search

wu-lab-uva / AMPHORA2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
32 stars 8 forks source link

BioPerl incompatibility #2

Open cjfields opened 10 years ago

cjfields commented 10 years ago

Re: the Bioperl issue, if you can provide a test case or file a bug regarding the errors you have we can try to address them. Thanks!

lakshwadeep commented 10 years ago

There is a TestData directory included, which will show errors if Perl is using BioPerl 1.6.9.

cjfields commented 10 years ago

Ok, that helps. Based on the error reported in the README it seems like something that changed with Newick parsing. I'll create a ticket and link it here.

wenqingchu commented 10 years ago

I met one error. perl Scripts/Phylotyping.pl -CPUs 2 > phylotype.result I typed the command above and got the error message below. Can't call method "id" on an undefined value at Scripts/Phylotyping.pl line 164, line 1.

159 for my $query (keys %support) { 160 $output .= "$query\t$marker"; 161 for my $edge (keys %{$support{$query}}) { 162 my @lineage = $tree_functions->get_lineage_nodes($ref_taxon{$edge}); 163 for my $taxon (@lineage, $ref_taxon{$edge}) { 164 $confidence{$query}{$taxon->id} += $support{$query}{$edge}; 165 } 166 }