Exception: amrfinder error! error code: 1 about bakta

[Daniel-VM]

Hi!,

I had the same issue with docker. In my case I used the database db-light.tar.gz from https://zenodo.org/records/7669534. it worked after amrfinder_update --force_update --database ${BAKTADB}/amrfinderplus-db.

Could the Bakta databases be updated in Zenodo to solve the issue by fixing amrfinderplus-db?.

Many thanks!

[Daniel-VM]

Downloading db-light with bakta v1.8.1(bakta_db download --type light) and running gene-annotation with bakta v1.8.2 wokrs.

It also works with bakta v1.8.1. See: Issue#221

[oschwengers]

Hi, @gidjes & @Daniel-VM ,
I just conducted another up-to-date round trip test in a fresh Conda environment for both Bakta v1.8.1 and v1.8.2 downloading v5.0 of the light db from Zenodo annotating the provided genome (55001924_1.fasta.zip). Of note, internally, AMRFinderplus v3.11.26 is used.

mamba create -p ./conda-env bakta=[1.8.1|1.8.2]
mamba activate conda-env
bakta_db download --type light
bakta --db ./db-light/ --verbose --output test 55001924_1.fasta

After fixing the FASTA header line of this file bakta succeeded w/o any errors.
So, unfortunately, I cannot reproduce this error. Maybe an update of AMRFinder itself might help?

[Daniel-VM]

Many thanks @oschwengers!!! I confirm that Bakta v1.8.2 works now with db-light 🚀 . So no need to mix versions :)