[question] Can I run ariba tool with all databases in one go?

[shigdon]

Hello!

I've setup Bactopia 2.2.0 on my institute HPC. In a previous run with Bactopia about a year ago, I was able to provide a path to a pre-configured ariba dataset and run the core workflow to generate ariba results for each isolate WGS library for each of the 8 or 9 databases configured (argannot,card,ncbi,megares,plasmidfinder,resfinder,srst2_argannot,vfdb_core,vfdb_full,virulencefinder). With the new version (2.2.0), and a new set of isolate WGS libraries, I tried to implement the workflow in as similar of a fashion as before by providing the path to the ariba databases when submitting the job, but ariba was not run at all.

The bactopia command I ran was:

bactopia \
    --samples FOFN.tsv \
    --centre CTMR \
    --sourmash_scale 1000 \
    --datasets /ceph/db/bactopia_2.0 \
    --use-bakta \
    --bakta_db /ceph/db/bakta/db \
    --run_checkm \
    --maxcpus 4 \
    --max_time 480 \
    --outdir bactopia_output \
    --nfconfig ctmr.config \
    -qs 96 \
    -resume

Is there an option I should have included to have ariba run with the main workflow?

Since discovering I have no ariba results, I've been exploring implementation of the ariba WF via bactopia-tools. I wrote another bash script for this, but when I try to provide a csv of all the databases to the ariba_db option I get an error that the specified comma-separated list of databases is invalid. I successfully ran the ariba-WF by providing a single database name, but what I actually want to do is run ariba for all of the isolates against each of the databases independently, in one go. Is this possible with the current release?

Thanks for the consideration.

[rpetit3]

Hi @shigdon,

I decided to move Ariba to a bactopia tool, a few versions ago, due to having to adjust the Bioconda recipe often enough that I didn't want it to affect the main pipeline too much.

I can see about allowing multiple databases through a CSV or something similar, in the latest dev version I'm working on.

Cheers,
Robert