There are interwiki & ipblocks with many other tables in both the current database and shared database. I am very sure that the account used for updater have full rights for both database.
However, the updater were failed to detect tables in shared database, and resulting create table already exits, which lead to error.
$wgSharedDB = 'wikidata';
$wgSharedTables[] = 'user';
$wgSharedTables[] = 'user_properties';
$wgSharedTables[] = 'user_groups';
$wgSharedTables[] = 'spoofuser';
$wgSharedTables[] = 'interwiki';
$wgEnableScaryTranscluding = true;
$wgSharedTables[] = 'ipblocks';
$wgSharedTables[] = 'abuse_filter';
$wgSharedTables[] = 'abuse_filter_action';
$wgSharedTables[] = 'abuse_filter_history';
php /var/www/wiki/maintenance/update.php --dbuser root --dbpass ******** --conf /var/www/wiki/LocalSettings.php --doshared --wiki moegirl --server https://zh.moegirl.org --nopurge
MediaWiki 1.28.0 Updater
Your composer.lock file is up to date with current dependencies!
Going to run database updates for moegirl
Depending on the size of your database this may take a while!
...echo_subscription doesn't exist.
Turning off Content Handler DB fields for this part of upgrade.
...ipblocks table does not exist, skipping new field patch.
...ipblocks table does not exist, skipping new field patch.
Creating interwiki table ...[0cd9644b7f61e6993060d51a] [no req] DBQueryError from line 1054 of /wiki/includes/libs/rdbms/database/Database.php: A database query error has occurred. Did you forget to run your application's database schema updater after upgrading?
Query: CREATE TABLE `wikidata`.`interwiki` (
iw_prefix varchar(32) NOT NULL,
iw_url blob NOT NULL,
iw_local BOOL NOT NULL,
UNIQUE KEY iw_prefix (iw_prefix)
) ENGINE=InnoDB
Function: Database::sourceFile( /wiki/maintenance/archives/patch-interwiki.sql )
Error: 1050 Table 'interwiki' already exists (10.0.0.113:3306)
Backtrace:
#0 /wiki/includes/libs/rdbms/database/Database.php(912): Database->reportQueryError(string, integer, string, string, boolean)
#1 /wiki/includes/libs/rdbms/database/Database.php(3136): Database->query(string, string)
#2 /wiki/includes/libs/rdbms/database/Database.php(3084): Database->sourceStream(unknown type, NULL, NULL, string, NULL)
#3 /wiki/includes/installer/DatabaseUpdater.php(690): Database->sourceFile(string)
#4 /wiki/includes/installer/MysqlUpdater.php(364): DatabaseUpdater->applyPatch(string, boolean, string)
#5 /wiki/includes/installer/DatabaseUpdater.php(472): MysqlUpdater->doInterwikiUpdate()
#6 /wiki/includes/installer/DatabaseUpdater.php(433): DatabaseUpdater->runUpdates(array, boolean)
#7 /wiki/maintenance/update.php(172): DatabaseUpdater->doUpdates(array)
#8 /wiki/maintenance/doMaintenance.php(111): UpdateMediaWiki->execute()
#9 /wiki/maintenance/update.php(217): require_once(string)
#10 {main}