Issue after pip install q2-greengenes2 in QIIME2 2026.1: QIIME fails to start after installation

Technical Support
1

I’m trying to install q2-greengenes2 in QIIME2 2026.1 (macOS). The installation fails and also QIIME2 does not work after the installation.

scikit-bio and scipy seem to be modified after installation but not sure what is the exact problem. Could someone please help me with this.

This is the output when I run pip install q2-greengenes2:

(qiime2-amplicon-2026.1) atpaok@royal-44-221 \~ % pip install q2-greengenes2

Collecting q2-greengenes2

  Using cached q2_greengenes2-2024.1-py3-none-any.whl

Requirement already satisfied: biom-format in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from q2-greengenes2) (2.1.16)

Requirement already satisfied: iow in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from q2-greengenes2) (1.0.5)

Collecting redbiom (from q2-greengenes2)

  Using cached redbiom-0.3.9-py3-none-any.whl

Requirement already satisfied: scikit-bio in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from q2-greengenes2) (0.6.2)

Requirement already satisfied: click in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from biom-format->q2-greengenes2) (8.1.8)

Requirement already satisfied: numpy>=1.9.2 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from biom-format->q2-greengenes2) (1.26.4)

Requirement already satisfied: scipy>=1.3.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from biom-format->q2-greengenes2) (1.13.0)

Requirement already satisfied: pandas>=0.20.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from biom-format->q2-greengenes2) (2.2.2)

Requirement already satisfied: h5py in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from biom-format->q2-greengenes2) (3.11.0)

Requirement already satisfied: python-dateutil>=2.8.2 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2.9.0.post0)

Requirement already satisfied: pytz>=2020.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2025.2)

Requirement already satisfied: tzdata>=2022.7 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2025.3)

Requirement already satisfied: six>=1.5 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas>=0.20.0->biom-format->q2-greengenes2) (1.17.0)

Collecting nose>=1.3.7 (from iow->q2-greengenes2)

  Using cached nose-1.3.7-py3-none-any.whl.metadata (1.7 kB)

Collecting cython>=0.24.1 (from iow->q2-greengenes2)

  Using cached cython-3.2.4-cp39-abi3-macosx_10_9_x86_64.whl.metadata (7.5 kB)

Collecting scikit-bio (from q2-greengenes2)

  Using cached scikit_bio-0.5.9-cp310-cp310-macosx_10_9_x86_64.whl

Requirement already satisfied: requests>=2.20.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (2.32.5)

Requirement already satisfied: decorator>=3.4.2 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (4.4.2)

Requirement already satisfied: IPython>=3.2.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (8.21.0)

Requirement already satisfied: matplotlib>=1.4.3 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (3.8.4)

Requirement already satisfied: natsort>=4.0.3 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (8.4.0)

Collecting scipy>=1.3.1 (from biom-format->q2-greengenes2)

  Using cached scipy-1.10.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (53 kB)

Requirement already satisfied: hdmedians>=0.14.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from scikit-bio->q2-greengenes2) (0.14.2)

Requirement already satisfied: jedi>=0.16 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.19.2)

Requirement already satisfied: matplotlib-inline in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.1)

Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.41 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (3.0.52)

Requirement already satisfied: pygments>=2.4.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (2.19.2)

Requirement already satisfied: stack-data in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.6.3)

Requirement already satisfied: traitlets>=5 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (5.9.0)

Requirement already satisfied: exceptiongroup in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (1.3.1)

Requirement already satisfied: pexpect>4.3 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (4.9.0)

Requirement already satisfied: wcwidth in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from prompt-toolkit<3.1.0,>=3.0.41->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.4.0)

Requirement already satisfied: parso<0.9.0,>=0.8.4 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from jedi>=0.16->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.8.5)

Requirement already satisfied: contourpy>=1.0.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.3.2)

Requirement already satisfied: cycler>=0.10 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (0.12.1)

Requirement already satisfied: fonttools>=4.22.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (4.61.1)

Requirement already satisfied: kiwisolver>=1.3.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.4.9)

Requirement already satisfied: packaging>=20.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (26.0)

Requirement already satisfied: pillow>=8 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (10.3.0)

Requirement already satisfied: pyparsing>=2.3.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (3.3.2)

Requirement already satisfied: ptyprocess>=0.5 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from pexpect>4.3->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.7.0)

Requirement already satisfied: charset_normalizer<4,>=2 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from requests>=2.20.0->scikit-bio->q2-greengenes2) (3.4.4)

Requirement already satisfied: idna<4,>=2.5 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from requests>=2.20.0->scikit-bio->q2-greengenes2) (3.11)

Requirement already satisfied: urllib3<3,>=1.21.1 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from requests>=2.20.0->scikit-bio->q2-greengenes2) (2.5.0)

Requirement already satisfied: certifi>=2017.4.17 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from requests>=2.20.0->scikit-bio->q2-greengenes2) (2026.1.4)

Requirement already satisfied: typing-extensions>=4.6.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from exceptiongroup->IPython>=3.2.0->scikit-bio->q2-greengenes2) (4.15.0)

Collecting nltk (from redbiom->q2-greengenes2)

  Using cached nltk-3.9.4-py3-none-any.whl.metadata (3.2 kB)

Requirement already satisfied: joblib in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from redbiom->q2-greengenes2) (1.5.3)

Collecting msgpack (from redbiom->q2-greengenes2)

  Using cached msgpack-1.1.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (8.1 kB)

Collecting regex>=2021.8.3 (from nltk->redbiom->q2-greengenes2)

  Using cached regex-2026.4.4-cp310-cp310-macosx_10_9_x86_64.whl.metadata (40 kB)

Requirement already satisfied: tqdm in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from nltk->redbiom->q2-greengenes2) (4.67.1)

Requirement already satisfied: executing>=1.2.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (2.2.1)

Requirement already satisfied: asttokens>=2.1.0 in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (3.0.1)

Requirement already satisfied: pure_eval in ./miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.3)

Using cached scipy-1.10.1-cp310-cp310-macosx_10_9_x86_64.whl (35.1 MB)

Using cached cython-3.2.4-cp39-abi3-macosx_10_9_x86_64.whl (2.9 MB)

Using cached nose-1.3.7-py3-none-any.whl (154 kB)

Using cached msgpack-1.1.2-cp310-cp310-macosx_10_9_x86_64.whl (81 kB)

Using cached nltk-3.9.4-py3-none-any.whl (1.6 MB)

Using cached regex-2026.4.4-cp310-cp310-macosx_10_9_x86_64.whl (291 kB)

Installing collected packages: nose, scipy, regex, msgpack, cython, nltk, scikit-bio, redbiom, q2-greengenes2

  Attempting uninstall: scipy

    Found existing installation: scipy 1.13.0

    Uninstalling scipy-1.13.0:

      Successfully uninstalled scipy-1.13.0

  Attempting uninstall: scikit-bio

    Found existing installation: scikit-bio 0.6.2

    Uninstalling scikit-bio-0.6.2:

      Successfully uninstalled scikit-bio-0.6.2

Successfully installed cython-3.2.4 msgpack-1.1.2 nltk-3.9.4 nose-1.3.7 q2-greengenes2-2024.1 redbiom-0.3.9 regex-2026.4.4 scikit-bio-0.5.9 scipy-1.10.1

(qiime2-amplicon-2026.1) atpaok@royal-44-221 \~ %

This this output when I check if qiime works after I have installed q2-greengenes2

(qiime2-amplicon-2026.1) atpaok@royal-44-221 \~ % conda deactivate

conda activate qiime2-amplicon-2026.1

qiime info

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/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/util.py", line 277, in get_plugin_manager

    return qiime2.sdk.PluginManager.reuse_existing()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/rachis/sdk/plugin_manager.py", line 64, in reuse_existing

    raise UninitializedPluginManagerError

rachis.sdk.plugin_manager.UninitializedPluginManagerError

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/bin/qiime", line 11, in <module>

    sys.exit(qiime())

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/click/core.py", line 1161, in \__call_\_

    return self.main(\*args, \*\*kwargs)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/click/core.py", line 1082, in main

    rv = self.invoke(ctx)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/click/core.py", line 1697, in invoke

    return \_process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/click/core.py", line 1443, in invoke

    return ctx.invoke(self.callback, \*\*ctx.params)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/click/core.py", line 788, in invoke

    return \__callback(\*args, \*\*kwargs)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/builtin/info.py", line 51, in info

    import q2cli.core.cache

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/core/cache.py", line 276, in <module>

    CACHE = DeploymentCache()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/core/cache.py", line 61, in \__init_\_

    self.\_state = self.\_get_cached_state(refresh=refresh)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/core/cache.py", line 107, in \_get_cached_state

    self.\_cache_current_state(current_requirements)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/core/cache.py", line 196, in \_cache_current_state

    state = self.\_get_current_state()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/core/cache.py", line 244, in \_get_current_state

    plugin_manager = q2cli.util.get_plugin_manager()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2cli/util.py", line 289, in get_plugin_manager

    return qiime2.sdk.PluginManager()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/rachis/sdk/plugin_manager.py", line 73, in \__new_\_

    self.\_init(add_plugins=add_plugins)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/rachis/sdk/plugin_manager.py", line 111, in \_init

    plugin = entry_point.load()

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/importlib/metadata/\__init_\_.py", line 171, in load

    module = import_module(match.group('module'))

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/importlib/\__init_\_.py", line 126, in import_module

    return \_bootstrap.\_gcd_import(name\[level:\], package, level)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2_vsearch/plugin_setup.py", line 12, in <module>

    import q2_vsearch.\_cluster_features

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/q2_vsearch/\_cluster_features.py", line 15, in <module>

    import skbio

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/\__init_\_.py", line 11, in <module>

    import skbio.io  # noqa

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/io/\__init_\_.py", line 244, in <module>

    import_module('skbio.io.format.clustal')

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/importlib/\__init_\_.py", line 126, in import_module

    return \_bootstrap.\_gcd_import(name\[level:\], package, level)

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/io/format/clustal.py", line 148, in <module>

    from skbio.alignment import TabularMSA

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/alignment/\__init_\_.py", line 203, in <module>

    from .\_tabular_msa import TabularMSA

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/alignment/\_tabular_msa.py", line 17, in <module>

    from skbio.metadata.\_mixin import MetadataMixin, PositionalMetadataMixin

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\__init_\_.py", line 27, in <module>

    from .\_interval import Interval, IntervalMetadata

  File "/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\_interval.py", line 13, in <module>

    from .\_intersection import IntervalTree

ImportError: dlopen(/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\_intersection.cpython-310-darwin.so, 0x0002): tried: '/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\_intersection.cpython-310-darwin.so' (duplicate LC_RPATH '/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib'), '/System/Volumes/Preboot/Cryptexes/OS/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\_intersection.cpython-310-darwin.so' (no such file), '/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib/python3.10/site-packages/skbio/metadata/\_intersection.cpython-310-darwin.so' (duplicate LC_RPATH '/Users/atpaok/miniconda3/envs/qiime2-amplicon-2026.1/lib')
2

Hey @tkvotsi,

Thanks for reaching out. This is unusual; that said, before we get too into the weeds, it looks like the most recent release for q2-greengenes2 was 2024.1, so I'd recommend trying to install this plugin in a QIIME 2 2024.2 environment.

Here's the URL for the environment file you'll want to use:

https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2024.2/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml

Once you have that environment installed, try pip installing q2-gg2 in that environment. If you still run into any issues, please share your full terminal output in your reply.

Cheers :lizard:

3

Thank you for your reply. I can try that by installing the 2024.1 environment, and keep you informed. However, as I have done all my downstream analysis so far e.g. joining paired ends, denoising etc on the 2026.1 environment could I only do the q2-greengenes2 (taxonomy) step in the 2024.1 environment and then continue to my original 2026.1? Can I switch between these 2 environments for different steps?

4

Hello!

Yes, one can use different versions of qiime2 for analyses.
However, due to some of the recent updates, qiime2 v2024.2 will not recognise files created by v.2026.1, while v2026.1 can accept files from v2024.2.

When I need to switch, I do the following:

  1. While in v2026.1, I export files that I will need to use in v2024.2.
  2. in v2024.2, I import files back and run some commands
  3. You can switch back to v2026.1 (no export/import is needed at this point).

Best,