Could you please ask around if this place has been empty / non-habited for more than 3 consecutive months in the past ?

Nevertheless, to get rid of whatever is troubling your dog and your nights, just do the following:

Read Psalm 110 (or any Psalm really, any of them will do, specially if you like one of them), out loud (not whispered), while in one room. Then read it again in the second room and so on. Don't do that in the bathrooms or in the shower rooms.

If you could read it in phonetic (English Hebrew) it's be great. If not, just read it in your mother's tongue (English I guess).

Do this preferably during the day, not during the night.