Log non indexed queries for multiple databases
To find all queries not using indexes, you need to do two things:


Enable the slow query log
Set the global variable log_queries_not_using_indexes to ON


In my.cnf for 5.6, this would look like:

[mysqld]
...
...
slow_query_log=ON
log_queries_not_using_indexes=ON


Both are dynamic variables and can be set on a running system like this:

mysql&gt; SET GLOBAL slow_query_log=ON;
mysql&gt; SET GLOBAL log_queries_not_using_indexes=ON;


Refer to https://dev.mysql.com/doc/refman/5.6/en/slow-query-log.html for full details and note that by default queries not using indexes are not logged to the slow query log, but if log_queries_not_using_indexes is enabled, ALL queries not using indexes will be logged, regardless of if they take longer than 'long_query_time' to execute.  If the number of queries logged is excessive, use log_throttle_queries_not_using_indexes to limit the number of queries not using indexes that will be logged per minute.  Like the other two global variables, this is dynamic and can be changed on a running system like this, e.g. to set it as 10 per minute:

mysql&gt; SET GLOBAL log_throttle_queries_not_using_indexes=10;


That ought to fix you up.