AMRProt

[Nanderson246]

Updated my databse and new version of armfinder is not working: The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus: No such file or directory.

[vbrover]

The amrfinder software version is now 3.12.9. It means that the database format has changed. Please install the new version of amrfinder.

[vbrover]

If the problem persists please post the complete screen output.

[dsurujon]

I got the same error as above with v3.12.8 which appears to be the latest release available

Running: amrfinder -l
Software directory: '/root/bin/amrfinder/'
Software version: 3.12.8
Database directory: '/root/bin/amrfinder/data/2024-01-31.1'

*** ERROR ***
The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus: No such file or directory

HOSTNAME: codon-okteto-5c4f5cb664-xkrg6
SHELL: ?
PWD: /root/res-2024/defne/2024-03-08_amrfinderplus_uci
PATH: /root/bin/amrfinder:/root/bin/hmmer-3.4/src:/root/bin/ncbi-blast-2.15.0+/bin:/opt/poetry/bin:/opt/pyenv/plugins/pyenv-virtualenv/shims:/root/.pyenv/shims:/opt/pyenv/bin:/root/opt/Flye/Flye/bin/:/root/opt/jellyfish/bin/:/root/opt/minimap2/minimap2/:/root/opt/samtools/samtools-1.9/:/opt/poetry/bin:/opt/pyenv/plugins/pyenv-virtualenv/shims:/opt/pyenv/bin:/root/miniconda3/bin:/root/miniconda3/condabin:/opt/poetry/bin:/opt/pyenv/plugins/pyenv-virtualenv/shims:/opt/pyenv/bin:/opt/google-cloud-sdk/bin:/root/.pyenv/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/kraken:/checkm-data:/usr/local/ncbi-blast/ncbi-blast-2.13.0+/bin:/root/bin
Progam name:  amrfinder
Command line: amrfinder -l

[dsurujon]

The solution for me was to run amrfinder --force_update. The amrfinder -u command was skipping the update because the target directory already had some files in it.

[vbrover]

We will try to improve this error message in the future versions.