[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species

[Gabriel Valiente]

Hi,

If you run the attached shell script you should be able to reproduce  
the problem. It is not about any species in particular, but about the  
total number of species: it crushes with more than 120 species. The  
resulting tree is not correct, I'm checking it further now. Thanks,

Gabriel

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On Dec 7, 2006, at 10:24 AM, Sendu Bala wrote:

> Gabriel Valiente wrote:
>> The following popped out when input more the 110 species to   
>> taxonomy2tree script version 1.4:
>>          (in cleanup)
>> ------------- EXCEPTION  -------------
>> MSG: Must supply a Bio::Taxon
>> STACK Bio::DB::Taxonomy::flatfile::ancestor Bio/DB/Taxonomy/  
>> flatfile.pm:260
>> STACK Bio::Taxon::ancestor Bio/Taxon.pm:476
>> STACK Bio::Taxon::remove_Descendent Bio/Taxon.pm:703
>> STACK Bio::Tree::Node::ancestor Bio/Tree/Node.pm:346
>> STACK Bio::Taxon::ancestor Bio/Taxon.pm:466
>> STACK Bio::Tree::Tree::cleanup_tree Bio/Tree/Tree.pm:325
>> STACK Bio::Root::Root::DESTROY Bio/Root/Root.pm:409
>> STACK (eval) taxonomy2tree.pl:0
>> STACK toplevel taxonomy2tree.pl:0
>> Any clues? Thanks,
>
> Are you able to narrow the problem down? What was your command  
> line, what species were you using? Does it work with the first 110  
> species you tried? Is there anything special about the 111th?
>
> Do I understand correctly that this was a problem during cleanup  
> only, and didn't affect the correctness and completeness of the  
> result?