First Install LetsEncrypt Plugin , there is a prebuilt script shipped in WHM , for the same login as root to the server. Assuming WHM is present there

]# /usr/local/cpanel/scripts/install_lets_encrypt_autossl_provider

Now Log in to WHM and navigate to the Manage AutoSSL interface (WHM > Home >  SSL/TLS > Manage AutoSSL).

Select LetsEncrypt there

Save and exit .

Now login to the respective cPanel account , Navigate to AutoSSL , select domains , Run Auto SSL

done