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Sorry to hear you’re facing problems 
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In order to help you as quickly as possible, before clicking Create Topic please provide as much of the below as you can. Feel free to use a pastebin service for logs, otherwise either indent short log examples with four spaces:
example
Or for longer, use three backticks above and below the code snippet:
longer
example
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Some or all of the below information will be requested if it isn’t supplied; for fastest response please provide as much as you can 
Nextcloud version (eg, 12.0.2): 16.0.3.0
Operating system and version (eg, Ubuntu 17.04): Debian 9
Apache or nginx version (eg, Apache 2.4.25): Apache 2.4.25
PHP version (eg, 7.1): 7.3.6
The issue you are facing:
When I attempted to log in to Nextcloud as the administrator user, I am prompted to update twofactor_totp. The update fails with the following output:
Set log level to debug
Updating database schema
Updated database
Updating <twofactor_totp> …
Doctrine\DBAL\Schema\SchemaException: The column ‘last_counter’ on table ‘oc_twofactor_totp_secrets’ already exists.
Update failed
Maintenance mode is kept active
Reset log level
If I disable twofacor_totp with occ, the admin user is still unable to login and receives an error that none of my TOTP options are available. I have a backup from when this was working correctly, but if I recover from backups I am presented with the same issue when I attempt to login.
Is this the first time you’ve seen this error? (Y/N): Y
Steps to replicate it:
- Recover from backup of working instance
- Attempt to login
- Prompted to update totp, update fails
The output of your Nextcloud log in Admin > Logging:
Unable to login to access interface
The output of your config.php file in /path/to/nextcloud (make sure you remove any identifiable information!):
<?php
$CONFIG = array (
'instanceid' => 'id',
'passwordsalt' => 'salt',
'secret' => 'secret',
'trusted_domains' =>
array (
0 => 'host.domain.org',
),
'datadirectory' => '/var/www/html/nextcloud/data',
'dbtype' => 'mysql',
'version' => '16.0.3.0',
'overwrite.cli.url' => 'https://host.domain.org',
'dbname' => 'nextcloud',
'dbhost' => 'localhost',
'dbport' => '',
'dbtableprefix' => 'oc_',
'mysql.utf8mb4' => true,
'dbuser' => 'dan',
'dbpassword' => 'dbpasswd',
'installed' => true,
'updater.release.channel' => 'stable',
'twofactor_enforced' => 'true',
'login_form_autocomplete' => false,
'memcache.local' => '\\OC\\Memcache\\APCu',
'twofactor_enforced_groups' =>
array (
),
'twofactor_enforced_excluded_groups' =>
array (
0 => 'New User Setup',
),
'maintenance' => true,
'theme' => '',
'loglevel' => 2,
'mail_from_address' => 'no_reply',
'mail_smtpmode' => 'smtp',
'mail_sendmailmode' => 'smtp',
'mail_domain' => 'domain.org',
'mail_smtpauthtype' => 'LOGIN',
'upgrade.disable-web' => true,
);
The output of your Apache/nginx/system log in /var/log/____:
PHP Warning: Module 'exif' already loaded in Unknown on line 0
PHP Warning: Module 'posix' already loaded in Unknown on line 0
PHP Warning: Module 'zip' already loaded in Unknown on line 0
PHP Warning: Module 'mysqlnd' already loaded in Unknown on line 0
PHP Warning: Module 'apc' already loaded in Unknown on line 0
PHP Warning: Module 'iconv' already loaded in Unknown on line 0
PHP Warning: Module 'curl' already loaded in Unknown on line 0
PHP Warning: Module 'imagick' already loaded in Unknown on line 0
PHP Warning: Module 'ctype' already loaded in Unknown on line 0
PHP Warning: Module 'PDO' already loaded in Unknown on line 0
PHP Warning: Module 'mysqli' already loaded in Unknown on line 0
PHP Warning: Module 'pdo_mysql' already loaded in Unknown on line 0
PHP Warning: Module 'xml' already loaded in Unknown on line 0
PHP Warning: Module 'sysvmsg' already loaded in Unknown on line 0
PHP Warning: Module 'gettext' already loaded in Unknown on line 0
PHP Warning: Module 'sockets' already loaded in Unknown on line 0
PHP Warning: Module 'xsl' already loaded in Unknown on line 0
PHP Warning: Module 'gd' already loaded in Unknown on line 0
PHP Warning: Module 'SimpleXML' already loaded in Unknown on line 0
PHP Warning: Module 'tokenizer' already loaded in Unknown on line 0
PHP Warning: Module 'intl' already loaded in Unknown on line 0
PHP Warning: Module 'mbstring' already loaded in Unknown on line 0
PHP Warning: Module 'shmop' already loaded in Unknown on line 0
PHP Warning: Module 'wddx' already loaded in Unknown on line 0
PHP Warning: Module 'dom' already loaded in Unknown on line 0
PHP Warning: Module 'xmlwriter' already loaded in Unknown on line 0
PHP Warning: Module 'readline' already loaded in Unknown on line 0
PHP Warning: Module 'apcu' already loaded in Unknown on line 0
PHP Warning: Module 'ftp' already loaded in Unknown on line 0
PHP Warning: Module 'Phar' already loaded in Unknown on line 0
PHP Warning: Module 'sysvsem' already loaded in Unknown on line 0
PHP Warning: Module 'calendar' already loaded in Unknown on line 0
PHP Warning: Module 'json' already loaded in Unknown on line 0
PHP Warning: Module 'fileinfo' already loaded in Unknown on line 0
PHP Warning: Module 'sysvshm' already loaded in Unknown on line 0
PHP Warning: Module 'xmlreader' already loaded in Unknown on line 0
[Tue Aug 20 10:50:41.000743 2019] [mpm_prefork:notice] [pid 4211] AH00163: Apac$
[Tue Aug 20 10:50:41.000760 2019] [core:notice] [pid 4211] AH00094: Command lin$
Cannot load Zend OPcache - it was already loaded
Cannot load Zend OPcache - it was already loaded
Cannot load Zend OPcache - it was already loaded
Cannot load Zend OPcache - it was already loaded
Any assistance in recovering my Nextcloud instance and ideally preventing this from occurring in the future would be greatly appreciated. Thank you.
