After seeing the coop and run photos, I would guess raccoon. Are there any loose spots anywhere on the run-netting, or any holes it can squeeze underneath? I have watched raccoons (at midnight) squeezing through tiny spots near the top of our runs, where they mold their bodies to look like jello. They are experts and ripping birds out of the coop also, even with only a 1/2" gap to reach through, usually in the door area. Sorry for your loss.