ValueError: invalid literal for int() with base 10: 'NA'

[taylorreiter]

Conda env:

channels:
 - conda-forge
 - bioconda
 - defaults
dependencies:
 - bakta=1.2.1

Configured db with:

bakta_db download --output inputs/bakta_db

Reprex:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/567/975/GCA_001567975.1_ASM156797v1/GCA_001567975.1_ASM156797v1_genomic.fna.gz
gunzip GCA_001567975.1_ASM156797v1_genomic.fna.gz
bakta --db inputs/bakta_db/db --prefix GCA_001567975.1 --locus-tag GCA_001567975.1 GCA_001567975.1_ASM156797v1_genomic.fna

std out & Error:

parse genome sequences...
        imported: 389
        filtered & revised: 389
        contigs: 389
predict tRNAs...
        found: 37
predict tmRNAs...
        found: 1
predict rRNAs...
        found: 3
predict ncRNAs...
        found: 4
predict ncRNA regions...
        found: 5
predict CRISPR arrays...
        found: 2
predict & annotate CDSs...
        predicted: 3903
        discarded spurious: 31
        detected IPSs: 3490
        found PSCs: 242
        found PSCCs: 39
        lookup annotations...
        conduct expert systems...
Traceback (most recent call last):
  File "/home/tereiter/github/2021-orpheum-refseq/.snakemake/conda/24979bf8344a46bbf88e8ed6dc80992f/bin/bakta", line 10, in <module>
    sys.exit(main())
  File "/home/tereiter/github/2021-orpheum-refseq/.snakemake/conda/24979bf8344a46bbf88e8ed6dc80992f/lib/python3.9/site-packages/bakta/main.py", line 279, in
main
    expert_amr_found = exp_amr.search(cdss, cds_aa_path)
  File "/home/tereiter/github/2021-orpheum-refseq/.snakemake/conda/24979bf8344a46bbf88e8ed6dc80992f/lib/python3.9/site-packages/bakta/expert/amrfinder.py", line 54, in search
    query_cov = int(alignment_length) / len(cds['aa'])
ValueError: invalid literal for int() with base 10: 'NA'

log file attached:
GCA_001567975.1.log

[oschwengers]

Hi @taylorreiter , thanks for reporting this!
Annotating this genome revealed an HMM-only AMRFinder hit. Interestingly, this never happened on all our test genomes - or we somehow never recognized it.

I pushed a fixing commit e9ff01c. I run a couple of tests and trigger a new patch release. I let you know once it is public.
Thanks again!

[oschwengers]

I tested the fixing commit mentioned above and released a new version v1.2.2.

It is now alive but it might take a moment until it's downloadable via BioConda.

Thanks again for pointing this out.
Best regards!