Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 to 0.3 #843

gxydevbot · 2025-05-12T05:01:14Z

Hello! This is an automated update of the following workflow: workflows/amplicon/qiime2/qiime2-III-VI-downsteam. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2025.4.0+dist.h1147124e
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2025.4.0+q2galaxy.2025.4.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2025.4.0+q2galaxy.2025.4.0

The workflow release number has been updated from 0.2 to 0.3.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

…o 0.3

github-actions · 2025-05-12T05:35:24Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	1
Error	0
Failure	1
Skipped	0

Failed Tests

❌ QIIME2-VI-diversity-metrics-and-estimations.ga_0

Problems:

Output with path /tmp/tmp1a15pp1d/beta_diversity_weighted_unifrac__3b9ba44c-451b-4228-bb03-7148adbf4cb0 different than expected
Expected file size to be in [400k:500k] found 504807

Workflow invocation details

Invocation Messages

Steps

Step 1: Sampling depth:
- step_state: scheduled
Step 2: Metadata:
- step_state: scheduled

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmppomf81kc/job_working_directory/000/19/configs/tmp3ptn2b4_'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 95990253-c5d5-4924-868a-432390b1cf03｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 12: Beta diversity - Bray-Curtis distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmppomf81kc/job_working_directory/000/20/configs/tmpv9_nuhsq'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 60069135-46e2-47d9-b865-f79e04ddc6a8｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 29, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 30, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 31, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 32, "src": "hda"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmppomf81kc/job_working_directory/000/22/configs/tmp3jnssos1'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 2dd30b1c-d8f5-4ea7-9df5-f3827e1fe485｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 28, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 26, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 25, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 27, "src": "hda"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 24, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 22, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 21, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 23, "src": "hda"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "rarefied_table"}, "input": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "faith_pd_vector"}, "input": {"values": [{"id": 17, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "observed_features_vector"}, "input": {"values": [{"id": 18, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "shannon_vector"}, "input": {"values": [{"id": 20, "src": "hda"}]}}, {"__index__": 4, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "eveness_vector"}, "input": {"values": [{"id": 19, "src": "hda"}]}}]

Step 3: Feature table:
- step_state: scheduled
Step 4: Rooted tree:
- step_state: scheduled
Step 5: Target metadata parameter (for beta diversity):
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2025.4.0+dist.h1147124e:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmppomf81kc/job_working_directory/000/14/configs/tmpl7jin51m'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 59, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmppomf81kc/job_working_directory/000/15/configs/tmp5nw8obab'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
  warn(f"{func.__name__} is deprecated as of {ver}.")
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.008592360631028074 and the largest is 5.250221977897388.
  warn(
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.08744210267781792 and the largest is 4.83121202245088.
  warn(
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.02238803416531163 and the largest is 2.2154065166410293.
  warn(
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.028624230910658778 and the largest is 0.6164051191609862.
  warn(

Standard Output:

｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣
｢sampling_depth: 2000｣
｢metadata: <Metadata>｣
｢with_replacement: False｣
｢ignore_missing_samples: False｣
                                                                                                                                                                                                                                                               
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/500490e2-e458-40a0-826e-d90a0cfc2c4c/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027831.22@uid=#1001/tmp/q2-OutPath-ydt017rx

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

ssu -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/500490e2-e458-40a0-826e-d90a0cfc2c4c/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027831.22@uid=#1001/tmp/q2-OutPath-wpasdq1s

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

ssu -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/500490e2-e458-40a0-826e-d90a0cfc2c4c/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027831.22@uid=#1001/tmp/q2-OutPath-ixxtk7be

Saved FeatureTable[Frequency] to: rarefied_table.qza
Saved SampleData[AlphaDiversity] to: faith_pd_vector.qza
Saved SampleData[AlphaDiversity] to: observed_features_vector.qza
Saved SampleData[AlphaDiversity] to: shannon_vector.qza
Saved SampleData[AlphaDiversity] to: evenness_vector.qza
Saved DistanceMatrix to: unweighted_unifrac_distance_matrix.qza
Saved DistanceMatrix to: weighted_unifrac_distance_matrix.qza
Saved DistanceMatrix to: jaccard_distance_matrix.qza
Saved DistanceMatrix to: bray_curtis_distance_matrix.qza
Saved PCoAResults to: unweighted_unifrac_pcoa_results.qza
Saved PCoAResults to: weighted_unifrac_pcoa_results.qza
Saved PCoAResults to: jaccard_pcoa_results.qza
Saved PCoAResults to: bray_curtis_pcoa_results.qza
Saved Visualization to: unweighted_unifrac_emperor.qzv
Saved Visualization to: weighted_unifrac_emperor.qzv
Saved Visualization to: jaccard_emperor.qzv
Saved Visualization to: bray_curtis_emperor.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"ignore_missing_samples": false, "with_replacement": false}`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`
sampling_depth	`"2000"`

Step 8: Alpha diversity metrics - Pielou's evenness:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmppomf81kc/job_working_directory/000/16/configs/tmpr1ejlqa9'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: 6bc07fc4-4f3c-483c-9f1c-51bb2bbb69bc｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmppomf81kc/job_working_directory/000/17/configs/tmpwhsebkhv'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: cb0c3a63-4761-47f3-8b58-492be9b76393｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Step 10: Alpha diversity metrics - Shannon's diversity index:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmppomf81kc/job_working_directory/000/18/configs/tmpdbfoel11'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: 91db387a-4628-4532-afda-15e7c33b3412｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"25011be22ef211f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Other invocation details
- history_id
  - 51588883e4a923bc
- history_state
  - ok
- invocation_id
  - 6608fcdda181eae8
- invocation_state
  - scheduled
- workflow_id
  - 6608fcdda181eae8

Passed Tests

✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Representative sequences:
- step_state: scheduled
Step 2: Feature table:
- step_state: scheduled
Step 3: Metadata:
- step_state: scheduled
Step 4: Minimum depth:
- step_state: scheduled
Step 5: Maximum depth:
- step_state: scheduled
Step 6: SEPP fragment insertion reference:
- step_state: scheduled
Step 7: Taxonomic classifier:
- step_state: scheduled

Step 8: Phylogenetic tree for diversity analysis:

step_state: scheduled

Subworkflow Steps

Step 1: DADA2 representative sequences:
- step_state: scheduled
Step 2: SEPP fragment insertion source file:
- step_state: scheduled

Step 3: Phylogenetic tree generation:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run fragment_insertion sepp '/tmp/tmppomf81kc/job_working_directory/000/6/configs/tmpksexrygp'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[05:23:43] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_48/pplacer.backbone.712szl08.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_48/pplacer.tree.2yupqwfv.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_48/pplacer.extended.0.o56e8bpo.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_48/pplacer.extended.0.o56e8bpo.jplace
[05:23:49] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_49/pplacer.backbone.czl0uyhb.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_49/pplacer.tree.s_z_m1o1.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_49/pplacer.extended.0.auxz5gnx.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_49/pplacer.extended.0.auxz5gnx.jplace
[05:23:53] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_50/pplacer.backbone.atc125jy.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_50/pplacer.tree.ccue4e58.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_50/pplacer.extended.0.1m3gb2mu.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_50/pplacer.extended.0.1m3gb2mu.jplace
[05:23:56] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_54/pplacer.backbone.89lhamkl.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_54/pplacer.tree.9ydfoe6g.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_54/pplacer.extended.0.fymdiiwr.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_54/pplacer.extended.0.fymdiiwr.jplace
[05:23:59] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_60/pplacer.backbone.kjvds6lj.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_60/pplacer.tree.uk3msqad.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_60/pplacer.extended.0.ktg2ng69.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_60/pplacer.extended.0.ktg2ng69.jplace
[05:24:02] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_61/pplacer.backbone.oprks7yg.fasta, tree_file:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_61/pplacer.tree.v6qqzdmt.tre, info_file:/tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_61/pplacer.extended.0.zbwzvzxy.fasta, output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf/root/P_61/pplacer.extended.0.zbwzvzxy.jplace
[05:24:37] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tmp-k3t2D1sUXO/q2-fragment-insertion_placement.json
[05:24:39] algorithm.py (line 213):     INFO: Current execution Finished in 640 seconds
[05:24:39] algorithm.py (line 215):     INFO: All checkpointed executions Finished in 640 cumulative time
[05:24:39] algorithm.py (line 224):     INFO: Temp files are left behind at /tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tempssd-uN7wJRxG50/q2-fragment-insertion.qnez9uyf

==> sepp-q2-fragment-insertion-out.log <==
root_p='/opt/conda/envs/qiime2-amplicon-2025.4/share/sepp/sepp'
output files are at q2-fragment-insertion_placement.json q2-fragment-insertion_placement.tog.relabelled.tre q2-fragment-insertion_placement.tog.relabelled.xml q2-fragment-insertion_placement.tog.tre q2-fragment-insertion_placement.tog.xml and more files are at /tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tmp-k3t2D1sUXO . Consider removing /tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tmp-k3t2D1sUXO if its files are not needed.
Removing /tmp/tmppomf81kc/tmp/tmp.u5O1AB3AgI/sepp-tmp-k3t2D1sUXO
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"4a60fc352eef11f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: DADA2 representative sequences:
- step_state: scheduled
Step 3: Taxonomic classifier:
- step_state: scheduled
Step 4: DADA2 feature table:
- step_state: scheduled

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmppomf81kc/job_working_directory/000/7/configs/tmpd50dq9yn'

Exit Code:

```
0
```

Standard Output:

｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢classifier: dc39ac42-8ecf-4093-8efa-14513ccde419｣
｢reads_per_batch: 'auto'｣
｢pre_dispatch: '2*n_jobs'｣
｢confidence: 0.7｣
｢read_orientation: 'auto'｣
                                                                                                                                                                                                                                                               
Saved FeatureData[Taxonomy] to: classification.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "pre_dispatch": "2*n_jobs", "read_orientation": "auto"}`
__workflow_invocation_uuid__	`"4a60fc362eef11f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run taxa barplot '/tmp/tmppomf81kc/job_working_directory/000/8/configs/tmpnwgvllhn'

Exit Code:

```
0
```

Standard Output:

｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
｢taxonomy: d4cb2706-1932-4d41-90d0-b814ce15dcee｣
｢metadata: <Metadata>｣
｢level_delimiter: None｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"4a60fc362eef11f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmppomf81kc/job_working_directory/000/9/configs/tmp4jh9sjf5'

Exit Code:

```
0
```

Standard Output:

｢input: <Metadata>｣
｢page_size: 100｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"4a60fc362eef11f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`[{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: DADA2 feature table:
- step_state: scheduled
Step 3: Rooted tree:
- step_state: scheduled
Step 4: Minimum depth:
- step_state: scheduled
Step 5: Maximum depth:
- step_state: scheduled

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_rarefaction '/tmp/tmppomf81kc/job_working_directory/000/10/configs/tmpukr9rxu8'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
  warn(f"{func.__name__} is deprecated as of {ver}.")
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_num
..
265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)

Standard Output:

｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
｢max_depth: 2019｣
｢phylogeny: 38884db0-e577-4364-ba8d-abde416cefc3｣
｢metrics: None｣
｢metadata: <Metadata>｣
｢min_depth: 1｣
｢steps: 10｣
｢iterations: 10｣
                                                                                                                                                                                                                                                               
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/0646f9bd-f71e-4fa0-a481-dc35c9163107/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-24xgfy_n

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c6e5fdad-271e-4438-b5f6-f0d4825a6f13/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-eq2ohj33

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/f6c401f3-51a6-4806-9680-e492ec8c4741/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-uuyocoyw

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/ba5b16ea-7101-414f-9947-769963b1350e/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-kz218es9

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/1d68927c-8348-4795-b289-7a52becd5087/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-ro8sk5b7

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/65ede320-e7e9-4aef-b1dd-c7b9687e775b/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-8e5diu_i

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/98710f50-e60e-4444-8787-829fe5935efb/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-5k3j4v6d

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/2203765f-6de4-4844-8938-25762b4847c3/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-jxi5ukzl

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/2630e195-5a28-41ab-a55f-35f540804e66/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-dgf16fks

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/1bfada33-8f05-4624-a354-d20724cc5bab/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-g9eb9j4t

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/7d3f3b89-443d-4aae-8dac-31949ed96df5/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-wkg4p8mv

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/f50cfd01-a6b1-4f1e-abf1-4b7180adb379/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-3dl_2s18

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a02aa697-9ac4-4b1a-b2f7-18520bf05242/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-wxlx200q

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/5187c224-fe6c-42c6-bfc2-62f83bdd00d9/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-9eulh0wo

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/41980cf4-4cb6-4336-9d9b-180a42411398/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-m8xbs3r0

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/2fdc2957-7b6d-4bf4-a4d7-f7acd6bdd480/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-2lwh1gre

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/d52a075b-0e8c-4e86-b3e6-8ba9a2c045be/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-irz11r9y

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/8b5117a6-9cf0-4659-a64d-ac7036576fa3/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-_44ihn6o

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/f8e15ab8-1955-4c01-962d-782f07718ec1/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-db2ku88c

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b717115a-b537-402c-b4c4-cdde73f86ba9/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-w25w11do

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/1a3289ab-5945-4745-8fcc-44d71c84b44a/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-stubi5xv

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c2b06c23-3960-431d-a6da-3f09cafefd9d/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-odwd2unm

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/65221768-6463-43bb-ab5f-4d84a43a0870/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-fd380ymi

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/0a8f6876-f706-4fd8-a7df-de7926ef6aa4/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-mtc1rz2d

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/88a0f128-77e1-4772-9bf2-2192a49aeca9/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-z0__id_x

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/56271f8f-d64a-4161-88f4-a8a4e0f097b8/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-f8u_mwts

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/dd1a7cd7-aabf-447c-8887-c5ba5253d3e3/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-49wackcf

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/9b0fd72e-2c22-44b4-a385-8b49aac323d0/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-8wu_jwws

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/3db54867-2e39-4c60-bad4-4607836a36c3/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-ycue5_kx

Runni
..
and being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/6260680f-e700-4607-8519-0cbf3096cb28/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-mg1zur5w

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c008e8f8-4f29-4422-afd6-fb9622998485/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-fmu3q72n

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/6e8aae8d-255d-4c8d-a871-d4a4f997bc77/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-3upx37lp

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c8d271a6-10e5-4308-8b83-c4ff6dec6b18/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-v7baioym

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/0cc699b4-fa79-452a-94a6-c28846fdcf58/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-acjc_2d2

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/10da3404-f20d-47c7-bfc6-aa9c08d1f490/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-x7kdtscc

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b2123ea9-ecb9-42d5-a0f8-148f0173ff82/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-lwym9fpf

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/8a13b81a-5130-4dc0-aebb-9c089855aa00/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-a5mkdwiu

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/202e7d12-6ec2-40ac-92e0-9559785b5270/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-3nuuplhm

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a074ae9a-d583-4963-9df6-1fe676b5f1b2/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-jf41c9a2

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/8ce4f4f5-8178-4092-9781-a0df4ee6025e/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-n2e651kh

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/7051b24c-29f6-40b9-816a-d079b18a30ae/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-pt8lnz_l

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/907bf15e-0921-482f-95b4-7c6f1d6aa59d/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-42c9uv67

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/d717855d-47d0-45a1-ba70-760dd2fc936f/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-4fpzpkcu

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/b1521a50-9e68-4bda-8957-a724dec0cdc8/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-8uqtd9p0

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/1b8688a8-3154-4b81-ba94-d0a0a584fa87/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-011s7j32

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c170227a-7c87-4e4d-b1a6-0f5ccf2a1453/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-v2ddnhuf

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/28ec733d-23b2-468d-94b3-722c11238cf2/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-5vvwwhga

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/d4d7f9be-0279-4213-be2e-6608dd3f364b/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-29ka4q5m

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/28b80160-6720-47ab-8485-68f89a8997d4/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-sk82sbcm

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/90dbeb7a-ad2f-4bd5-ae78-4b0076820aba/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-g5osbn7d

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/ee684a84-08b3-4aba-94f3-d186c9b4273f/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-hdz1hpp0

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/8fdd80ab-1b71-42aa-957a-1f0514a8cc26/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-vhflsy2z

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/bee080ab-1121-4202-9c16-6c86f1597192/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-y8q2fpn9

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/a52514c1-a52f-4523-92aa-c035c8554f2e/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-wi3p1iq1

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/500a8859-8ac6-4614-9523-f6b17d575ad9/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-hkgof15f

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/d5f05859-179c-43ee-a747-f8b77431e9dd/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-xlhvzrh7

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/eafca7ab-a8a2-4faf-a8a5-ab5f2680218d/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-cy38gezu

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/91a53ecc-a85a-4fda-8251-f0f609d90b7c/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-eba6u6f8

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/62f3024c-2a42-44a3-8c3f-ac5a0609d0ca/data/feature-table.biom -t /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/data/c1e96f28-86f3-4bdb-b372-8694da0edda5/data/tree.nwk -o /tmp/tmppomf81kc/tmp/qiime2/uid=#1001/processes/52-1747027578.14@uid=#1001/tmp/q2-OutPath-uc1khcmt

Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"4a60fc372eef11f0a452000d3a17e462"`
chromInfo	`"/tmp/tmppomf81kc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- history_id
  - a9671a3be5151c44
- history_state
  - ok
- invocation_id
  - a9671a3be5151c44
- invocation_state
  - scheduled
- workflow_id
  - 0a79a9a95ddd0a22

Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 t…

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Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 to 0.3 #843

Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 to 0.3 #843

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Workflow invocation details

Workflow invocation details

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Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 to 0.3 #843

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Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.2 to 0.3 #843

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Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details

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