【报错解决】snakePipes处理scRNAseq流程报错及解决汇总

本文链接：https://blog.csdn.net/Maud000/article/details/135042127

1. inconsistent use of tabs and spaces in indentation

1.1 报错

很诡异的问题，因为所有py脚本都是snakePipes自带的，我根本没动过。

1.2 解决

先找到哪一步报错： scRNAseq脚本中cf.runAndCleanup这一步：
找到cf也就是snakePipes.common_functionsmodule： 路径：/path_to/anaconda3/envs/mamba/envs/snakePipes/lib/python3.12/site-packages/snakePipes/common_functions.py
查看runAndCleanup：

继续找出问题的脚本：
因为上述报错是在运行下面这个命令后出错的，所以先找到cmd：
snakePipes会将cmd输出到log中，查找后得知出问题的应该在snakefile，也就是/path_to/anaconda3/envs/mamba/envs/snakePipes/lib/python3.12/site-packages/snakePipes/workflows/scRNAseq/Snakefile：

检查出问题脚本：
先备份该脚本
vscode打开，找之前报错的line 118，发现确实是indentation混用的问题
解决：ctrl+shift+p，然后选择Convert Identation to Tabs

2. The ‘mamba’ command is not available in the shell

2.1 报错

2.2 原因及解决把mamba的bin加入到环境变量中即可

3. Could not resolve host: mirrors.tuna.tsinghua.edu.cn

3.1 报错

3.2 原因及解决

原因：mamba env create会使用conda设置中默认的、优先级最前的channel，我的设置里是conda-forge:https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/，所以最后会变成以下报错：
RuntimeError: Download error (28) Timeout was reached [https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/repodata.json]
而这个地址是不存在的。

解决：
备份.condarc
修改.condarc：
修改channels里优先级
在custom_channels中添加mpi-ie: https://conda.anaconda.org/.
channels:
  - mpi-ie
  - conda-forge
  - defaults 
show_channel_urls: true 
custom_channels: 	
  	mpi-ie: https://conda.anaconda.org/ ```

4. ERROR: Could not open file for download /data/extended/mambaf8uLNT88UCo: No such file or directory

4.1 报错

Could not create conda environment from
/path_to/anaconda3/envs/mamba/envs/snakePipes/lib/python3.12/site-packages/snakePipes/shared/rules/envs/shared.yaml:
Command: mamba env create --quiet --file
"/path_to/anaconda3/envs/mamba/envs/8a730fff6bfd761c1a1a279a0c048d44_.yaml"
--prefix "/path_to/anaconda3/envs/mamba/envs/8a730fff6bfd761c1a1a279a0c048d44_"
Output: ERROR   Could not open file for download
/data/extended/mambaf8uLNT88UCo: No such file or directory