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;

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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]

In reply to Re^3: Got some problem with read write file by choroba
in thread Got some problem with read write file by SilverWol

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