Created the subdirectories and uloaded a test file into it. Can't browse http://yycre.ca/.well-known/acme-challenge/testfile
Tried every combination of permissions, checked the .htaccess file and not able to browse the test file..
Started over and installed cerbot into the /opt folder and ran it from there based on this article.
Was able to create the certificates for the sub domain this way. Set up a virtual host for the mapped subdomains and with a virtual host setup it is partially working with a B grade on SSL Labs - 'This server's certificate chain is incomplete. Grade capped to B'
Following the instructions from Bitnami
https://docs.bitnami.com/google/components/apache/#how-to-generate-and-install-a-certificate-for-your-domain-using-the-lets-encrypt-client
Certificates created then copied:
sudo cp /etc/letsencrypt/live/DOMAIN/cert.pem /opt/bitnami/apache2/conf/server.crt$
sudo cp /etc/letsencrypt/live/DOMAIN/privkey.pem /opt/bitnami/apache2/conf/server.key
I am sure that there is another portion I am missing....
Virtual Host is as follows:
<VirtualHost *:80>
ServerName yycre.ca
ServerAlias www.yycre.ca
DocumentRoot "/opt/bitnami/apps/wordpress/htdocs"
Include "/opt/bitnami/apps/wordpress/conf/httpd-app.conf"
<VirtualHost *:443>
ServerName yycre.ca
ServerAlias www.yycre.ca
DocumentRoot "/opt/bitnami/apps/wordpress/htdocs"
SSLEngine on
SSLCertificateFile "/opt/bitnami/apache2/conf/server2.crt"
SSLCertificateKeyFile "/opt/bitnami/apache2/conf/server2.key"
Include "/opt/bitnami/apps/wordpress/conf/httpd-app.conf"