[Moving Picture Tutorial] Issues when running the "core-metrics-phylogeny" pipeline in "diversity" plugin

[hoangle]

HI @lizgehret,
I have deactivated conda and reinstalled QIIME2. Here's what I get:

qiime info

returns

System versions
Python version: 3.9.19
QIIME 2 release: 2024.5
QIIME 2 version: 2024.5.0
q2cli version: 2024.5.0

Installed plugins
alignment: 2024.5.0
composition: 2024.5.0
cutadapt: 2024.5.0
dada2: 2024.5.0
deblur: 2024.5.0
demux: 2024.5.0
diversity: 2024.5.0
diversity-lib: 2024.5.0
emperor: 2024.5.0
empress: 1.2.0
feature-classifier: 2024.5.0
feature-table: 2024.5.0
fragment-insertion: 2024.5.0
longitudinal: 2024.5.0
metadata: 2024.5.0
phylogeny: 2024.5.0
quality-control: 2024.5.0
quality-filter: 2024.5.0
rescript: 2024.5.0
sample-classifier: 2024.5.0
taxa: 2024.5.0
types: 2024.5.0
vsearch: 2024.5.0

Application config directory
/Users/phamnguyenhoangle/miniconda3/envs/qiime2-amplicon-2024.5/var/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

and

conda list scikit-bio

returns

# packages in environment at /Users/miniconda3/envs/qiime2-amplicon-2024.5:
#
# Name                    Version                   Build  Channel
scikit-bio                0.6.0            py39h5b4affa_4    conda-forge

However, the channel list is still the same:

channels:
  - r
  - bioconda
  - conda-forge
  - defaults

I will try to run the Moving Picture tutorial again and let you know if I encounter any problem. Thanks a lot~!

[SoilRotifer (Mike Robeson)]

I can confirm @Iyarit's observation.

• The base install does indeed have scikit-bio v0.6.0.
• After I install greengenes, with pip install q2-greengenes2, I get: scikit-bio v0.5.9.

[SoilRotifer (Mike Robeson)]

The same issue arises when installing empress, i.e. scikit-bio v0.5.9 and may also occur with other external plugins too.