Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 #498

gxydevbot · 2024-08-12T04:16:38Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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

github-actions · 2024-08-12T04:48:57Z

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:

q2galaxy run fragment_insertion sepp '/tmp/tmpwrqbeckx/job_working_directory/000/6/configs/tmp0jatzhqt'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[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:

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	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmpwrqbeckx/job_working_directory/000/7/configs/tmp_5_bu3ks'

Exit Code:

```
1
```

Standard 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.

Standard Output:

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:

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	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"53cb5a54586311ef835e79bd337787c6"`
chromInfo	`"/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"53cb5a55586311ef835e79bd337787c6"`
chromInfo	`"/tmp/tmpwrqbeckx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

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

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/19/configs/tmpbufrlhwm'

Exit Code:

```
0
```

Standard Error:

/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:

｢distance_matrix: e6a17b55-b199-4948-a9f9-541d71fad240｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"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"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/20/configs/tmpq0tcb5o4'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/22/configs/tmp48pwplsf'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

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"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

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

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpwrqbeckx/job_working_directory/000/14/configs/tmpumv2f1cx'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

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"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmpwrqbeckx/job_working_directory/000/15/configs/tmpixc7sfl0'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/16/configs/tmpootc2iju'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: 04761deb-ea58-4ac6-afde-433779ec6b08｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/17/configs/tmp8hel52hp'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: c206655c-c511-4dde-a62e-09797e82e9ae｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpwrqbeckx/job_working_directory/000/18/configs/tmpg1cyo7fc'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: 4bb4d8c3-38b4-4bb3-8409-3541cfbfae14｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Other invocation details
- history_id
  - 9b93904bc451528c
- history_state
  - ok
- invocation_id
  - c41ca451b0165f3b
- invocation_state
  - scheduled
- workflow_id
  - c41ca451b0165f3b

mvdbeek · 2024-08-12T08:38:51Z

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 ?

github-actions · 2024-08-22T16:17:32Z

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:

q2galaxy run fragment_insertion sepp '/tmp/tmp_4egxnd8/job_working_directory/000/6/configs/tmpaeac_3i8'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[16:07:34] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_48/pplacer.backbone.wbza5ex7.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_48/pplacer.tree.l_hkb6yx.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_48/pplacer.extended.0.jcm55rum.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_48/pplacer.extended.0.jcm55rum.jplace
[16:07:41] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_49/pplacer.backbone.cvc8cwtq.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_49/pplacer.tree.5f0jd2av.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_49/pplacer.extended.0.drr8cvo0.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_49/pplacer.extended.0.drr8cvo0.jplace
[16:07:45] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_50/pplacer.backbone.akx9o100.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_50/pplacer.tree.0zh9tie9.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_50/pplacer.extended.0._o69js_5.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_50/pplacer.extended.0._o69js_5.jplace
[16:07:48] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_54/pplacer.backbone.8ap4fy90.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_54/pplacer.tree.b5ap00w5.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_54/pplacer.extended.0.2tpiksbr.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_54/pplacer.extended.0.2tpiksbr.jplace
[16:07:51] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_60/pplacer.backbone.oihp79p6.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_60/pplacer.tree.ubeezlsv.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_60/pplacer.extended.0.z5lmq_a6.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_60/pplacer.extended.0.z5lmq_a6.jplace
[16:07:54] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_61/pplacer.backbone.qn58bo22.fasta, tree_file:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_61/pplacer.tree.t7c0lb78.tre, info_file:/tmp/tmp_4egxnd8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_61/pplacer.extended.0.4s07fl_o.fasta, output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56/root/P_61/pplacer.extended.0.4s07fl_o.jplace
[16:08:30] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tmp-iPF91lmQz4/q2-fragment-insertion_placement.json
[16:08:32] algorithm.py (line 196):     INFO: Current execution Finished in 619 seconds
[16:08:32] algorithm.py (line 198):     INFO: All checkpointed executions Finished in 619 cumulative time
[16:08:32] algorithm.py (line 207):     INFO: Temp files are left behind at /tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tempssd-XEooMwPsnK/q2-fragment-insertion.cvaswf56

==> 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/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tmp-iPF91lmQz4 . Consider removing /tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tmp-iPF91lmQz4 if its files are not needed.
Removing /tmp/tmp_4egxnd8/tmp/tmp.hffzqdseZd/sepp-tmp-iPF91lmQz4
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"fecf3ce7609e11efb9ad9977ff3515d7"`
chromInfo	`"/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmp_4egxnd8/job_working_directory/000/7/configs/tmp4agaa01w'

Exit Code:

```
1
```

Standard 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.

Standard Output:

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:

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	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"fecf3ce8609e11efb9ad9977ff3515d7"`
chromInfo	`"/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

q2galaxy run diversity alpha_rarefaction '/tmp/tmp_4egxnd8/job_working_directory/000/10/configs/tmpm3cooi20'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"fecf3ce9609e11efb9ad9977ff3515d7"`
chromInfo	`"/tmp/tmp_4egxnd8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 992ad748fa45d2ac
- history_state
  - error
- invocation_id
  - 992ad748fa45d2ac
- invocation_state
  - scheduled
- workflow_id
  - 2992b73dbc619cf5

Passed Tests

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

Workflow invocation details

Invocation Messages

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/19/configs/tmpahyln7kp'

Exit Code:

```
0
```

Standard Error:

/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:

｢distance_matrix: 9c9cbe09-7a4e-4ee6-8db5-d9bfd8a79701｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"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"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/20/configs/tmpzxskbfw1'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/22/configs/tmpiyw040m2'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

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"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

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

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp_4egxnd8/job_working_directory/000/14/configs/tmptqsxtj32'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

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"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmp_4egxnd8/job_working_directory/000/15/configs/tmpg247u5er'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/16/configs/tmpdosnxdwk'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: f93c4558-302f-4902-a28e-80c63ae8a79e｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/17/configs/tmpl1vv9yn0'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: b797bb54-dd78-4946-b96e-3540b4d8a432｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp_4egxnd8/job_working_directory/000/18/configs/tmp_xb7770c'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: c64103d6-5d3c-496d-ad4d-d81afdfe3c55｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Other invocation details
- history_id
  - c328fcbebfd7714e
- history_state
  - ok
- invocation_id
  - cc5354ff594645c2
- invocation_state
  - scheduled
- workflow_id
  - cc5354ff594645c2

gxydevbot · 2024-08-26T04:28:35Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-02T04:32:16Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-09T04:30:40Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-16T04:28:55Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T04:32:54Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T14:08:59Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:09:17Z

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:

q2galaxy run fragment_insertion sepp '/tmp/tmpi_mq8140/job_working_directory/000/6/configs/tmpy3x_j68j'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[15:00:45] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_48/pplacer.backbone._iq5hj7r.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_48/pplacer.tree.9ta8sdj3.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_48/pplacer.extended.0.0iop85di.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_48/pplacer.extended.0.0iop85di.jplace
[15:00:51] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_49/pplacer.backbone.j1jbgqq1.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_49/pplacer.tree.2c0hcnli.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_49/pplacer.extended.0.b7kmkxf5.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_49/pplacer.extended.0.b7kmkxf5.jplace
[15:00:56] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_50/pplacer.backbone.ts2fj060.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_50/pplacer.tree.h8jy8bl5.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_50/pplacer.extended.0.tq5y2af8.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_50/pplacer.extended.0.tq5y2af8.jplace
[15:00:59] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_54/pplacer.backbone.3byu4_h9.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_54/pplacer.tree.f3ffdw9f.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_54/pplacer.extended.0.crgquz3l.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_54/pplacer.extended.0.crgquz3l.jplace
[15:01:01] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_60/pplacer.backbone.eivtv3ho.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_60/pplacer.tree.r1vw1syc.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_60/pplacer.extended.0.76pwt_cn.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_60/pplacer.extended.0.76pwt_cn.jplace
[15:01:05] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_61/pplacer.backbone.qf9urvv9.fasta, tree_file:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_61/pplacer.tree.c_qysvtw.tre, info_file:/tmp/tmpi_mq8140/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_61/pplacer.extended.0._xgf642m.fasta, output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k/root/P_61/pplacer.extended.0._xgf642m.jplace
[15:01:41] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tmp-oKpnOKZyQ6/q2-fragment-insertion_placement.json
[15:01:43] algorithm.py (line 196):     INFO: Current execution Finished in 619 seconds
[15:01:43] algorithm.py (line 198):     INFO: All checkpointed executions Finished in 619 cumulative time
[15:01:43] algorithm.py (line 207):     INFO: Temp files are left behind at /tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tempssd-zWQNzZGwiv/q2-fragment-insertion.67au8k8k

==> 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/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tmp-oKpnOKZyQ6 . Consider removing /tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tmp-oKpnOKZyQ6 if its files are not needed.
Removing /tmp/tmpi_mq8140/tmp/tmp.KQ1n2FBlFZ/sepp-tmp-oKpnOKZyQ6
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"f3c41ec379ba11efa64a3ff5e2ea4f1a"`
chromInfo	`"/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmpi_mq8140/job_working_directory/000/7/configs/tmpsvyrlyo0'

Exit Code:

```
1
```

Standard 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.

Standard Output:

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:

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	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"f3c41ec479ba11efa64a3ff5e2ea4f1a"`
chromInfo	`"/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"f3c41ec579ba11efa64a3ff5e2ea4f1a"`
chromInfo	`"/tmp/tmpi_mq8140/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 722a690baa4e9232
- history_state
  - error
- invocation_id
  - 722a690baa4e9232
- invocation_state
  - scheduled
- workflow_id
  - 65b0255a3f08c5f8

Passed Tests

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

Workflow invocation details

Invocation Messages

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/19/configs/tmpkbukpmdg'

Exit Code:

```
0
```

Standard Error:

/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:

｢distance_matrix: ddbd5b13-7d2f-493d-9229-a4d5a9ab666c｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"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"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/20/configs/tmph24tr2lo'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/22/configs/tmpr1sxp0h0'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

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"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

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

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpi_mq8140/job_working_directory/000/14/configs/tmp96wxaak4'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

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"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmpi_mq8140/job_working_directory/000/15/configs/tmpdjnlbin9'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/16/configs/tmp782kj2pb'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: 7eeda4d7-9b49-40c1-9d65-bdbb9292c277｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/17/configs/tmpv_tqhmld'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: d0f0aea0-1ed4-4788-adfb-a8d703ce65d7｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpi_mq8140/job_working_directory/000/18/configs/tmpaf0_bxi_'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: 0f182372-fa80-4c32-8869-51e85aedd336｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Other invocation details
- history_id
  - 7d2c5d9c7bed683f
- history_state
  - ok
- invocation_id
  - 1f3540163abdebfe
- invocation_state
  - scheduled
- workflow_id
  - 1f3540163abdebfe

gxydevbot · 2024-09-24T13:49:41Z

There are new updates, they have been integrated to the PR, check the file diff.

lldelisle · 2024-09-24T13:56:16Z

Youhou 2 workflows updated at the same time!!

github-actions · 2024-09-24T14:18:20Z

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:

q2galaxy run fragment_insertion sepp '/tmp/tmp0g3jfc9u/job_working_directory/000/6/configs/tmpvsw0xqh2'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[14:10:14] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_48/pplacer.backbone.q8bsb4la.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_48/pplacer.tree.lf_yds43.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_48/pplacer.extended.0._i6l_gk4.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_48/pplacer.extended.0._i6l_gk4.jplace
[14:10:21] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_49/pplacer.backbone.4lu3pllh.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_49/pplacer.tree.t1qf6zmp.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_49/pplacer.extended.0.e64tnk73.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_49/pplacer.extended.0.e64tnk73.jplace
[14:10:25] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_50/pplacer.backbone.vsu7uv5j.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_50/pplacer.tree.z772mmf9.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_50/pplacer.extended.0.31367roe.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_50/pplacer.extended.0.31367roe.jplace
[14:10:28] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_54/pplacer.backbone.u6f5h9cl.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_54/pplacer.tree.f2kyllxa.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_54/pplacer.extended.0.v9xvc69x.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_54/pplacer.extended.0.v9xvc69x.jplace
[14:10:31] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_60/pplacer.backbone.1egshtx_.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_60/pplacer.tree.vn1558rl.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_60/pplacer.extended.0.qhmiu9hx.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_60/pplacer.extended.0.qhmiu9hx.jplace
[14:10:34] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_61/pplacer.backbone.bng34os3.fasta, tree_file:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_61/pplacer.tree.hvs14tyo.tre, info_file:/tmp/tmp0g3jfc9u/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_61/pplacer.extended.0.ni0dmkqp.fasta, output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo/root/P_61/pplacer.extended.0.ni0dmkqp.jplace
[14:11:12] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tmp-pI0zmUz5Gl/q2-fragment-insertion_placement.json
[14:11:14] algorithm.py (line 196):     INFO: Current execution Finished in 627 seconds
[14:11:14] algorithm.py (line 198):     INFO: All checkpointed executions Finished in 627 cumulative time
[14:11:14] algorithm.py (line 207):     INFO: Temp files are left behind at /tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tempssd-uguLcWHWMg/q2-fragment-insertion.bwkyi3oo

==> 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/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tmp-pI0zmUz5Gl . Consider removing /tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tmp-pI0zmUz5Gl if its files are not needed.
Removing /tmp/tmp0g3jfc9u/tmp/tmp.tDBM4jbf6V/sepp-tmp-pI0zmUz5Gl
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"0de251d17a7d11ef8f11c9241a440b00"`
chromInfo	`"/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmp0g3jfc9u/job_working_directory/000/7/configs/tmpye8h7afn'

Exit Code:

```
1
```

Standard 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.

Standard Output:

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:

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	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"0de251d27a7d11ef8f11c9241a440b00"`
chromInfo	`"/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"0de251d37a7d11ef8f11c9241a440b00"`
chromInfo	`"/tmp/tmp0g3jfc9u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - b0bd5651c6206d96
- history_state
  - error
- invocation_id
  - b0bd5651c6206d96
- invocation_state
  - scheduled
- workflow_id
  - 7048359c644d5db2

Passed Tests

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

Workflow invocation details

Invocation Messages

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/19/configs/tmpifatv7ju'

Exit Code:

```
0
```

Standard Error:

/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:

｢distance_matrix: c24162c7-094e-4af7-9d5d-b39128d2ba04｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"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"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/20/configs/tmpc6x8cbub'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/22/configs/tmp1_u8ezy3'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

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"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"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"}]}}]

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

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp0g3jfc9u/job_working_directory/000/14/configs/tmp97_6uh26'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

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"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmp0g3jfc9u/job_working_directory/000/15/configs/tmpf_klp9b4'

Exit Code:

```
0
```

Standard Error:

/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:

｢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:

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"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/16/configs/tmpc5nguiu9'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: d7110a32-6bef-49f4-a080-70865adb54a3｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/17/configs/tmpc5f7rlnz'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: eb73378b-952c-42a0-9d08-0b3f00e08e61｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp0g3jfc9u/job_working_directory/000/18/configs/tmpixttj0bq'

Exit Code:

```
0
```

Standard Error:

/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:

｢alpha_diversity: 4c87e577-4394-46ea-84b8-677b8355efac｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

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"}}]`

Other invocation details
- history_id
  - b9411eadefc9f988
- history_state
  - ok
- invocation_id
  - 65344635f770f36f
- invocation_state
  - scheduled
- workflow_id
  - 65344635f770f36f

…o 0.2

gxydevbot · 2024-11-04T04:32:01Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-11-04T04:59:47Z

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:

q2galaxy run fragment_insertion sepp '/tmp/tmp1m3tq5ie/job_working_directory/000/6/configs/tmpsnq7wtsa'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[04:53:06] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_48/pplacer.backbone.0xj0y3xk.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_48/pplacer.tree.jod8zhnh.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_48/pplacer.extended.0.2dckkb2y.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_48/pplacer.extended.0.2dckkb2y.jplace
[04:53:12] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_49/pplacer.backbone.yhh68iuh.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_49/pplacer.tree.o2u7hw3b.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_49/pplacer.extended.0.d3b4axdv.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_49/pplacer.extended.0.d3b4axdv.jplace
[04:53:16] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_50/pplacer.backbone.x6qn8l7p.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_50/pplacer.tree.57_r5o3q.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_50/pplacer.extended.0.pu2wc084.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_50/pplacer.extended.0.pu2wc084.jplace
[04:53:19] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_54/pplacer.backbone.xaydifq0.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_54/pplacer.tree.4zicyvb_.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_54/pplacer.extended.0.hvrbavmc.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_54/pplacer.extended.0.hvrbavmc.jplace
[04:53:22] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_60/pplacer.backbone.3q6u15o6.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_60/pplacer.tree.aw07ksri.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_60/pplacer.extended.0.olju17hd.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_60/pplacer.extended.0.olju17hd.jplace
[04:53:25] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_61/pplacer.backbone.bq04ig3y.fasta, tree_file:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_61/pplacer.tree.b7bc90jt.tre, info_file:/tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_61/pplacer.extended.0.o0618tle.fasta, output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e/root/P_61/pplacer.extended.0.o0618tle.jplace
[04:54:01] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tmp-ms4KRzia0v/q2-fragment-insertion_placement.json
[04:54:03] algorithm.py (line 213):     INFO: Current execution Finished in 586 seconds
[04:54:03] algorithm.py (line 215):     INFO: All checkpointed executions Finished in 586 cumulative time
[04:54:03] algorithm.py (line 224):     INFO: Temp files are left behind at /tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tempssd-I94ACZIRcZ/q2-fragment-insertion.0yter31e

==> sepp-q2-fragment-insertion-out.log <==
root_p='/opt/conda/envs/qiime2-amplicon-2024.10/share/sepp/sepp'
output files are at q2-fragment-insertion_placement.json q2-fragment-insertion_placement.tog.relabelled.tre q2-fragment-insertion_placement.tog.relabelled.xml q2-fragment-insertion_placement.tog.tre q2-fragment-insertion_placement.tog.xml and more files are at /tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tmp-ms4KRzia0v . Consider removing /tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tmp-ms4KRzia0v if its files are not needed.
Removing /tmp/tmp1m3tq5ie/tmp/tmp.GRvFOaCzqN/sepp-tmp-ms4KRzia0v
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"19f815ff9a6711ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmp1m3tq5ie/job_working_directory/000/7/configs/tmpxm60usj3'

Exit Code:

```
1
```

Standard 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-2024.10/bin/q2galaxy", line 11, in <module>
    sys.exit(root())
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2galaxy/__main__.py", line 98, in run
    action_runner(plugin, action, config)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2galaxy/core/drivers/action.py", line 31, in action_runner
    results = _execute_action(action, action_kwargs,
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
    return function(*args, **kwargs)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/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-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 296, in bound_callable
    self.signature.transform_and_add_callable_args_to_prov(
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 401, in transform_and_add_callable_args_to_prov
    self._transform_and_add_input_to_prov(
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 434, in _transform_and_add_input_to_prov
    transformed_input = _input._view(spec.view_type, recorder)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 420, in _view
    result = transformation(self._archiver.data_dir)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 70, in transformation
    new_view = transformer(view)
  File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/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:

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:

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__	`"19f816009a6711ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"19f816009a6711ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"19f816009a6711ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`[{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"19f816019a6711ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 2fe8ef0de6784092
- history_state
  - error
- invocation_id
  - 2fe8ef0de6784092
- invocation_state
  - scheduled
- workflow_id
  - 7303aed5af6a8923

Passed Tests

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

Workflow invocation details

Invocation Messages

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/19/configs/tmpu9irz4wf'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 089d77b7-ccb8-43e4-ae33-bd20d8388451｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/20/configs/tmp_a4xg2f0'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 5a8e4c1a-7a45-4d38-a132-f30843acc4b2｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 29, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 30, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 31, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 32, "src": "hda"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/22/configs/tmpnn4f037j'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 366fe256-5dc8-45e3-a489-8bbff2b76256｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 28, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 26, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 25, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 27, "src": "hda"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 24, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 22, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 21, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 23, "src": "hda"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "rarefied_table"}, "input": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "faith_pd_vector"}, "input": {"values": [{"id": 17, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "observed_features_vector"}, "input": {"values": [{"id": 18, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "shannon_vector"}, "input": {"values": [{"id": 20, "src": "hda"}]}}, {"__index__": 4, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "eveness_vector"}, "input": {"values": [{"id": 19, "src": "hda"}]}}]

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

Step 6: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp1m3tq5ie/job_working_directory/000/14/configs/tmp5nx3xq4y'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 58, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmp1m3tq5ie/job_working_directory/000/15/configs/tmpbyovuvuw'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
  warn(f"{func.__name__} is deprecated as of {ver}.")
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.009778913164700325 and the largest is 5.211357714408949.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.08824245824800393 and the largest is 4.8280724273827005.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.022133707291771255 and the largest is 2.1668533967018413.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.02734134562638538 and the largest is 0.6265284251274377.
  warn(

Standard Output:

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

Command:

faithpd -i /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/97e21b03-7d39-4bc3-9173-90d2e8874a4a/data/feature-table.biom -t /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/processes/23-1730696169.29@uid=#1001/tmp/q2-OutPath-obryff_t

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/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/97e21b03-7d39-4bc3-9173-90d2e8874a4a/data/feature-table.biom -t /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/processes/23-1730696169.29@uid=#1001/tmp/q2-OutPath-js6j_jgl

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/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/97e21b03-7d39-4bc3-9173-90d2e8874a4a/data/feature-table.biom -t /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmp1m3tq5ie/tmp/qiime2/uid=#1001/processes/23-1730696169.29@uid=#1001/tmp/q2-OutPath-7rqu2vs8

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"ignore_missing_samples": false, "with_replacement": false}`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`
sampling_depth	`"2000"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/16/configs/tmp61u68jy3'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: d6e3ab06-5ff0-4e58-a06a-b7dca2d789ab｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/17/configs/tmp7gow50n5'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: ac4eb1c6-26b8-481b-a6de-b7d3a0fc5f1b｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmp1m3tq5ie/job_working_directory/000/18/configs/tmpjofwlj5f'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: f509ea63-1e4a-4df3-bd84-7c7b0c38d02b｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f17d19a9a6911ef93a121a68daad63c"`
chromInfo	`"/tmp/tmp1m3tq5ie/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Other invocation details
- history_id
  - d36726ed74b536ef
- history_state
  - ok
- invocation_id
  - 3c5f0d82a87d6e30
- invocation_state
  - scheduled
- workflow_id
  - 3c5f0d82a87d6e30

github-actions · 2024-11-23T19:21:27Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

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

Problems:

Output with path /tmp/tmphxbgjqdt/taxonomy_classification__82913fe5-afb1-42f7-b23c-2fa76d9a38fa different than expected
Expected file size to be in [70k:80k] found 52534

Workflow invocation details

Invocation Messages

Steps

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

Step 8: Phylogenetic tree for diversity analysis:

step_state: scheduled

Subworkflow Steps

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

Step 3: Phylogenetic tree generation:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run fragment_insertion sepp '/tmp/tmpktfgor32/job_working_directory/000/6/configs/tmpih407znp'

Exit Code:

```
0
```

Standard Output:

｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣
｢alignment_subset_size: 1000｣
｢placement_subset_size: 5000｣
｢debug: False｣
                                                                                                                                                                                                                                                               
==> sepp-q2-fragment-insertion-err.log <==
[19:12:51] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_48/pplacer.backbone.j2f5uw0l.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_48/pplacer.tree.oa0y93cz.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_48/pplacer.extended.0.s76a35zm.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_48/pplacer.extended.0.s76a35zm.jplace
[19:12:57] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_49/pplacer.backbone.rqeq8iqs.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_49/pplacer.tree.hjip6wph.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_49/pplacer.extended.0.hcjax3e5.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_49/pplacer.extended.0.hcjax3e5.jplace
[19:13:01] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_50/pplacer.backbone.ehkxpd2u.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_50/pplacer.tree.1dhrr4wg.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_50/pplacer.extended.0.kdpallcv.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_50/pplacer.extended.0.kdpallcv.jplace
[19:13:03] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_54/pplacer.backbone.w8ldvjdu.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_54/pplacer.tree.p1yyvn55.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_54/pplacer.extended.0.fh527il_.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_54/pplacer.extended.0.fh527il_.jplace
[19:13:06] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_60/pplacer.backbone.w2rtmqcs.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_60/pplacer.tree.zdg9ebqt.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_60/pplacer.extended.0.yuqhepc8.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_60/pplacer.extended.0.yuqhepc8.jplace
[19:13:09] jobs.py (line 131):     INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_61/pplacer.backbone.gqatld_j.fasta, tree_file:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_61/pplacer.tree.7lfvi1e7.tre, info_file:/tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_61/pplacer.extended.0.606r4_b2.fasta, output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f/root/P_61/pplacer.extended.0.606r4_b2.jplace
[19:13:44] jobs.py (line 131):     INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tmp-n5cIqJ1Z0U/q2-fragment-insertion_placement.json
[19:13:46] algorithm.py (line 213):     INFO: Current execution Finished in 582 seconds
[19:13:46] algorithm.py (line 215):     INFO: All checkpointed executions Finished in 582 cumulative time
[19:13:46] algorithm.py (line 224):     INFO: Temp files are left behind at /tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tempssd-VYehUMWB1m/q2-fragment-insertion.vbqvk7_f

==> sepp-q2-fragment-insertion-out.log <==
root_p='/opt/conda/envs/qiime2-amplicon-2024.10/share/sepp/sepp'
output files are at q2-fragment-insertion_placement.json q2-fragment-insertion_placement.tog.relabelled.tre q2-fragment-insertion_placement.tog.relabelled.xml q2-fragment-insertion_placement.tog.tre q2-fragment-insertion_placement.tog.xml and more files are at /tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tmp-n5cIqJ1Z0U . Consider removing /tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tmp-n5cIqJ1Z0U if its files are not needed.
Removing /tmp/tmpktfgor32/tmp/tmp.hrswo3vCc9/sepp-tmp-n5cIqJ1Z0U
Saved Phylogeny[Rooted] to: tree.qza
Saved Placements to: placements.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000"}`
__workflow_invocation_uuid__	`"4d863ea9a9cd11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Taxonomic analysis:

step_state: scheduled

Subworkflow Steps

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

Step 5: Taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_classifier classify_sklearn '/tmp/tmpktfgor32/job_working_directory/000/7/configs/tmp1266ts_f'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "pre_dispatch": "2*n_jobs", "read_orientation": "auto"}`
__workflow_invocation_uuid__	`"4d863eaaa9cd11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: Taxonomy barplot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run taxa barplot '/tmp/tmpktfgor32/job_working_directory/000/8/configs/tmpe2kij2nq'

Exit Code:

```
0
```

Standard Output:

｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
｢taxonomy: 80f23d06-9960-4963-bac9-b120677f4143｣
｢metadata: <Metadata>｣
｢level_delimiter: None｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}}`
__workflow_invocation_uuid__	`"4d863eaaa9cd11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Tabulate taxonomy classification:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmpktfgor32/job_working_directory/000/9/configs/tmp2vabztip'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"4d863eaaa9cd11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`[{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}]`

Step 10: Rarefaction:

step_state: scheduled

Subworkflow Steps

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

Step 6: Alpha rarefaction:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_rarefaction '/tmp/tmpktfgor32/job_working_directory/000/10/configs/tmpqhu5w34j'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
  warn(f"{func.__name__} is deprecated as of {ver}.")
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecate
..
ntation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:260: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  summary_df = data.stack(level=0)
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_alpha/_visualizer.py:265: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  stacked_counts = counts.stack(level=0)

Standard Output:

｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
｢max_depth: 2019｣
｢phylogeny: 0073fde0-1e6c-4291-a889-323dbbac9549｣
｢metrics: None｣
｢metadata: <Metadata>｣
｢min_depth: 1｣
｢steps: 10｣
｢iterations: 10｣
                                                                                                                                                                                                                                                               
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/24c2a92c-ecb0-41f1-afca-135f59a90e80/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-rb2a8v24

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/2179c7e2-0f54-46d6-a569-fa848aa4cb3d/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-ukyc0o7i

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/233e450b-1813-4ac0-bad9-68f4b60f7911/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-k7b9ee_d

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/5a51ee8a-69ef-43df-a936-6e573475ea48/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-m68qe55_

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/292abf15-70fb-414a-af74-1d7c3230a424/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-43aq84ey

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/89e59448-4ab6-4abc-af61-52bfdcc4569c/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-rtj7wxfp

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/f439ef19-f795-4396-aeb6-63487803092a/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-ffzdcs5u

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/710733c7-06ab-4274-9c6e-ad85942e2538/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-idl8c5bg

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/b290531d-611f-4135-a015-c9ef1dee4c5c/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-cf72a005

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/04947d58-4baf-404f-bb9e-4fa1d35f2631/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-525pz92l

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/ba3f1914-96ca-4ca6-8c22-ad32b6e8ca9a/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-hdjs8s9j

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/dd1473e2-200c-4d55-913a-0e030e362f8f/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-_z7fbu71

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/1b05b453-b46e-4ea3-b7ea-a345d053e536/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-0fnjwodm

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/26de0475-47be-4a0e-8c48-6193e4795792/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-2xy5zh8h

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/e376cd45-394c-4852-9756-fcea83ca67d9/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-y5zvehk6

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/404705ad-1d93-4c5e-950c-079cd29df3f1/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-u7pngspb

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/4902c66d-e5a8-41e4-8869-61b8d72f86de/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-90yy_rig

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/27c6d2f4-bbc2-4222-b039-e14732b08498/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-60udeyb2

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/eee3c18f-fb2a-497c-a51b-cad7b2e08189/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-0c2dl4ss

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/4ce57091-73b0-4d72-b3e2-c0aa25ed16e3/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-kfszdm5t

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/22c0310b-7cc8-4168-ad15-d4e657a751db/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-25666iu0

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/76716f07-6ce2-45ff-9fef-b2ab20613058/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-fd3gjar9

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/918bf59d-86c9-4b12-8aea-a2200104f328/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-y55m1dij

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/e0f4ce5c-4dab-4ffe-aec4-7443cc1d9936/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-3km9_gwm

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/8254cc35-ca6b-40e2-b706-b4143e802ce6/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-3evtv6hm

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/e4fc7881-403a-48b6-ad23-35f8415463eb/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-30669ogy

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/4fb74393-4c38-432e-88e5-1d8f0b6057e7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-837mvl7w

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/3eddeffd-bf18-4b6e-943b-428b125256f7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-yr8oq4w9

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/5e8b6a5c-2f97-455a-975d-e6eeb27ba3ee/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-anqvd0ly

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

Command:

faithpd -i /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/de22a53f-9c46-4944-b41a-6e9696e8ba22/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-s6tfw2y7

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/685b0bf2-2a0a-410f-9091-61c9b6ddf5f9/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-uip0ljtc

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/d2aaa8a1-e867-4cca-b9b0-b2883ceedb58/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-v46arhmw

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/e8bfe22a-ad30-458c-9736-ab41b6018f03/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-og4no54p

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/ab467a99-9f9a-464c-acab-0444a95e2794/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-vfl7bc_9

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/839d6e52-d9c8-48ba-8363-f7c9d1c11334/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-uayvncvj

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/5b8b74b3-e2b8-4bcc-bc58-dcaf91ac38d6/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-24yqccm0

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/506a1ab3-d322-43dc-a46b-974ee8f74f7a/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-4b5yi3bm

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/3ee2f3a8-238d-40e9-9b19-f59d8c505f2a/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-csbwk174

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/8a66d3c6-9b6e-4828-b31b-e79db7c39f9a/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-_32zc4lu

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/abe5b9ea-9c98-443e-87b4-a63f6c0e2169/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-kidv_slg

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/dd56449a-9c59-4338-b77a-586e1f6d4b26/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-ds2m7m9k

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/fc8b9e79-f82d-4320-beb0-4d957d9b01e7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-c5l7aq6b

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/0f13edaa-288f-4781-a5d0-5c7f49838e1c/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-3szhqy2e

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/c65f1a3f-abe8-4e63-8c89-889e11deaebc/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-gqvawfby

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/84ea1025-418c-4216-a994-25a15ae09ffd/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-3dxb51ov

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/48d07a74-116c-4e24-abe5-41955692c06f/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-vcrkqfwq

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/075d3775-978e-44bb-acf5-b7eeff46793e/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-q1x3vpgo

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/b8eed5bd-5297-41c8-ae66-3b83e1b1ade7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-nyq7glby

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/d9eb4c39-5966-42c1-9add-598c004ae2ca/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-mdtti529

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/d6136015-559d-4188-8ffa-a4b8efbb90ab/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-1c9yy9cw

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/ea2d8998-4cf4-4e52-a0a1-46a8dbf9abf2/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-g6_3xh_q

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/a6ee0a91-e205-43cf-9b99-2d685f84c9cc/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-o7szk37u

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/e769ec0a-fe42-449c-9f3c-1497893257d7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-63re9nvf

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/de78ad85-22fe-457b-83bb-d330e41929fa/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-hb19liep

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/670d541b-6ca4-4dc0-a8a3-cb94c6376aa0/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-hw5pwky7

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/5edd5bc2-354a-44c8-b16d-c63fed765513/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-gj4haca8

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/95acd278-a3d3-4d4f-bd34-9b0f896949b7/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-thuwoffv

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/78ef9c4a-837d-4e3b-a804-647b20783348/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-jp4mh9lt

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/9b957221-9f11-4b1e-8ca6-3b4065261a7e/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/5100f290-16e6-4bd2-b1ce-2af4c4214df9/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/24-1732389311.05@uid=#1001/tmp/q2-OutPath-hg9g2f0q

Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"}`
__workflow_invocation_uuid__	`"4d863eaba9cd11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
max_depth	`"2019"`

Other invocation details
- history_id
  - 3fe08938d224cac0
- history_state
  - ok
- invocation_id
  - 3fe08938d224cac0
- invocation_state
  - scheduled
- workflow_id
  - ff6e1a33cc042d92

Passed Tests

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

Workflow invocation details

Invocation Messages

Steps

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

Step 11: Beta diversity - Jaccard distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpktfgor32/job_working_directory/000/19/configs/tmp06le0jz7'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 73a0a3c7-f234-467b-b751-37ab2b6bcc86｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpktfgor32/job_working_directory/000/20/configs/tmpgo9qgro5'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 7cf94112-915d-4154-b5d0-f9ccb2b6ec10｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 13: Emperor plot collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 29, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 30, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 31, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 32, "src": "hda"}]}}]

Step 14: Beta diversity - weighted UniFrac distance matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity beta_group_significance '/tmp/tmpktfgor32/job_working_directory/000/22/configs/tmpiiuptlkx'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_beta/_visualizer.py:174: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  pairs_summary = pd.concat([pairs_summary, group_pairs_summary])

Standard Output:

｢distance_matrix: 333de73c-d369-400d-bdd6-64da67d2f100｣
｢metadata: <CategoricalMetadataColumn name='cage_id' id_count=48>｣
｢method: 'permanova'｣
｢pairwise: False｣
｢permutations: 999｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"method": "permanova", "pairwise": false, "permutations": "999"}`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`{"__current_case__": 1, "column": "cage_id", "source": {"values": [{"id": 15, "src": "hda"}]}, "type": "qza"}`

Step 15: PCoA collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 28, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 26, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 25, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 27, "src": "hda"}]}}]

Step 16: Distance matrix collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "unweighted_unifrac"}, "input": {"values": [{"id": 24, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "weighted_unifrac"}, "input": {"values": [{"id": 22, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "jaccard"}, "input": {"values": [{"id": 21, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "bray_curtis"}, "input": {"values": [{"id": 23, "src": "hda"}]}}]

Step 17: Richness and evenness collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
datasets	[{"__index__": 0, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "rarefied_table"}, "input": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "faith_pd_vector"}, "input": {"values": [{"id": 17, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "observed_features_vector"}, "input": {"values": [{"id": 18, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "shannon_vector"}, "input": {"values": [{"id": 20, "src": "hda"}]}}, {"__index__": 4, "id_cond": {"__current_case__": 2, "id_select": "manual", "identifier": "eveness_vector"}, "input": {"values": [{"id": 19, "src": "hda"}]}}]

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

Step 6: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpktfgor32/job_working_directory/000/14/configs/tmpld16y8lz'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 58, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 7: Diversity metrics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity core_metrics_phylogenetic '/tmp/tmpktfgor32/job_working_directory/000/15/configs/tmp3u3q52r3'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
  warn(f"{func.__name__} is deprecated as of {ver}.")
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.012088089524238852 and the largest is 5.226842011297444.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.10210269173294123 and the largest is 4.815356998067746.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.021402208971835323 and the largest is 2.178696781150897.
  warn(
/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.02795250953518607 and the largest is 0.6032181133453333.
  warn(

Standard Output:

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

Command:

faithpd -i /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/93a4253c-c203-4020-aa9b-a9124fd7f968/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/23-1732389434.76@uid=#1001/tmp/q2-OutPath-3u_fesoy

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/93a4253c-c203-4020-aa9b-a9124fd7f968/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m unweighted -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/23-1732389434.76@uid=#1001/tmp/q2-OutPath-c7jxaydg

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/tmpktfgor32/tmp/qiime2/uid=#1001/data/93a4253c-c203-4020-aa9b-a9124fd7f968/data/feature-table.biom -t /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/data/b37f57aa-ce89-466a-82e7-14a9417b8cd0/data/tree.nwk -m weighted_unnormalized -o /tmp/tmpktfgor32/tmp/qiime2/uid=#1001/processes/23-1732389434.76@uid=#1001/tmp/q2-OutPath-tvhvd4rn

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"ignore_missing_samples": false, "with_replacement": false}`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`
sampling_depth	`"2000"`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpktfgor32/job_working_directory/000/16/configs/tmpr0_r8zw6'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: b5d6c6a3-4890-4c67-9ca3-27a56cc5d4f8｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Step 9: Alpha diversity metrics - Observed features:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpktfgor32/job_working_directory/000/17/configs/tmpg9pr0m0e'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: 8af5e0f8-951c-47ba-907c-a55cae4a849c｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run diversity alpha_group_significance '/tmp/tmpktfgor32/job_working_directory/000/18/configs/tmp59unrh0h'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_types/sample_data/_deferred_setup/_transformers.py:28: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')

Standard Output:

｢alpha_diversity: c033a269-82a0-4eab-912d-0fe64d87bf65｣
｢metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"82cc4acea9cf11ef9deef76adf930bfe"`
chromInfo	`"/tmp/tmpktfgor32/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
metadata	`[{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 12, "src": "hda"}]}, "type": "tsv"}}]`

Other invocation details
- history_id
  - 2c6696977afc7088
- history_state
  - ok
- invocation_id
  - fd816ef332e0fdf1
- invocation_state
  - scheduled
- workflow_id
  - fd816ef332e0fdf1

lldelisle

Looks good to me. (Usually I review and merge the autoupdate PR of the workflows I put in IWC, feel free to do the same).

gxydevbot changed the title ~~Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2~~ Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 Aug 22, 2024

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-III-VI-downsteam branch from 72b8e32 to f75c4d8 Compare August 22, 2024 15:49

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-III-VI-downsteam branch from f75c4d8 to 68fb231 Compare September 23, 2024 14:08

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-III-VI-downsteam branch from 68fb231 to a813d1f Compare September 24, 2024 13:49

Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 t…

df9a79f

…o 0.2

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-III-VI-downsteam branch from a813d1f to df9a79f Compare November 4, 2024 04:32

Update classifier

542ee0c

Update QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml

f387426

lldelisle approved these changes Nov 25, 2024

View reviewed changes

mvdbeek approved these changes Nov 25, 2024

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mvdbeek merged commit f140bc4 into galaxyproject:main Nov 25, 2024
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Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 #498

Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 #498

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Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 #498

Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 #498

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