KeyError: 'ampC-promoter'

[Ryan James Kennedy]

I am running Resfinder 4.1.11 with the most recent commit of the master branch from pointfinder_db and resfinder_db and I keep getting the following error:

Traceback (most recent call last):
    File "/usr/local/lib/python3.8/runpy.py", line 194, in _run_module_as_main
      return _run_code(code, main_globals, None,
    File "/usr/local/lib/python3.8/runpy.py", line 87, in _run_code
      exec(code, run_globals)
    File "/usr/local/lib/python3.8/site-packages/resfinder/__main__.py", line 5, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.8/site-packages/resfinder/run_resfinder.py", line 485, in main
      finder.write_results(
    File "/usr/local/lib/python3.8/site-packages/resfinder/cge/pointfinder.py", line 376, in write_results
      result_str = self.results_to_str(res_type=res_type,
    File "/usr/local/lib/python3.8/site-packages/resfinder/cge/pointfinder.py", line 323, in results_to_str
      str_tuple = self.mut2str(gene, gene_name, mis_matches,
    File "/usr/local/lib/python3.8/site-packages/resfinder/cge/pointfinder.py", line 1880, in mut2str
      gene_mut_name, resistence, pmid = self.look_up_known_muts(
    File "/usr/local/lib/python3.8/site-packages/resfinder/cge/pointfinder.py", line 2039, in look_up_known_muts
      if codon_pos in self.known_mutations[gene_ID][mut]:
  KeyError: 'ampC-promoter'

I would love to know what I’m doing wrong. I will try roll back to the most recent tag for the respective dbs.

[RolfKaas]

Hi Ryan. Due to a bug we unfortunately had to change some of the formatting for the pointfinder_db database, and hence it will unfortunately only be compatible with at least ResFinder version 4.4.2. You may need to roll back to pointfinder_db version 3.0.1 or 2.0.1. In general if a database major version number changes it will often have undergone some format changes that may make it incompatible with previous ResFinder app version. We always strive towards making changes backwards compatible if possible. It was unfortunately not possible this time. We are sorry about the inconvenience this has caused.

[Ryan James Kennedy]

No problem! Please could push the latest version as a singularity image to galaxy project? Thank you for your help!

[RolfKaas]

Hi Ryan. We officially only publish via pip and docker hub, as we are a small team with limited resources. It is not us who has uploaded the image that is already there. With that said, I wouldn’t mind pushing the docker image to the Galaxy project if its just an extra command or something like that. However, I can’t seem to find any documentation for how to push it to the Galaxy project?

[Ryan James Kennedy]

As I understand it, it’s done by contributing to bioconda by creating a PR to the bioconda repository (specifically this yaml file). Once merged, it will add it to the galaxy project automatically.

[RolfKaas]

Ah ok, I see. Then we probably have to decline. I wish we had the time to publish our applications wider, but as I said we are a very small team and need to prioritize. With that said, we do have some volunteers within our group who are working on getting some of the CGE applications into Conda. You can find it here: https://anaconda.org/genomicepidemiology. They had to abandon bioconda, as adding to bioconda requires a manual review process and approval, and getting something published took several months. But anyone can push things to bioconda, so if you know someone, they are more than welcome to update ResFinder in bioconda