When a server shuts down, it hangs on "[18:36:14 INFO]: [LP] Closing storage..." infinitely

[18:36:14 INFO]: Stopping server
[18:36:14 INFO]: [ChatGuard] Disabling ChatGuard v7.3
[18:36:14 INFO]: [ClansGameserver] Disabling ClansGameserver v4.59.5
[18:36:14 INFO]: [AAC] Disabling AAC v3.3.2
[18:36:14 INFO]: [AAC] Disabling checks...
[18:36:14 INFO]: [AAC] Saving log file...
[18:36:14 WARN]: [AAC] Could not save log file as none was created.
[18:36:14 INFO]: [BedwarsRel] Disabling BedwarsRel v1.2.8
[18:36:14 INFO]: [Multiverse-Core] Disabling Multiverse-Core v2.4-b527
[18:36:14 INFO]: [Multiverse-Core] - Disabled
[18:36:14 INFO]: [ProtocolLib] Disabling ProtocolLib v4.3.0
[18:36:14 INFO]: [PigParty] Disabling PigParty v1.0
[18:36:14 INFO]: [Vault] Disabling Vault v1.5.6-b49
[18:36:14 INFO]: [ViaVersion] Disabling ViaVersion v1.3.0
[18:36:14 INFO]: [ViaVersion] ViaVersion is disabling, if this is a reload and you experience issues consider rebooting.
[18:36:14 INFO]: [CommandForward] Disabling CommandForward v0.1
[18:36:14 INFO]: [ConditionalCommands] Disabling ConditionalCommands v1.2
[18:36:14 INFO]: [IPWhitelist] Disabling IPWhitelist v1.7
[18:36:14 INFO]: [BWLuckyBlockAddon] Disabling BedwarsLuckyBlockAddon v1.0.0
[18:36:14 INFO]: [BedWars] The Luckyblock addon is successfully disabled.
[18:36:14 INFO]: [PigStaff] Disabling PigStaff v0.1
[18:36:14 INFO]: [LuckPerms] Disabling LuckPerms v4.1.25
[18:36:14 INFO]: [LP] Closing storage...

LuckyPerms Info prints the following:

[23:52:45 INFO]: [LP] Running LuckPerms v4.1.25 by Luck.
[23:52:45 INFO]: [LP] - Platform: Bukkit
[23:52:45 INFO]: [LP] - Server Brand: CraftBukkit
[23:52:45 INFO]: [LP] - Server Version:
[23:52:45 INFO]: [LP] - git-PaperSpigot-"8b18730" (MC: 1.8.8) - 1.8.8-R0.1-SNAPSHOT
[23:52:45 INFO]: [LP] - Storage:
[23:52:45 INFO]: [LP] - Type: MySQL
[23:52:45 INFO]: [LP] - Ping: 1ms
[23:52:45 INFO]: [LP] - Connected: true
[23:52:45 INFO]: [LP] - Messaging: None
[23:52:45 INFO]: [LP] - Instance:
[23:52:45 INFO]: [LP] - Static contexts: None
[23:52:45 INFO]: [LP] - Online Players: 0 (0 unique)
[23:52:45 INFO]: [LP] - Uptime: 32s
[23:52:45 INFO]: [LP] - Local Data: 0 users, 18 groups, 0 tracks
`

Do you control the server yourself?
Ideally I need a thread dump when the server is disabling.

You can use the jstack command to do this.