BioPerl incompatibility about amphora2 HOT 3 OPEN

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

from amphora2.

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.

from amphora2.

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 }

from amphora2.