Running spigot 1.13.1 with the latest version of luckperms off spigot at this date.

Error happens after leaving the server on over night then logging in with no players on.

https://hastebin.com/nizexepeva.shell

Please see this page:
https://github.com/lucko/LuckPerms/wiki/Storage-system-errors#luckperms-cannot-connect-to-my-mysql-server

https://github.com/lucko/LuckPerms/wiki/Storage-system-errors#mysql-no-operations-allowed-after-connection-closed-error

^ is the appropriate section for you.