[Observium] Database service crashes after update

After updating to the latest version 18.5.9221 (stable) I ran the discovery.php -u to update it said (update syslog, may be long operation ~30-45min) after about 5 min I get an error Critical error: (2013) Lost connection to MySQL server during query. Restarting the service nor rebooting the server helps and I had to do a rollback from a checkpoint to get Observium to function again. Can you help me with this error?