$file = 'test_predictions_1';
open (FH, "<EXAMPLE");
while (<FH>) {

    chop;  # remove trailing newline

    $id = $_;
    if (exists $data{$file}{$id}) {print "match\n";}
}
[download]

<update>

Having a second look at your code:

    if (exists $data{$file}{$id}) {print "match\n";}
[download]

Does the key $file to the hash $data even exist in the hash?

You could use Data::Dumper to dump your HoH and check if it's what you expect.

</update>

--shmem

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}