search

davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
673 stars 186 forks source link

Species tree make_ultrameric.py not working #905

Closed aebaci closed 1 month ago

aebaci commented 2 months ago

Hi: I'm trying to convert the species tree to ultrameric to use in CAFE, so I would like to know which of the trees (rooted or rooted _node_labels.txt) is best to use.

However, I have this issue: ./make_ultrametric.py --help Traceback (most recent call last): File "/opt/software/OrthoFinder/./make_ultrametric.py", line 12, in from scripts_of import tree, util ModuleNotFoundError: No module named 'scripts_of'

I have Orthofinder version 2.5.5, and these are the files in the Orthofinder folder:

bin convert_orthofinder_tree_ids.py init.py orig_config.json orthogroup_gene_count.py tools config.json create_files_for_hogs.py License.md orthofinder primary_transcript.py version_2.5.5 config_orthofinder_user.json ExampleData make_ultrametric.py OrthoFinder-manual.pdf README.md

bin folder

diamond fastme mcl

tools folder

convert_orthofinder_tree_ids.py make_ultrametric.py primary_transcript.py I tried running both the one in the main folder and in the tools folder, and both gave the same error.

I would appreciate if you help me with this issue. Thanks.

aebaci commented 2 months ago

I installed the conda orthofinder in an environment, and there the make_ultrameric.py worked