MySql - How can I improve this query?
What are you trying to achieve here? I am not a MySQL programmer; however, as I understand SQL in general, every column that is not listed in the GROUP BY clause must be part of an aggregate like

SELECT
    MAX(id) AS max_id,
    chain, subchain, job_type
FROM
    `job_logs`
WHERE
    user_id = ? AND
    workflow_state = ?
GROUP BY
    chain, subchain, job_type 




SELECT * in a grouping query will not work in most (if not all) SQL implementations.



UPDATE

In order to get the row with the highest id for each group you would have to embed the query above in an "outer" query.

SELECT *
FROM `job_logs`
WHERE id IN (
    SELECT
        MAX(id) AS max_id
    FROM
        `job_logs`
    WHERE
        user_id = ? AND
        workflow_state = ?
    GROUP BY
        chain, subchain, job_type 
)


This query is deterministic and should work with most SQL dialects.



Some query engines perform better with joins than with "IN subquery". You can give this a try

SELECT A.*
FROM
    `job_logs` A
    INNER JOIN (
        SELECT
            MAX(id) AS max_id
        FROM
            `job_logs`
        WHERE
            user_id = ? AND
            workflow_state = ?
        GROUP BY
            chain, subchain, job_type) B
    ON A.id = B.max_id;