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

Chris Fields cjfields at uiuc.edu
Thu Dec 7 10:22:47 EST 2006


> Hi,
> 
> 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,
> 
> Gabriel

Gabriel, 

My guess is this may have to do with using an old taxonomy dump file.  I got
this to work on winXP using the latest NCBI taxonomy.  I had to modify
taxonomy2tree and your shell script to get it to play nice with Windows, but
I didn't get the error and I did get a tree (abbreviated for brevity):

(((((("Agrobacterium tumefaciens str. C58","Sinorhizobium
meliloti")Rhizobiaceae,...

chris



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