Thanks Bliako for your suggestions. I corrected the code as you said and it worked. Could you help me to understand the results? I have two similar files. For an input file which worked well, the output is:

While another file which does not work generates this output:

Both files have some different titles with the same length after them (1000 digits) What it means? Thank you in advance!

2020-06-01 Athanasius added <code> tags.

I can not see anything wrong with that part of the code, unless some other more Monks can see something wrong.

So, let's see what happens at the root of the problem. Can you also do this change in same file:

    for my $oligo_indice ( 0 .. $#{ $self->{oligo_ref} } ) {
        # INSERT debug code below - this must be around line 474 :
        for my $j (0 ..  $#{ $self->{hd_matrix_ref}->[$oligo_indice] }
+){
            die "problem with hd_matrix_ref index '$oligo_indice/$j'" 
+unless defined $self->{hd_matrix_ref}->[$oligo_indice][$j];
        }
        # END insert debug code
        $hd_sum[$oligo_indice] =
            List::Util::sum( @{ $self->{hd_matrix_ref}->[$oligo_indice
+] } );
    }
[download]

EDIT: for clearer output, for the moment, can you edit the PREVIOUS debug code to comment-out all print statements? But leave the die there. It should now be:

for my $oligo_indice ( 0 .. $#{ $self->{oligo_ref} } ) {
 #print "index: $oligo_indice (";
 for my $count_indice ( 0 .. $#{ $self->{count_matrix_ref} } ) {
   if( ! defined $hd_matrix[$oligo_indice][$count_indice] ){ die "prob
+lem at [$oligo_indice][$count_indice]" }
   #print $hd_matrix[$oligo_indice][$count_indice].","
 }
 #print "\n";
}
[download]

Can you please edit your last 2 posts and wrap the info you provided within code tags c and /c (i.e. the long output lines and error messages) in <readmore> </readmore> tags.

Sorry for the delay. I could run the Perl module with some files and I was working on that. With anothers I'm having the same problem of this issue. I add your suggestion for the EDIT part in 'Finder.pm' file and I recieved the following error comments.

Read more... (11 kB)

I really appreciate your help, thanks in advance. Rocío

there seem to be extra spaces in the pasted string $ # {$ self -> {oligo_ref}} compared to the original $#{ $self->{oligo_ref} }

If you click on the [download] link under debug code you will be able to copy-paste safely.