That's normal. Give it a few weeks and the diatome's will die off. However, if you are using anything but ro/di water (or water from your lfs) it will keep coming back.
Yes, you can still run the lights. Diatoms are very normal, and are food for the bacteria breeding in the tank. The bacteria is needed to get your tank ready for livestock, as it is part of the biological filtration your tank needs.