BioQ limits how long a single query may execute and how much disk space is used for the query. If it determines that the query has gone on for too long is using up too much space it may terminate the query, and possibly remove the corresponding data from the server. If this occurs, a message should be displayed, after which you may execute a new query that should attempt to consume less time and storage than the original. Currently the time limit for queries is about 10 minutes, although the actual time allowed may vary for technical reasons.
There are also certain technical limitations placed on the queries. Subqueries, for example, are not allowed because they can lead to very inefficient and computationally demanding queries. BioQ will also attempt to determine if the query will perform an excessive number of comparisons, such as a join on a non-indexed column. The query may be rejected in these situations and the solution is to reduce the complexity of the query. If you require more complex queries please consider downloading and installing a local MySQL implementation of the database using the utilities provided on the downloads page for that database (see dbSNP Build 134 for example).