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

Sendu Bala bix at sendu.me.uk
Thu Dec 7 04:24:39 EST 2006

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?

More information about the Bioperl-l mailing list