nginx just quit on me , so I ran some test.
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nginx -t
nginx: [alert] could not open error log file: open() "/var/log/nginx/error.log" failed (13: Permission denied)
2018/09/05 20:08:10 [warn] 1750#1750: the "user" directive makes sense only if the master process runs with super-user privileges, ignored in /etc/nginx/nginx.conf:1
2018/09/05 20:08:10 [emerg] 1750#1750: BIO_new_file("/etc/letsencrypt/live/mydomain/fullchain.pem") failed (SSL: error:0200100D:system library:fopen:Permission denied:fopen('/etc/letsencrypt/live/mydomain/fullchain.pem','r') error:2006D002:BIO routines:BIO_new_file:system lib)
nginx: configuration file /etc/nginx/nginx.conf test failed
----------------------------------------
Then
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certbot --nginx
The following error was encountered:
[Errno 13] Permission denied: '/var/log/letsencrypt/.certbot.lock'
Either run as root, or set --config-dir, --work-dir, and --logs-dir to writeable paths.
-----------------------
sudo certbot --nginx
Saving debug log to /var/log/letsencrypt/letsencrypt.log
The requested nginx plugin does not appear to be installed
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Its something to do with cert permissions. I saw the Nginx plugin disabled at one point. I thought I enabled it. Maybe it got disabled again. I am not sure what to do after this.