Linux下Snakemake运行报错：module 'asyncio' has no attribute 'coroutine'

问题详情 #

在Linux机器上通过以下步骤安装Snakemake：

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

安装无异常，但执行命令snakemake -s Snakemake_job -j n时出现报错：

Building DAG of jobs...
Traceback (most recent call last):
  File "/home/debian/.conda/envs/snakemake/lib/python3.11/site-packages/snakemake/__init__.py", line 747, in snakemake
    success = workflow.execute(
              ^^^^^^^^^^^^^^^^^
  File "/home/debian/.conda/envs/snakemake/lib/python3.11/site-packages/snakemake/workflow.py", line 949, in execute
    self.scheduler = JobScheduler(
                     ^^^^^^^^^^^^^
  File "/home/debian/.conda/envs/snakemake/lib/python3.11/site-packages/snakemake/scheduler.py", line 109, in __init__
    from ratelimiter import RateLimiter
  File "/home/debian/.conda/envs/snakemake/lib/python3.11/site-packages/ratelimiter.py", line 36, in <module>
    class RateLimiter(object):
  File "/home/debian/.conda/envs/snakemake/lib/python3.11/site-packages/ratelimiter.py", line 127, in RateLimiter
    __aexit__ = asyncio.coroutine(__exit__)
                ^^^^^^^^^^^^^^^^^
AttributeError: module 'asyncio' has no attribute 'coroutine'

已尝试重装Snakemake、pip安装asyncio，均未解决。

错误原因 #

Python 3.10+版本中移除了asyncio.coroutine API，但当前环境中安装的ratelimiter版本过旧，仍在调用该废弃接口，导致兼容性报错。

解决方案 #

方案1：重建兼容的Snakemake环境 #

直接创建包含适配Python3.11依赖的Snakemake环境：

1. 删除现有环境：

conda remove -n snakemake --all

2. 创建新环境，指定兼容版本的Snakemake：

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake>=7.32.4 python=3.11
conda activate snakemake

方案2：更新现有环境中的ratelimiter #

无需重建环境，直接升级ratelimiter到适配Python3.10+的版本：

conda activate snakemake
pip install --upgrade ratelimiter>=1.2.0.post0

验证 #

执行以下命令确认版本正常：

snakemake --version

之后重新运行你的任务：

snakemake -s Snakemake_job -j n

内容的提问来源于stack exchange，提问作者chippycentra