[Error] Mamba/ Mambaforge (Conda) 완전삭제 방법

어제부터 QIIME 분석만 하면 "QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment."이라고 오류가 뜬다. 오류의 전문은 아래와 같다. 

 

(qiime2-amplicon-2024.2) [ksy@localhost HMP]$ qiime feature-classifier classify-sklearn --i-classifier /data/Reference/16S/QIIME2/Greengenes/2022-10/gg_2022_10_backbone_full_length.nb.qza --i-reads ./representative_sequences.qza  --o-classification taxonomy_gg.qza
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/util.py", line 279, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/click/core.py", line 1157, in **call**
return self.main(*args, **kwargs)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/click/core.py", line 1682, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/click/core.py", line 1729, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 100, in get_command
plugin = self._plugin_lookup[name]
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in <module>
CACHE = DeploymentCache()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in **init**
self._state = self._get_cached_state(refresh=refresh)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/util.py", line 291, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in **new**
self._init(add_plugins=add_plugins)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/pkg_resources/**init**.py", line 2496, in load
return self.resolve()
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/pkg_resources/**init**.py", line 2502, in resolve
module = **import**(self.module_name, fromlist=['**name**'], level=0)
File "/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/rescript/plugin_setup.py", line 11, in <module>
from q2_types.genome_data import GenomeData, Loci, Proteins, Genes, DNASequence
ImportError: cannot import name 'DNASequence' from 'q2_types.genome_dat**a' (/home/ksy/mambaforge/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_types/genome_data/init.py)**

 

 

다른 Conda 계정에서 보니 문제가 없다 => 그럼 mamba오류로 추정 

 

 

1. Mamba, Mambaforge 삭제 

킹 받는 점은 mamba 문서에 삭제 방법이 기술되어있지 않음. 

https://github.com/conda-forge/miniforge/issues/407

No uninstall instructions for mamba · Issue #407 · conda-forge/miniforge

여기서도 적어달라고 문의했는데, 아직까지도 없다..

 

삭제 방법은 아래 링크 참고

https://github.com/conda-forge/miniforge?tab=readme-ov-file#uninstallation

GitHub - conda-forge/miniforge: A conda-forge distribution.

 

 

conda init --reverse --dry-run
conda init --reverse
CONDA_BASE_ENVIRONMENT=$(conda info --base)

echo The next command will delete all files in ${CONDA_BASE_ENVIRONMENT}
rm -rf ${CONDA_BASE_ENVIRONMENT}

echo ${HOME}/.condarc will be removed if it exists
rm -f "${HOME}/.condarc"
echo ${HOME}/.conda and underlying files will be removed if they exist.
rm -fr ${HOME}/.conda

 

 

 

2. Conda 재설치

- 공식문서: https://docs.anaconda.com/anaconda/install/

Installing Anaconda Distribution — Anaconda documentation

yum install libXcomposite libXcursor libXi libXtst libXrandr alsa-lib mesa-libEGL libXdamage mesa-libGL libXScrnSaver
 curl -O https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh
bash ~/Anaconda3-2024.10-1-Linux-x86_64.sh
conda update conda

 

 

 

Picrust2때문에 mamba 썼는데, 그것 때문에 환경 오류 나고 난리 났다. 

역시 믿음직한 Conda를 쓰는 것이 제일인가보다.

 

다음부터 도커와 Nextflow를 써보자...ㅎㅎ