I accepted the request from the GUI "Owncloud want to display notification" and the server died completly. Here is the log.
[Tue Jul 11 12:37:00.120742 2017] [:error] [pid 40849] [client 81.235.28.244:10249] PHP Fatal error: Uncaught InvalidArgumentException: Identifier "command.dbUpgrade" is not defined. in /var/www/owncloud/updater/vendor/pimple/pimple/src/Pimple/Container.php:96\nStack trace:\n#0 /var/www/owncloud/updater/app/config/container.php(152): Pimple\Container->offsetGet('command.dbUpgra...')\n#1 /var/www/owncloud/updater/vendor/pimple/pimple/src/Pimple/Container.php(113): {closure}(Object(Pimple\Container))\n#2 /var/www/owncloud/updater/app/config/container.php(171): Pimple\Container->offsetGet('commands')\n#3 /var/www/owncloud/updater/vendor/pimple/pimple/src/Pimple/Container.php(113): {closure}(Object(Pimple\Container))\n#4 /var/www/owncloud/updater/src/Controller/IndexController.php(97): Pimple\Container->offsetGet('application')\n#5 /var/www/owncloud/updater/index.php(29): Owncloud\Updater\Controller\IndexController->dispatch()\n#6 {main}\n thrown in /var/www/owncloud/updater/vendor/pimple/pimple/src/Pimple/Container.php on line 96