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

Gabriel Valiente valiente at lsi.upc.edu
Fri Dec 15 19:45:27 EST 2006


> I don't think that can be true. Your error message contains 'Must  
> supply
> a Bio::Taxon'. Bio::Taxon only exists in 1.5.2 (or cvs live).
>
> If you uninstall the fink installation and install 1.5.2 using cpan  
> (with root privileges by going sudo cpan) that should at least get  
> rid of the error messages...
>
>
>> The tree is not correct (I've parsed it from R to have a double
>> check) but don't know yet what the problem is with it.
>
> ... But if the tree is wrong anyway... Let me know what you find out.

I've uninstalled the fink installation and used the cvs instead, and  
the error message is gone. However, on a larger set of 190 species,  
which are all present in the NCBI taxonomy, the resulting tree has  
only 178 taxa. I suspect, something must be wrong with the  
merge_lineage method in the major rewrite of the taxonomy2tree  
script. Can someone please check this? I'm attaching the 190 species  
call to the script. Thanks,

Gabriel

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