You can replace directive #4 with this small script to get the links for the genomic.fna.gz only downloads. Save the contents in down.pl. And then do perl down.pl assembly_summary_complete_genomes.txt > wget_links.

use strict;
use warnings;

my $datafile1 = $ARGV[0];

open (IN, $datafile1) or die "can't open the datafile: $datafile1\n";

while (my $line = <IN>) {
        chomp($line);
        my @things = split(/\//, $line);
        print "wget -P GbBac ".$line."/".$things[9]."_genomic.fna.gz"."\n";
}

close (IN);

You can use: https://github.com/kblin/ncbi-genome-download