Please fill out the fields below so we can help you better. Note: you must provide your domain name to get help. Domain names for issued certificates are all made public in Certificate Transparency logs (e.g. https://crt.sh/?q=example.com), so withholding your domain name here does not increase secrecy, but only makes it harder for us to provide help.
It produced this output: The apache plugin is not working; there may be problems with your existing configuration.
The error was: NoInstallationError('Could not find configuration root')
My web server is (include version): * Apache/2.4.46 (cPanel)
The operating system my web server runs on is (include version): * CENTOS 7.9 kvm [server1]
I can login to a root shell on my machine (yes or no, or I don't know): Yes Via Terminal
I'm using a control panel to manage my site (no, or provide the name and version of the control panel): Am using Cpanel & WHM
The version of my client is (e.g. output of certbot --version or certbot-auto --version if you're using Certbot): cannot create user data directory: /home/uname/snap/certbot/793: Permission denied
This indicates a problem with the Apache configuration.
I see that you are running cPanel (it should have handled this cert process for you).
So I don't know why you are having to run certbot manually.
Nonetheless, certbot should have worked.
Is it possible that anyone has also made changes to the Apache configuration manually?
Let's have a look at the basic Apache IP:port:FQDN assignments with: sudo apachectl -S
You have all your vhosts in the single file: /etc/apache2/conf/httpd.conf
[That makes things unnecessarily difficult - you should split them into individual files]
Anyhow, I find this same name in multiple places and some sections were included more than once:
port 80 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:295)
port 80 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:316)
: server1.nnaira.website (/etc/apache2/conf/httpd.conf:346)
port 443 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:6719)
port 443 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:6719)
port 443 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:6855)
port 443 namevhost server1.nnaira.website (/etc/apache2/conf/httpd.conf:6855)
*:443 server1.nnaira.website (/etc/apache2/conf/httpd.conf:6855)
Then you need to understand how wildcards work.
You can only cover one field with a wildcard.
And that must be the first one (left most).
So if you want: company.com.your.domain
You need a wildcard for: *.com.your.domain
For: another-company.co.uk.your.domain
You need a wildcard for: *.co.uk.your.domain