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mdmparis / defense-finder

Systematic search of all known anti-phage systems.
GNU General Public License v3.0
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Failed to run via singularity #3

Closed YuyaKiguchi closed 6 months ago

YuyaKiguchi commented 3 years ago

Hi,

Thanks for great tool for analyzing the phage defense system. I made the image of singularity, and run the defense-finder. Unfortunately, I got the error below. Could you solve this problem?

Traceback (most recent call last): File "/usr/local/bin/macsyfinder", line 8, in sys.exit(main()) File "/usr/local/lib/python3.8/dist-packages/macsypy/scripts/macsyfinder.py", line 837, in main macsypy.init_logger(log_file=os.path.join(config.working_dir(), config.log_file()), File "/usr/local/lib/python3.8/dist-packages/macsypy/init.py", line 48, in init_logger logging = colorlog.logging.logging AttributeError: module 'colorlog' has no attribute 'logging' Traceback (most recent call last): File "/usr/local/bin/defense-finder", line 8, in sys.exit(cli()) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1137, in call return self.main(args, kwargs) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1062, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1668, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 763, in invoke return __callback(args, **kwargs) File "/usr/local/lib/python3.8/dist-packages/defense_finder_cli/main.py", line 46, in run defense_finder_posttreat.run(outdir) File "/usr/local/lib/python3.8/dist-packages/defense_finder_posttreat/init.py", line 7, in run bs = best_solutions.get() File "/usr/local/lib/python3.8/dist-packages/defense_finder_posttreat/best_solutions.py", line 4, in get parsed = parse_all() File "/usr/local/lib/python3.8/dist-packages/defense_finder_posttreat/best_solutions.py", line 8, in parse_all tsv_file = open('/tmp/defense-finder/all_best_solutions.tsv') FileNotFoundError: [Errno 2] No such file or directory: '/tmp/defense-finder/all_best_solutions.tsv'

charlottecc commented 2 years ago

Hi, I'm having this same issue, has any one figured out how to fix it? Thanks!

github-actions[bot] commented 6 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.