The CodeIgniter database module automatically saves all queries you ran in the request, apparently for profiling. You can see the code here:

https://github.com/bcit-ci/CodeIgniter/blob/3.0-stable/system/database/DB_driver.php#L633

This can really eat into your memory, especially if you are running a large script via CodeIgniter CLI, processing a large amount of data.

Thankfully this is faily easy to stop. Just set the flag below to FALSE. It's in the DB_driver.php file, same as above.

    /**
     * Save queries flag
     *
     * Whether to keep an in-memory history of queries for debugging purposes.
     *
     * @var bool
     */
    public $save_queries        = TRUE;

I haven't found a way to dynamically turn this on/off (at least through officially supported means), but ideally I think this should be able to be set on/off depending on your environment. In a production environment where you rarely would be using the CodeIgniter profiler, this will just be a waste of memory, and can be very harmful to your application.
Until that dynamic configuration is possible, I suggest just turning it off everywhere, and turning it on only when you need it.

I wish this becomes configurable...