Try pausing Cloudflare before running this:
VIA COMMAND LINE
For this, you need ssh access of your web server. Open terminal, and type command:
certbot certonly -d example.com -d ~www.example.com
(put your website in place of example.com, remove the ~ symbol from above line)
It will ask for putting webroot path. Write down the path of your documentRoot.
https://pastebin.com/embed_iframe/h12HFmYs
How would you like to authenticate with the ACME CA?
1: Apache Web Server plugin - Beta (apache)
2: Place files in webroot directory (webroot)
3: Spin up a temporary webserver (standalone)
Select the appropriate number [1-3] then [enter] (press 'c' to cancel): 2
Starting new HTTPS connection (1): acme-v01.api.letsencrypt.org
Cert is due for renewal, auto-renewing...
Renewing an existing certificate
Performing the following challenges:
http-01 challenge for example.com
http-01 challenge for www.example.com
Select the webroot for example.com:
1: Enter a new webroot
Press 1 [enter] to confirm the selection (press 'c' to cancel): 1
Input the webroot for gyanbyte.com: (Enter 'c' to cancel):/var/www/example/
Select the webroot for www.example.com:
1: Enter a new webroot
2: /var/www/example/
Select the appropriate number [1-2] then [enter] (press 'c' to cancel): 2
Waiting for verification...
Cleaning up challenges
Generating key (2048 bits): /etc/letsencrypt/keys/0004_key-certbot.pem
Creating CSR: /etc/letsencrypt/csr/0004_csr-certbot.pem
IMPORTANT NOTES:
- Congratulations! Your certificate and chain have been saved at
/etc/letsencrypt/live/example.com/fullchain.pem. Your cert will
expire on 2017-10-20. To obtain a new or tweaked version of this
certificate in the future, simply run certbot again. To
non-interactively renew all of your certificates, run "certbot
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
Source: How to renew SSL certificate from Lets-encrypt when your website is using cloudflare | GyanBlog