Im struggling with the exact same Problem.
Installed on Digital Ocean VPS (CentOS7).
Added frappe user to wheel
renamed site to erp.mysite.com
Created A record on my domains DNS pointing to DO Public IP (works).
Here I add my output from:
sudo bench setup lets-encrypt erp.mydomain.com (my site name is the same)
File “/usr/lib/python2.7/site-packages/virtualenv.py”, line 796, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /opt/eff.org/certbot/venv/bin/python2.7 - setuptools pip wheel failed with error code 1
INFO:bench.utils:sudo systemctl start nginx
There was a problem trying to setup SSL for your site
Any help is very appreciated!