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?

1 Like

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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