Just a guess without code to look at, but you may be try to perhaps open the $filename you are getting? ala

my $filename = $query->param("file_uploaded");
open(FH, "<$filename or die "cannot open!");
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If so, don't do that. Just process the $filename which is a file handle.

my $filename = $query->param("file_uploaded");
while (<$filename>) {
 # do something
}
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well I hope I guessed right :-), good luck!