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

**URL:** https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668
**Category:** User Support
**Created:** [June 30, 2024, 1:39pm UTC](https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668 "2024-06-30T13:39:18Z")
**Posts on this page:** 4
**Page:** 2

<div class="post-metadata">

### Author: ![hoangle](https://forum.qiime2.org/user_avatar/forum.qiime2.org/hoangle/32/18823_2.png) [@hoangle](https://forum.qiime2.org/u/hoangle)
#### Post date: [July 15, 2024, 4:18am UTC](https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668/26 "2024-07-15T04:18:38Z")

</div>

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

```auto
qiime info

```

returns

```auto
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

```auto
conda list scikit-bio

```

returns

```auto
# 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:

```auto
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~!

---

<div class="post-metadata">

### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [July 17, 2024, 6:07pm UTC](https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668/27 "2024-07-17T18:07:55Z")

</div>

I can confirm @Iyarit's observation.

- The base install does indeed have `scikit-bio v0.6.0`.
- After I install [greengenes](https://github.com/biocore/q2-greengenes2/), with `pip install q2-greengenes2`, I get: `scikit-bio v0.5.9`.

---

<div class="post-metadata">

### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [July 17, 2024, 6:23pm UTC](https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668/28 "2024-07-17T18:23:13Z")

</div>

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

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 18, 2024, 12:23am UTC](https://forum.qiime2.org/t/moving-picture-tutorial-issues-when-running-the-core-metrics-phylogeny-pipeline-in-diversity-plugin/30668/29 "2024-08-18T00:23:45Z")

</div>

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