Your post isn't very clear, you should write a small example so that we can better understand what data you are processing. See How do I post a question effectively?. And you should give more information about the sizes and complexity you have to deal with (how big is the big file, and how many smaller files do you process?)

The first thing you need to do is identify which part (or parts) is taking so long. Since you are talking about minutes , you can make a pretty rough measure (in seconds) with code like:

my $start_time = time;
# Big step here
print "First step ended at time: ", $start_time - time;
# Other big step
print "Second step ended at time: ", $start_time - time;
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Try to find out exactly which part is taking most of the time, and then we can focus on that :).

Edit s/you're/your/ :D