I have a server that has a chronic problem with skipping ticks and then being shut down by the Watchdog. To be clear, this is not a problem with the Watchdog feature. I know how to disable it, and it does not help because although the server does not shut down, it lags severely and still needs to be manually restarted. Do not mark it as a duplicate of the Watchdog issue, as I have seen done to many similar threads.

The server is a quad-core i7 2.7 GHz with 16GB of RAM, 4 of which are dedicated to Minecraft. CPU usage and disk activity on the server are both very low during the times that the server is lagging. The messages shown in the log are pasted below, and the crash report is attached. The crash occurred when no players were on the server and can happen at any time.

The crash occurs frequently, usually at least every 2 or 3 days and often more than once per day.

[10:57:45] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 2107ms behind, skipping 42 tick(s)
[13:14:28] [Server Watchdog/FATAL]: A single server tick took 60.00 seconds (should be max 0.05)
[13:14:28] [Server Watchdog/FATAL]: Considering it to be crashed, server will forcibly shutdown.
[13:18:26] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 298344ms behind, skipping 5966 tick(s)
[13:18:26] [Server Watchdog/ERROR]: This crash report has been saved to: /snip/crash-reports/crash-2015-10-18_13.14.28-server.txt
[13:18:26] [Server Shutdown Thread/INFO]: Stopping server
[13:18:26] [Server Shutdown Thread/INFO]: Saving players