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evolbioinfo / pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees
https://pastml.pasteur.fr
GNU General Public License v3.0
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not able to run Albanian example data #15

Closed TYMichaelsen closed 3 years ago

TYMichaelsen commented 3 years ago

Hi,

I tried to download the Albanian testset (Albanian.tree.152tax.tre and data.txt) and run pastml from within the same directory, first through singularity:

singularity run docker://evolbioinfo/pastml --tree Albanian.tree.152tax.tre --data data.txt --columns Country --data_sep ,

And through a conda env, made according to guidelines:

pastml --tree Albanian.tree.152tax.tre --data data.txt --columns Country --data_sep ,

I consistently get the error: pastml:ERROR Did not manage to save the annotated tree in nexus format due to the following error: 'list' object has no attribute 'read'

I also tried the version of the Albanian dataset downloadable from here: https://pastml.pasteur.fr/. I cannot figure out what I'm doing wrong, any help will be much appreciated! Thanks, Thomas

annazhukova commented 3 years ago

Hi Thomas,

Thanks for trying PastML and for reporting this issue. I will look at this soon and fix the nexus output in the future versions of PastML.

But in the meanwhile you can safely use PastML as is, just ignoring this error message: It does not affect the other results and only means that the conversion of the tree with named internal nodes from newick (produced among the output files) to nexus did not work. If you ever need nexus you can convert for example with gotree.

Sorry about it.

Cheers, Anna

annazhukova commented 3 years ago

Sorry for such a long delay. The issue should be solver in v1.9.34