Database requires sofware version at least 3.10.16

[pedrofteixeira]

Hello,

I have just installed the AMRfinder Plus through Bioconda. Once I try to update the database an error occurs:

% amrfinder -u Running: amrfinder -u Software directory: '/Users/utilizador/opt/anaconda3/envs/AMRFinder_env/bin/' Software version: 3.10.1 Running: /Users/utilizador/opt/anaconda3/envs/AMRFinder_env/bin/amrfinder_update -d /Users/utilizador/opt/anaconda3/envs/AMRFinder_env/share/amrfinderplus/data Looking up databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/ Downloading AMRFinder database version 2022-10-11.2 into '/Users/utilizador/opt/anaconda3/envs/AMRFinder_env/share/amrfinderplus/data/2022-10-11.2/' Indexing Database directory: '/Users/utilizador/opt/anaconda3/envs/AMRFinder_env/share/amrfinderplus/data/2022-10-11.2' Database version: 2022-10-11.2

ERROR Database requires sofware version at least 3.10.16 To download the latest version to the default directory run: amrfinder -u

HOSTNAME: ? SHELL: /bin/zsh PWD: /Users/utilizador/Documents/REQUIMTE/Genomes/Gardnerella/AllGenomes/FASTA Progam name: amrfinder Command line: amrfinder -u

[vbrover]

The current version of AMRFinderPlus in github is 3.10.45. We will investigate Bioconda.

[pedrofteixeira]

Thank you @vbrover

[evolarjun]

Hi @pedrofteixeira,

I'm not sure how you got such an old version of AMRFinderPlus, but maybe it's not coming from the correct conda channel? That was the problem for some other people in issue https://github.com/ncbi/amr/issues/81.

Could you try running

conda update -c bioconda -c conda-forge ncbi-amrfinderplus

And let us know if that installs the current version (3.10.45) and allows you to update with amrfinder -u?

You can also check the software version by running amrfinder --version .

Thanks! Arjun

[vbrover]

You can check the software version by running amrfinder --version.

[pedrofteixeira]

Hi @evolarjun,

I tried updating amrfinder and for some reason it installed the software version 3.10.1. After running amrfinder -u, the same error occurred.

Thank tou, Pedro Teixeira

[evolarjun]

So I am confused by this, but most likely the cause is something else in the environment that is dependent on old versions of BLAST, HMMER, or libcurl. You can try to force a version update like:

conda update --force-reinstall -c bioconda -c conda-forge ncbi-amrfinderplus=3.10.45

But I'm guessing that will not work.

Another option would be to create a new environment for AMRFinderPlus E.g.:

conda create -y -c bioconda -c conda-forge  -n amrfinder ncbi-amrfinderplus=3.10.45

Then you'd have to use conda activate amrfinder to get into that environment.

Let us know if either of those options work for you.

[vbrover]

Another solution would be to install AMRFinderPlus without Conda.

[pedrofteixeira]

@evolarjun I tried both updating and reinstalling the 3.10.45 version of amrfinder plus but they both resulted in conflicts due to incompatible packages.

@vbrover is it recommended the installation without conda?

[evolarjun]

Installation from binaries is usually pretty easy. The only thing you need is BLAST and HMMER in your path (which you can install with conda if you need to). See https://github.com/ncbi/amr/wiki/Install-with-binary#installing-amrfinderplus-itself for instructions on how to install AMRFinderPlus itself.

[pedrofteixeira]

@evolarjun @vbrover I think I just solved this issue. I installed AMRFinderPlus using the Anaconda Navigator and it installed the latest version. Thank you both for your help.

[evolarjun]

Glad it worked for you finally. Sorry for the frustrating experience; bioconda doesn't always behave as we expect it to.