Cant Complete the setup process

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My domain is: example.com

I ran this command: sudo certbot --apache

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]

My hosting provider, if applicable, is: Namecheap

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

Hi, and welcome to the LE community forum.

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

the output is very long

You can....
Cut it and post it in pieces
Use a third party site - like paste.bin

But we really need to have a look at it.
I'm 99.9% sure the problem will be found there.

That was clever!

i actually want to set up SSL for all wildcards subdomains on my site like

letsencrypt.org.example.com
amazon.co.uk.example.com

I need it to cover both second level and third level subdomains

I didnt find an option in cpanel to do this,

Why would you want to do that?
It sounds very Phishy!

no, its not

take a look at

https://letsencrypt.org.cutestat.com

I am building a similar web analysis tool, so i will be having unlimited dynamic subdomains

back to the issue, how can i solve it

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)

Instead of this:

Can you just do this?:

example.com/letsencrypt.org/
example.com/amazon.co.uk/

oops, am new on terminal, i dont know how to clean that up
Is there no easier way to make it work?

You choose:
Basically undo whatever was done to make it that way (via menu options).
OR
Fix it manually.

yes, i can do that , but its not how my competitors do it, they would outrank me on seo easily

please go easy , what menu options
I havent tampered with anything in my cpanel

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

Then you cut&pasted some sections in more than once.
So then there is no fix this by menu option.

yes, exactly what am trying to achieve

so what do you suggest i do
I can contact namecheap to assist me on my server end, but what do i tell them

I suggest we review the error message and try to fix whatever it needs:

It seems to want "configuration root".
Which it fails to find via normal process.
Luckily the docs show a way to pass it in the command line:
image