I changed the way it reads in tax_file to this

my $taxon = $ARGV[3];
unless($taxon){
    $taxon = "";#default is blank
}
$annotation .= "\t$taxon";
my @taxList = split(/\|/, $taxon);
open(tax_file, "..".$slash."dataset".$slash."taxonomy.tab") or die "co
+uldn't open taxonomy.tab";
#my @taxR = <tax_file>;
my %taxR;
if($taxon){
    while(<tax_file>){
        foreach my $tempTax (@taxList){
            if($_ =~ m/$tempTax/i){
                my @tempTax = split(/\t/, $_);
                $taxR{$tempTax[1]} = 1;
            }
        }
    }
    
}
close tax_file;
[download]

I get the same results as last time. I also had the opportunity to test it on a unix machine and the program works fine on that machine.

As far as use warnings goes, I need to do a lot of editing or parsing because my program relies heavily on uninitialized values counting as false, so I'm going to work on that now.