orthofinder鑑定物種間的同源蛋白

github主頁

https://github.com/davidemms/OrthoFinder

我直接使用conda安裝

conda install orthofinder

運行命令

orthofinder -f test_data/ -M msa -S diamond -T fasttree -a 8 -t 8

遇到一個報錯

Traceback (most recent call last):
  File "/home/myan/anaconda3/envs/orthofinder/bin/scripts_of/stride.py", line 506, in GetRoot
    speciesTree = tree.Tree(speciesTreeFN, format=2)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/myan/anaconda3/envs/orthofinder/bin/scripts_of/tree.py", line 221, in __init__
    read_newick(newick, root_node = self, format=format)
  File "/home/myan/anaconda3/envs/orthofinder/bin/scripts_of/newick.py", line 208, in read_newick
    nw = open(newick, 'rU').read()
         ^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'

During handling of the above exception, another exception occurred:

主要是這個報錯

    nw = open(newick, 'rU').read()
         ^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'

查了一下，我這個虛擬環境下的python是3.11,這個版本的python打開文本文件的時候已經沒有-U模式了，找到

/home/myan/anaconda3/envs/orthofinder/bin/scripts_of/newick.py這個腳本中的nw = open(newick, 'rU').read()代碼把U去掉就行了

這行代碼在208行

208: nw = open(newick, 'r').read()

測試數據是4個物種的蛋白質序列，8個核心，運行了1個小時多一點 還挺快的