Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bakta database bug ("amrfinder error") #90

Open
zachary-foster opened this issue Aug 14, 2024 · 1 comment
Open

Bakta database bug ("amrfinder error") #90

zachary-foster opened this issue Aug 14, 2024 · 1 comment
Labels
bug Something isn't working

Comments

@zachary-foster
Copy link
Contributor

Happens occasionally, but I am not sure what causes it. It might be good to add this code to the download step.

Exception: amrfinder error! error code: 1. Please, try 'amrfinder_update --force_update --database /home/fosterz/data/files/projects/current/pathogensurveillance/path_surveil_data/bakta_db/db-light/amrfinderplus-db' to update AMRFinderPlus's internal database.
@zachary-foster zachary-foster added the bug Something isn't working label Aug 14, 2024
@zachary-foster
Copy link
Contributor Author

Looks like this is fixed by deleting the saved database and redownloading.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@zachary-foster