I got my reference number when I received their detailed response on my second email. The reference number starts with a W then followed by 9 numbers that is written on the subject line. The email is written as follows:
Dear Sir/Madam,
This is in response to your recent email enquiry.
Your application is still under process within our standard processing times.
We trust that this information will be of assistance.
Immigration Section / Section de l'immigration/DK
Canadian Embassy / Ambassade du Canada
Abu Dhabi
After two days from this response, I received my passport stamped with the visa and a letter attached to it with the same reference number that I got from the email.