CakePHP SQLSTATE[HY000][14] error

I'm trying to upgrade my current CakePHP 2.x application to 3.x.

I fixed namespace and folder structure issues. Now I have problems with database. In my test server, I created same MySQL database and grant access to users. Then I changed config\app.php configuration file. But when I try my application I get following error. What would be the problem ? It seems like Cakephp tries to use Sqlite but I use MySQL ?

Inside config\app.php

'Datasources' => [
    'default' => [
        'className' => 'Cake\Database\Connection',
        'driver' => 'Cake\Database\Driver\Mysql',
        'persistent' => false,
        'host' => 'localhost',
        /**
         * CakePHP will use the default DB port based on the driver selected
         * MySQL on MAMP uses port 8889, MAMP users will want to uncomment
         * the following line and set the port accordingly
         */
        //'port' => 'nonstandard_port_number',
        'username' => 'myuser',
        'password' => 'mypass',
        'database' => 'mydatabase',
        'encoding' => 'utf8',
        'timezone' => 'UTC',
        'cacheMetadata' => true,

        /**
         * Set identifier quoting to true if you are using reserved words or
         * special characters in your table or column names. Enabling this
         * setting will result in queries built using the Query Builder having
         * identifiers quoted when creating SQL. It should be noted that this
         * decreases performance because each query needs to be traversed and
         * manipulated before being executed.
         */
        'quoteIdentifiers' => false,
    ],
],

Error

Error: [PDOException] SQLSTATE[HY000] [14] unable to open database file
Request URL: /mycontroller/
Stack Trace:
#0 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Driver/PDODriverTrait.php(48): PDO->__construct('sqlite:/var/www...', NULL, NULL, Array)
#1 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Driver/Sqlite.php(61): Cake\Database\Driver\Sqlite->_connect('sqlite:/var/www...', Array)
#2 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Schema/BaseSchema.php(46): Cake\Database\Driver\Sqlite->connect()
#3 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Dialect/SqliteDialectTrait.php(169): Cake\Database\Schema\BaseSchema->__construct(Object(Cake\Database\Driver\Sqlite))
#4 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Schema/Collection.php(52): Cake\Database\Driver\Sqlite->schemaDialect()
#5 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Schema/CachedCollection.php(44): Cake\Database\Schema\Collection->__construct(Object(Cake\Database\Connection))
#6 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Database/Connection.php(319): Cake\Database\Schema\CachedCollection->__construct(Object(Cake\Database\Connection), true)
#7 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/debug_kit/src/Model/Table/LazyTableTrait.php(40): Cake\Database\Connection->schemaCollection()
#8 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/debug_kit/src/Model/Table/RequestsTable.php(43): DebugKit\Model\Table\RequestsTable->ensureTables(Array)
#9 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/ORM/Table.php(285): DebugKit\Model\Table\RequestsTable->initialize(Array)
#10 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/ORM/TableRegistry.php(196): Cake\ORM\Table->__construct(Array)
#11 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/debug_kit/src/Routing/Filter/DebugBarFilter.php(186): Cake\ORM\TableRegistry::get('DebugKit.Reques...')
#12 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Event/EventManager.php(389): DebugKit\Routing\Filter\DebugBarFilter->afterDispatch(Object(Cake\Event\Event), Object(Cake\Network\Request), Object(Cake\Network\Response))
#13 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Event/EventManager.php(355): Cake\Event\EventManager->_callListener(Array, Object(Cake\Event\Event))
#14 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Event/EventManagerTrait.php(78): Cake\Event\EventManager->dispatch(Object(Cake\Event\Event))
#15 /var/www/vhosts/example.com/httpdocs/vendor/cakephp/cakephp/src/Routing/Dispatcher.php(92): Cake\Routing\Dispatcher->dispatchEvent('Dispatcher.afte...', Array)
#16 /var/www/vhosts/example.com/httpdocs/webroot/index.php(37): Cake\Routing\Dispatcher->dispatch(Object(Cake\Network\Request), Object(Cake\Network\Response))
#17 {main}

If you look a little closer at the stacktrace, you'll notice that this doesn't stem from your apps connections, but from the DebugKit plugin, which by default uses SQLite for storing panel and request details, and most probably the target directory/file isn't writable.

Cookbook > DebugKit

[...]

DebugKit Storage

By default, DebugKit uses a small SQLite database in your application’s /tmp directory to store the panel data. If you’d like DebugKit to store its data elsewhere, you should define a debug_kit connection.

Database Configuration

By default DebugKit will store panel data into a SQLite database in your application’s tmp directory. If you cannot install pdo_sqlite, you can configure DebugKit to use a different database by defining a debug_kit connection in your config/app.php file.

[...]