mdmparis / defense-finder

Systematic search of all known anti-phage systems.
GNU General Public License v3.0
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AttributeError: 'NoneType' object has no attribute 'split' #44

Closed liucong2016 closed 2 months ago

liucong2016 commented 8 months ago

i met a question. can you give me some advice?

(vs2) defense-finder run --db-type gembase bacteria_cluster-23.10.4-protein.fa --models-dir /home/liu-c/.macsyfinder/models -w 60

2024-01-06 17:09:56 | INFO | Received file bacteria_cluster-23.10.4-protein.fa 2024-01-06 17:09:56 | WARNING | Out directory /home/liu-c/virus-data/tuanjuti-virome/defense_finder_output-24.1.5 already exists. Existing DefenseFinder output will be overwritten 2024-01-06 17:09:56 | WARNING | Temporary directory /home/liu-c/virus-data/tuanjuti-virome/defense_finder_output-24.1.5/defense-finder-tmp already exists. Overwriting it. 2024-01-06 17:09:56 | INFO | Running DefenseFinder 2024-01-06 21:03:05 | INFO | Post-treatment of the data Traceback (most recent call last): File "/software1/envs/vs2/bin/defense-finder", line 8, in sys.exit(cli()) File "/software1/envs/vs2/lib/python3.10/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/software1/envs/vs2/lib/python3.10/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/software1/envs/vs2/lib/python3.10/site-packages/click/core.py", line 1659, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/software1/envs/vs2/lib/python3.10/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/software1/envs/vs2/lib/python3.10/site-packages/click/core.py", line 754, in invoke return __callback(args, **kwargs) File "/software1/envs/vs2/lib/python3.10/site-packages/defense_finder_cli/main.py", line 145, in run defense_finder_posttreat.run(tmp_dir, outdir, os.path.splitext(os.path.basename(filename))[0]) File "/software1/envs/vs2/lib/python3.10/site-packages/defense_finder_posttreat/init.py", line 11, in run bs = best_solution.get(tmp_dir) File "/software1/envs/vs2/lib/python3.10/site-packages/defense_finder_posttreat/best_solution.py", line 15, in get return format_best_solution(acc) File "/software1/envs/vs2/lib/python3.10/site-packages/defense_finder_posttreat/best_solution.py", line 56, in format_best_solution gene_ref_elements = split_def_name(gene_ref) File "/software1/envs/vs2/lib/python3.10/site-packages/macsypy/registries.py", line 49, in split_def_name split = fqn.split(_SEPARATOR) AttributeError: 'NoneType' object has no attribute 'split'

github-actions[bot] commented 6 months ago

Stale issue message

jeanrjc commented 4 months ago

your protein file is probably not gembase

github-actions[bot] commented 2 months ago

This issue has been inactive for 60 days and is now marked as stale. It will be closed in 7 days without further activity.