报错:

/root/miniconda3/envs/rna/lib/python2.7/site-packages/multiqc/utils/config.py:45: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  configs = yaml.load(f)
/root/miniconda3/envs/rna/lib/python2.7/site-packages/multiqc/utils/config.py:51: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  sp = yaml.load(f)
[WARNING]         multiqc : MultiQC Version v1.8 now available!
[INFO   ]         multiqc : This is MultiQC v1.4
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/root/project/rnaseq/01raw_data/'
Traceback (most recent call last):
  File "/root/miniconda3/envs/rna/bin/multiqc", line 751, in <module>
    multiqc()
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/root/miniconda3/envs/rna/bin/multiqc", line 398, in multiqc
    template_mod = config.avail_templates[config.template].load()
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2340, in load
    self.require(*args, **kwargs)
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2363, in require
    items = working_set.resolve(reqs, env, installer, extras=self.extras)
  File "/root/miniconda3/envs/rna/lib/python2.7/site-packages/pkg_resources/__init__.py", line 872, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (kiwisolver 0.1.3 (/root/miniconda3/envs/rna/lib/python2.7/site-packages), Requirement.parse('kiwisolver>=1.0.1'), set(['matplotlib']))

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原因

这个版本的multiqc是python2.7编写的，而python2.7在2020年1月1日以后就停止更新了，相应的包慢慢地也可能会有各种bug。

解决

安装python3.版的multiqc。

#创建rnaseq3.7环境
conda create --name rnaseq3.7 python=3.7 
#激活环境
conda activate rnaseq3.7
#安装mulyiqc， 默认是最新版

##pip安装
pip install multiqc
##conda安装
conda install -c bioconda -c conda-forge multiqc

which multiqc #显示你的路径 说明安装成功，进入路径就可以直接用了
multiqc --help #运行multiqc