Hi,
when I ran $ conda update conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.13.0
latest version: 23.7.2
Please update conda by running
$ conda update -n base -c defaults conda
All requested packages already installed.
I followed the recommended instruction:
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.13.0
latest version: 23.7.2
Please update conda by running
$ conda update -n base -c defaults conda
All requested packages already installed.
I have Python 3.9.17
$ conda config --show-sources
==> /home/raiz.condarc <==
channels:
- bioconda
- defaults
I am worried about upgrading the environment since I have many conda env for a different software, and currently, I have an issue with qiime2 env (qiime2-2022.2) after installing Songbird plugin that generated another issue when activating the env or when running any q2 commands or even installing a new qiime2 version (qiime2-2023.5) to skip this messed up env. This warning message is as follows:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
2023-08-15 08:33:36.880401: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-08-15 08:33:36.909950: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-08-15 08:33:36.910304: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-08-15 08:33:37.425176: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Traceback (most recent call last):
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/util.py”, line 224, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File “/home/miniconda3/envs/qiime2-2022.2/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/miniconda3/envs/qiime2-2022.2/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 829, in call
return self.main(*args, **kwargs)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 781, in main
with self.make_context(prog_name, args, **extra) as ctx:
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 700, in make_context
self.parse_args(ctx, args)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/click/command.py”, line 43, in parse_args
return super().parse_args(ctx, args)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 1209, in parse_args
echo(ctx.get_help(), color=ctx.color)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 570, in get_help
return self.command.get_help(self)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 975, in get_help
self.format_help(ctx, formatter)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py”, line 1003, in format_help
self.format_options(ctx, formatter)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/click/command.py”, line 157, in format_options
for subcommand in self.list_commands(ctx):
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py”, line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py”, line 76, in _plugin_lookup
import q2cli.core.cache
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py”, line 285, in
CACHE = DeploymentCache()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py”, line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py”, line 205, in _cache_current_state
state = self._get_current_state()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py”, line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/util.py”, line 236, in get_plugin_manager
return qiime2.sdk.PluginManager()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py”, line 67, in new
self._init(add_plugins=add_plugins)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py”, line 105, in _init
plugin = entry_point.load()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/pkg_resources/init.py”, line 2465, in load
return self.resolve()
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/pkg_resources/init.py”, line 2471, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/q2/init.py”, line 2, in
from ._method import multinomial
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/q2/_method.py”, line 8, in
from songbird.multinomial import MultRegression
File “/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/multinomial.py”, line 3, in
from tensorflow.contrib.distributions import Multinomial, Normal
ModuleNotFoundError: No module named ‘tensorflow.contrib’
Sorry for including different issues in the post, but I thought I should clarify the current running issues with conda env.
However, other env including other software are working properly.
Thanks!