jeanrjc
commented
4 months ago You need to install it with pip and not with conda.
mamba create -n defensefinder
mamba activate defensefinder
pip install mdmparis_defense_finder
mamba install hmmer -c biocondaThey did not pin the correct version of macsyfinder in the conda version. Let me know if there is still a problem
Hi! Thanks for making this tool, I'm excited to use it!
I believe I'm experiencing the same issue noted here. It looks like it was fixed in version 1.2.2, but that's the version I'm using. I've just installed for the first time and the models are freshly updated. My hmmer version is 3.3.2. Macsyfinder version is 2.1.3. Here's the error:
`Traceback (most recent call last): File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/profile.py", line 70, in get_profile path = model_location.get_profile(gene.name) File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/registries.py", line 344, in get_profile return self._profiles[name] KeyError: 'Rst_RT-Tm__RT-Tm'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/automounts/workspace/workspace/rweed/TR_phage_redo/defensefinder_env/bin/defense-finder", line 10, in
sys.exit(cli())
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(args, kwargs)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(args, **kwargs)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/defense_finder_cli/main.py", line 147, in run
defense_finder.run(protein_file_name, dbtype, workers, coverage, tmp_dir, models_dir, no_cut_ga, loglevel)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/defense_finder/init.py", line 29, in run
macsyfinder.main(args=msf_cmd)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/scripts/macsyfinder.py", line 1193, in main
all_systems, rejected_candidates = search_systems(config, model_registry, models_def_to_detect, logger)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/scripts/macsyfinder.py", line 529, in search_systems
parser.parse(models_def_to_detect)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/definition_parser.py", line 85, in parse
self._fill_gene_bank(model_node, model_location, def_loc)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/definition_parser.py", line 287, in _fill_gene_bank
self.gene_bank.add_new_gene(model_location, gene_name, self.profile_factory)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/gene.py", line 102, in add_new_gene
gene = CoreGene(model_location, name, profile_factory)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/gene.py", line 114, in init
self._profile = profile_factory.get_profile(self, model_location)
File "/workspace/rweed/TR_phage_redo/defensefinder_env/lib/python3.10/site-packages/macsypy/profile.py", line 72, in get_profile
raise MacsypyError(f"'{model_location.name}/{gene.name}': No such profile")
macsypy.error.MacsypyError: 'defense-finder-models/Rst_RT-Tm__RT-Tm': No such profile`
I would appreciate any help you have to offer! Thanks so much!