Open gxydevbot opened 2 months ago
Test State | Count |
---|---|
Total | 2 |
Passed | 1 |
Error | 1 |
Failure | 0 |
Skipped | 0 |
</details>
- **Step 9: Taxonomic analysis**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is error
**Command Line:**
* ```console
q2galaxy run feature_classifier classify_sklearn '/tmp/tmpwrqbeckx/job_working_directory/000/7/configs/tmp_5_bu3ks'
```
**Exit Code:**
* ```console
1
```
**Standard Error:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-amplicon-2024.5/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/__main__.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 152, in _execute_action
return action(**action_kwargs)
File "<decorator-gen-311>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 339, in bound_callable
self.signature.transform_and_add_callable_args_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 396, in transform_and_add_callable_args_to_prov
self._transform_and_add_input_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 429, in _transform_and_add_input_to_prov
transformed_input = _input._view(spec.view_type, recorder)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 406, in _view
result = transformation(self._archiver.data_dir)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 59, in _1
raise ValueError('The scikit-learn version (%s) used to generate this'
ValueError: The scikit-learn version (0.24.1) used to generate this artifact does not match the current version of scikit-learn installed (1.4.2). Please retrain your classifier for your current deployment to prevent data-corruption errors.
```
**Standard Output:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
「reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a」
「classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858」
「reads_per_batch: 'auto'」
「pre_dispatch: '2*n_jobs'」
「confidence: 0.7」
「read_orientation: 'auto'」
```
**Traceback:**
* ```console
```
**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\_\_ | ` "53cb5a54586311ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 6: Taxonomy barplot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**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\_\_ | ` "53cb5a54586311ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 7: Tabulate taxonomy classification**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "53cb5a54586311ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/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"}}] ` |
</details>
</details>
- **Step 10: Rarefaction**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is queued
**Traceback:**
* ```console
```
**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\_\_ | ` "53cb5a55586311ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| max\_depth | ` "2019" ` |
</details>
</details>
</details>
- **Step 12: Beta diversity - Bray-Curtis distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/20/configs/tmpq0tcb5o4'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: 968ee25e-39fa-4c1a-a88b-d6b1d8e2083a」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 13: Emperor plot collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| 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"}]}}] ` |
</details>
- **Step 14: Beta diversity - weighted UniFrac distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/22/configs/tmp48pwplsf'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: ee5af1fb-f8cb-4978-ae81-87d38aca7e82」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 15: PCoA collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| 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"}]}}] ` |
</details>
- **Step 16: Distance matrix collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| 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"}]}}] ` |
</details>
- **Step 17: Richness and evenness collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| 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"}]}}] ` |
</details>
- **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/2024.5.0+dist.he540b0b0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run tools import '/tmp/tmpwrqbeckx/job_working_directory/000/14/configs/tmpumv2f1cx'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
「type: ImmutableMetadata」
「format: ImmutableMetadataFormat」
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |
</details>
- **Step 7: Diversity metrics**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmpwrqbeckx/job_working_directory/000/15/configs/tmpixc7sfl0'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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-2024.5/lib/python3.9/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 -0.011742216606406829 and the largest is 5.215386479954058.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.08997199986316493 and the largest is 4.818783989980348.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.02078465446871078 and the largest is 2.1990190147116433.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.02894878886111258 and the largest is 0.5950124619520928.
warn(
```
**Standard Output:**
* ```console
「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/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/ea55d940-e62c-4eca-b4fd-5d98fdec99f0/data/feature-table.biom -t /tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmpwrqbeckx/tmp/q2-AlphaDiversityFormat-pv5g9_dy
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/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/ea55d940-e62c-4eca-b4fd-5d98fdec99f0/data/feature-table.biom -t /tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmpwrqbeckx/tmp/q2-LSMatFormat-ej2w978r
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/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/ea55d940-e62c-4eca-b4fd-5d98fdec99f0/data/feature-table.biom -t /tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmpwrqbeckx/tmp/q2-LSMatFormat-u4kvxqj8
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:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"ignore_missing_samples": false, "with_replacement": false} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/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" ` |
</details>
- **Step 8: Alpha diversity metrics - Pielou's evenness**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/16/configs/tmpootc2iju'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: 04761deb-ea58-4ac6-afde-433779ec6b08」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/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"}}] ` |
</details>
- **Step 9: Alpha diversity metrics - Observed features**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/17/configs/tmp8hel52hp'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: c206655c-c511-4dde-a62e-09797e82e9ae」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/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"}}] ` |
</details>
- **Step 10: Alpha diversity metrics - Shannon's diversity index**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/18/configs/tmpg1cyo7fc'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: 4bb4d8c3-38b4-4bb3-8409-3541cfbfae14」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "584a17c4586511ef835e79bd337787c6" ` |
| chromInfo | ` "/tmp/tmpwrqbeckx/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"}}] ` |
</details>
</details>
This is the error:
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-amplicon-2024.5/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/__main__.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 152, in _execute_action
return action(**action_kwargs)
File "<decorator-gen-311>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 339, in bound_callable
self.signature.transform_and_add_callable_args_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 396, in transform_and_add_callable_args_to_prov
self._transform_and_add_input_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 429, in _transform_and_add_input_to_prov
transformed_input = _input._view(spec.view_type, recorder)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 406, in _view
result = transformation(self._archiver.data_dir)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 59, in _1
raise ValueError('The scikit-learn version (%s) used to generate this'
ValueError: The scikit-learn version (0.24.1) used to generate this artifact does not match the current version of scikit-learn installed (1.4.2). Please retrain your classifier for your current deployment to prevent data-corruption errors.
Any idea here @bernt-matthias ?
Test State | Count |
---|---|
Total | 2 |
Passed | 1 |
Error | 1 |
Failure | 0 |
Skipped | 0 |
</details>
- **Step 9: Taxonomic analysis**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is error
**Command Line:**
* ```console
q2galaxy run feature_classifier classify_sklearn '/tmp/tmp_4egxnd8/job_working_directory/000/7/configs/tmp4agaa01w'
```
**Exit Code:**
* ```console
1
```
**Standard Error:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-amplicon-2024.5/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/__main__.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 152, in _execute_action
return action(**action_kwargs)
File "<decorator-gen-311>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 339, in bound_callable
self.signature.transform_and_add_callable_args_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 396, in transform_and_add_callable_args_to_prov
self._transform_and_add_input_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 429, in _transform_and_add_input_to_prov
transformed_input = _input._view(spec.view_type, recorder)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 406, in _view
result = transformation(self._archiver.data_dir)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 59, in _1
raise ValueError('The scikit-learn version (%s) used to generate this'
ValueError: The scikit-learn version (0.24.1) used to generate this artifact does not match the current version of scikit-learn installed (1.4.2). Please retrain your classifier for your current deployment to prevent data-corruption errors.
```
**Standard Output:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
「reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a」
「classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858」
「reads_per_batch: 'auto'」
「pre_dispatch: '2*n_jobs'」
「confidence: 0.7」
「read_orientation: 'auto'」
```
**Traceback:**
* ```console
```
**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\_\_ | ` "fecf3ce8609e11efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 6: Taxonomy barplot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**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\_\_ | ` "fecf3ce8609e11efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 7: Tabulate taxonomy classification**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fecf3ce8609e11efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/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"}}] ` |
</details>
</details>
- **Step 10: Rarefaction**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is running
**Command Line:**
* ```console
q2galaxy run diversity alpha_rarefaction '/tmp/tmp_4egxnd8/job_working_directory/000/10/configs/tmpm3cooi20'
```
**Traceback:**
* ```console
```
**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\_\_ | ` "fecf3ce9609e11efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| max\_depth | ` "2019" ` |
</details>
</details>
</details>
- **Step 12: Beta diversity - Bray-Curtis distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/20/configs/tmpzxskbfw1'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: 97ec504d-3ddd-41fb-9be6-9a5005514d6e」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 13: Emperor plot collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| 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"}]}}] ` |
</details>
- **Step 14: Beta diversity - weighted UniFrac distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/22/configs/tmpiyw040m2'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: fecf946e-18d5-4061-91b0-eb04ca7afd4b」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 15: PCoA collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| 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"}]}}] ` |
</details>
- **Step 16: Distance matrix collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| 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"}]}}] ` |
</details>
- **Step 17: Richness and evenness collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| 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"}]}}] ` |
</details>
- **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/2024.5.0+dist.he540b0b0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run tools import '/tmp/tmp_4egxnd8/job_working_directory/000/14/configs/tmptqsxtj32'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
「type: ImmutableMetadata」
「format: ImmutableMetadataFormat」
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |
</details>
- **Step 7: Diversity metrics**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmp_4egxnd8/job_working_directory/000/15/configs/tmpg247u5er'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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-2024.5/lib/python3.9/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 -0.00975452515361931 and the largest is 5.250163073575461.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.09110894389218684 and the largest is 4.808646852428832.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.021825527042658253 and the largest is 2.233502021364367.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.0310210683519113 and the largest is 0.6116012002505453.
warn(
```
**Standard Output:**
* ```console
「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/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a795716d-3937-4ab4-acb3-632725cf91e7/data/feature-table.biom -t /tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmp_4egxnd8/tmp/q2-AlphaDiversityFormat-w25nolvw
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/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a795716d-3937-4ab4-acb3-632725cf91e7/data/feature-table.biom -t /tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmp_4egxnd8/tmp/q2-LSMatFormat-7cywtt74
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/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a795716d-3937-4ab4-acb3-632725cf91e7/data/feature-table.biom -t /tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmp_4egxnd8/tmp/q2-LSMatFormat-v6d4pn4m
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:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"ignore_missing_samples": false, "with_replacement": false} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/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" ` |
</details>
- **Step 8: Alpha diversity metrics - Pielou's evenness**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/16/configs/tmpdosnxdwk'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: f93c4558-302f-4902-a28e-80c63ae8a79e」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/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"}}] ` |
</details>
- **Step 9: Alpha diversity metrics - Observed features**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/17/configs/tmpl1vv9yn0'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: b797bb54-dd78-4946-b96e-3540b4d8a432」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/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"}}] ` |
</details>
- **Step 10: Alpha diversity metrics - Shannon's diversity index**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/18/configs/tmp_xb7770c'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: c64103d6-5d3c-496d-ad4d-d81afdfe3c55」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "083ff46260a111efb9ad9977ff3515d7" ` |
| chromInfo | ` "/tmp/tmp_4egxnd8/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"}}] ` |
</details>
</details>
There are new updates, if you want to integrate them, close the PR and delete branch.
There are new updates, if you want to integrate them, close the PR and delete branch.
There are new updates, if you want to integrate them, close the PR and delete branch.
There are new updates, if you want to integrate them, close the PR and delete branch.
There are new updates, if you want to integrate them, close the PR and delete branch.
There are new updates, they have been integrated to the PR, check the file diff.
Test State | Count |
---|---|
Total | 2 |
Passed | 1 |
Error | 1 |
Failure | 0 |
Skipped | 0 |
</details>
- **Step 9: Taxonomic analysis**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is error
**Command Line:**
* ```console
q2galaxy run feature_classifier classify_sklearn '/tmp/tmpi_mq8140/job_working_directory/000/7/configs/tmpsvyrlyo0'
```
**Exit Code:**
* ```console
1
```
**Standard Error:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-amplicon-2024.5/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/__main__.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 152, in _execute_action
return action(**action_kwargs)
File "<decorator-gen-311>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 339, in bound_callable
self.signature.transform_and_add_callable_args_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 396, in transform_and_add_callable_args_to_prov
self._transform_and_add_input_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 429, in _transform_and_add_input_to_prov
transformed_input = _input._view(spec.view_type, recorder)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 406, in _view
result = transformation(self._archiver.data_dir)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 59, in _1
raise ValueError('The scikit-learn version (%s) used to generate this'
ValueError: The scikit-learn version (0.24.1) used to generate this artifact does not match the current version of scikit-learn installed (1.4.2). Please retrain your classifier for your current deployment to prevent data-corruption errors.
```
**Standard Output:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
「reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a」
「classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858」
「reads_per_batch: 'auto'」
「pre_dispatch: '2*n_jobs'」
「confidence: 0.7」
「read_orientation: 'auto'」
```
**Traceback:**
* ```console
```
**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\_\_ | ` "f3c41ec479ba11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 6: Taxonomy barplot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**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\_\_ | ` "f3c41ec479ba11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 7: Tabulate taxonomy classification**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "f3c41ec479ba11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/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"}}] ` |
</details>
</details>
- **Step 10: Rarefaction**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**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\_\_ | ` "f3c41ec579ba11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| max\_depth | ` "2019" ` |
</details>
</details>
</details>
- **Step 12: Beta diversity - Bray-Curtis distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/20/configs/tmph24tr2lo'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: d38e73dd-7ad8-4c47-aebf-b106f8cf7b53」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 13: Emperor plot collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| 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"}]}}] ` |
</details>
- **Step 14: Beta diversity - weighted UniFrac distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/22/configs/tmpr1sxp0h0'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: d1589056-1c46-4fef-b41f-e2bf5b364882」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 15: PCoA collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| 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"}]}}] ` |
</details>
- **Step 16: Distance matrix collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| 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"}]}}] ` |
</details>
- **Step 17: Richness and evenness collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| 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"}]}}] ` |
</details>
- **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/2024.5.0+dist.he540b0b0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run tools import '/tmp/tmpi_mq8140/job_working_directory/000/14/configs/tmp96wxaak4'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
「type: ImmutableMetadata」
「format: ImmutableMetadataFormat」
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |
</details>
- **Step 7: Diversity metrics**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmpi_mq8140/job_working_directory/000/15/configs/tmpdjnlbin9'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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-2024.5/lib/python3.9/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 -0.011988286356780594 and the largest is 5.249348163803918.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.101688226993198 and the largest is 4.8306845574651.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.022335119428744818 and the largest is 2.2087367279958734.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.02915430115244917 and the largest is 0.607807923535416.
warn(
```
**Standard Output:**
* ```console
「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/tmpi_mq8140/tmp/qiime2/uid=#1001/data/5e08bc17-87e1-4893-b1ce-15926265cb6b/data/feature-table.biom -t /tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmpi_mq8140/tmp/q2-AlphaDiversityFormat-vpjqry6n
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/tmpi_mq8140/tmp/qiime2/uid=#1001/data/5e08bc17-87e1-4893-b1ce-15926265cb6b/data/feature-table.biom -t /tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmpi_mq8140/tmp/q2-LSMatFormat-ao5ycj9s
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/tmpi_mq8140/tmp/qiime2/uid=#1001/data/5e08bc17-87e1-4893-b1ce-15926265cb6b/data/feature-table.biom -t /tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmpi_mq8140/tmp/q2-LSMatFormat-jxjhcjsn
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:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"ignore_missing_samples": false, "with_replacement": false} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/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" ` |
</details>
- **Step 8: Alpha diversity metrics - Pielou's evenness**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/16/configs/tmp782kj2pb'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: 7eeda4d7-9b49-40c1-9d65-bdbb9292c277」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/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"}}] ` |
</details>
- **Step 9: Alpha diversity metrics - Observed features**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/17/configs/tmpv_tqhmld'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: d0f0aea0-1ed4-4788-adfb-a8d703ce65d7」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/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"}}] ` |
</details>
- **Step 10: Alpha diversity metrics - Shannon's diversity index**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/18/configs/tmpaf0_bxi_'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: 0f182372-fa80-4c32-8869-51e85aedd336」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "fd1bc12679bc11efa64a3ff5e2ea4f1a" ` |
| chromInfo | ` "/tmp/tmpi_mq8140/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"}}] ` |
</details>
</details>
There are new updates, they have been integrated to the PR, check the file diff.
Youhou 2 workflows updated at the same time!!
Test State | Count |
---|---|
Total | 2 |
Passed | 1 |
Error | 1 |
Failure | 0 |
Skipped | 0 |
</details>
- **Step 9: Taxonomic analysis**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is error
**Command Line:**
* ```console
q2galaxy run feature_classifier classify_sklearn '/tmp/tmp0g3jfc9u/job_working_directory/000/7/configs/tmpye8h7afn'
```
**Exit Code:**
* ```console
1
```
**Standard Error:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-amplicon-2024.5/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/__main__.py", line 98, in run
action_runner(plugin, action, config)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
results = _execute_action(action, action_kwargs,
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2galaxy/core/drivers/action.py", line 152, in _execute_action
return action(**action_kwargs)
File "<decorator-gen-311>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 339, in bound_callable
self.signature.transform_and_add_callable_args_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 396, in transform_and_add_callable_args_to_prov
self._transform_and_add_input_to_prov(
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 429, in _transform_and_add_input_to_prov
transformed_input = _input._view(spec.view_type, recorder)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 406, in _view
result = transformation(self._archiver.data_dir)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 59, in _1
raise ValueError('The scikit-learn version (%s) used to generate this'
ValueError: The scikit-learn version (0.24.1) used to generate this artifact does not match the current version of scikit-learn installed (1.4.2). Please retrain your classifier for your current deployment to prevent data-corruption errors.
```
**Standard Output:**
* ```console
This plugin encountered an error:
The scikit-learn version (0.24.1)
used to generate this artifact does
not match the current version of
scikit-learn installed (1.4.2).
Please retrain your classifier for
your current deployment to prevent
data-corruption errors.
:(
「reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a」
「classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858」
「reads_per_batch: 'auto'」
「pre_dispatch: '2*n_jobs'」
「confidence: 0.7」
「read_orientation: 'auto'」
```
**Traceback:**
* ```console
```
**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\_\_ | ` "0de251d27a7d11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 6: Taxonomy barplot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**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\_\_ | ` "0de251d27a7d11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
</details>
- **Step 7: Tabulate taxonomy classification**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "0de251d27a7d11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/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"}}] ` |
</details>
</details>
- **Step 10: Rarefaction**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **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
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**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\_\_ | ` "0de251d37a7d11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| max\_depth | ` "2019" ` |
</details>
</details>
</details>
- **Step 12: Beta diversity - Bray-Curtis distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/20/configs/tmpc6x8cbub'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: 998729e6-620b-4859-a9a6-77ab58a5d765」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 13: Emperor plot collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| 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"}]}}] ` |
</details>
- **Step 14: Beta diversity - weighted UniFrac distance matrix**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity beta_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/22/configs/tmp1_u8ezy3'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_diversity/_beta/_visualizer.py:181: 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:**
* ```console
「distance_matrix: 9d66024a-0bbd-4b2f-93b3-d26df15cbb47」
「metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>」
「method: 'permanova'」
「pairwise: False」
「permutations: 999」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"method": "permanova", "pairwise": false, "permutations": "999"} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| metadata | ` {"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"} ` |
</details>
- **Step 15: PCoA collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| 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"}]}}] ` |
</details>
- **Step 16: Distance matrix collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| 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"}]}}] ` |
</details>
- **Step 17: Richness and evenness collection**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| 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"}]}}] ` |
</details>
- **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/2024.5.0+dist.he540b0b0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run tools import '/tmp/tmp0g3jfc9u/job_working_directory/000/14/configs/tmp97_6uh26'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
「type: ImmutableMetadata」
「format: ImmutableMetadataFormat」
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |
</details>
- **Step 7: Diversity metrics**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmp0g3jfc9u/job_working_directory/000/15/configs/tmpf_klp9b4'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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-2024.5/lib/python3.9/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 -0.012360783176750509 and the largest is 5.269766641027056.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.09302798594569282 and the largest is 4.826113652040095.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.020249709938765646 and the largest is 2.2212992124750954.
warn(
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/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 -0.027476618509378478 and the largest is 0.6029259953446836.
warn(
```
**Standard Output:**
* ```console
「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/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/98013c5a-9128-4e2f-98ac-add0c4783ad5/data/feature-table.biom -t /tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmp0g3jfc9u/tmp/q2-AlphaDiversityFormat-9bu2xci7
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/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/98013c5a-9128-4e2f-98ac-add0c4783ad5/data/feature-table.biom -t /tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmp0g3jfc9u/tmp/q2-LSMatFormat-5hwc0jl6
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/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/98013c5a-9128-4e2f-98ac-add0c4783ad5/data/feature-table.biom -t /tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmp0g3jfc9u/tmp/q2-LSMatFormat-s6kfmc6r
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:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"ignore_missing_samples": false, "with_replacement": false} ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/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" ` |
</details>
- **Step 8: Alpha diversity metrics - Pielou's evenness**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/16/configs/tmpc5nguiu9'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: d7110a32-6bef-49f4-a080-70865adb54a3」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/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"}}] ` |
</details>
- **Step 9: Alpha diversity metrics - Observed features**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/17/configs/tmpc5f7rlnz'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: eb73378b-952c-42a0-9d08-0b3f00e08e61」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/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"}}] ` |
</details>
- **Step 10: Alpha diversity metrics - Shannon's diversity index**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/18/configs/tmpixttj0bq'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_types/sample_data/_transformer.py:27: 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:**
* ```console
「alpha_diversity: 4c87e577-4394-46ea-84b8-677b8355efac」
「metadata: <Metadata>」
Saved Visualization to: visualization.qzv
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "20379a5a7a7f11ef8f11c9241a440b00" ` |
| chromInfo | ` "/tmp/tmp0g3jfc9u/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"}}] ` |
</details>
</details>
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/2023.5.0+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.5.0+q2galaxy.2024.5.0
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2
should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.5.0+q2galaxy.2024.5.0
The workflow release number has been updated from 0.1 to 0.2.
The workflow release number has been updated from 0.1 to 0.2.