It's not uncommon to wake up when you realize that your dreaming. You brain doesn't know what to make of it because it's never been in the situation before so it panics. It tries to figure out what happened and to do that it needs the logical part of the brain to turn on, that wakes you up.

After a few of these quick awakenings your brain should be conditioned to transitioning from regular dreaming to lucid dreaming and realize it without having to turn on your logic centre.

Even though you just had a long one, don't get frustrated if your next one is short to. The first couple will have random lengths, after a few more you should have stable long lucid dreams.