I had the same issue with the magenta ink and tried the deep clean but that did not do the trick this time. After some research, I tried the Ink Flush from the operational panel. It solved the issue and is now printing all colors. You have to make sure all your ink containers are full before starting the process because it does use a large amount of ink.
If you have tried cleanings and deep cleanings and the magenta is missing completely. you can try the steps in the link HERE to perform a color only ink flush. If that does not resolve the issue, it looks like the color print head needs to be replaced or the printer needs service. You can view your available service options from your MyCanon account.
