Here is the procedure that I've used to create a letsencrypt certificate in manual mode using a DNS record for registration.

sudo letsencrypt certonly -d -d  --manual --preferred-challenges dns     

The procedure will guide to the creation of a DNS TXT record used to verify the ownership of the domain.

After that the certificate can be found in /etc/letsencrypt/live/

For any of you using Plesk remember that privkey.pem is the privateKey, cert.pem is the Certificate and chain.pem is the CA

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