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nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing
https://nf-co.re/pathogensurveillance
MIT License
13 stars 5 forks source link

Bakta database bug ("amrfinder error") #90

Closed zachary-foster closed 2 weeks ago

zachary-foster commented 3 months ago

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 commented 3 months ago

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