That’s not the error message.
pymysql.err.OperationalError: (1045, "Access denied for user '_46bb7e3c2f0d01a3'@'localhost' (using password: YES)")
This is the error message. There seems to be an authentication issue for your site. Set a new password for the user _46bb7e3c2f0d01a3 perhaps and update it in the site_config.json. Then try again, that should work for you.
There’s a thread: Bench update i get this - pymysql.err.OperationalError: (1045, u"Access denied for user regarding a similar issue.