One issue is opening the output file inside the loop and closing it outside the loop. Move the 'open' to before the loop. Also at the top of your script place the following line: use autodie;.
But to give an effective answer to your question we would need to know how the code you posted is failing, as well as see a brief sample of the input files. Phrasing it in the form of a question may add clarity as well.
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