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

Gabriel Valiente valiente at lsi.upc.edu
Thu Dec 7 04:38:03 EST 2006


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,


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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?

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