You'll need to escape the meta-characters in $comm e.g

## note the \Q before $comm
if(($line eq $comm) || ($line =~ /\Q$comm/)){
  print"Line $i: $comm";
}
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And it looks like a simple index would be better suited in this situation since you're just testing to see whether $comm is in $line e.g

if(($line eq $comm) || (index($line, $comm) > -1)){
  print"Line $i: $comm";
}
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See. perlre and quotemeta for more info on escaping regex meta-characters and perldiag for a more detailed explanation of your error.
HTH

_________
broquaint