Issues with VFDB Integration and Gene Detection in Abricate

[mirulee]

Hello,

I've been primarily using Abricate with the VFDB database and have encountered a couple of issues that I hope can be addressed.

1. I noticed that Abricate utilizes the VFDB's setA (core dataset) for its database. Attempting to create a custom database using setB (all dataset) from VFDB, I've run into a problem. While Abricate neatly extracts and organizes gene names in its output, the VFDB database format combines gene names with additional information, such as "VFG032131(gb|WP_009917653) (actA) actin-assembly inducing protein precursor [ActA (VF0066) - Motility (VFC0204)] [Listeria monocytogenes SLCC2540]", making it difficult to separately identify gene names. How does Abricate manage to extract gene names separately when using its default database?

2. For certain samples, specific genes are not detected by Abricate, yet when I submit the same samples directly to the VFDB site, those genes are identified. What could be causing this discrepancy?

Thank you for your assistance in resolving these matters. I look forward to your guidance and suggestions.