Database unclear
Hi Mustafa,
I have an issue with running your pipeline. The last error message mentioned a problem:
Activating conda environment: .snakemake/conda/799412dbd3c8e1dde671c5e3095cd32c_
[Wed Aug 30 20:08:31 2023]
Error in rule amrfinder:
jobid: 11
input: results/assembly/Pool-12_S14_L001_R1_001/contigs.fasta
output: results/amrfinder/Pool-12_S14_L001_R1_001.tsv
conda-env: /mnt/localdata/homes/mul21@helmholtz-hzi.de/ARpip/ARpip/.snakemake/conda/799412dbd3c8e1dde671c5e3095cd32c_
shell:
amrfinder --plus --threads 4 --ident_min 0.6 --coverage_min 0.6 -n results/assembly/Pool-12_S14_L001_R1_001/contigs.fasta -o results/amrfinder/Pool-12_S14_L001_R1_001.tsv
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
It seems to start amrfinder, but in the config.yaml I specified.
amr_tool:
amr_finder_plus: False
abricate: True
Do I have to provide the databases ncbi/card on my own and specify it somewhere or is it automatically downloading the databases? Haven't found a line in the provided scripts. Can you make this clear to me?
Thanks for any advice!
Best, Markus