I modified your code to the following:

#!/usr/bin/perl

 use strict;
 use warnings;

my $outfile = "HUGO_dummyResults.txt";

open( OUT, "> $outfile" ) or die "cannot create the output file";

open (DUMMY_GENEFILE, 'DummyGenes.txt') or die "cannot open file conta
+ining genes";

open (DUMMYHUGO,'DummyHugo.txt') or die "cannot open file containing H
+UGO IDs";

#################################################
#Operations
#################################################

#make array HUGO
my @hugo = <DUMMYHUGO>;

foreach (<DUMMY_GENEFILE>) #Changed from (<DUMMY_GENEFILE>)

{
    #make array genes
    my @genes = split ( /\b/, $_ );
    
    foreach my $i ( 4 .. 7 )   
    {
      if ($genes[2] eq $hugo[$i])
      {
        print OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]\t$hugo[1
+]\n";
      }
            
      print OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]\tNo HUGO I
+D\n";
    }    
    
    
}
close (DUMMYHUGO);
close (DUMMY_GENEFILE);
close (OUT);
exit;
[download]

This results in:

ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID
[download]

Could you tell me what you expected to see, so I can refine this further?

Modifictions:

• Define @hugo, @genes and $i.
• References to DUMMYHUGO and DUMMY_GENEFILE should be surrounded by < and >.
• genes[3] changed to $genes[3]
• my $i defined tightened up slightly