Bitbucket
安装
mamba create --name vContact2 biopython=1.78
mamba install -c bioconda vcontact2=0.11.3
vim ~/envs/vContact2/lib/python3.9/site-packages/vcontact2/exports/summaries.py
把 np.warnings.filterwarnings('ignore')
改成
import warnings
warnings.filterwarnings('ignore')
## 下载聚类软件，移动到conda/bin路径
wget -c http://www.paccanarolab.org/static_content/clusterone/cluster_one-1.0.jar
## 下载MCL
mamba install -c bioconda mcl使用
#使用自带函数构建[gene-to-genome mapping file]
vcontact2_gene2genome -p （faa文件） -o （输出文件） -s Prodigal-FAA
#正式运行
运行失败报错
----------------------------------Loading data----------------------------------
INFO:vcontact2: Read 422588 entries (dropped 3534 singletons) from fetal_vc2/vConTACT_profiles.csv
Traceback (most recent call last):
File "/home/zhongpei/mambaforge/envs/vContact2/bin/vcontact2", line 834, in <module>
main(options)
File "/home/zhongpei/mambaforge/envs/vContact2/bin/vcontact2", line 602, in main
matrix, singletons = vcontact2.pcprofiles.build_pc_matrices(profiles, contigs_csv_df, pcs_csv_df)
File "/home/zhongpei/mambaforge/envs/vContact2/lib/python3.9/site-packages/vcontact2/pcprofiles.py", line 358, in build_pc_matrices
matrix = sparse.coo_matrix(([1]*len(profiles), (zip(*profiles.values))), shape=(len(contigs), len(pcs)),
File "/home/zhongpei/mambaforge/envs/vContact2/lib/python3.9/site-packages/scipy/sparse/_coo.py", line 99, in __init__
self._check()
File "/home/zhongpei/mambaforge/envs/vContact2/lib/python3.9/site-packages/scipy/sparse/_coo.py", line 188, in _check
raise ValueError('mismatching number of index arrays for shape; '
ValueError: mismatching number of index arrays for shape; got 0, expected 2
算了不用它了
