Hi everyone, I'm trying to run bacass using bakta. I've downloaded version 5.1 of the bakta database from https://zenodo.org/records/10522951. I've untarred the database to a folder called

db

I'm running version 2.4.0 of the pipeline (though the dev version gives the same error) on the following system:

Nextflow version: 24.10.5 build 5935
Java version: openjdk 17.0.6 2023-01-17 LTS
Operating system: Rocky Linux, VERSION="8.8 (Green Obsidian)",ID_LIKE="rhel centos fedora")
Bash version: version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Apptainer: V1.3.3
Executor: slurm or direct

Hardware HPC -- submitting pipeline from <http://tower.nf|tower.nf>
Tower Agent version 0.5.0 (build d758993)

Which gives this error:

predict rRNAs...
    found: 0
predict ncRNAs...
    found: 0
predict ncRNA regions...
    found: 0
predict CRISPR arrays...
    found: 1
predict & annotate CDSs...
    predicted: 116
    discarded spurious: 2
    revised translational exceptions: 0
    detected IPSs: 5
    found PSCs: 30
    found PSCCs: 27
    lookup annotations...
    conduct expert systems...
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/bakta/main.py", line 275, in main
    expert_amr_found = exp_amr.search(cdss, cds_aa_path)
  File "/usr/local/lib/python3.10/site-packages/bakta/expert/amrfinder.py", line 47, in search
    raise Exception(f"amrfinder error! error code: {proc.returncode}. Please, try 'amrfinder_update --force_update --database {amrfinderplus_db_path}' to update AMRFinderPlus's internal database.")
Exception: amrfinder error! error code: 1. Please, try 'amrfinder_update --force_update --database /mnt/scratch/projects/biol-tf-2018/nextflow/Data/bakta_db/2024.01.19_ver5.1/db/amrfinderplus-db' to update AMRFinderPlus's internal database.

Any thoughts on how to resolve this? Thanks.

Hi there, I am sorry but I dont get what

I'm trying to run bacass using bakta.

means. Could you elaborate?

Yes, sorry that's a little ambiguous. I'm trying to run bacass using bakta as the

--annotation_tool

. The pipeline is failing at the NFCORE_BACASSBACASSBAKTA_DBDOWNLOAD_RUN:BAKTA_BAKTA stage with the errors I outlined above.

Ah I see! Well, the error message seems clear:

Exception: amrfinder error! error code: 1. Please, try 'amrfinder_update --force_update --database /mnt/scratch/projects/biol-tf-2018/nextflow/Data/bakta_db/2024.01.19_ver5.1/db/amrfinderplus-db' to update AMRFinderPlus's internal database.

That means the database that you have set up doesnt apper to be as bakta wants. Did you try to apply the above command to your database (i.e. not to the one on scratch as indicated above ofc)?

I admit I've not tried that, I wasn't sure if this was an issue that others had come across. As I'm using the database that is provided by the author of bakta (i.e. from https://zenodo.org/records/10522951) I didn't know if there was another issue (e.g. apptainer container issue). I will setup the tool chain and try updating the database and see if that helps.

When I used bakta in the past I did need to update the db with armfinder also occasionally. So yes, I did come across that error, but not when running bacass but when running bakta in other settings.

That's useful to know. Thank you.