macsyfinder: "No such model definition: 'CasFinder'"

[liaohu1231]

2023-11-02 14:09:40 | INFO | Received file bins/1-1_bin.1/1-1_bin.1.faa 2023-11-02 14:09:40 | WARNING | Out directory /home/liaohu01/thawed_soil_metagenome already exists. Existing DefenseFinder output will be overwritten 2023-11-02 14:09:40 | WARNING | Temporary directory /home/liaohu01/thawed_soil_metagenome/defense-finder-tmp already exists. Overwriting it. 2023-11-02 14:09:49 | INFO | Running DefenseFinder macsyfinder: "No such model definition: 'CasFinder'"

[liliancaesarbio]

I am having the same issue:

"macsyfinder: "No such model definition: 'CasFinder'""

[eranbosis]

Hi everyone, I am having the same issue: macsyfinder: "No such model definition: 'CasFinder'" The previous version of defense-finder worked properly. Any ideas how to resolve it? Thanks, Eran

[gjzheng]

I am having the same issue too macsyfinder: "No such model definition: 'CasFinder'"

[gjzheng]

finally I solve my problem by download the CasFinder file on https://github.com/macsy-models/CasFinder or you can Use command like : macsydata install CasFinder . Then move the ‘’CasFinder‘’ to a folder which must contain the original defense-finder-models . then use --models-dir to specific your models place. and you can finally run defense-finder

[eranbosis]

Thanks for the info. In my case, there was a problem with the defense-finder models. So, I deleted the /data directory where the models are stored and re-installed them using defense-finder update and the name of the directory where I store the models.

[balamalaha]

I countered the error "KeyError: "No such model definition: 'RloC'"". How can I solve it?

[jeanrjc]

Hello everyone,

Could you give more details about your issues (ideally in separate issues if the problem differs from the one in the issue, although it's still vague what's the problem here).

First make sure Defense Finder software is up to date as well as the defense finder's models.

If it's still not working, please give a sample dataset on which you have the problem and the path of where the models are stored

Thanks

[balamalaha]

Hi this is the error I got. I installed the latest version of the program and database. I have checked that RolC is in the database files.

Traceback (most recent call last): File "/home/ana/.conda/envs/main/bin/defense-finder", line 8, in sys.exit(cli()) File "/home/ana/.local/lib/python3.7/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/home/ana/.local/lib/python3.7/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/home/ana/.local/lib/python3.7/site-packages/click/core.py", line 1659, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/ana/.local/lib/python3.7/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/ana/.local/lib/python3.7/site-packages/click/core.py", line 754, in invoke return __callback(args, **kwargs) File "/home/ana/.conda/envs/main/lib/python3.7/site-packages/defense_finder_cli/main.py", line 143, in run defense_finder.run(protein_file_name, dbtype, workers, coverage, tmp_dir, models_dir, no_cut_ga, loglevel) File "/home/ana/.conda/envs/main/lib/python3.7/site-packages/defense_finder/init.py", line 29, in run macsyfinder.main(args=msf_cmd) File "/home/ana/.local/lib/python3.7/site-packages/macsypy/scripts/macsyfinder.py", line 903, in main all_systems, rejected_clusters = search_systems(config, model_registry, models_def_to_detect, logger) File "/home/ana/.local/lib/python3.7/site-packages/macsypy/scripts/macsyfinder.py", line 483, in search_systems parser.parse(models_def_to_detect) File "/home/ana/.local/lib/python3.7/site-packages/macsypy/definition_parser.py", line 80, in parse model_location = self.model_registry[def_loc.family_name] File "/home/ana/.local/lib/python3.7/site-packages/macsypy/registries.py", line 119, in getitem raise KeyError(f"No such model definition: '{name}'") KeyError: "No such model definition: 'RloC'"

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