So I want to do about 16 million grep counts on a 1.4 Gigabyte file. I'm simply counting how many times a Z or Z pops up relative to another variable. It will take me 10 years to do this with nested greps. And 545 years to do this via the perl script you recommended.

Load an array by greping the file for only those lines that contain 'Z' (or 'Z'????) and then grep that resultant subset foreach of your 16e6 seartch terms and it should take around 15 seconds per; which would reduce your total time to 7.6 days.

Do the 'Z' (or 'Z'???) filter as once pass and then you can run your 16 million secondary filters concurrently 1 per core and reduce that to a little under two days assuming 4 cores.

And in the first quarter of next year you'll be able buy a sub-$2000 machine that will allow 8-cores/16-threads that will reduce that to half a day.