Some plugins in WordPress are causing high CPU usage. Running atop command i can see that can php-cgi and mysql services are causing the load. Is there a way i can see via CLI what plugins are causing this mess?
No. Try to disable all plug-in and enable them one at a time.
Sometime the mytop could help you to find if the database is a problem (lack of index) and possibly also the plugin which do slow/bad queries (like many SEO plugins).