Repetitive message "QIIME is caching your current deployment for improved performance"

After installing songbird, I ran the command “qiime dev refresh-cache”. Now, when I try to run any qiime command, I get the following message and the command does not run:
“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 “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/bin/qiime”, line 11, in
sys.exit(qiime())
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py”, line 829, in call
return self.main(*args, **kwargs)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py”, line 782, in main
rv = self.invoke(ctx)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py”, line 1254, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py”, line 1297, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py”, line 100, in get_command
plugin = self._plugin_lookup[name]
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py”, line 76, in _plugin_lookup
import q2cli.core.cache
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py”, line 406, in
CACHE = DeploymentCache()
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py”, line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py”, line 200, in _cache_current_state
state = self._get_current_state()
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py”, line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 54, in new
self._init(add_plugins=add_plugins)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 81, in _init
plugin = entry_point.load()
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py”, line 2471, in load
self.require(*args, **kwargs)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py”, line 2494, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File “/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py”, line 790, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.19.1 (/Users/emilykunselman/opt/anaconda2/envs/qiime2-2020.8/lib/python3.6/site-packages), Requirement.parse(‘numpy<1.19.0,>=1.16.0’), {‘tensorflow’})”

How can prevent this from happening and run my qiime commands like normal again?

Unfortunately, Songbird depends on an old version of TensorFlow, and that old version of TensorFlow depends on an old version of NumPy – which breaks newer versions of QIIME 2 right now.

For now, you should be able to fix your QIIME 2 environment by uninstalling Songbird and rerunning the qiime dev refresh-cache command. (You may need to also uninstall TensorFlow if that isn’t automatically done when Songbird is uninstalled.)

The current workaround for using Songbird in QIIME 2 is using an old version of QIIME 2 to run Songbird – going by this post, I think QIIME 2 2020.6 should work.

4 Likes

I tried the older version of Qiime2 (2020.2) that I had and that solved the problem. Thank you!

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