search

DessimozLab / pyham

MIT License
9 stars 5 forks source link

(Error in treeprofile) KeyError: '2 node(s) founded for the ancestral genome #14

Closed maiumy closed 2 years ago

maiumy commented 3 years ago

I ran treeprofile for one specific tree and everything went well, but when I tried to run it for another tree I get this error. I already tried running the analysis again, but it didn't work. I can only assume that this is some with the new tree that I'm using, but I'm not sure what could be wrong with it.

The full error line is:

KeyError: '2 node(s) founded for the ancestral genome named centruroides_sculpturatus/parasteatoda_tepidariorum/limulus_polyphemus/ixodes_scapularis/dermacentor_silvarum/rhipicephalus_microplus/hyalomma_asiaticum/tetranychus_urticae/dermatophagoides_pteronyssinus/varroa_destructor/varroa_jacobsoni/dermanyssus_gallinae/daphnia_pulex/tribolium_castaneum'

And my tree is: (((((centruroides_sculpturatus,parasteatoda_tepidariorum),limulus_polyphemus),(((ixodes_scapularis,(dermacentor_silvarum,(rhipicephalus_microplus,hyalomma_asiaticum))),(tetranychus_urticae,dermatophagoides_pteronyssinus)),((varroa_destructor,varroa_jacobsoni),dermanyssus_gallinae))),(daphnia_pulex,tribolium_castaneum)));

Does anyone know how I can solve this? Thank you.

gmartinezredondo commented 2 years ago

I believe that the problem is that your tree has extra parentheses at the beginning and end. If you check the tree with http://etetoolkit.org/treeview/ you can see that there are two nodes at the root of the tree. imagen

Removing the extra parentheses, the problem should be solved. This would be the fixed tree: ((((centruroides_sculpturatus,parasteatoda_tepidariorum),limulus_polyphemus),(((ixodes_scapularis,(dermacentor_silvarum,(rhipicephalus_microplus,hyalomma_asiaticum))),(tetranychus_urticae,dermatophagoides_pteronyssinus)),((varroa_destructor,varroa_jacobsoni),dermanyssus_gallinae))),(daphnia_pulex,tribolium_castaneum));

maiumy commented 2 years ago

Oh, that's right. I missed those extra parentheses. Thank you!