in reply to Re^3: Use of uninitialized value in subroutine entry at /home/roarce/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Seeder/Finder.pm line 476, <IN> line 8192.
in thread Use of uninitialized value in subroutine entry at /home/roarce/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Seeder/Finder.pm line 476, <IN> line 8192.

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: 

index: 4094 (0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
+,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,
index: 4095 (0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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+1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

[download]

While another file which does not work generates this output:

index: 4094 (0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,
+0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0
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+0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1
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+0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0
+,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,1,2,0,0
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+0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,
+0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,1
+,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,
+1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0
+,0,1,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,1
+,0,0,0,0,0,0,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,
+0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,1,0,0,0,0,1,0,2,0,0
+,0,0,0,0,1,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,
index: 4095 (0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,1,0,0,0,0,0,
+0,0,0,0,0,0,0,0,0,0,0,0,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0
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+0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0
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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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[download]

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.

  • Comment on Re^4: Use of uninitialized value in subroutine entry at /home/roarce/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Seeder/Finder.pm line 476, <IN> line 8192.
  • Select or Download Code

Replies are listed 'Best First'.
Re^5: Use of uninitialized value in subroutine entry at /home/roarce/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Seeder/Finder.pm line 476, <IN> line 8192.
by bliako (Abbot) on May 26, 2020 at 08:58 UTC

    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.

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[d/l]
[select]

      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

[reply]
[d/l]

        Hi Rocio,

        there must be some tiny bug like a missing bracket somewhere? Anyway, it is trivial debugging code. But right now I can't remember what was the problem and I will not start looking at it again. Perhaps another Monk here can help you or the author of said module. If you are willing to share the data causing the problem it will be better. If you can't find anyone to help you, you can post an offer to https://jobs.perl.org

[reply]

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