Given that your lines are already unique, this is the shell-way to find the intersection of 2 uniq files:
    $ sort file1.txt file2.txt | uniq -d > matches.txt

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This approach would work on very large files efficiently.

In reply to Re: Comparing strings (exact matches) in LARGE numbers FAST by repellent
in thread Comparing strings (exact matches) in LARGE numbers FAST by perlSD

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