mdmparis / defense-finder

Systematic search of all known anti-phage systems.
GNU General Public License v3.0
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[BUG]Issue with -A Option in DefenseFinder v3.1.0 #67

Open maocheng2020 opened 2 weeks ago

maocheng2020 commented 2 weeks ago

Hello,

I'm using DefenseFinder, and I believe I have the latest version installed (v3.1.0) (defense-finder update). According to the release notes for v1.3.0, the tool should support the following options:

--antidefense to run AntiDefense models alongside DefenseFinder --antidefense-only to run only AntiDefense models However, when I attempt to use the -a or --antidefense-only options in my command, it returns an error stating "No such option: -A". Additionally, when I run defense-finder run -h to check the available options, I do not see any mention of -a or --antidefense.Here is the exact command I used: defense-finder run vRhyme_955.faa -o test -A

Usage: defense-finder run [OPTIONS] FILE Try 'defense-finder run -h' for help. Error: No such option: -A

Could you please help me understand why this option is not being recognized? Is there something I'm missing, or could this be an issue with the current release?

Thank you for your assistance!