Hello,
I have been using qiime2 for a while without issues. I tried to set up a Jupyter notebook to use qiime2 API with it and could not figure it out. I guess I must have messed something up in the process because when I gave up and went back to using cli, this error popped up regardless of what qiime command I put in.
I have been using qiime2-2022.8, natively installed with conda on a WSL (Windows 10).
Here is the code and error:
(qiime2-2022.8) dzagal@QUERCETIN:/mnt/c/Users/dzagal3/Desktop/dzagal3/0_PhD_Microbiome/1_NGS/Data_Processing/qiime_data_v4$ qiime tools import \
--input-path Input_Files/Fungi_Files/taxa_table.biom
--type 'FeatureTable[Frequency]'
--input-format BIOMV100Format
--output-path Input_Files/Fungi_Files/feature_table.qza
Traceback (most recent call last):
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 265, in import_data
view_type = qiime2.sdk.parse_format(view_type)
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/util.py", line 88, in parse_format
pm = qiime2.sdk.PluginManager()
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/init.py", line 2471, in load
return self.resolve()
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/init.py", line 2477, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_feature_table/init.py", line 12, in
from ._summarize import (summarize, tabulate_seqs)
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_feature_table/_summarize/init.py", line 9, in
from ._visualizer import (summarize, tabulate_seqs)
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_feature_table/_summarize/_visualizer.py", line 16, in
import seaborn as sns
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/seaborn/init.py", line 5, in
from .relational import * # noqa: F401,F403
File "/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/seaborn/relational.py", line 8, in
from ._core import (
ImportError: cannot import name 'VectorPlotter' from 'seaborn._core' (/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/seaborn/_core/init.py)
An unexpected error has occurred:
cannot import name 'VectorPlotter' from 'seaborn._core' (/home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/seaborn/_core/init.py)
Here is what I have done to try to solve it:
- Searched the error on the forum and nothing came up, although there seem to be a common issue with seaborn and python(?) when searching on Google.
- Updated conda, but everything was up to date.
- Tried to reinstall seaborn with pip, but requirements were already satisfied:
(qiime2-2022.8) dzagal@QUERCETIN:/mnt/c/Users/dzagal3/Desktop/dzagal3/0_PhD_Microbiome/1_NGS/Raw_Data/DZ_processing_Oct2022/Miseq640_Daniel_Zagal_28299_ITS-249135893$ pip install seaborn
Requirement already satisfied: seaborn in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (0.12.0)
Requirement already satisfied: pandas>=0.25 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from seaborn) (1.4.4)
Requirement already satisfied: matplotlib>=3.1 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from seaborn) (3.5.2)
Requirement already satisfied: numpy>=1.17 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from seaborn) (1.23.1)
Requirement already satisfied: fonttools>=4.22.0 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (4.25.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (1.4.2)
Requirement already satisfied: pillow>=6.2.0 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (9.2.0)
Requirement already satisfied: python-dateutil>=2.7 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (2.8.2)
Requirement already satisfied: cycler>=0.10 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (0.11.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (3.0.9)
Requirement already satisfied: packaging>=20.0 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from matplotlib>=3.1->seaborn) (21.3)
Requirement already satisfied: pytz>=2020.1 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from pandas>=0.25->seaborn) (2022.1)
Requirement already satisfied: six>=1.5 in /home/dzagal/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages (from python-dateutil>=2.7->matplotlib>=3.1->seaborn) (1.16.0)
I am almost certain I must have inadvertently changed something while trying to troubleshoot importing qiime on a Jupyter notebook. I apologize, I cannot recall everything I did while trying this, but I hope it hints at what may be the problem.
Thanks,
Daniel