in reply to Re^3: Searching and Coutning using 2 files with multiple columns
in thread Searching and Coutning using 2 files with multiple columns

It would just hang. It ended up running all night. The processor was still processing, but I wasn't getting any data out. I will try to index my MySQL table to make it run faster. I have to learn how to do it, but for now I am doing

mysql> create index Chr_start_end using btree on H3K36me3 (chrom,start,end)

Thanks for the suggestion!