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I just compiled and ran your code on my own Mayfly board (replacing the Loop function with the one I edited above), and commenting out anything relate to the Atlas sensors since I don’t have any here for testing, and the Mayfly board slept properly, woke up every minute and took a “sample”, wrote data to the card, and went back to sleep.
If you board isn’t waking up and you don’t even have the two header lines on your memory card, then that means your board isn’t even getting to the main loop. I would guess there’s problem with either your memory card, memory card socket, RTC chip or battery (you have the positive side of the coin cell facing up, right?), or something wrong in your sensor wiring that is either shorting something out or causing the sketch to lock up before it can run.