github-actions[bot]
commented
2 months ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 2 |
| Passed | 1 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
*❌ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
**Execution Problem:**
* ```
Failed to run workflow, at least one job is in [error] state.
```
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Phylogenetic tree for diversity analysis**: * step_state: scheduled *Subworkflow Steps
- **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpwrqbeckx/job_working_directory/000/6/configs/tmp0jatzhqt' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [04:40:17] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_48/pplacer.backbone.1gxs1x8a.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_48/pplacer.tree.jd5za6is.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_48/pplacer.extended.0.abqt2wcm.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_48/pplacer.extended.0.abqt2wcm.jplace [04:40:23] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_49/pplacer.backbone.k93dra4i.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_49/pplacer.tree.1bd010os.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_49/pplacer.extended.0.yz7ox972.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_49/pplacer.extended.0.yz7ox972.jplace [04:40:27] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_50/pplacer.backbone.6n5c1u3o.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_50/pplacer.tree.cdb5c828.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_50/pplacer.extended.0.s0_wiouz.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_50/pplacer.extended.0.s0_wiouz.jplace [04:40:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_54/pplacer.backbone.4ie5dy_r.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_54/pplacer.tree.sxy9oyos.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_54/pplacer.extended.0.5v9hag9t.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_54/pplacer.extended.0.5v9hag9t.jplace [04:40:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_60/pplacer.backbone.dv0_6jtu.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_60/pplacer.tree.ua6bkif7.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_60/pplacer.extended.0.mse8z4tc.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_60/pplacer.extended.0.mse8z4tc.jplace [04:40:36] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_61/pplacer.backbone.kye6vre5.fasta, tree_file:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_61/pplacer.tree.vcmmyhwd.tre, info_file:/tmp/tmpwrqbeckx/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_61/pplacer.extended.0.ksbqsqyl.fasta, output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef/root/P_61/pplacer.extended.0.ksbqsqyl.jplace [04:41:11] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tmp-8DDTS6PesT/q2-fragment-insertion_placement.json [04:41:13] algorithm.py (line 196): INFO: Current execution Finished in 610 seconds [04:41:13] algorithm.py (line 198): INFO: All checkpointed executions Finished in 610 cumulative time [04:41:13] algorithm.py (line 207): INFO: Temp files are left behind at /tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tempssd-dpJT71x3lS/q2-fragment-insertion.aizszdef ==> sepp-q2-fragment-insertion-out.log <== output files are at q2-fragment-insertion_placement.json q2-fragment-insertion_placement.tog.relabelled.tre q2-fragment-insertion_placement.tog.relabelled.xml q2-fragment-insertion_placement.tog.tre q2-fragment-insertion_placement.tog.xml and more files are at /tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tmp-8DDTS6PesT . Consider removing /tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tmp-8DDTS6PesT if its files are not needed. Removing /tmp/tmpwrqbeckx/tmp/tmp.inucFtCcUs/sepp-tmp-8DDTS6PesT Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "53cb5a53586311ef835e79bd337787c6" ` | | chromInfo | ` "/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | </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>-
Other invocation details
- **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 2b0a1b23e0ff0c7d - **history_state** * error - **invocation_id** * 2b0a1b23e0ff0c7d - **invocation_state** * scheduled - **workflow_id** * 89d2afded7b9e012
Passed Tests
*✅ QIIME2-VI-diversity-metrics-and-estimations.ga_0
#### Workflow invocation details
* Invocation Messages
* ｣
｢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"} ` |
Steps
- **Step 1: Sampling depth**: * step_state: scheduled - **Step 2: Metadata**: * step_state: scheduled - **Step 11: Beta diversity - Jaccard distance matrix**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/19/configs/tmpbufrlhwm' ``` **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: e6a17b55-b199-4948-a9f9-541d71fad240｣ ｢metadata: - **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>-
Other invocation details
- **history_id** * 9b93904bc451528c - **history_state** * ok - **invocation_id** * c41ca451b0165f3b - **invocation_state** * scheduled - **workflow_id** * c41ca451b0165f3b
mvdbeek
gxydevbot
lldelisle
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.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.5.0+q2galaxy.2024.5.0toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2should be updated totoolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.5.0+q2galaxy.2024.5.0The 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.