12.0.3 to 12.0.5 upgrade has made web side very slow

Nextcloud version: 12.0.5
Operating system and version: Debian 8.10
Linux nextcloud 3.16.0-4-amd64 #1 SMP Debian 3.16.51-3 (2017-12-13) x86_64 GNU/Linux
Apache or nginx version: Apache 2.4.10
PHP version: 5.6.33
PHP 5.6.33-0+deb8u1 (cli) (built: Jan 5 2018 15:46:26)
Copyright © 1997-2016 The PHP Group
Zend Engine v2.6.0, Copyright © 1998-2016 Zend Technologies
with Zend OPcache v7.0.6-dev, Copyright © 1999-2016, by Zend Technologies

The issue you are facing:

I ran the upgrade via the web client last week from 12.0.3 to 12.0.5 and ever since the web side is far slower when visiting any page. SNMP monitoring shows no obvious issues, CPU, RAM and network usage all have nothing out of the ordinary. The logs in NextCloud web (although took an age to load) have no indications of where the problem might lie. There appears to be no noticeable change in the speed from the desktop client, or when downloading files via the web client (when it finally loads). All plugins have been updated to the latest version. All file permissions are set correctly, as per the instructions for setting strong file permissions.

Is this the first time you’ve seen this error? Yes

The output of your Nextcloud log in Admin > Logging:

{"reqId":"ke9U941vfYOXDOYCv1za","level":1,"time":"2018-01-30T21:14:45+00:00","remoteAddr":"151.231.126.248","user":"--","app":"updater","method":"GET","url":"\/core\/ajax\/update.php?requesttoken=aofNA3fs5ezaBLrQrGDa6JUOxOfErasJgAyH8sYojMM%3D%3AJrODcBaYgdq7fYqVlRHr3dFZk76i%2Bd1Yw03ftKNP7fo%3D","message":"\\OC\\Updater::updateEnd: Update successful","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"ke9U941vfYOXDOYCv1za","level":1,"time":"2018-01-30T21:14:45+00:00","remoteAddr":"151.231.126.248","user":"--","app":"updater","method":"GET","url":"\/core\/ajax\/update.php?requesttoken=aofNA3fs5ezaBLrQrGDa6JUOxOfErasJgAyH8sYojMM%3D%3AJrODcBaYgdq7fYqVlRHr3dFZk76i%2Bd1Yw03ftKNP7fo%3D","message":"\\OC\\Updater::maintenanceDisabled: Turned off maintenance mode","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"ke9U941vfYOXDOYCv1za","level":1,"time":"2018-01-30T21:14:45+00:00","remoteAddr":"151.231.126.248","user":"--","app":"updater","method":"GET","url":"\/core\/ajax\/update.php?requesttoken=aofNA3fs5ezaBLrQrGDa6JUOxOfErasJgAyH8sYojMM%3D%3AJrODcBaYgdq7fYqVlRHr3dFZk76i%2Bd1Yw03ftKNP7fo%3D","message":"\\OC\\Updater::resetLogLevel: Reset log level to Warning(2)","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"wHBd0SGpWbCEtfPEF2dR","level":2,"time":"2018-01-30T21:22:07+00:00","remoteAddr":"151.231.126.248","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"151.231.126.248\" tried to access using \"storage.alexwinder.net\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"vt6QxClDgoHTw0viDIFG","level":2,"time":"2018-01-30T21:22:07+00:00","remoteAddr":"151.231.126.248","user":"--","app":"core","method":"GET","url":"\/index.php\/js\/core\/merged-template-prepend.js?v=a7b44c06cdf32ca1cf344bf6446cc19c-16","message":"Trusted domain error. \"151.231.126.248\" tried to access using \"storage.alexwinder.net\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"vuqfOKASx7MO9yse0uRv","level":2,"time":"2018-01-30T21:27:53+00:00","remoteAddr":"151.231.126.248","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"151.231.126.248\" tried to access using \"storage.alexwinder.net\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"bo5T8nvBCGPabtqSD9CJ","level":2,"time":"2018-01-30T21:27:53+00:00","remoteAddr":"151.231.126.248","user":"--","app":"core","method":"GET","url":"\/index.php\/js\/core\/merged-template-prepend.js?v=a7b44c06cdf32ca1cf344bf6446cc19c-16","message":"Trusted domain error. \"151.231.126.248\" tried to access using \"storage.alexwinder.net\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.119 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"HS955PErpyvN6WMamNPb","level":2,"time":"2018-01-30T23:52:41+00:00","remoteAddr":"62.233.65.182","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"62.233.65.182\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"JDRGhURCy1F55YOhJebL","level":2,"time":"2018-01-31T00:45:04+00:00","remoteAddr":"62.233.65.182","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"62.233.65.182\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"yzJYAEtp1xxWNpnAfJFu","level":2,"time":"2018-01-31T02:54:38+00:00","remoteAddr":"107.170.232.242","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"107.170.232.242\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"yrzwRos9hHfGYjPACC3T","level":2,"time":"2018-01-31T13:15:06+00:00","remoteAddr":"216.218.206.69","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"216.218.206.69\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"51NjElK2Y8QQ7yyrYIYO","level":2,"time":"2018-01-31T23:26:48+00:00","remoteAddr":"209.126.136.7","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"209.126.136.7\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/57.0.2987.133 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"rIHQYKD5mgpPmcesDWsp","level":2,"time":"2018-02-01T05:04:04+00:00","remoteAddr":"80.82.77.33","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"80.82.77.33\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (X11; Linux x86_64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/34.0.1847.137 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"iTlDe3vZkxFr410XfpQz","level":2,"time":"2018-02-01T13:31:25+00:00","remoteAddr":"216.218.206.69","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"216.218.206.69\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"T0dN20Vve5IbysCclQPs","level":3,"time":"2018-02-01T16:15:44+00:00","remoteAddr":"27.151.114.81","user":"--","app":"PHP","method":"GET","url":"\/phpMyAdmin","message":"Exception: The requested uri(\/phpMyAdmin) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/4.0 (compatible; MSIE 9.0; Windows NT 6.1)","version":"12.0.5.3"}
{"reqId":"5j3jYSFs03OdCqAjeOu4","level":2,"time":"2018-02-01T19:09:26+00:00","remoteAddr":"141.212.122.81","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"141.212.122.81\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"Nm2557ER1RYRzGa9VJQj","level":2,"time":"2018-02-02T03:57:54+00:00","remoteAddr":"141.212.122.96","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"141.212.122.96\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"opzwZCkvn9nSxTN69CWL","level":2,"time":"2018-02-02T08:57:22+00:00","remoteAddr":"71.6.202.204","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"71.6.202.204\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/56.0.2924.87 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"YmDT3NluYQvXJht7shNb","level":2,"time":"2018-02-02T11:10:53+00:00","remoteAddr":"169.229.3.91","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"169.229.3.91\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"gcDKAk6oK29OGNwUIhgI","level":2,"time":"2018-02-02T11:55:31+00:00","remoteAddr":"139.162.116.133","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"139.162.116.133\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; WOW64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/50.0.2661.102 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"KwTXkdaufLxXgEF2Wcpw","level":3,"time":"2018-02-02T12:17:12+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/.ftpconfig","message":"Exception: The requested uri(\/.ftpconfig) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"QXbXSNdZ2YhFBwp7YD1Q","level":3,"time":"2018-02-02T12:17:13+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/.remote-sync.json","message":"Exception: The requested uri(\/.remote-sync.json) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"cFP4aPzJMZ2Hk2JQ1Ri1","level":3,"time":"2018-02-02T12:17:13+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/.vscode\/ftp-sync.json","message":"Exception: The requested uri(\/.vscode\/ftp-sync.json) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"Edub7NixJiZWntCAYi9U","level":3,"time":"2018-02-02T12:17:13+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/sftp-config.json","message":"Exception: The requested uri(\/sftp-config.json) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"gGBP1uPMarPNevTL3efB","level":3,"time":"2018-02-02T12:17:14+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/deployment-config.json","message":"Exception: The requested uri(\/deployment-config.json) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"40nDrr3eQ2DWSpIOamcC","level":2,"time":"2018-02-02T13:47:15+00:00","remoteAddr":"74.82.47.4","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"74.82.47.4\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"RtGZPuSgSFhTbY5FSecR","level":2,"time":"2018-02-02T15:38:08+00:00","remoteAddr":"164.52.6.150","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"164.52.6.150\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 6.1; WOW64; rv:52.0) Gecko\/20100101 Firefox\/52.0","version":"12.0.5.3"}
{"reqId":"VR9WvVY7puBzDLzjOzTK","level":3,"time":"2018-02-02T17:01:11+00:00","remoteAddr":"223.167.245.104","user":"--","app":"PHP","method":"GET","url":"\/current_config\/passwd","message":"Exception: The requested uri(\/current_config\/passwd) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"--","version":"12.0.5.3"}
{"reqId":"jPTmoDrYgVSmp6fMbAG4","level":2,"time":"2018-02-02T21:42:31+00:00","remoteAddr":"60.191.38.77","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"60.191.38.77\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"m6TlRlMAmeTVkLOQmk3K","level":2,"time":"2018-02-03T07:09:58+00:00","remoteAddr":"71.6.202.204","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"71.6.202.204\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/56.0.2924.87 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"zEP8oyKlKdVLsvDYidId","level":2,"time":"2018-02-03T14:45:45+00:00","remoteAddr":"184.105.139.67","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"184.105.139.67\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"RvLZzHwV9GdSft0sjcvw","level":2,"time":"2018-02-04T05:50:52+00:00","remoteAddr":"107.170.252.110","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"107.170.252.110\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"CdtRk9PuhUtXnjVfVBKZ","level":2,"time":"2018-02-04T11:21:13+00:00","remoteAddr":"139.162.113.204","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"139.162.113.204\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; WOW64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/50.0.2661.102 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"YeDqWBPIv4F1iQxqiVqm","level":2,"time":"2018-02-04T13:54:38+00:00","remoteAddr":"184.105.139.68","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"184.105.139.68\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"Q1h2U84IQYRo2HR6TX4X","level":2,"time":"2018-02-04T18:09:22+00:00","remoteAddr":"107.170.255.4","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"107.170.255.4\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"gZy8MEDfDfKGL1roMsjf","level":2,"time":"2018-02-04T20:15:33+00:00","remoteAddr":"151.231.126.248","user":"--","app":"core","method":"POST","url":"\/index.php\/login","message":"Login failed: 'REMOVED_FOR_SECURITY' (Remote IP: '151.231.126.248')","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.140 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"yXdXfwXerG4ktyyqVq9D","level":2,"time":"2018-02-04T21:03:22+00:00","remoteAddr":"60.191.38.77","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"60.191.38.77\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"N7cNFmeCMKeIKUmUDukl","level":3,"time":"2018-02-05T02:51:54+00:00","remoteAddr":"195.22.127.249","user":"--","app":"PHP","method":"GET","url":"\/.git\/HEAD","message":"Exception: The requested uri(\/.git\/HEAD) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/62.0.3202.94 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"jgWRCOj3UR7N6DJ3DK5b","level":3,"time":"2018-02-05T06:12:20+00:00","remoteAddr":"172.104.115.143","user":"--","app":"PHP","method":"GET","url":"\/favicon.ico","message":"Exception: The requested uri(\/favicon.ico) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"JBkZu8NtXsQVuP3LEYwa","level":2,"time":"2018-02-05T10:01:04+00:00","remoteAddr":"71.6.202.204","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"71.6.202.204\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/56.0.2924.87 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"s9UEpFQaTwB4pwb7JnXU","level":3,"time":"2018-02-05T13:03:59+00:00","remoteAddr":"46.21.150.141","user":"--","app":"PHP","method":"GET","url":"\/etc\/lib\/pChart2\/examples\/index.php?Action=View&Script=..\/..\/..\/..\/cnf\/db.php","message":"Exception: The requested uri(\/etc\/lib\/pChart2\/examples\/index.php) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"HTTP_Request2\/0.5.2 (http:\/\/pear.php.net\/package\/http_request2) PHP\/5.3.3","version":"12.0.5.3"}
{"reqId":"gprpfP0EVkZpOcgMPbuN","level":2,"time":"2018-02-05T14:42:13+00:00","remoteAddr":"216.218.206.66","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"216.218.206.66\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"1IN7ppiSMgUD43nUxEFI","level":3,"time":"2018-02-05T14:45:20+00:00","remoteAddr":"46.21.150.141","user":"--","app":"PHP","method":"GET","url":"\/etc\/lib\/pChart2\/examples\/index.php?Action=View&Script=..\/..\/..\/..\/cnf\/db.php","message":"Exception: The requested uri(\/etc\/lib\/pChart2\/examples\/index.php) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"HTTP_Request2\/0.5.2 (http:\/\/pear.php.net\/package\/http_request2) PHP\/5.3.3","version":"12.0.5.3"}
{"reqId":"rcgdC9DfxdQ8MumPMiMs","level":2,"time":"2018-02-05T15:01:40+00:00","remoteAddr":"60.191.38.77","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"60.191.38.77\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"Uff1ZBJyZeuS0rarxXub","level":2,"time":"2018-02-06T09:10:36+00:00","remoteAddr":"139.162.106.181","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"139.162.106.181\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; WOW64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/50.0.2661.102 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"MPoHu9KXaUlaDmdaXwF2","level":2,"time":"2018-02-06T09:52:06+00:00","remoteAddr":"164.132.91.13","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"164.132.91.13\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Chrome\/41.0.2228.0 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"xCh5fxCjfisnksouxTfl","level":2,"time":"2018-02-06T10:22:04+00:00","remoteAddr":"209.126.136.7","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"209.126.136.7\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/57.0.2987.133 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"cyf3zTa5dZ1GLCfG4eZl","level":2,"time":"2018-02-06T14:06:05+00:00","remoteAddr":"184.105.139.67","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"184.105.139.67\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"KDNBoGpl9m3h0p3dWfj4","level":2,"time":"2018-02-06T17:30:17+00:00","remoteAddr":"139.162.78.135","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"139.162.78.135\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; WOW64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/45.0.2454.101 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"RrqpwCIHUx19ReTdz6DF","level":3,"time":"2018-02-07T07:33:01+00:00","remoteAddr":"27.151.114.81","user":"--","app":"PHP","method":"GET","url":"\/pmd\/","message":"Exception: The requested uri(\/pmd\/) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/4.0 (compatible; MSIE 9.0; Windows NT 6.1)","version":"12.0.5.3"}
{"reqId":"A26ZdRr1T9NWa2Sl6onL","level":2,"time":"2018-02-07T08:20:42+00:00","remoteAddr":"107.170.251.213","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"107.170.251.213\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"VyD7PPmJHL05jLvWm7Mu","level":3,"time":"2018-02-07T10:34:38+00:00","remoteAddr":"78.129.130.53","user":"--","app":"PHP","method":"GET","url":"\/xmlrpc.php","message":"Exception: The requested uri(\/xmlrpc.php) cannot be processed by the script '\/core\/templates\/404.php') at \/var\/www\/nextcloud\/lib\/private\/AppFramework\/Http\/Request.php#729","userAgent":"Mozilla\/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko\/20070725 Firefox\/2.0.0.6","version":"12.0.5.3"}
{"reqId":"5xflmDtfMWyhygtN1N8z","level":2,"time":"2018-02-07T14:24:23+00:00","remoteAddr":"184.105.139.69","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"184.105.139.69\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"k7sfHqUNOBwekq4b9aUe","level":2,"time":"2018-02-07T21:03:12+00:00","remoteAddr":"60.191.38.77","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"60.191.38.77\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"amVYIIAoFPGMdKfyvQDG","level":2,"time":"2018-02-07T23:32:15+00:00","remoteAddr":"107.170.225.228","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"107.170.225.228\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 zgrab\/0.x","version":"12.0.5.3"}
{"reqId":"CgSJYiv1qznZe0jmzXGL","level":2,"time":"2018-02-08T00:38:16+00:00","remoteAddr":"164.52.6.150","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"164.52.6.150\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 6.1; WOW64; rv:52.0) Gecko\/20100101 Firefox\/52.0","version":"12.0.5.3"}
{"reqId":"dYE5wg2rqDg0l1DvUee7","level":2,"time":"2018-02-08T02:41:36+00:00","remoteAddr":"71.6.202.204","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"71.6.202.204\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"Mozilla\/5.0 (Windows NT 10.0; WOW64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/63.0.3239.132 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"C5oOa74EvZtHjUnLi7aB","level":2,"time":"2018-02-08T06:55:48+00:00","remoteAddr":"183.129.160.229","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"183.129.160.229\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"dDLs0kRqcQZWCELNG8yQ","level":2,"time":"2018-02-08T10:21:40+00:00","remoteAddr":"84.92.92.163","user":"--","app":"core","method":"POST","url":"\/index.php\/login","message":"Login failed: 'REMOVED_FOR_SECURITY' (Remote IP: '84.92.92.163')","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.140 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"yjuhOBtoHnWLbDspDCSq","level":2,"time":"2018-02-08T14:40:29+00:00","remoteAddr":"216.218.206.66","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"216.218.206.66\" tried to access using \"REMOVED_FOR_SECURITY\" as host.","userAgent":"--","version":"12.0.5.3"}
{"reqId":"A8mNOzAE1G8DQ5sHmoO3","level":2,"time":"2018-02-08T18:07:32+00:00","remoteAddr":"185.226.74.78","user":"--","app":"core","method":"POST","url":"\/index.php\/login","message":"Login failed: 'REMOVED_FOR_SECURITY' (Remote IP: '185.226.74.78')","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.140 Safari\/537.36","version":"12.0.5.3"}
{"reqId":"fEZYM4Biy6eY0IFev2rQ","level":2,"time":"2018-02-08T20:55:07+00:00","remoteAddr":"60.191.38.77","user":"--","app":"core","method":"GET","url":"\/","message":"Trusted domain error. \"60.191.38.77\" tried to access using \"REMOVED_FOR_SECURITY:443\" as host.","userAgent":"Mozilla\/5.0 (Macintosh; Intel Mac OS X 10.11; rv:47.0) Gecko\/20100101 Firefox\/47.0","version":"12.0.5.3"}
{"reqId":"OeG636UEHaOyrYsf35Ns","level":3,"time":"2018-02-08T23:34:16+00:00","remoteAddr":"185.70.135.6","user":"REMOVED_FOR_SECURITY","app":"no app in context","method":"GET","url":"\/index.php\/settings\/admin\/logging","message":"Exception: {\"Exception\":\"OCP\\\\AppFramework\\\\QueryException\",\"Message\":\"Could not resolve OCA\\\\BruteForceSettings\\\\Settings\\\\IPWhitelist! Class OCA\\\\BruteForceSettings\\\\Settings\\\\IPWhitelist does not exist\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Utility\\\/SimpleContainer.php(117): OC\\\\AppFramework\\\\Utility\\\\SimpleContainer->resolve('OCA\\\\\\\\BruteForceS...')\\n#1 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/ServerContainer.php(132): OC\\\\AppFramework\\\\Utility\\\\SimpleContainer->query('OCA\\\\\\\\BruteForceS...')\\n#2 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Settings\\\/Manager.php(262): OC\\\\ServerContainer->query('OCA\\\\\\\\BruteForceS...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Settings\\\/Manager.php(353): OC\\\\Settings\\\\Manager->query('OCA\\\\\\\\BruteForceS...')\\n#4 \\\/var\\\/www\\\/nextcloud\\\/settings\\\/Controller\\\/AdminSettingsController.php(138): OC\\\\Settings\\\\Manager->getAdminSettings('security')\\n#5 \\\/var\\\/www\\\/nextcloud\\\/settings\\\/Controller\\\/AdminSettingsController.php(72): OC\\\\Settings\\\\Controller\\\\AdminSettingsController->getNavigationParameters('logging')\\n#6 [internal function]: OC\\\\Settings\\\\Controller\\\\AdminSettingsController->index('logging')\\n#7 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Http\\\/Dispatcher.php(160): call_user_func_array(Array, Array)\\n#8 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Http\\\/Dispatcher.php(90): OC\\\\AppFramework\\\\Http\\\\Dispatcher->executeController(Object(OC\\\\Settings\\\\Controller\\\\AdminSettingsController), 'index')\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/App.php(114): OC\\\\AppFramework\\\\Http\\\\Dispatcher->dispatch(Object(OC\\\\Settings\\\\Controller\\\\AdminSettingsController), 'index')\\n#10 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Routing\\\/RouteActionHandler.php(47): OC\\\\AppFramework\\\\App::main('AdminSettingsCo...', 'index', Object(OC\\\\AppFramework\\\\DependencyInjection\\\\DIContainer), Array)\\n#11 [internal function]: OC\\\\AppFramework\\\\Routing\\\\RouteActionHandler->__invoke(Array)\\n#12 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Route\\\/Router.php(299): call_user_func(Object(OC\\\\AppFramework\\\\Routing\\\\RouteActionHandler), Array)\\n#13 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(1004): OC\\\\Route\\\\Router->match('\\\/settings\\\/admin...')\\n#14 \\\/var\\\/www\\\/nextcloud\\\/index.php(48): OC::handleRequest()\\n#15 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Utility\\\/SimpleContainer.php\",\"Line\":102}","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit\/537.36 (KHTML, like Gecko) Chrome\/64.0.3282.140 Safari\/537.36","version":"12.0.5.3"}

The output of your config.php file in /path/to/nextcloud (make sure you remove any identifiable information!):

$CONFIG = array (
  'instanceid' => 'REMOVED',
  'passwordsalt' => 'REMOVED',
  'secret' => 'REMOVED',
  'trusted_domains' =>
  array (
    0 => 'REMOVED',
  ),
  'datadirectory' => '/var/www/nextcloud/data',
  'overwrite.cli.url' => 'http://REMOVED/nextcloud',
  'dbtype' => 'mysql',
  'version' => '12.0.5.3',
  'dbname' => 'REMOVED',
  'dbhost' => 'REMOVED',
  'dbport' => 'REMOVED',
  'dbtableprefix' => 'REMOVED',
  'dbuser' => 'REMOVED',
  'dbpassword' => 'REMOVED',
  'logtimezone' => 'UTC',
  'installed' => true,
  'memcache.local' => '\\OC\\Memcache\\APCu',
  'mail_smtpmode' => 'smtp',
  'mail_smtpauthtype' => 'LOGIN',
  'mail_smtpauth' => 1,
  'mail_from_address' => 'REMOVED',
  'mail_domain' => 'REMOVED',
  'mail_smtphost' => 'smtp.gmail.com',
  'mail_smtpsecure' => 'ssl',
  'mail_smtpport' => '465',
  'mail_smtpname' => 'REMOVED',
  'mail_smtppassword' => 'REMOVED',
  'maintenance' => false,
  'theme' => '',
  'loglevel' => 2,
  'updater.secret' => 'REMOVED',
);

The output of your Apache/nginx/system log in /var/log/____:

[Thu Feb 08 06:25:03.473044 2018] [mpm_prefork:notice] [pid 733] AH00163: Apache/2.4.10 (Debian) OpenSSL/1.0.1t configured -- resuming normal operations
[Thu Feb 08 06:25:03.473077 2018] [core:notice] [pid 733] AH00094: Command line: '/usr/sbin/apache2'
[Thu Feb 08 10:44:38.995887 2018] [authz_core:error] [pid 14493] [client 84.92.92.163:22497] AH01630: client denied by server configuration: /var/www/nextcloud/data/.ocdata
[Thu Feb 08 10:45:29.317699 2018] [authz_core:error] [pid 18570] [client 84.92.92.163:22513] AH01630: client denied by server configuration: /var/www/nextcloud/data/.ocdata
[Thu Feb 08 18:08:50.894192 2018] [authz_core:error] [pid 18567] [client 185.226.74.78:11824] AH01630: client denied by server configuration: /var/www/nextcloud/data/.ocdata
[Thu Feb 08 23:12:06.994498 2018] [authz_core:error] [pid 18567] [client 185.70.135.6:27800] AH01630: client denied by server configuration: /var/www/nextcloud/data/.ocdata
[Thu Feb 08 23:34:26.892886 2018] [authz_core:error] [pid 2833] [client 185.70.135.6:30393] AH01630: client denied by server configuration: /var/www/nextcloud/data/.ocdata

Update:

There is a slowdown when listing folders on the client side for selection also.

Any help would be most appreciated.

Update:

This has now been resolved. It was caused due to a federated share being no longer available and thus timing out. Removing the share has fixed the issue. However, this seems very odd that the whole system becomes unusable, even when I’m not accessing even the parent folder of where the share lives. I’m also pretty sure that the share link was still unavailable before my upgrade to 12.0.5.

In this case, please report it on the bugtracker on github.com/nextcloud/server/issues