error in taxonomy prediction

[Lu Yang]

Hi, 

I am using phylophlan in taxonomy prediction. However, I got the error as indicated in the attached file. Is there anyone who can help me with this?

Millions of thanks.

Sincerely.

[Francesco Asnicar]

Hi,

Unfortunately the automatic taxonomic prediction in PhyloPhlAn is not working at present. But I can suggest you two other ways to get a taxonomic assignment from the phylogeny you obtained form PhyloPhlAn.

1)

As you managed to integrate your proteomes into the PhyloPhlAn tree of life, one thing you can do is to attach the taxonomic information to the reference proteomes of the tree of life (you can have a look at the "ppafull.tax.txt" file present in the "data" folder of the repository for getting the taxonomic labels).

If your proteomes are not too many, you can manually inspect with an interactive visualization software (like Archeopteryx: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx) to see where your proteomes are falling in the tree of life.

2)

Another a bit less manual way could be to use the "tree_pairwisedists.py" script from https://bitbucket.org/nsegata/pyphlan/src/default/ to compute all pairwise distances, you should then filter them to your input proteomes and consider only the closest reference proteomes in PhyloPhlAn. Then using the taxonomic labels from the above file you can see which is the phylogenetically closest species.

Many thanks,

Francesco

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