Hi everyone,
First of all, my apologies for not providing a domain. I never used certbot before this and I did this mistake on a company domain and I am scared they will find this if they google the domain. I don't want this to be known 
I am using certbot 1.20.0
So here is the situation:
1-) I created the certificate using following command:
sudo certbot certonly --standalone --non-interactive --agree-tos -m myemail@myemail.com -d "mydomain.com"
2-) Then I configured a NGINX in a docker. There is nothing special about this except the NGINX is running inside a container, so the nginx executable and libraries are not visible to certbot.
3-) Now it is time to renew the certificates but I cant do this because I keep getting errors.
REGULAR RENEW FAILS BECAUSE NGINX IN CONTAINER IS USING PORT 80
Command:
sudo certbot renew --force-renewal
Error:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
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Processing /etc/letsencrypt/renewal/mydomain.com.conf
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Renewing an existing certificate for mydomain.com
Failed to renew certificate mydomain.com with error: Could not bind TCP port 80 because it is already in use by another process on this system (such as a web server). Please stop the program in question and then try again.
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All renewals failed. The following certificates could not be renewed:
/etc/letsencrypt/live/mydomain.com/fullchain.pem (failure)
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1 renew failure(s), 0 parse failure(s)
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
TRYING TO USE --preferred-challenges dns FAILS WITH FOLLOWING
Command:
sudo certbot renew --force-renewal --preferred-challenges dns
Error:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
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Processing /etc/letsencrypt/renewal/mydomain.com.conf
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Renewing an existing certificate for mydomain.com
Failed to renew certificate mydomain.com with error: None of the preferred challenges are supported by the selected plugin
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All renewals failed. The following certificates could not be renewed:
/etc/letsencrypt/live/mydomain.com/fullchain.pem (failure)
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1 renew failure(s), 0 parse failure(s)
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
TRYING TO USE NGINX FAILS BECAUSE NGINX IS IN A CONTAINER/DOCKER
Command:
sudo certbot renew --force-renewal --nginx
Error:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
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Processing /etc/letsencrypt/renewal/mydomain.com.conf
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Failed to renew certificate mydomain.com with error: The nginx plugin is not working; there may be problems with your existing configuration.
The error was: NoInstallationError("Could not find a usable 'nginx' binary. Ensure nginx exists, the binary is executable, and your PATH is set correctly.")
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All renewals failed. The following certificates could not be renewed:
/etc/letsencrypt/live/mydomain.com/fullchain.pem (failure)
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1 renew failure(s), 0 parse failure(s)
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
TRYING TO USE DIFFERENT PORT FAILS BECAUSE REQUEST STILL GOES TO PORT 80
Command:
sudo certbot renew --force-renewal --http-01-port 5566
Error:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
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Processing /etc/letsencrypt/renewal/mydomain.com.conf
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Renewing an existing certificate for mydomain.com
Certbot failed to authenticate some domains (authenticator: standalone). The Certificate Authority reported these problems:
Domain: mydomain.com
Type: unauthorized
Detail: Invalid response from https://mydomain.com/.well-known/acme-challenge/U2NIpzq13L6ap_t0_4du-IkGfL7pK1tycGl1xMTE-Lg [xx.xx.xx.xx]: "<html>\r\n<head><title>404 Not Found</title></head>\r\n<body>\r\n<center><h1>404 Not Found</h1></center>\r\n<hr><center>nginx</center>\r\n"
Hint: The Certificate Authority failed to download the challenge files from the temporary standalone webserver started by Certbot on port 5566. Ensure that the listed domains point to this machine and that it can accept inbound connections from the internet.
Failed to renew certificate mydomain.com with error: Some challenges have failed.
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All renewals failed. The following certificates could not be renewed:
/etc/letsencrypt/live/mydomain.com/fullchain.pem (failure)
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1 renew failure(s), 0 parse failure(s)
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
IS THERE A WAY FOR ME TO RENEW THE CERTIFICATE WITHOUT STOPPING NGINX?
I read that I can stop the container by using --pre-hook and --post-hook commands. I did not try those yet but I wanted to ask the experts before I ended up stopping the company servers for a minute or two. If I do this, it will be visible to my boss.
My domain is:
I ran this command:
It produced this output:
My web server is (include version):
The operating system my web server runs on is (include version):
My hosting provider, if applicable, is:
I can login to a root shell on my machine (yes or no, or I don't know):
I'm using a control panel to manage my site (no, or provide the name and version of the control panel):
The version of my client is (e.g. output of certbot --version or certbot-auto --version if you're using Certbot):