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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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Cant build new (my own) database #206

Open UzmaBasit opened 4 months ago

UzmaBasit commented 4 months ago

Hello, I'm attempting to create my own database, but it's not showing up in the list, even though the command seems to be working correctly:

makeblastdb -in sequences -title Uzma_prev -dbtype nucl -hash_index

However, when I use the abricate --list command, the recently built database isn't appearing in the list. Could you please provide some advice on this matter?

Thanks

nandan75 commented 4 months ago

Hi

I am actually getting the exact same problem as above!

I am running the command using a singularity container.

singularity exec $base_path/singularity_containers/abricate_1.0.1--ha8f3691_2.sif makeblastdb -in sequences -title PLSDB -dbtype nucl -hash_index

The command runs fine but I am unable to see a new entry in abricate --list and hence cannot use this database.

Appreciate your assistance,

regards,

Nandan

Note: Abricate works great for me with the default databases. thanks.

UzmaBasit commented 4 months ago

I believe the issue arises from the directory in which Abricate stores all the databases. In my case, it's my current directory, which was causing the problem. Upon installing Abricate via conda, I could observe my new database listed in the Abricate database.

buihoangphuc412 commented 4 months ago

Should you check the directory of miniconda3?. In my case, the abricate --list will list db in this folder: /lustre7/home/buihoangphuc412/miniconda3/db. Not from abricate database.