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foreach my $line (@array) {
    if ($line =~ /^JOB=/) {
        $array[$counter] = "RMT=$file\n";
    }
    $counter++;
}

foreach my $line (@array) {
    $line =~ s/^JOB=/RMT=$file\n/;
}

s/^JOB=/RMT=$file\n/ for @array;