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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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Issue after updating databases #165

Open Walwa opened 3 years ago

Walwa commented 3 years ago

I had abricate running then I updated the standard databases (except card and megares) and it now runs but does not detect except for specific databases I built. I got error messages when I failed to update megares and card, that said the compressed files could not be downloaded. Then I downloaded the databases via my browser and put them in the database folders but they do not get recognised as present. I run Abricate v1.0.1 on Red Hat Linux kernel version 3.10.0-1160.21.1el7.x86_64 . I do not get any error messages when checking genomes against a database, just a 0 genes found comment. When I run my bespoke databases I get gene detection, so it appears to be something about my updated databases. Thank you for the software and your help.

andersgs commented 3 years ago

@Walwa can you elaborate on how you built the databases?

Can you also confirm the version of blast you are using, and that it has not been recently updated?

Thank you.

Walwa commented 3 years ago

Hi and thank you for your fast response.

update database : abricate-get_db —db card build database : abricate —setupdb

BLAST v 2.10.2 dowloaded from anaconda when installed abricate in an enviroment.

Barbara

On 7/04/2021, at 12:34 PM, Anders Goncalves da Silva @.***> wrote:

@Walwa https://github.com/Walwa can you elaborate on how you built the databases?

Can you also confirm the version of blast you are using, and that it has not been recently updated?

Thank you.

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