1) Login to your server via SSH.
2) Execute the command given below.
mysql -uDB_USERNAME_HERE -pDB_USER_PASSWORD_HERE -DYOUR_WORDPRESS_DB_NAME_HERE -e "DELETE FROM wp_comments WHERE comment_approved = '0';"
( Please note that, if your WordPress database prefix is something else, please replace “wp_” with that prefix. )
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Regards,
Vinod T K