MySQL Error 1093 - Can't specify target table for update in FROM clause

Update: This answer covers the general error classification. For a more specific answer about how to best handle the OP's exact query, please see other answers to this question

In MySQL, you can't modify the same table which you use in the SELECT part.
This behaviour is documented at: http://dev.mysql.com/doc/refman/5.6/en/update.html

Maybe you can just join the table to itself

If the logic is simple enough to re-shape the query, lose the subquery and join the table to itself, employing appropriate selection criteria. This will cause MySQL to see the table as two different things, allowing destructive changes to go ahead.

UPDATE tbl AS a
INNER JOIN tbl AS b ON ....
SET a.col = b.col

Alternatively, try nesting the subquery deeper into a from clause ...

If you absolutely need the subquery, there's a workaround, but it's ugly for several reasons, including performance:

UPDATE tbl SET col = (
  SELECT ... FROM (SELECT.... FROM) AS x);

The nested subquery in the FROM clause creates an implicit temporary table, so it doesn't count as the same table you're updating.

... but watch out for the query optimiser

However, beware that from MySQL 5.7.6 and onward, the optimiser may optimise out the subquery, and still give you the error. Luckily, the optimizer_switch variable can be used to switch off this behaviour; although I couldn't recommend doing this as anything more than a short term fix, or for small one-off tasks.

SET optimizer_switch = 'derived_merge=off';

Thanks to Peter V. Mørch for this advice in the comments.

Example technique was from Baron Schwartz, originally published at Nabble, paraphrased and extended here.

NexusRex provided a very good solution for deleting with join from the same table.

If you do this:

DELETE FROM story_category
WHERE category_id NOT IN (
        SELECT DISTINCT category.id AS cid FROM category 
        INNER JOIN story_category ON category_id=category.id
)

you are going to get an error.

But if you wrap the condition in one more select:

DELETE FROM story_category
WHERE category_id NOT IN (
    SELECT cid FROM (
        SELECT DISTINCT category.id AS cid FROM category 
        INNER JOIN story_category ON category_id=category.id
    ) AS c
)

it would do the right thing!!

Explanation: The query optimizer does a derived merge optimization for the first query (which causes it to fail with the error), but the second query doesn't qualify for the derived merge optimization. Hence the optimizer is forced to execute the subquery first.

The inner join in your sub-query is unnecessary. It looks like you want to delete the entries in story_category where the category_id is not in the category table.

Do this:

DELETE FROM story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category);

Instead of that:

DELETE FROM story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category INNER JOIN
         story_category ON category_id=category.id);