Hi,
I finished successfully the tutorial on "Moving Pictures".
Then I installed Songbird GitHub - biocore/songbird: Vanilla regression methods for microbiome differential abundance analysis and since then I get the following error message and qiime does not work anymore:
pkg_resources.VersionConflict: (tensorflow 1.15.0 (/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages), Requirement.parse('tensorflow<2,>=1.15.2'))
who can help??
all the best
Hi @rotifer!
Sounds like something went wrong with the installation of songbird. All you need to do is follow the installation instructions for QIIME 2 again (you can start with creating the conda env): it should go very fast since you have already installed this version of QIIME 2 once before, so you should have all these packages in your cache.
:qiime2:
I followed your advice but qiime does not work anymore ...
I did:
conda create -n songbird_env songbird "pandas>=0.18.0,<1" -c conda-forge
I copy and paste some important/interesting pieces:
Remove existing environment (y/[n])? y
==> WARNING: A newer version of conda exists. <==
current version: 4.8.2
latest version: 4.8.3
tensorboard conda-forge/osx-64::tensorboard-1.15.0-py37_0
tensorflow pkgs/main/osx-64::tensorflow-1.15.0-mkl_py37hb249377_0
tensorflow-base pkgs/main/osx-64::tensorflow-base-1.15.0-mkl_py37h032239d_0
tensorflow-estima~ pkgs/main/noarch::tensorflow-estimator-1.15.1-pyh2649769_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
pandas-0.25.3 | 10.3 MB | ################################################################################################################################################## | 100%
importlib_metadata-1 | 3 KB | ################################################################################################################################################## | 100%
tensorflow-base-1.15 | 75.8 MB | ################################################################################################################################################## | 100%
songbird-1.0.2 | 27 KB | ################################################################################################################################################## | 100%
setuptools-46.1.3 | 636 KB | ################################################################################################################################################## | 100%
tensorflow-1.15.0 | 4 KB | ################################################################################################################################################## | 100%
importlib-metadata-1 | 42 KB | ################################################################################################################################################## | 100%
wcwidth-0.1.9 | 20 KB | ################################################################################################################################################## | 100%
prompt-toolkit-3.0.5 | 232 KB | ################################################################################################################################################## | 100%
numpy-1.18.1 | 5.1 MB | ################################################################################################################################################## | 100%
tensorboard-1.15.0 | 3.8 MB | ################################################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
then I did:
conda activate songbird_env
conda activate qiime2-2020.2
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 "/Users/uli/miniconda3/envs/qiime2-2020.2/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 716, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 641, in make_context
self.parse_args(ctx, args)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 1086, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 516, in get_help
return self.command.get_help(self)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 879, in get_help
self.format_help(ctx, formatter)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/click/core.py", line 898, in format_help
self.format_options(ctx, formatter)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 404, in <module>
CACHE = DeploymentCache()
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in __new__
self._init(add_plugins=add_plugins)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2444, in load
self.require(*args, **kwargs)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2467, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 792, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.VersionConflict: (tensorflow 1.15.0 (/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages), Requirement.parse('tensorflow<2,>=1.15.2'))
(qiime2-2020.2) Ulis-MacBook-Pro:redsea uli$
Looks like you have a bit of a mess on your hands: first off, I don't see where you actually reinstalled QIIME 2 again - did you do that? I would recommend just removing all of the broken conda envs with
conda env remove -n $NAME
where $NAME is the name of the broken conda env.
Then, before you do anything else, make sure that your base env is clean by running conda list in it - there should not be any packages like tensorflow or scikit-learn in your root env - this will cause you all kinds of heartache. Once you sort out your base env, then go back to reinstalling QIIME 2 (not songbird, just the base QIIME 2 environment):
https://docs.qiime2.org/2020.2/install/native/
:qiime2:
PS -
This bit, where you activate an environment within an environment, will always lead to sadness and suffering. I strongly encourage you to just use one environment at a time! They are practically disposable, and quick and easy to make, it'll make your life so much easier.
I am happy to tell you that qiime works again :o)
I would like to work with Songbird
conda install songbird -c conda-forge
Next, run the following command to get QIIME 2 to "recognize" Songbird:
qiime dev refresh-cache
I still have songbird_env
how should I proceed now?
Hi @rotifer,
It looks like the original error you got was my fault -- we've been having some problems with Songbird on conda recently.
We're currently working on a fix to the conda-forge installation of Songbird, but in the meantime you should be able to install Songbird through pip: just run the following commands while in a QIIME 2 conda environment --
pip install songbird
qiime dev refresh-cache
qiime info
Let me know how this works for you! If you run into problems, you may need to run conda uninstall songbird first.
hurrah, it worked!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
many thanks for your kind help
Great! thanks Fedarko, it solved our problem with Songbird as well.