Let's take one piece of your code and rewrite it a bit:

open (FILE, "$file") || die "Can't open $file";
       $tmp=<FILE>;
           foreach(split(/\t/,$tmp)){
               push(@hashkeys, $_);
           
       }
[download]

This takes only the first line of the file. I think what you want is:

my @hashkeys;
open (FILE, "$file") || die "Can't open $file";
       my @lines=<FILE>;
           foreach my $line (@lines){
               my @fields = (split(/\t/,$line){
                push(@hashkeys, $fields[0]); # or perhaps it's some ot
+her 
                                             # field you want?
           }
[download]

This isn't meant as a definitive answer but merely a small illustrative example to help you sort out exactly what you want to do