Wow, that was obvious! Apologies for missing such a mistake, and thanks for your answer.

OUT1 is re-opened just to clear it's contents, then it is re-filled with the next section of the file I need to analyse. I'm not sure this is the best way of doing this, but it seems to work.

Now I've added that missing ;, I'm getting an error message: Use of uninitialized value $columnsA2 in addition (+) at phastCons_multiples_ids3.pl line 19

I'm not sure why this is, it's declared within the first if statement?

In reply to Re^2: Error opening file handle within while loop by rjc33
in thread Error opening file handle within while loop by rjc33

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