same fix worked for me. Thanks for all the effort you put into bakta and for sharing it pre-publication. I'm running it on several genomes now and I'm curious to see how it compares!

Back on topic: for ease of use, I had the following two ideas:

1. Perhaps it's worth time/effort to include amrfinder --update in bakta_db download by default. At least that seems logical to me as long as bakta will halt on this amrfinder issue.
2. Secondly, how about a "pre-flight check" for amrfinder along with other dependencies in utils.py. Perhaps one check for amrfinder presence, and a second for the version number of the database in envs/bakta/share/amrfinderplus/data/latest/version.txt

Thanks again!

edit-----------
corrected version.txt path above.
Also, commit 750396f already is super helpfull for future users indeed.

[oschwengers]

Thanks @lauralwd for the confirmation and your suggestions - excellent ideas!

1. will be added as soon as possible.
2. is already implemented, just needs some testing.

[lauralwd]

Sound like great progress. If you'd appreciate a pull request just let me know. I'm not that fluent in python but I think I can handle this.

off-topic------------
annotations are looking great to me. At least similar to previous tools I used and trust, but the bakta names for genes are a bit more verbose which makes it easier for me to interpret. My favourite feature is the extra information for hypothetical proteins.

[oschwengers]

@lauralwd thanks for the offered help but it's already implemented: https://github.com/oschwengers/bakta/tree/catch-amrfinderplus-db-issue
I'm just running some final tests.