orthofinder鉴定物种间的同源蛋白

github主页

https://github.com/davidemms/OrthoFinder

我直接使用conda安装

conda install orthofinder

运行命令

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

遇到一个报错

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:

主要是这个报错

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

查了一下，我这个虚拟环境下的python是3.11,这个版本的python打开文本文件的时候已经没有-U模式了，找到

/home/myan/anaconda3/envs/orthofinder/bin/scripts_of/newick.py这个脚本中的nw = open(newick, 'rU').read()代码把U去掉就行了

这行代码在208行

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

测试数据是4个物种的蛋白质序列，8个核心，运行了1个小时多一点 还挺快的