As others have said, the message you’re getting is a warning, not an error, and it’s likely coming from the line:

print PLP_FILE   "$aa_pos\t".$split_query_for_PLP[$s]."\t".$hash_plp_l
+bl_barrel_region_only{$s}."\n";
[download]

in which case either the array element $split_query_for_PLP[$s] or the hash element $hash_plp_lbl_barrel_region_only{$s} is undefined for some value(s) of $s.

For general debugging advice, see toolic’s Basic debugging checklist. In this case, something like this:

for (my $s = $start_of_barrel_region; $s <= (($start_of_barrel_region 
++ $length_of_barrel_region)); $s++)
{
    my $aa_pos = $s + 1;
    warn "\$aa_pos is undefined when \$s is $s"               unless d
+efined $aa_pos;
    warn "\$split_query_for_PLP[$s] is undefined"             unless d
+efined $split_query_for_PLP[$s];
    warn "\$hash_plp_lbl_barrel_region_only{$s} is undefined" unless d
+efined $hash_plp_lbl_barrel_region_only{$s};
    print PLP_FILE "$aa_pos\t".$split_query_for_PLP[$s] . "\t" . $hash
+_plp_lbl_barrel_region_only{$s} . "\n";    
}
[download]

should solve the mystery.

Hope that helps,