That partly depends on the situation. You can use certbot options to do that, but with some plugins, you might be able to just run the command certbot and use the questions interactively asked by certbot.
Unfortunately, for some reason you didn’t get or you’ve deleted the questionnaire which was presented to you when you started this thread in the Help section. Please answer all questions to the best of your knowledge:
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.
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):
I assumed you already corrected the error which was pointed out to you earlier.
No, you need to understand what you're doing incorrectly. Please read @JuergenAuer s first post, it contains your answer. Also please count the amount of -d options you've used between your single and multiple subdomain commands. If you don't know what the -d option does, please read about it in the documentation linked earlier by @JuergenAuer.
I am however curious why you’re using --certonly? Because you said earlier you’re using nginx. Is there a reason why you’re not using the nginx plugin? Perhaps because you want to install your certificate manually into the nginx configuration? Even if that’s the case and you don’t want to automatically install the certificate and keep certbot away from your nginx configuration, you might want to look at the webroot plugin. Because with --standalone you’ll need to stop nginx every time you have to renew your certificate (which can be done automatically with specific hooks). With the webroot plugin, you can just let nginx run.
I Like to have more manual control over things that is why im using --certonly . I tried webroot before but it fail to verify. i even tried to debug it and everything was fine but it didnt worked and i didnt put much effort into it to make it work.
The webroot plugin should be really simple: just use the same path as your root option in the nginx configuration for that virtualhost as -w option for certbot.