To get wildcard supported certificates, we need to pass the challenge which requires adding TXT records in your dns records.

To get certificates for single domains, there is no need to modify dns records. Check this link https://micropyramid.com/blog/configure-ssl-with-letsencrypt-and-nginx/  for more info.

Your distribution may have old version of certbot, so we will try with latest certbot from github repository. This solution is based on https://github.com/certbot/certbot/issues/5719, thanks to talyguryn.

git clone https://github.com/certbot/certbot

cd certbot

./certbot-auto certonly --manual -d *.mydomain.com -d mydomain.com --agree-tos --manual-public-ip-logging-ok --preferred-challenges dns-01 --server https://acme-v02.api.letsencrypt.org/directory

Output:

Please deploy a DNS TXT record under the name
_acme-challenge.mydomain.com with the following value:

qasdli_thisissometxtvalueherebrrrrrlaisd

Before continuing, verify the record is deployed.

-------------------------------------------------------------------------------

Press Enter to Continue

-------------------------------------------------------------------------------

Please deploy a DNS TXT record under the name
_acme-challenge.pietrack.com with the following value:

aldsfj_onemorevalueheredurrrrrrrrlaisdj

Before continuing, verify the record is deployed.

-------------------------------------------------------------------------------

Press Enter to Continue
Waiting for verification...
Cleaning up challenges

IMPORTANT NOTES:

 - Congratulations! Your certificate and chain have been saved at:
 /etc/letsencrypt/live/mydomain.com/fullchain.pem
 Your key file has been saved at:
 /etc/letsencrypt/live/mydomain.com/privkey.pem
 Your cert will expire on 2018-07-21. To obtain a new or tweaked
 version of this certificate in the future, simply run certbot-auto
 again. To non-interactively renew *all* of your certificates, run
 "certbot-auto renew"
 - If you like Certbot, please consider supporting our work by:

 Donating to ISRG / Let's Encrypt:   https://letsencrypt.org/donate

 Donating to EFF:      https://eff.org/donate-le

As the above suggests, in your dns records add TXT record, with

name: _acme-challenge.mydomain.com

and values

1. qasdli_thisissometxtvalueherebrrrrrlaisd

2. aldsfj_onemorevalueheredurrrrrrrrlaisdj

On successfull verifcation you should have certificates in /etc/letsencrypt/live directory.

Troubleshoot:

Error: Failed authorization procedure.

In this case, check that your TXT records are updated, for that you can run:

host -t txt _acme-challenge.mydomain.com

Nginx configuration:

Now that we have certificates in /etc/letsecrypt/live, add those certificates in nginx configuration:

server {
 listen 443 ssl;
 server_name mydomain.com;
 ssl_certificate /etc/letsencrypt/live/mydomain.com/fullchain.pem;
 ssl_certificate_key /etc/letsencrypt/live/mydomain.com/privkey.pem;
  }