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Hugely appreciate the time you've taken to help me out. I'll now take sometime to break this down, read around, and hopefully digest ;)

It runs in about 3 hours on the 'real' dataset.

You're a...

With the second set of test data:

Scrutinizers script incorrectly identifies the second line of file 2 as a match:
100
50 - This one should be NA
25
40
NA
NA
22
NA
NA
21
12
35
90
80...

Apologies, if there was any confusion. Please find below some data which matches the reality of the files.

Note:
Column 1 in File 1 & 2 is not a complete list of Scxxxx names, some are missing....

In reality the files I have, that are millions of rows in size, are not contiguous or even nearly as uniform as File1 (many gaps exist). The data sets (and results) would not make sense if File1 was...

Hey thanks for the help, I'm away from a unix box to test at the moment....... I'll try tomorrow and get back to you.

You're a legend! If this works hopefully you can help me understand the code...

Please know that I am very new to unix and trying to learn 'on the job'. I'm only manipulating large tab-delimited files (millions of rows), but I'm stuck and don't know how to proceed with the...