I wasn't sure what they would be called. But, I thought it was strange to find the flies there. So, I did a search on ' sewer flies' sure enough, there are such a thing. I guess the drain will have to be cleaned before the toilet goes on. I assume this by reading off the net.
Sewer flies can be found in most sewers and I would not clean your drain line just because you found a fly. Just cover up the hole well until you get your toilet installed. Just my opinion.