How do I empty the trash?

Where are the db-es located? On the storage drive? Or on a SSD or a USB3 SSD flash drive?
If not, you should consider moving them. I have coming some Corsair flash drives with SSD tech. They will be more than enough to keep databases happy.
Try to vacuum them, also.
https://forum.storj.io/t/database-maintenance-integrity-check-vacuum/25047