Let's Encrypt creates new /home/public_html duplicate directory

[nilands55s]

In virtualmin when I request a new Cert it dose not use /home/nilandtrading/public_html/.well-known/acme-challenge. ,but creates /home/nilandtrading/home/nilandtrading/public_html/.well-known/acme-challenge owned by root:root, so this is a duplicate /home directory with the wrong owner. My sub-server chat.nilandtrading.com did not do this and I got the cert. So the continuing error is;

Obtaining a new certificate
Performing the following challenges:
http-01 challenge for nilandtrading.com
http-01 challenge for www.nilandtrading.com
Using the webroot path /home/nilandtrading/home/nilandtrading/public_html for all unmatched domains.
Waiting for verification…
Cleaning up challenges
Unable to clean up challenge directory /home/nilandtrading/home/nilandtrading/public_html/.well-known/acme-challenge
Failed authorization procedure. nilandtrading.com (http-01): urn:acme:error:unauthorized :: The client lacks sufficient authorization :: Invalid response from http://nilandtrading.com/.well-known/acme-challenge/GtNOihoJHlx0gy9YBanDI4FSqZFiWE_Ghnb-1AadP6g: "

404 Not Found

404 Not Found

---

" IMPORTANT NOTES: - The following errors were reported by the server:

Domain: nilandtrading.com
Type: unauthorized
Detail: Invalid response from
http://nilandtrading.com/.well-known/acme-challenge/GtNOihoJHlx0gy9YBanDI4FSqZFiWE_Ghnb-1AadP6g:
"

404 Not Found

404 Not Found

---

"

To fix these errors, please make sure that your domain name was
entered correctly and the DNS A/AAAA record(s) for that domain
contain(s) the right IP address.
My server runs through No-IP DUC for the connection as TWC/Septrum even for a commercial account want’s my first born for a Static IP, but I can get to http//…/.well-known ok in a brawser. Checked all the Permissions?
the server is an HP X9400 with 8 cores and 32GB of RAM, Linux/apache2, Ubuntu-server 14.04.5
I do use a Ubutnu-Gnome GUI As I can do multiple things with it (don’t want to hear about server purity and command line only). My interface is Virtualmin/webmin latest version 6.00/1.852

[jared.m]

Please use the prompts given when you created this topic to make sure you provide all information requested. Specifically in this case, please post the exact command you were using.

[nilands55s]

Ok not sure what “prompts” you are asking for, but I was not using Let’s Encrypt from comand line, but rater from the Virtualmin >> Server Configuration >> Manage SSL Certificate >> Let’s Encrypt Tab.
Where do I find these prompts?
Further from doing a text search (sagasu) for “/home/nilandtrading/home/nilandtrading/public_html” I discovered it is being done by Lets’ Encrypt RE: Let’s Encrypt Log Sept-20

2017-09-20 15:40:44,854:DEBUG:certbot.main:certbot version: 0.17.0
2017-09-20 15:40:44,854:DEBUG:certbot.main:Arguments: ['-a', 'webroot', '-d', 'nilandtrading.com', '-d', 'www.nilandtrading.com', '-d', 'autoconfig.nilandtrading.com', '-d', 'autodiscover.nilandtrading.com', '--webroot-path', '/home/nilandtrading/home/nilandtrading/public_html', '--duplicate', '--manual-public-ip-logging-ok', '--config', '/tmp/.webmin/590663_25148_1_letsencrypt.cgi', '--rsa-key-size', '2048']
2017-09-20 15:40:44,854:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#apache,PluginEntryPoint#manual,PluginEntryPoint#null,PluginEntryPoint#standalone,PluginEntryPoint#webroot)
2017-09-20 15:40:44,882:DEBUG:certbot.log:Root logging level set at 20

So I am assuming the COMMAND is something from Virtualmin, but i could not tell Why and Virtualmin support does not seem to know anything about it, but asked me to Validate the server with no further reply:

Beginning validation of selected virtual servers. Any problems found will be shown in red …
nilandtrading.com
Home directory : Sub-directory home/nilandtrading/public_html under home directory does not exist
Apache website : Missing Apache block for HTML directory /home/nilandtrading/home/nilandtrading/public_html
SSL website : No SSL certificate file specified in Apache virtual host
Git repositories : Missing Git Location from Apache configuration

There should not be any nilandtrading.com subdirectory. I have sub-server and not subdirectories. i.e.
nilandtrading.tld
chat.nilandtrading.com (sub-server)
forum.nilandtrading.com (sub-server)

By the way chat.nilandtrading.com installed once I removed the sites-enabled <VirtualHost *:443> section, That I was told by webmin support “this should not work”. but it would not install the Cert until I did this?
additional info Apache version 2.4.10, bind9 PHP5.5.9

[schoen]

Hi @nilands55s,

This looks likely to be some kind of Virtualmin bug to me (where Virtualmin is misinterpreting/misparsing your Apache configuration and then passing incorrect information to Certbot). You are welcome to keep discussing it here, but you might get better results over on

https://www.virtualmin.com/forum

Or if you prefer, you could try to use Certbot outside of Virtualmin—but I’m not sure what effects that would have for using Virtualmin to manage your site afterward.