My bad, I think I deleted live and archive folders from /etc/letsencrypt but I’m not very sure. Anyway, I tried certbot-auto update_symlinks but nothing changed. It writes a log file though:
2017-03-18 14:49:34,887:DEBUG:certbot.main:Root logging level set at 20
2017-03-18 14:49:34,888:INFO:certbot.main:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2017-03-18 14:49:34,889:DEBUG:certbot.main:certbot version: 0.12.0
2017-03-18 14:49:34,889:DEBUG:certbot.main:Arguments: []
2017-03-18 14:49:34,890:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#standalone,PluginEntryPoint#manual,PluginEntryPoint#nginx,PluginEntryPoint#webroot,PluginEntryPoint#apache,PluginEntryPoint#null)