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

Sendu Bala bix at sendu.me.uk
Thu Dec 7 04:33:18 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,

Oh, does it work with option -e? Or does it work if you delete your old 
indexes of the nodes and names files and let it re-create them?


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