It seems that the certbot, the recommended script to install and update the LetsEncrypt certificates requires root permissions. Well, I found several tutorials and forums where people claimed that they ran it without root permissions but they all said they needed root permissions to do something else for certbot to work and then I ran this simple command:
Requesting to rerun ./certbot-auto with root privileges...
[sudo] password for eleni:
and decided to give up and search for an alternative method. 🙂