AMRFinderPlus database not installed!

[dfeistel3]

I keep getting this error: ERROR: AMRFinderPlus database not installed! Please, install AMRFinderPlus's internal database by executing: 'amrfinder_update --database <database-path>/amrfinderplus-db'. This must be done only once.

I have tried to updated the amrfinderplus database, and the entire database. I have tried to use --db or export $BAKTA_DB with the realpath but that is not working either.

bakta was installed using condo and I'm working in a cluster

[oschwengers]

Hi, this is most certainly an AMRFinder issue related to a symlink within the AMRFinder db. It's a symlink pointing to an absolute path and this often gets broken when the database is manually copied to another directory. Therefore, I'd like to kindly refer you to https://github.com/oschwengers/bakta/issues/151

A possible solution would be to delete the entire content within the amrfinderplus-db directory including the symbolic link and then re-install the AMRFinder db via amrfinder_update --database <database-path>/amrfinderplus-db.

cd <BAKTA_DB_PATH>
rm -rf amrfinderplus-db/*
amrfinder_update --database amrfinderplus-db/

BTW, I also recommend to update AMRFinder to the latest version 3.10.42

[oschwengers]

Thanks to the AMRFinder developers https://github.com/ncbi/amr/issues/101, this should not happen anymore after using release v3.10.45

[oschwengers]

I hope the information above and within #151 helped to solve this issue. I'll close this issue for now. Just in case, please do not hesitate to re-open it if it remains.