I have searched for related issues. The previous solution was to upgrade glibc to 2.17, but my system already has this version and I still encounter this problem.
Qiime2 2023.9, installed by Conda on CentOS6
conda info:
active environment : base
active env location : /share/data2/pmid/miniconda3
shell level : 1
user config file : /home/pmid/.condarc
populated config files :
conda version : 4.12.0
conda-build version : not installed
python version : 3.8.13.final.0
virtual packages : __linux=2.6.32=0
__glibc=2.17=0
__unix=0=0
__archspec=1=x86_64
base environment : /share/data2/pmid/miniconda3 (writable)
conda av data dir : /share/data2/pmid/miniconda3/etc/conda
conda av metadata url : None
channel URLs : main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /share/data2/pmid/miniconda3/pkgs
/home/pmid/.conda/pkgs
envs directories : /share/data2/pmid/miniconda3/envs
/home/pmid/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.8.13 Linux/2.6.32-754.10.1.el6.x86_64 centos/6.10 glibc/2.17
UID:GID : 555:558
netrc file : None
offline mode : False
detail Error when I run qiime --help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/ijson/backends/init.py:22: UserWarning: Cannot determine yajl version, assuming <1.0.12
warnings.warn('Cannot determine yajl version, assuming <1.0.12')
Traceback (most recent call last):
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/q2cli/util.py", line 279, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/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 "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/bin/qiime", line 11, in
sys.exit(qiime())
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1077, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 943, in make_context
self.parse_args(ctx, args)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1644, in parse_args
rest = super().parse_args(ctx, args)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1408, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 2400, in handle_parse_result
value = self.process_value(ctx, value)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 2362, in process_value
value = self.callback(ctx, self, value)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1300, in show_help
echo(ctx.get_help(), color=ctx.color)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 704, in get_help
return self.command.get_help(self)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1325, in get_help
self.format_help(ctx, formatter)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/click/core.py", line 1358, in format_help
self.format_options(ctx, formatter)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self.plugin_lookup)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/commands.py", line 76, in plugin_lookup
import q2cli.core.cache
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init
self.state = self.get_cached_state(refresh=refresh)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in get_cached_state
self.cache_current_state(current_requirements)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in cache_current_state
state = self.get_current_state()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2cli/util.py", line 291, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self.init(add_plugins=add_plugins)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in init
plugin = entry_point.load()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/pkg_resources/init.py", line 2518, in load
return self.resolve()
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/pkg_resources/init.py", line 2524, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2_diversity/init.py", line 11, in
from .beta import (beta, beta_phylogenetic, bioenv,
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2_diversity/beta/init.py", line 9, in
from q2_diversity_lib.beta import METRICS
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 11, in
import sklearn.metrics
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe_/lib/python3.8/site-packages/sklearn/init.py", line 83, in
from .utils.show_versions import show_versions
File "/share/data2/pmid/miniconda3/envs/7f5b1f1ae050f6ff2c48bda21fe04afe/lib/python3.8/site-packages/sklearn/utils/_show_versions.py", line 12, in
from ._openmp_helpers import _openmp_parallelism_enabled
ImportError: dlopen: cannot load any more object with static TLS