Ok, thanks!
I just tried installing qiime2-2021.2, and that worked fine. However, it seems like somehow everything is stuck inside my qiime2-2020.6 env (not sure if this is the right terminology)?
See below for what happens when I try and activate the new qiime2-2021.2 conda environment:
(base) [[email protected]@bc-login03 ~]$ conda activate qiime2-2021.2
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-1/[email protected]/miniconda3/envs/qiime2-2020.6/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 781, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 700, in make_context
self.parse_args(ctx, args)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1209, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 570, in get_help
return self.command.get_help(self)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 975, in get_help
self.format_help(ctx, formatter)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1003, in format_help
self.format_options(ctx, formatter)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in <module>
CACHE = DeploymentCache()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in __new__
self._init(add_plugins=add_plugins)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2461, in load
return self.resolve()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2467, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/scratch/groups/ksandel1/q2-picrust2-2021.2_0/q2_picrust2/__init__.py", line 9, in <module>
from ._full_pipeline import full_pipeline
File "/scratch/groups/ksandel1/q2-picrust2-2021.2_0/q2_picrust2/_full_pipeline.py", line 7, in <module>
from picrust2.default import (default_ref_dir, default_tables,
ImportError: cannot import name 'default_ref_dir'
(qiime2-2021.2) [[email protected]@bc-login03 ~]$ which pip
~/miniconda3/envs/qiime2-2020.6/bin/pip
(qiime2-2021.2) [[email protected]@bc-login03 ~]$ conda activate qiime2-2020.6
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-1/[email protected]/miniconda3/envs/qiime2-2020.6/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 781, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 700, in make_context
self.parse_args(ctx, args)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1209, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 570, in get_help
return self.command.get_help(self)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 975, in get_help
self.format_help(ctx, formatter)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1003, in format_help
self.format_options(ctx, formatter)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in <module>
CACHE = DeploymentCache()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in __new__
self._init(add_plugins=add_plugins)
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2461, in load
return self.resolve()
File "/home-1/[email protected]/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2467, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/scratch/groups/ksandel1/q2-picrust2-2021.2_0/q2_picrust2/__init__.py", line 9, in <module>
from ._full_pipeline import full_pipeline
File "/scratch/groups/ksandel1/q2-picrust2-2021.2_0/q2_picrust2/_full_pipeline.py", line 7, in <module>
from picrust2.default import (default_ref_dir, default_tables,
ImportError: cannot import name 'default_ref_dir'
and this is what happens when I navigate to the base environment and then input "which pip":
(qiime2-2020.6) [[email protected]@bc-login03 ~]$ conda env list
# conda environments:
#
base /home-1/[email protected]/miniconda3
picrust2 /home-1/[email protected]/miniconda3/envs/picrust2
qiime2-2019.10 /home-1/[email protected]/miniconda3/envs/qiime2-2019.10
qiime2-2019.7 /home-1/[email protected]/miniconda3/envs/qiime2-2019.7
qiime2-2020.2 /home-1/[email protected]/miniconda3/envs/qiime2-2020.2
qiime2-2020.6 * /home-1/[email protected]/miniconda3/envs/qiime2-2020.6
qiime2-2021.11 /home-1/[email protected]/miniconda3/envs/qiime2-2021.11
qiime2-2021.2 /home-1/[email protected]/miniconda3/envs/qiime2-2021.2
(qiime2-2020.6) [[email protected]@bc-login03 ~]$ conda activate base
(base) [[email protected]@bc-login03 ~]$ which pip
~/miniconda3/envs/qiime2-2020.6/bin/pip