That makes sense. I understand what you mean that the discrepancies will be much lesser with smaller inputs. In fact, I have seen that happen with my tool too. Considering I'm using Parallel::ForkManager now (please see Update 2 of my original post), I should be able to implement this idea relatively easily.

But I won't be able to modify the output of the tool. As I mentioned in my other post, I cannot edit this tool in anyway. So I guess I will still have to deal with multiple files, which is not too much of a problem though. I can use a specific prefix for the output files generated by a single input, and merge them later. Not the best way, but certainly an easier way (given the noob I am).

Will update how it goes. Thanks a lot for the detailed explanation.