20 minutes..... that's indeed your system slowed down, most likely one of your HDDs is failing, that usually causes the slowdown you're suffering. I suggest you to first try to boot with only the HDD where you have your OS installed connected and see if the problem goes away, that would mean the 2nd HDD (the one you disconnected) is the faulty one, else it means the HDD where you have the OS installed is the problem, once you've identified the failing HDD try to access to it and backup all critical info to not lose that data.
You could try then to format (full format not the "quick" one) the failing HDD and see if that solves the problem, but when facing a failing HDD the best thing to do is to get a new one.