Hello abhikalrt53,

You need to close the filehandle before you can unlink the file:

...
open my $fh, '<', $file or die "Cannot open file $file: $!";
my $headers = grep /^>/, <$fh>;
close $fh or die "Cannot close file $file: $!";

if ($headers <= 3) {
    unlink ...
[download]

Hope that helps,