Looking at the source, the message "<IN> line 8192." is irrelevant if not misleading because IN was never closed as it should. In sub _read_bkgd(). So, all subsequent warns report it and rightly so as it is still open, alas they are irrelevant.

Line 476 of the source file is:

sub _get_seed {
    my $self       = shift;
    my $n_bkgd_seq = List::Util::sum( @{ $self->{bkgd_ref}->[0] } );
    my @hd_sum;
    for my $oligo_indice ( 0 .. $#{ $self->{oligo_ref} } ) {
        $hd_sum[$oligo_indice] =
            List::Util::sum( @{ $self->{hd_matrix_ref}->[$oligo_indice
+] } ); # 476
    }
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Which suggests that there is something wrong with $self->{hd_matrix_ref}->[$oligo_indice]. Either $self->{hd_matrix_ref} is not an arrayref or if it is, the index $oligo_indice exceeds its size, or $self->{hd_matrix_ref}->[$oligo_indice] is not an arrayref. The construction of $self->{hd_matrix_ref} is done in line 325 (sub _build_hd_matrix).

From a glance at line 325, I think the first and second hypotheses can be ruled out because the index spans the exact same range as in line 476, that is:

for my $oligo_indice ( 0 .. $#{ $self->{oligo_ref} } ) {

That is, the array has correct dimensions but may contain "holes" or has undef in its 2D span. (Edit: by "holes" i mean array elements which were never set to a value, as opposed to the "undef" which means array elemets were set to an undef value which was the result of a calculation/transformation which went wrong, and was not detected, or just bad input).

If you want to debug this, then perhaps you can add a couple of debug prints to see what's going on with that array. I would start just before line 387 (before return), with this (untested):

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";
}
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bw, bliako