I did run in apache mode..
The command was:
certbot --apache -d mydomain.com
Apparently it needs modifications because seafile uses a reverse proxy, and perhaps also perhaps because my domain is behind Cloudflare. I'm running Debian jessie. Anyway after struggling a lot with this setting up rules for apache conf for the reverse proxy, I ended up using certbot in manual mode using TXT file authentication. The command is:
certbot -d mydomain.com --manual --preferred-challenges dns certonly