#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