The size of an app has nothing to do with how long it might take to run that app's script. Likewise, the data model is not helpful in this regard.
You've included a partial log of a failed run, so there's no way to see what takes the extra time during a successful run. However, it does look like the time is being spent reading data from your database. If that's the case, the way to optimize it would be to improve the queries, add indexes, etc. on the database side. I'd suggest taking it up with the database-side developers or DBA.
