First, follow the advice given. Go through your script and correct *all* the items Discipulus pointed out. Second, when in doubt, print out the value of your variables.

use Data::Dumper;
...
foreach my $id (keys %id2seq) {
    warn "ID: $id";

    my @segments = split /\|/, $id;
    warn "Segments: " . Dumper \@segments;

    my $filename = $segments[0];

    ...
}
[download]

Once the code is working right, remove the debug statements.