Anyone knows what I am doing wrong here?

Asking questions about one piece of code while posting another.

It doesn't produce the results you describe, and you would have noticed you're chomping the wrong variable.

while($evalue = <DATA>){
chomp;                        # Should be chomp( $evalue );
   if($evalue < 0.001){
      print $evalue, "\n";
    }
}
close DATA;

__DATA__
1e-005
2e-090
0.00
0.67
1.0
4e-065
[download]

1e-005

2e-090

0.00

4e-065
[download]