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TheBrownLab / PhyloFisher

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
MIT License
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heterotachy.py error #124

Open thesamuanels opened 1 month ago

thesamuanels commented 1 month ago

Hello, I have been trying to use the heterotachy.py script (phylofisher v1.2.14):

heterotachy.py -tr matrix_FULL.fa.treefile -m matrix_FULL.fa -s 2216

*.treefile is the output tree from iqtree2 matrix_FULL.fa is the original matrix constructed at the end of the phylofisher workflow

However, here is what happens when I try to run it:

Traceback (most recent call last):
  File "/opt/Anaconda3/envs/fisher_1.2.14/lib/python3.7/site-packages/ete3/coretype/tree.py", line 235, in __and__
    first_match = next(self.iter_search_nodes(name=value))
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/Anaconda3/envs/fisher_1.2.14/bin/heterotachy.py", line 289, in <module>
    series, size = get_branch_lens()
  File "/opt/Anaconda3/envs/fisher_1.2.14/bin/heterotachy.py", line 93, in get_branch_lens
    node2 = tree & taxon2
  File "/opt/Anaconda3/envs/fisher_1.2.14/lib/python3.7/site-packages/ete3/coretype/tree.py", line 238, in __and__
    raise TreeError("Node not found")
ete3.coretype.tree.TreeError: 'Node not found'

I have used the same data for the fast_site_removal.py script, and that one worked perfectly. Any idea why this happens? Thanks

robert-ervin-jones commented 1 month ago

Hi @thesamuanels,

I suspect there may be an issue with your tree file. Do you mind sharing your tree file and matrix so I can try to reproduce the error?

Best, Robert