mdmparis

mdmparis/defense-finder

Systematic search of all known anti-phage systems.

16 good first / help-wanted issues · Python · last activity Jul 6, 2026

176 stars 25 forks 176 watchers Python GNU General Public License v3.0

16 Open Issues Need Help Last updated: Jul 6, 2026

Open Issues Need Help

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[HELP] Code for operon synteny and clustering analysis about 1 month ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] Find duplicates results in file _systems.tsv 4 months ago

help wanted stale

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]How should same-locus conflicting calls between DefenseFinder and PADLOC be reconciled? 5 months ago

help wanted stale

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] Understanding system classification for VP1853 6 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] FileNotFoundError: [Errno 2] No such file or directory: '/gpfs1/schlecker/home/lawal/.macsyfinder/models/defense-finder-models/definitions/profiles' 6 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]macsypy.error.MacsypyError: unable to parse model definition 'CasFinder/CAS_Class1-Type-IV' : The model definition CAS_Class1-Type-IV.xml has not the right version. version supported is '2.0'. Please update your model.” 6 months ago

help wanted stale

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] Error when I ran the update command 6 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]TimeoutError: [Errno 110] Connection timed out 7 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] New error after fixing seq.name.decode() issue – MacSyFinder model version incompatibility 7 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] Error when running DefenseFinder: 'str' object has no attribute 'decode' 7 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]CasFinder 3.1.1 incompatibility with defense-finder 2.0.1 (MacsypyError: version mismatch) and inability to download older CasFinder versions 8 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] Why are there duplicate lines in the defensefinder results? 8 months ago

help wanted stale

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] macsypy.error.MacsypyError: unable to parse model definition 'CasFinder/CAS_Class1-Subtype-III-F' : The model definition CAS_Class1-Subtype-III-F.xml has not the right version. version supported is '2.0'. Please update your model. 10 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP] 11 months ago

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]Whether the anti-defense systems are capable of targeting all subtypes of their corresponding defense systems about 1 year ago

help wanted stale

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python

[HELP]requesting a complete set of models about 1 year ago

AI Summary: A user downloaded `defense-finder-models-v2.0.2.tar.gz` but encountered an "Uncomplete defense-finder models" error when running the tool, indicating missing or incomplete models despite the presence of 'Cas' and 'defense-finder' directories. As the `defense-finder update` command is blocked in China, the user is requesting a complete set of models, preferably via an alternative download method like Google Drive.

Complexity: 4/5

help wanted

mdmparis/defense-finder

176

Systematic search of all known anti-phage systems.

Python