SQLite multiple command

I am new to SQLite and python and would like some help with a command. I have created a table, 'gRNAs' with 11 columns and imported a .tab file into it to organize my data. I am trying to extract information with the following command:

select count(*) from gRNAs a where chr='chr5' and pos > 500000 and pos < 4000000 and a.rowid in (select b.rowid from grnas b where chr='chr5' and pos > 500000 and pos < 4000000 and mm0=0 and mm1=0 and b.rowid is not null and a."DHS" = b."DHS" order by mm0, mm1, mm2, mm3 limit 25) order by a."DHS";

I was using this sqlite command with an older Mac and it worked fine, but I recently purchased a new Mac and the command stopped working. I don't get an error or anything but the command used to take 20min or so and now it just runs for hours without giving me a number. If I just use a single command such as :

select count(*) from grnas where pos > 1000 and pos < 4000000 and chr="chr5" and mm0=0 and mm1=0 and mm2=0;

I get a number back very quickly. Please advise, thanks in advance.