Why is the same SQLite query being 30 times slower when fetching only twice as many results?

Question

I have been working on speeding up a query I\'m using for about a week now and asked several questions about it here ( How can I speed up fetching the results after running an s

Answer 1

I suggest you try using an R*Tree index, They're designed for efficient range queries.

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I haven't actually used R*Tree much, just read the documentation, but I think you might be using it incorrectly. You may want to try changing your query to use

WHERE convexhull_edges.rtMin <= spectrum.scan_start_time AND convexhull_edges.rtMax >= spectrum.scan_start_time AND
convexhull_edges.mzMin <= MSMS_precursor.ion_mz AND convexhull_edges.mzMax >= MSMS_precursor.ion_mz

which should be equivalent to your current query, but I think should be faster (You should be picking a range out of the R*Tree, rather than comparing the point to the range)