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Note: This is a tutorial was made for the purposes of running bakta on the Cooper Lab’s beagle server. This is also still a working draft so please reach out if you get stuck or if anything is unclear.



Create a bakta virtual environment


See my tutorial on virtual environments to create a virtual environment in beagle. Then follow the instructions in the bakta GitHub repo to install.

Bakta version installed must be compatible with the bakta database version. For example, bakta v1.8 can work with database v5.0 but not with database v4.0. Likewise, bakta v1.6 works with database v4.0 but not v5.0.

Note that the database is large (~30.83G for version 5.0) so make sure there is enough space before doing this.

Make sure that you activate your virtual environment before installing bakta. bakta can be installed on beagle using the following command as outlined in bakta’s GitHub repo:

conda install -c conda-forge -c bioconda bakta



Update Database


The bakta database can be found here: https://zenodo.org/records/7669534

To update, do the following:

wget https://zenodo.org/record/7669534/files/db.tar.gz #change link as needed
tar -xzf db.tar.gz
rm db.tar.gz
amrfinder_update --force_update --database db/amrfinderplus-db/



Run bakta


For the input data, bakta can run on fasta format (zipped or unzipped).

The general format is as follows. Make sure to change the file path for the database to where your bakta database is located:

bakta --db /home/nak177/bakta/DB genome.fasta


Additional parameters can be found here: