#!usr\bin\perl -w
open HUBFILE,"1048_undefined.tsv";
@hub=();
while(my $line = <HUBFILE>){
         while ($line =~ /\d \t (\w+) \t/x) {
        push(@hub,$1);
            }
            }close HUBFILE;
            $L=@hub;
    open OUT,">hubs.txt";
    for($i=0;$i<$L;$i++){
    print OUT "HUB:$hub[$i]\n";
    }
    close OUT;
[download]

Why is the second while there? Do you want to find several occurences on the same line? Also, you probably don't want to print all the genes found so far after finding a gene, you want to print them once all of them have been found:

#!/usr/bin/perl
use warnings;
use strict;

open my $HUBFILE, '<', '1048_undefined.tsv' or die $!;
my @hubs;
while (my $line = <$HUBFILE>) {
    push @hubs, $1 if $line =~ /\d \t (\w+) \t/x;
}
close $HUBFILE;

open my $OUT, '>', 'hubs.txt' or die $!;
for my $hub (@hubs) {
    print {$OUT} "HUB:$hub\n";
}
close $OUT;
[download]

Notice I modified some other parts of the code, too: I switched to 3-argument open with lexical filehandles, foreach style loop instead of the C-style one, etc.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]

Thought wrong about the second while, I want to print in the second file a list with all the gene names but it just print only the 1st gene name. I didn't know about the lexical filehandles, thank you!