open(OUT,">$outfile");
open(F1, "<$infile")   or die "Could not open $infile for reading!\n";
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I realize that this is just an example snippet, but.... verbally fail if $infile won't open, and silently fail if the output file can't be opened? Also, have a look at the first paragraph or two of chomp and how it reacts to changes to $/. You're not removing the trailing newline characters.