Hi all,
To preface, I'm pretty new to most coding-related stuff, and I'm having trouble figuring out how to properly load the QIIME2 environment. For reference, I'm using MobaXterm on Windows 10.
I used the following lines of code to install/activate QIIME2:
wget https://data.qiime2.org/distro/core/qiime2-2021.11-py38-linux-conda.yml
conda env create -n qiime2-2021.11 --file qiime2-2021.11-py38-linux-conda.yml
conda activate qiime2-2021.11
However, when I run that, I get the following error message:
(base) -bash-4.2$ conda activate qiime2-2021.11
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 "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 716, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 641, in make_context
self.parse_args(ctx, args)
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 1086, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 516, in get_help
return self.command.get_help(self)
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 879, in get_help
self.format_help(ctx, formatter)
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/click/core.py", line 898, in format_help
self.format_options(ctx, formatter)
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in <module>
CACHE = DeploymentCache()
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/util.py", line 221, in get_plugin_manager
import qiime2.sdk
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/__init__.py", line 9, in <module>
from qiime2.sdk import Artifact, Visualization
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/__init__.py", line 10, in <module>
from .action import Action, Method, Visualizer, Pipeline
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 20, in <module>
import qiime2.core.type as qtype
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/type/__init__.py", line 10, in <module>
from .semantic import SemanticType, Properties
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/type/semantic.py", line 15, in <module>
from qiime2.core.type.util import is_semantic_type, is_qiime_type
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/type/util.py", line 13, in <module>
from qiime2.core.type.primitive import Int, Float, Bool, Str
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/type/primitive.py", line 13, in <module>
import qiime2.metadata as metadata
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/metadata/__init__.py", line 9, in <module>
from .metadata import (Metadata, MetadataColumn, NumericMetadataColumn,
File "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/metadata/metadata.py", line 16, in <module>
import pandas as pd
File "/opt/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/site-packages/pandas/__init__.py", line 16, in <module>
raise ImportError(
ImportError: Unable to import required dependencies:
numpy:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.8 from "/mnt/home/bagchioi/miniconda3/envs/qiime2-2021.11/bin/python"
* The NumPy version is: "1.21.3"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: No module named 'numpy.core._multiarray_umath'
I ended up removing the environment and reinstalling everything with the following:
conda env remove -n qiime2-2021.11
conda clean -y --all
conda update conda
conda install wget
wget https://data.qiime2.org/distro/core/qiime2-2021.11-py38-linux-conda.yml
conda env create -n qiime2-2021.11 --file qiime2-2021.11-py38-linux-conda.yml
And I am still getting the exact same issue. When I check which version of python I am using, it says I'm on version 3.7.2. However, when I look at the environment, the version there is 3.8 something, so I do not know (or understand) why it's using 3.7.2. Code is shown below.
(qiime2-2021.11) -bash-4.2$ which python
/opt/software/Python/3.7.2-GCCcore-8.2.0/bin/python
Any and all help would be appreciated.