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Galaxy Workflows maintained by the Intergalactic Workflow Commission
https://dockstore.org/organizations/iwc
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QIIME2 downstream workflows #372

Closed debjyoti197 closed 1 month ago

debjyoti197 commented 5 months ago

TODOs:

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 3
Passed 0
Error 3
Failure 0
Skipped 0
Errored Tests *
❌ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
**Execution Problem:** * ``` File [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data/Import DADA2 representative sequences.qza] does not exist - parent directory [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data] does not exist, cwd is [/home/runner/work/iwc/iwc] ```
  • ❌ QIIME2-IV-rarefaction.ga_0
    **Execution Problem:** * ``` File [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data/Metadata.qiime2.tabular] does not exist - parent directory [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data] does not exist, cwd is [/home/runner/work/iwc/iwc] ```
  • ❌ QIIME2-V-taxonomic-analysis.ga_0
    **Execution Problem:** * ``` File [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data/Metadata.qiime2.tabular] does not exist - parent directory [/home/runner/work/iwc/iwc/workflows/amplicon/qiime2/qiime2-III-V-downsteam/test-data] does not exist, cwd is [/home/runner/work/iwc/iwc] ```

bernt-matthias commented 5 months ago

@debjyoti197 in each of these workflows only one tool is called. Would it make sense to join some of them to one. E.g. the steps separated by checkpoints in https://docs.qiime2.org/2024.2/tutorials/pd-mice/.

Seems that ony qiime diversity core-metrics-phylogenetic uses the sampling depth determined in the rarefaction step. So essentially only these need to be separated in workflows.

But we also do not need to clump everything together in one .. might have to many outputs that confuse users.

Should we discuss this?

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 3
Passed 2
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ QIIME2-V-taxonomic-analysis.ga_0
**Execution Problem:** * ``` Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '14' (Import DADA2 representative sequences) is not optional and no input provided.","err_code":0} ```

Passed Tests *
✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpco260g0y/job_working_directory/000/3/configs/tmpw2tcf48f' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [14:49:36] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_47/pplacer.backbone.c07sfczf.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_47/pplacer.tree.pjp46qcs.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_47/pplacer.extended.0.ux0om8ji.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_47/pplacer.extended.0.ux0om8ji.jplace [14:49:42] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_48/pplacer.backbone.nglz4oar.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_48/pplacer.tree.ol4dq72h.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_48/pplacer.extended.0.6e71naif.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_48/pplacer.extended.0.6e71naif.jplace [14:49:48] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_49/pplacer.backbone.p173hw1o.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_49/pplacer.tree.7g26b9me.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_49/pplacer.extended.0.uh7x6cuu.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_49/pplacer.extended.0.uh7x6cuu.jplace [14:49:52] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_50/pplacer.backbone.grl21obx.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_50/pplacer.tree.bkt79qvl.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_50/pplacer.extended.0.ljg9hvqu.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_50/pplacer.extended.0.ljg9hvqu.jplace [14:49:55] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_54/pplacer.backbone.nq326wh0.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_54/pplacer.tree.ga8q_faq.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_54/pplacer.extended.0.lboltwzd.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_54/pplacer.extended.0.lboltwzd.jplace [14:49:58] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_60/pplacer.backbone.4o_bnf4q.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_60/pplacer.tree.xhxlu0dz.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_60/pplacer.extended.0.lczijsy2.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_60/pplacer.extended.0.lczijsy2.jplace [14:50:01] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_61/pplacer.backbone.ux15lefw.fasta, tree_file:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_61/pplacer.tree.nesrlc8p.tre, info_file:/tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_61/pplacer.extended.0.ndqcfy6x.fasta, output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tempssd-o8eylChwxX/q2-fragment-insertion.ve76pdmm/root/P_61/pplacer.extended.0.ndqcfy6x.jplace [14:50:42] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tmp-Iz9efSbDme/q2-fragment-insertion_placement.json [14:50:44] algorithm.py (line 195): INFO: Current execution Finished in 603 seconds [14:50:44] algorithm.py (line 197): INFO: All checkpointed executions Finished in 603 cumulative time ==> 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/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tmp-Iz9efSbDme . Consider removing /tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tmp-Iz9efSbDme if its files are not needed. Removing /tmp/tmpco260g0y/tmp/tmp.mrYN4siPO6/sepp-tmp-Iz9efSbDme Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "ee77d2baf74711ee8995617597dc976a" ` | | chromInfo | ` "/tmp/tmpco260g0y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
  </details>
  • Other invocation details - **history_id** * 791aa15b9af0d506 - **history_state** * ok - **invocation_id** * 791aa15b9af0d506 - **invocation_state** * scheduled - **workflow_id** * 791aa15b9af0d506

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmpco260g0y/job_working_directory/000/7/configs/tmperkm_snf' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmpco260g0y/tmp/qiime2/uid=#1001/data/7cddb5ee-525e-4829-a589-d3113e85c880/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-ibsxj_rj 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c6e0dd44-d79f-410f-a5de-8484d7a69711/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-tzcu6mni 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/952a2c97-4bf9-42a4-901c-02b2e6351b05/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-kwmprc9u 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/b7f7244b-7ecb-4e45-83b0-fa7ee1718de2/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-_s42755t 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/ff65100d-f272-4731-b1e8-8adbdfd72062/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-wu3std3y 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/e7852bf3-b610-4340-87d6-1706fa431a39/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-23rmd0ne 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c4b3c239-065e-4b5a-9260-41c09acdcedd/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-jwrhif16 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/b460aab7-21cf-4734-b671-76670061aa6e/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-phfjj6dw 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/8bad9b2c-1260-4cd8-9327-9020afa471c0/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-dskbxw5_ 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/96c2e041-4025-44c8-bccc-7022c6a7605b/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-z7vyd6ky 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/a9740944-9950-4e38-b775-83e9ad4ad035/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-3ppy01q0 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/b96f507a-81e1-4d0b-8d83-e2405733c234/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-tkl66x7o 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/0ae4a719-af08-4e49-bf08-f3018adbe8b6/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-7alyazcy 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/61680d9b-6727-4f9e-ac9f-4de9935fbd49/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-m4yjenc_ 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c250e2fa-490a-437d-8a6e-dc3192eaab17/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-t6j5v_yo 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/a926fb44-21ae-43ea-be8e-c756e0fb5bc4/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-lxmj326g 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c7856b18-8d10-4ebd-80ac-93a203307523/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-4q6x5iiu 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/2f0af14d-36ca-49c5-9d9c-8c6d64b45ed0/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-53aeezu1 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/280740bb-7bd6-4578-90f2-f3d3edbba8ad/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-svit6_0x 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/f8c2d88b-c9f1-4f87-9e95-ff693ae3ea99/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-9ke35zvj 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/6645acd1-62d5-4562-9b9c-1b360cb261b8/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-t92vnuga 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/7e54ede5-0668-4c02-8090-505aafdf948c/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-fkesq8zt 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/f24973f3-a0de-456b-898a-3daa459fb774/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-_5rd7r9z 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/83c638b2-28b5-492d-80e8-d7d3cb29997f/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-8gkp3l9n 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/8edd3edc-ae58-40c5-af3b-de20e3558db2/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-18hs02eo 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/2f1af53e-4da3-415e-a2cc-14f7fdf97a2e/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-ry170o58 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/57bcf849-cc88-4d09-aa31-7e8c9c0451e7/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-ybrm5485 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/b8c21273-edb7-4a99-ab35-c23f3cf305e1/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-myr4wovm 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/91bfe186-015e-4754-82a3-227815f9e1c2/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-zuy2hjnw 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/526148f2-c51f-45db-b4d3-3af1ebd919a7/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-txrvq09d 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/5c575609-48ed-4c53-bb4f-e35b90236abd/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-n1mzce9k 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c7b2867d-e3e1-4f0 .. y/tmp/qiime2/uid=#1001/data/14e6786a-8a31-4eb5-8762-53b63d4202f8/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-spifhk64 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/263021c9-62c3-447b-b782-24443c1359b7/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-5g_b5bzb 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/bd72a63d-2c3f-4ca0-9b34-144ae7de6b18/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-j94vjcus 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/aaff73ac-a65c-4e2b-a63c-cab67e070d6f/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-qc79zrjc 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/043ce953-62fa-49c6-a707-bb6f3d4ddeae/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-6hq8snau 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/6b064046-0f6d-4ed4-bfa2-346adac4b392/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-zyr7p5uz 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/63a25abc-9e48-4f46-ad57-c8e6b4155343/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-ivciifxh 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/bf0ba898-1eb7-4eed-8612-dd1d0d790575/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-qgd6lcwe 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/ac0728ab-4bb1-40a7-b65c-01e5aa7070ec/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-mnradfm7 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/f1fc4fee-d01a-4093-bf24-2d5669a8ab51/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-byszgfij 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/763ce67a-5c9f-45ec-b406-bbf5fcc72dc0/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-iqibo5y9 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/59f4c89a-a5fd-4779-89ca-8262c8df6a68/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-y5t05h4c 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/586854d2-3808-4471-84ad-0b6a49cbd57b/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-09fd8gwy 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/e92a42ad-986d-49d1-9980-496d86b1d7ff/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-v85aht3u 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/5c53b507-8137-43b3-bed9-4388ee7f827f/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-cl1nz1vx 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/e9c8c08a-2d84-4580-ad55-96065b6da19c/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-er9ake4y 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/6f612856-0a65-4909-95c3-ba01864b9b7f/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-r3h49c4v 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/a5bb7624-c31d-4c8e-b20a-19877ba67b53/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-ugy_np6z 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/79f7f36c-8935-4b0e-9b5b-d491be49facb/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-dsbbl6k0 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/eee0db5b-25e0-4587-a2d7-37d0a6073445/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-9zhdp3z7 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/12af2f81-b4a1-49e3-bcd9-1fcd38629a4b/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-atydgmpn 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/ae060d6c-9c07-4c44-9873-f0abee928b20/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-4d3akelv 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/ae3aa69d-3bdb-458c-ab4e-079112275fa9/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-xa2r_3j0 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/41f2dd03-30a1-4b88-9e3e-d112b2895549/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-gs3u_3_l Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. Command: faithpd -i /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/06d23393-fc32-434a-8f72-22efef4992b9/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-lz9d3nhb 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/79d3a0ff-2014-48f3-8079-85c8f278b717/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-kg61pwgn 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/d3357b8d-e2b1-4ad1-bfb5-28f7bffe7ac1/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-30za7w1a 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/a9cf83e4-da6e-41b0-bd46-0d4e877518f6/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-o2az8k5o 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/c844961c-79f4-4b13-b129-db902fd37f17/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-lfoe224n 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/e69e5664-d1fd-4dc3-a36a-959c6d709e25/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-0sl8mbhc 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/b239ef1f-62c6-435c-8e0f-aed2a7da4896/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-1w6x_eti 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/a212317d-8d54-483c-be06-1f2af32eb0c1/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-izu9g5nt 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/tmpco260g0y/tmp/qiime2/uid=#1001/data/f828f892-fb1f-4bb4-b8fc-2656edb31d65/data/feature-table.biom -t /tmp/tmpco260g0y/tmp/qiime2/uid=#1001/data/1c010934-b89c-424a-bbf1-9ea2764fb6e3/data/tree.nwk -o /tmp/tmpco260g0y/tmp/q2-AlphaDiversityFormat-9g0xlm8y Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 7, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "efd3e1cef74911ee8995617597dc976a" ` | | chromInfo | ` "/tmp/tmpco260g0y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 92c78ef533821e82 - **history_state** * ok - **invocation_id** * 92c78ef533821e82 - **invocation_state** * scheduled - **workflow_id** * 92c78ef533821e82

debjyoti197 commented 5 months ago

@debjyoti197 in each of these workflows only one tool is called. Would it make sense to join some of them to one. E.g. the steps separated by checkpoints in https://docs.qiime2.org/2024.2/tutorials/pd-mice/.

Seems that ony qiime diversity core-metrics-phylogenetic uses the sampling depth determined in the rarefaction step. So essentially only these need to be separated in workflows.

But we also do not need to clump everything together in one .. might have to many outputs that confuse users.

Should we discuss this?

I'm in Edinburgh this week. We can discuss over Zoom. How does tomorrow morning sound for a meeting? Around 8-30 or 9 am?

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 3
Passed 3
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmppv48ifv0/job_working_directory/000/3/configs/tmpiabta3__' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [10:23:35] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_47/pplacer.backbone.y4obm6lm.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_47/pplacer.tree.ytpgliyx.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_47/pplacer.extended.0.px1orlfp.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_47/pplacer.extended.0.px1orlfp.jplace [10:23:41] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_48/pplacer.backbone.5n52s_0m.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_48/pplacer.tree.v9nqve34.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_48/pplacer.extended.0.2td45pl2.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_48/pplacer.extended.0.2td45pl2.jplace [10:23:47] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_49/pplacer.backbone.taotzfp6.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_49/pplacer.tree.a_1zozt3.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_49/pplacer.extended.0.7etcjgxf.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_49/pplacer.extended.0.7etcjgxf.jplace [10:23:51] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_50/pplacer.backbone.fndtjdg2.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_50/pplacer.tree.34ps376d.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_50/pplacer.extended.0.z24t3puf.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_50/pplacer.extended.0.z24t3puf.jplace [10:23:54] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_54/pplacer.backbone.bg7xvflf.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_54/pplacer.tree.76za7fht.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_54/pplacer.extended.0.jb8akcj0.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_54/pplacer.extended.0.jb8akcj0.jplace [10:23:57] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_60/pplacer.backbone.ycionzh9.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_60/pplacer.tree.6uesrg7p.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_60/pplacer.extended.0.i1epp_29.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_60/pplacer.extended.0.i1epp_29.jplace [10:24:00] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_61/pplacer.backbone.z4od0g7z.fasta, tree_file:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_61/pplacer.tree.letqgu21.tre, info_file:/tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_61/pplacer.extended.0.dsvgrjoy.fasta, output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tempssd-JmkkoTRkB8/q2-fragment-insertion.nsbxk30o/root/P_61/pplacer.extended.0.dsvgrjoy.jplace [10:24:41] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tmp-SNUCHEwsRq/q2-fragment-insertion_placement.json [10:24:43] algorithm.py (line 195): INFO: Current execution Finished in 607 seconds [10:24:43] algorithm.py (line 197): INFO: All checkpointed executions Finished in 607 cumulative time ==> 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/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tmp-SNUCHEwsRq . Consider removing /tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tmp-SNUCHEwsRq if its files are not needed. Removing /tmp/tmppv48ifv0/tmp/tmp.tMIfim6dif/sepp-tmp-SNUCHEwsRq Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "f8471202f7eb11eeadfecba1fb709b24" ` | | chromInfo | ` "/tmp/tmppv48ifv0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
  </details>
  • Other invocation details - **history_id** * 651470f3a152d1fc - **history_state** * ok - **invocation_id** * 651470f3a152d1fc - **invocation_state** * scheduled - **workflow_id** * 651470f3a152d1fc

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmppv48ifv0/job_working_directory/000/7/configs/tmpeifqi0vm' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/0b580cc3-a0ad-49a8-9b60-5341a91a8428/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-zti7rnx7 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/c745aed2-4a99-4973-84a3-94bc350a7471/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-_mh3iisr 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/9485caab-4241-4ab1-b6ed-0ec390972643/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-xq5ibc2n 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/b43e9aa6-7ae6-45f2-a2d2-6f2dcac6ee11/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-129rux95 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7cf665fd-cd61-44fc-810e-5509667cd8b1/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-5jlinnh1 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/fc274ad7-706d-477e-969b-b1c99c5e7af0/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-732ru0f9 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/3ba9953c-1321-4a81-b1f4-0833198f2fba/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-zartksc3 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/a449a9ab-57ce-40c6-9f98-c628d67475ca/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-mvi4l56n 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/e4debc55-b845-4b58-a996-52d1630c5a00/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-83d0x36z 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/3da7cf0a-7d49-4045-9fad-eee57e122bf4/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-86e3n6b0 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/cb190b9c-4624-4e63-aa7f-cb84343a3f1f/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-yu__36me 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/55f3f71d-bc66-40e3-86fb-7c1de3b60a07/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-t4xwuti4 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/9e55b602-c885-46eb-a0ce-d639fba75e1f/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-1u8nd8ui 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/ea253abe-92e0-417b-a0a1-0589ec062cf9/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-ayleh4zy 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/bcfd9c02-0c52-4607-af61-7987f4cfc62d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-4kac339c 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/447d0867-aea3-4414-b1bf-902efc54f333/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-17m4ktsn 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/01cf62e0-03ab-4689-a29a-2bd492d687bc/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-rhlcl_oc 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/031f7954-bd7f-4fad-b07c-db75a54a4ac5/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-1gc3uge9 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/0e7478d4-e917-4b68-b9e1-edfcdfe3c174/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-l91lzpvu 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/65c7304d-1290-416d-aa0d-c0401309785e/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-7jf7u28a 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/ee529da6-cd41-4b42-baba-b57649f9130d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-mjs8h5_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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/145dc5c0-0864-4d7a-bcb1-90b58118378b/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-_mto9x3o 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/d3c4e2d8-bb46-4bf3-976b-bd63a60a6c89/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-b8jt5nqv 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/2b3f30c6-9345-43e2-af31-4d3debc9ad4e/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-4zs9sngt 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/cf44452b-492b-4ffd-ba77-d2a84a1828d3/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-08bl95df 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/b066a701-b9be-4125-b475-2efb41f7ded0/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-l4zilb44 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/e86bcb11-4846-4019-a8f3-69989cbfac46/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-la6x2mvh 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/bbdfe358-6b5a-4ebe-a36b-3353ed2ac9e4/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-2v5smw5g 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/9629c245-6e9c-4dce-b820-7f1a62a09036/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-34owlwnw 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/6036b10b-f5c6-481c-9c3a-9cf813d41342/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-e6gfd4oo 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/cde94111-ceba-421e-ab55-bc5a8ceb4867/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-4rqeibo0 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/27d20b90-3040-4fa .. 0/tmp/qiime2/uid=#1001/data/e7ee7777-ebbe-4a27-88df-88bb1e81ead5/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-b7v5iy6s 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/0db3deaf-6fcf-42c7-afc0-45f3dfec6d99/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-udd00t2s 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/59f6aa97-ad85-4aca-bebe-3f1970f329e5/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-v_tjvmzf 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/c373ea8e-9ad7-4157-9bd8-f332b2118bee/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-kfmeoxhs 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/431d9e0f-2711-4b6d-ae9d-943f299ad9f1/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-sofsj1zn 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/dbb133cb-c543-43d9-af37-804398139f70/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-xehfiytc 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/ee645ef0-cc27-43a3-8bc8-0bf0afea4275/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-xf3lx3bu 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/0c18fcb2-6e59-4cf6-a61f-96556225884d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-hs_8buro 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/15f087d6-78aa-4e62-833b-3f35672f5a1e/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-osb71o23 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/79922c41-6a09-4c21-b0cc-4e2009df5c97/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-75bd19az 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/3a02ba77-4be6-4695-bc28-9effb4d8a505/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-07uogvxh 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/f5196b57-e9ad-49b2-a0ce-7e7f4eccd28e/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-lhbnw8ey 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7a1ce471-6413-41d6-a357-4a7d20cf1e9d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-r4iwyxxn 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/371c1151-9e2a-4fd4-8c95-1eb9d623329d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-x_iiq0di 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/3bdc5ae0-4c44-4726-8763-d770229cab8f/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-trv0l1ww 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/64d71b72-6766-4bc2-a111-abfb0cd55834/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-mlx8lks1 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/05936084-5f39-4ee3-9fbd-31525db0e8e9/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-u02iqksp 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/b0856dd8-3b35-407e-8c28-d0084f6835ec/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-ty5yl719 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/bfe46848-ea9c-4d85-bdbc-d4c32d75ad32/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-_r8vc0g3 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/1298f2db-f965-446e-85ee-2f41fd3d45f0/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-rbp8bzk9 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/1fb6e83c-3d2e-4369-a1ef-38e9319cd95b/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-xkkp5lik 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/45bf8e79-28fb-42e9-8477-d9952acfb242/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-qqi_cc24 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/811752f3-c0e3-4a12-9322-bad467b3a05c/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-g6moehoc 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/83df6f42-dc0f-4666-9c8d-bb14eb9bbfff/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-vj0vu7iz 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/fd0bc127-6987-45b0-bbca-c9486c1fd3bc/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-02ql3yqk 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/67cfd2ba-6aa8-48ac-ad00-773d4866561a/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-urwgwsge 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7a8f191d-ffb8-434f-a139-5b565720c4ee/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-y9jvpbf1 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/84b2ae20-3e25-4a46-97f0-7d71dab48d85/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-apqscsut 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/51bf6e7d-5d61-40f4-bb0f-081e32ff8d63/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-_x4kd96p 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/8b339613-7ccc-4c66-8088-6b8f59cd6394/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-pl4uu_uu 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/587524a9-147e-46d1-8185-ce1295118f9d/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-9kwpu0ns 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/ccc89d30-d92e-42d8-b3a6-fcb7d289130a/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-u0a7pt_z 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/tmppv48ifv0/tmp/qiime2/uid=#1001/data/69e27b6f-e9ff-4625-889b-34f6278632c0/data/feature-table.biom -t /tmp/tmppv48ifv0/tmp/qiime2/uid=#1001/data/7ed922ee-4f27-4320-b726-158801ea2640/data/tree.nwk -o /tmp/tmppv48ifv0/tmp/q2-AlphaDiversityFormat-p1jq9947 Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 7, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "f42fc6bcf7ed11eeadfecba1fb709b24" ` | | chromInfo | ` "/tmp/tmppv48ifv0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 68f8171a910eb816 - **history_state** * ok - **invocation_id** * 68f8171a910eb816 - **invocation_state** * scheduled - **workflow_id** * 68f8171a910eb816

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmppv48ifv0/job_working_directory/000/12/configs/tmpl7mi3s_u' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "38996a2ef7ee11eeadfecba1fb709b24" ` | | chromInfo | ` "/tmp/tmppv48ifv0/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:** * ```console q2galaxy run taxa barplot '/tmp/tmppv48ifv0/job_working_directory/000/13/configs/tmppenktvpe' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: dda19181-91a2-4e33-9879-722b996329c4｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 9, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 13, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "38996a2ef7ee11eeadfecba1fb709b24" ` | | chromInfo | ` "/tmp/tmppv48ifv0/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmppv48ifv0/job_working_directory/000/14/configs/tmphgs3n6fk' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "38996a2ef7ee11eeadfecba1fb709b24" ` | | chromInfo | ` "/tmp/tmppv48ifv0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 13, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * 2e7a84383b7bc651 - **history_state** * ok - **invocation_id** * 2e7a84383b7bc651 - **invocation_state** * scheduled - **workflow_id** * 2e7a84383b7bc651

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 3
Passed 3
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpbwxoptbi/job_working_directory/000/3/configs/tmpjyazi9uv' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [08:20:38] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_47/pplacer.backbone.yjnskz6j.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_47/pplacer.tree.tyyujybq.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_47/pplacer.extended.0.j0hnhv1g.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_47/pplacer.extended.0.j0hnhv1g.jplace [08:20:45] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_48/pplacer.backbone.clce_mxq.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_48/pplacer.tree.i7hzq8vt.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_48/pplacer.extended.0.plxifl6c.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_48/pplacer.extended.0.plxifl6c.jplace [08:20:51] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_49/pplacer.backbone.duumawjv.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_49/pplacer.tree.px6mzb2g.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_49/pplacer.extended.0.c9u1j11q.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_49/pplacer.extended.0.c9u1j11q.jplace [08:20:55] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_50/pplacer.backbone.uctnv7py.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_50/pplacer.tree.jbbl9x34.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_50/pplacer.extended.0.4b5ov3lo.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_50/pplacer.extended.0.4b5ov3lo.jplace [08:20:58] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_54/pplacer.backbone.a75xgycp.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_54/pplacer.tree.823shk3n.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_54/pplacer.extended.0.jf6rkpcx.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_54/pplacer.extended.0.jf6rkpcx.jplace [08:21:01] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_60/pplacer.backbone.0_2tmopf.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_60/pplacer.tree.b7dqlsq5.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_60/pplacer.extended.0.eo48azho.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_60/pplacer.extended.0.eo48azho.jplace [08:21:04] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_61/pplacer.backbone.sg22_tup.fasta, tree_file:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_61/pplacer.tree.i_vri_cx.tre, info_file:/tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_61/pplacer.extended.0.axq7svqu.fasta, output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tempssd-Jh462lzdIa/q2-fragment-insertion.bmc54hnp/root/P_61/pplacer.extended.0.axq7svqu.jplace [08:21:46] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tmp-kbbIzn2OhD/q2-fragment-insertion_placement.json [08:21:48] algorithm.py (line 195): INFO: Current execution Finished in 607 seconds [08:21:48] algorithm.py (line 197): INFO: All checkpointed executions Finished in 607 cumulative time ==> 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/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tmp-kbbIzn2OhD . Consider removing /tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tmp-kbbIzn2OhD if its files are not needed. Removing /tmp/tmpbwxoptbi/tmp/tmp.5gN88LVJO0/sepp-tmp-kbbIzn2OhD Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "f70f1340f8a311ee9ad937312e715a30" ` | | chromInfo | ` "/tmp/tmpbwxoptbi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
  </details>
  • Other invocation details - **history_id** * b443d753d0671932 - **history_state** * ok - **invocation_id** * b443d753d0671932 - **invocation_state** * scheduled - **workflow_id** * b443d753d0671932

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmpbwxoptbi/job_working_directory/000/7/configs/tmpiye3vl5x' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/7141231f-9b02-4054-942a-07de483b4c24/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-v83p2lmj 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/047cc72f-21bc-442f-a525-6b209e5cf06f/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ensr_49t 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/0773f816-39fa-46e3-b0fb-3d79a0d517b8/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-_qscwcip 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/201f6165-777f-492a-95a2-942cf1eefa85/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-yvqtrwz3 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/7ed9f487-2620-4456-b8b0-4080a9bdddcb/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-5klqsy_b 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a92ee9e7-f94b-4fd8-9624-c3115b76cb5c/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-hcue0hz9 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/191b4b6c-6850-4299-ad48-b4ee703a6520/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-g0tgl3nb 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/7afb78fb-87b2-4d02-8cfc-60372ca685a4/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-tkw8znwg 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/331cd984-68c9-4427-82c6-a0caf0db6e79/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3ylapej6 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/16e4b678-ed6d-4f9c-82ac-29c3d4d67530/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-mm7lqtri 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/97f95605-d19a-49b1-8b65-eab170fc0169/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3orxtcww 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/66acc1b7-dadf-4a5d-b130-9258c0662e87/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-nyg9g7rx 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/65db0c7e-a059-49d2-a567-fa5071971215/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-bj1qzr_r 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/4590eb85-8ec5-46fd-804b-18aeedd99dcf/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-g_j2dupb 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/0f5aca9b-a286-4d12-81c6-5155e5cb6279/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-q2dqbbdd 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/8d65e6c0-a31f-4171-bbcd-6c2236b2082f/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3ckjvgs4 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/24415675-ec0b-4c3f-b840-77fdeb40f28e/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-pjyyrslp 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3fd8c8e4-ab95-4fb4-9c13-bdd077c94a29/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-1qmjnmt1 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/faa8ec0b-8042-4dfc-8129-c00bcdd21090/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-htwmin00 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/eebb385e-3695-4f76-a7f5-12a3949c9c24/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-rbvlx8er 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/1e88b9d9-475c-4b9c-9947-c800db0ade92/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-v2ykz_sq 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/018c03d0-fc9a-4bbe-a274-06c8fca2aa2e/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-pelf11zn 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3abe7f8a-e10a-4876-94bf-b196a828fd5e/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3wccc2qf 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/9614372d-a0bb-4a32-9e88-3a74c81dcbdf/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-6x802lr9 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/b05637bf-3e2e-4c62-b4a5-448f835c4498/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ry15hndx 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/6495de6c-e7fc-4a2a-ac20-7980d2faacec/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-91y2qifp 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/713532d5-e63e-4b33-8371-0a3c17511487/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-zfo_lb9e 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/1042bacf-1bed-4351-b7e0-3fa0f105d9c0/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-4bhxi1hm 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/056543aa-9d0d-482c-aa7a-d115fe5ae073/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-78oweoq6 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/743994c8-eb49-4aee-9b12-f5eb0bf0b3dd/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-qc5ieru9 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/48a11f19-a827-4647-adfc-257a62c9eedb/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-464sclhb 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/9a4233c1-b294-4da .. i/tmp/qiime2/uid=#1001/data/580e45ae-e079-448e-8555-9bc764bc8531/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-jec8xi3v 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/83b7da9e-4d35-4802-beb8-d731ff469253/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-jtters2m 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/5be57a10-5385-44b1-b036-e44ddf1004cc/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-lek7815t 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/4ec5757e-9854-4aa6-bcb8-beba942c331d/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-q595c08b 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/2d04a20d-63d3-4e57-8174-51c6dd3e2ba8/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ssmdu_8p 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/aa5446a4-41b4-4265-aee7-29d1571cc8c7/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-2oa2v5ri 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/adc1ae27-5b3c-4425-a825-a4e1543c1dfc/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-a7ylofjc 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/8a2ee8fd-ed92-419e-977b-dd61e6db586b/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-sy0jir6_ 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/30317feb-1a78-4172-a226-d89cc0fcc172/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3_2oi2sc 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/340d5b64-ebdb-47bb-bbd2-2a169617af86/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-1zoi7v4u 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/fc097bec-bfc0-42b7-b8e0-d135e5ddb7fe/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-r2pp7ts5 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3e735355-38ec-458d-a5bd-4289a987ca07/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ovbztyy2 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/2b704193-9d51-400c-978a-30000f178f6a/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-tmvsko_e 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/6b78e594-e18c-4e20-a97a-e9e8bede8a0b/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-9f5k7kh1 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3fe04e6a-07f2-4c84-a182-841cfc39aad5/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-pdv_h_uf 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/d04ce520-0e46-4219-95df-4605784715b6/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-emty62uf 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/adc9ee74-3b9f-4628-a323-2f5d547554bf/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-l99n0fb1 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3077f94e-1df9-4ff1-abdc-9b38465bd43f/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-hubtaxio 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/b7e3d65e-b9dc-4cf8-a1d6-494c73c14ad6/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3iv9f55q 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/e4192014-f024-4c0b-868e-e8939f417a50/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-x5hr5lbq 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/d3842c84-7cc3-4d00-a708-fdb450834718/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-6l0ix0x9 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/c629a813-faa9-441e-980e-77a8fe7c9a35/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-xrrdluni 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/03fe35fb-0c90-43fb-8add-d9abfe6dde03/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-6uz4wg2g 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/a6a03798-c17e-4742-9ef3-a9981329577f/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ik6f6vdt 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/9ccea89a-3bb5-41cd-81a7-fc59b2cb5d53/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-ys_f37d5 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/da4a3b94-2f7e-4cf2-bce0-c1d596265ca7/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-3fc3p7hd 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/081abdeb-a319-4c75-ac82-5d3ff6230401/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-wuqr0u0u 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/430c9f02-028b-4ad9-b589-62ea3daf1f36/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-h1wfc_lu 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/2f0256fd-086c-4674-81b5-c6e6577ef8c1/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-shi1vzc0 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/0494361e-0aaa-405e-826c-e9c24efe43f7/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-m6iq175k 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/4e673593-67cf-4b21-81d0-18e4cad8201a/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-0fmx_g5k 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/caad02f5-c850-46d4-8025-96c9f6798c35/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-b8c2tmhr 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/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/1d6a60d7-99fc-46a8-a729-cc27debf86ef/data/feature-table.biom -t /tmp/tmpbwxoptbi/tmp/qiime2/uid=#1001/data/3b83c2b8-aaca-4e19-998b-0f4c9b4052c5/data/tree.nwk -o /tmp/tmpbwxoptbi/tmp/q2-AlphaDiversityFormat-1xiea_sp Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 7, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "f41a5800f8a511ee9ad937312e715a30" ` | | chromInfo | ` "/tmp/tmpbwxoptbi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * a047f118bf4fc5e7 - **history_state** * ok - **invocation_id** * a047f118bf4fc5e7 - **invocation_state** * scheduled - **workflow_id** * a047f118bf4fc5e7

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmpbwxoptbi/job_working_directory/000/12/configs/tmp4fuxy8pz' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "376a36def8a611ee9ad937312e715a30" ` | | chromInfo | ` "/tmp/tmpbwxoptbi/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:** * ```console q2galaxy run taxa barplot '/tmp/tmpbwxoptbi/job_working_directory/000/13/configs/tmphj_6v2yq' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: 0d32febc-ba05-4fe3-9f56-ec6c1f682357｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 9, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 13, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "376a36def8a611ee9ad937312e715a30" ` | | chromInfo | ` "/tmp/tmpbwxoptbi/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmpbwxoptbi/job_working_directory/000/14/configs/tmps7koqp1o' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "376a36def8a611ee9ad937312e715a30" ` | | chromInfo | ` "/tmp/tmpbwxoptbi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 13, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * 2d43be394ec21c16 - **history_state** * ok - **invocation_id** * 2d43be394ec21c16 - **invocation_state** * scheduled - **workflow_id** * 2d43be394ec21c16

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 3
Passed 3
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpojnjs_jh/job_working_directory/000/3/configs/tmph_gtnm9c' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [09:21:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_47/pplacer.backbone.qepf4dhc.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_47/pplacer.tree.ektoinvv.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_47/pplacer.extended.0.nk8kkcs1.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_47/pplacer.extended.0.nk8kkcs1.jplace [09:21:36] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_48/pplacer.backbone.j53g6bw4.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_48/pplacer.tree.b_gosjjq.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_48/pplacer.extended.0.c6alf1fe.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_48/pplacer.extended.0.c6alf1fe.jplace [09:21:42] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_49/pplacer.backbone.0x3spy7d.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_49/pplacer.tree.btmzr09g.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_49/pplacer.extended.0.6on5ef8w.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_49/pplacer.extended.0.6on5ef8w.jplace [09:21:46] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_50/pplacer.backbone.td_4hlqc.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_50/pplacer.tree.pcdq7_f5.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_50/pplacer.extended.0.yooktmqa.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_50/pplacer.extended.0.yooktmqa.jplace [09:21:49] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_54/pplacer.backbone.7_plzh4q.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_54/pplacer.tree.l7ocxbta.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_54/pplacer.extended.0.4gwh4_4a.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_54/pplacer.extended.0.4gwh4_4a.jplace [09:21:52] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_60/pplacer.backbone.g6rymg7s.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_60/pplacer.tree.di7tlq3m.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_60/pplacer.extended.0.lmb_ecz4.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_60/pplacer.extended.0.lmb_ecz4.jplace [09:21:55] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_61/pplacer.backbone.ob5zmcrz.fasta, tree_file:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_61/pplacer.tree.af1bgfyt.tre, info_file:/tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_61/pplacer.extended.0.171i6k4m.fasta, output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tempssd-g1DyqccixO/q2-fragment-insertion.07d_zbsx/root/P_61/pplacer.extended.0.171i6k4m.jplace [09:22:36] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tmp-kA1YO0l0Gz/q2-fragment-insertion_placement.json [09:22:38] algorithm.py (line 195): INFO: Current execution Finished in 602 seconds [09:22:38] algorithm.py (line 197): INFO: All checkpointed executions Finished in 602 cumulative time ==> 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/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tmp-kA1YO0l0Gz . Consider removing /tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tmp-kA1YO0l0Gz if its files are not needed. Removing /tmp/tmpojnjs_jh/tmp/tmp.igACAG1siw/sepp-tmp-kA1YO0l0Gz Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "7adc8fbaf8ac11ee926aa1767afe511c" ` | | chromInfo | ` "/tmp/tmpojnjs_jh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
  </details>
  • Other invocation details - **history_id** * 4fb66cfa8953f7bc - **history_state** * ok - **invocation_id** * 4fb66cfa8953f7bc - **invocation_state** * scheduled - **workflow_id** * 4fb66cfa8953f7bc

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmpojnjs_jh/job_working_directory/000/7/configs/tmp44k_yh8s' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1ed89a9f-e227-4964-afed-890fa2e5bf45/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-2hqgdsu3 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/aee8b353-713a-4281-a2cd-fa3de8589148/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-3xgz0lzv 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/42751335-cea8-4366-8e10-298aa0d78e76/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-e5u46k52 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/99e1c4ae-05c9-4e7c-b09e-99cbf904f30b/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-denow391 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/0a07619d-eb13-42ce-805d-582692bea6a3/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-pb596qb4 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/9eaadf66-2c11-4ff6-a1c9-c9e5e73d82f1/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-as7x_vrl 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/291ccf34-5fd9-47c6-86d2-95044ffd9e81/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-uxwicqcz 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a351702c-baa7-4cb3-84e8-dc53b5c4d925/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-zozlgo76 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/ee15788a-b2ca-4636-9e10-f227da28eb3c/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-jw8xtf9o 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/5d797626-07b1-4f41-bbd1-43990554c24e/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-mgarjj7v 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a09bf306-f367-4a9d-92f8-7e239858617d/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ooblrif5 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/55d2d77e-9c86-4115-b901-f5d9bb72b2bf/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-apsfy2zw 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/9e7c2937-8ce0-41fb-a923-b3ad1ebc6d01/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-e_kuj862 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a9e9083c-f9d8-43f0-84f9-fb9c19dbc0da/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-79wq0yyd 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/6933922c-a2a2-4742-9368-c1a8424a0411/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-wow68b0v 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/f2a1e89f-a0b5-4b4f-9be1-070d512952cc/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-omrh7kkq 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/70babfc7-4898-4777-af5e-f215c4ac467d/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-44q_7otm 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/59d2f901-0b68-4449-9832-006e195fb605/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-8d7fw14r 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/5643f928-2658-4832-99d1-2a00797bc7ce/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-1kh_w9l2 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/e1356bf4-12ff-4878-a7de-d831d8618b44/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-9_juxnua 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/93458bde-6977-49f6-8fa1-dfc9ce2a6027/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-o6yh_0d8 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/479cecf8-037f-42e5-9797-01da44c9d3a1/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-td6u9stt 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/9851548a-a383-48c7-b46b-a61a2ef6d197/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-8jnxe4ef 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/18d6b109-aa94-4e32-a665-c3c7bad2a2f8/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-zkboinrp 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/80fa92ab-f99b-4d8d-85e8-f714135bbd32/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-btpxfmv3 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/139a1a65-acd9-4d6a-8924-43dfc62de457/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-_ti7oxct 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/568b36fd-ea36-45df-a2f9-1603a3cac8dd/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-8mb8p_nq 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/187f22b7-44d9-4435-8960-aa38511f3381/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-phz_y8mh 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/c9b0dec8-de76-48e3-8aa6-827c51f35743/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-2hbqfkdk 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/c02a9060-8304-4a9f-acf1-49d267e5f15b/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-f2tajgu4 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/bde0f070-5c01-4e31-a160-53656f10ede9/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-7lai9bzy 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/a83c0f21-cb29-444 .. h/tmp/qiime2/uid=#1001/data/846560f2-b67d-4607-abad-de98cd376973/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-8dch4_ov 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/0e5baba4-ca1a-42c6-bb93-f094fa9322c7/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-zau0q510 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/02a4fb68-46fe-4cca-b6f7-528d06d5931a/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-_epx__e4 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/379040e4-eb8b-48e3-a6e4-e4b8d6317009/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ilxssk96 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/366ef8a9-0d9c-4bae-85b2-196607f52b63/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-stljk79u 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/9a7611ff-b459-41c4-8608-4d0717488895/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-1v26ciiy 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/4555e163-998b-49f5-8132-979348b2accb/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ybp3wlrf 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/72f1dd57-414a-4fcf-8d2e-605036f76101/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-880qy7r3 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/c61af42a-551e-4472-8415-d148f342be27/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-87s9p5aj 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/0d5e5607-d6bb-4b3c-b6ea-2f57b96de071/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-6i7snfrc 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/c6447cba-fe7a-4760-a817-ff61ecbb18df/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-1n53ckq8 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/fef8a390-66bb-4a63-bd87-4656af36d18f/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-gwe27xod 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/17ee7c98-dd1d-4011-a537-3fa18cc4e0fa/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-osm4ps8i 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/32dc5efd-dd5e-4b66-96c8-85c2188264ee/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ebcbwlzj 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b59c1f29-b8b9-400e-ac7b-bbc9d4c17cde/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ote2gp1n 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/99dc736e-e7fc-4e70-8a2e-bf82c5bfa244/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-jmzqqllq 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/24c88b4b-00b1-42c4-8e15-c4a6766f1c7d/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-skamiq2k 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b2134d91-fddd-4ed8-8772-1d600d9a82c3/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-nxaodf9l 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/9437c07c-8fe0-4444-bacd-77722e4dec47/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-u9cz8jh9 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/56b77e5b-ddc8-4155-96a3-a4d19df9996a/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-haf6g6vy 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b27a32d8-35af-48d3-8506-b019e32be630/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-9c3jtudn 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/d0536d97-d4c7-4186-a56f-f62f9f1d49fa/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-1i5dxq54 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/d4453c95-0681-44b2-a505-cfb149c698fd/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-ylwm8he7 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/d009629e-5031-4bee-9d1b-7f0808f1c1bf/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-d_cnd6g5 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b29f8242-1218-411d-8061-b163d3261d66/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-pi4rfiju 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/053914a0-1a9d-4734-a638-cc66716bf4fc/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-vrk4qs9_ 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/04933168-5ba2-4a4d-8b00-0d106307a612/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-rh9exgdk 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/d3d0b531-222b-4713-b42e-83d8d57adf90/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-pl375dvy 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b1447fd0-c90e-4180-ab7a-324fc2e4a5e6/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-u0t92h2j 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/bdcad4dd-1a80-41c5-9ede-58b7c22ea26c/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-oosugx4c 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/b2d62f16-30f5-48e4-9eb8-a938c87d275b/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-51x1bdh9 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/dd135cce-46a8-4ea0-bd70-7442223504d1/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-v95dhhmo 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/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/c942fe5a-30be-42da-9f82-e043392a2ccc/data/feature-table.biom -t /tmp/tmpojnjs_jh/tmp/qiime2/uid=#1001/data/1b7f7fde-3454-4b2d-ae53-18c8c12aded3/data/tree.nwk -o /tmp/tmpojnjs_jh/tmp/q2-AlphaDiversityFormat-nm4bxhx3 Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 7, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "7104dd06f8ae11ee926aa1767afe511c" ` | | chromInfo | ` "/tmp/tmpojnjs_jh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 0b4980ad5df2a60a - **history_state** * ok - **invocation_id** * 0b4980ad5df2a60a - **invocation_state** * scheduled - **workflow_id** * 0b4980ad5df2a60a

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmpojnjs_jh/job_working_directory/000/12/configs/tmpkhovjmod' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "b1c302dcf8ae11ee926aa1767afe511c" ` | | chromInfo | ` "/tmp/tmpojnjs_jh/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:** * ```console q2galaxy run taxa barplot '/tmp/tmpojnjs_jh/job_working_directory/000/13/configs/tmp4a_ix3ux' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: dcb295a4-a0b5-40de-8bb9-c682c6025d36｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 9, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 13, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "b1c302dcf8ae11ee926aa1767afe511c" ` | | chromInfo | ` "/tmp/tmpojnjs_jh/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmpojnjs_jh/job_working_directory/000/14/configs/tmpu7cojglj' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "b1c302dcf8ae11ee926aa1767afe511c" ` | | chromInfo | ` "/tmp/tmpojnjs_jh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 13, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * 3f51d2fa24a737e5 - **history_state** * ok - **invocation_id** * 3f51d2fa24a737e5 - **invocation_state** * scheduled - **workflow_id** * 3f51d2fa24a737e5

github-actions[bot] commented 5 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Unlabelled step**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp91xuue3w/job_working_directory/000/6/configs/tmphx9ylig6' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [10:04:19] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_47/pplacer.backbone.3fbbli3m.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_47/pplacer.tree.wkwv184n.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_47/pplacer.extended.0.p9_otlfi.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_47/pplacer.extended.0.p9_otlfi.jplace [10:04:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_48/pplacer.backbone.z6lsjglb.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_48/pplacer.tree.ugyqj60x.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_48/pplacer.extended.0.nj3h48ca.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_48/pplacer.extended.0.nj3h48ca.jplace [10:04:31] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_49/pplacer.backbone.c4p8qvgm.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_49/pplacer.tree.o2uadbu5.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_49/pplacer.extended.0.ea0k8mjz.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_49/pplacer.extended.0.ea0k8mjz.jplace [10:04:35] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_50/pplacer.backbone.3n3vej4f.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_50/pplacer.tree.6w8gqlly.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_50/pplacer.extended.0.spocqlrx.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_50/pplacer.extended.0.spocqlrx.jplace [10:04:38] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_54/pplacer.backbone.2aj6x1o1.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_54/pplacer.tree.u3t2f1eh.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_54/pplacer.extended.0.ns9ki5xe.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_54/pplacer.extended.0.ns9ki5xe.jplace [10:04:40] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_60/pplacer.backbone.w6ahdm2n.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_60/pplacer.tree.rnpyz9sx.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_60/pplacer.extended.0.gwi87mq_.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_60/pplacer.extended.0.gwi87mq_.jplace [10:04:44] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_61/pplacer.backbone.y_38yr40.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_61/pplacer.tree.wzmsjcy3.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_61/pplacer.extended.0.slpo6r1m.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tempssd-I5XA9dCsJi/q2-fragment-insertion.9kb1jm5m/root/P_61/pplacer.extended.0.slpo6r1m.jplace [10:05:25] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tmp-YMCn7EjRog/q2-fragment-insertion_placement.json [10:05:27] algorithm.py (line 195): INFO: Current execution Finished in 611 seconds [10:05:27] algorithm.py (line 197): INFO: All checkpointed executions Finished in 611 cumulative time ==> 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/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tmp-YMCn7EjRog . Consider removing /tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tmp-YMCn7EjRog if its files are not needed. Removing /tmp/tmp91xuue3w/tmp/tmp.8pWP3yvh48/sepp-tmp-YMCn7EjRog Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "6d6f163bf8b211eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Unlabelled step**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmp91xuue3w/job_working_directory/000/7/configs/tmpi7nxiioe'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "6d6f163cf8b211eea1c979b956b379de" ` |
                  | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmp91xuue3w/job_working_directory/000/8/configs/tmpswnexfc7'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: a3204bb9-7634-4185-8a7e-312e5afcc9ef｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "6d6f163cf8b211eea1c979b956b379de" ` |
                  | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmp91xuue3w/job_working_directory/000/9/configs/tmp_9y46brh'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "6d6f163cf8b211eea1c979b956b379de" ` |
                  | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Unlabelled step**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmp91xuue3w/job_working_directory/000/10/configs/tmpwqdvcd6n'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: c0545bbe-4176-4eb1-b44f-fce83805da6e｣
                ｢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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/4e20020e-2713-47d0-8b83-c40897137426/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ye0eyliv

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/3add4ab3-a5ac-49ff-9b90-cb60724b3089/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-4nzdz65k

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/86557e98-bb9a-40f8-8e56-3d81ef818304/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-f7wuvl8d

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8150f711-f889-4b24-9f8a-036b6fd19c06/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-u_x6h5pv

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/3d425b79-7a5b-448f-bb76-c77b25059c7e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-512zun77

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/3da11407-21d1-4712-a940-e53062e28e96/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-rsunqkim

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5fbfd28a-f123-44b3-8700-cce898d01568/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5iu_915s

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/73e0ef90-9998-4b64-a52e-0f156ea799d8/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-qyu_7q4z

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8ab0cd19-3480-4f69-85db-f4db685374ef/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-_q8ppewi

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/ecbe97a5-13f9-4b83-b883-b2df18d96bbb/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-gh94abvu

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c899f6ee-5895-4af3-b7f8-da546e6594af/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-l1kho2o5

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c2a130d2-042d-439b-8bd3-a8e18ee7435f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-d34r3d4c

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/cdd372a1-2b14-483d-b017-7b7526279f72/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-3_u3jxmq

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/71a9f890-5c3e-4b23-acc9-a6cad2aa6e81/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-eat9wc_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:

                faithpd -i /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/aa911d68-b235-48c7-be7c-22992513db0e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-jnqm2nys

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/31317454-11af-445d-a668-2856585141c5/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-elhvupf7

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c15e0c8c-f15b-48e3-82c4-ee59ff195ff5/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-smatvlnr

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/ac851321-8b95-4e42-a2b0-036c4bbc1310/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-8tdkimm_

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0c449d8e-d16c-45d1-946f-6b913d479bc5/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-bfz4cscw

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/57976ae7-2126-4fb7-9e7d-5f85208853f4/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-hha1101a

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a786b745-3be1-4b77-abd2-ef8c7f26b088/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-16oe033x

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a7ccbafa-3839-4bad-817a-17f8f29c7957/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-4ogp8jqm

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/6de14171-db43-4f4b-becd-92a8cb6a6b2c/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ymoolq49

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/931a9ebd-76aa-4c19-b689-595aec093d3b/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-uk20j8de

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/88d6f2a2-1031-43b3-aa4c-638d000f93ac/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-25clzcy5

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/cf0b6787-7b30-476e-accb-e57302ccf878/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-lctvkgik

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/1f35b70b-a65b-405c-a645-fd5fc0dadca8/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-oeq7n8fa

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b677b063-0921-410a-99b1-eda4f342a28a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-16o75lor

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/dbd63db0-095c-42dd-aeab-cc95d85c5407/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5l2lqxkl

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/4a413ef1-c0e8-4465-8e75-2e923b5bd89b/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2fd8iw_w

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/9402ae46-3c06-4cb6-ab22-44ef601967a1/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-sh3gosdt

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/91d64d86-7fa1-4bd
                ..
                w/tmp/qiime2/uid=#1001/data/decafef1-5265-4e4f-8d24-89237e71fc11/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-7or8du5w

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/096342b3-f6be-4094-a219-648c001cd43e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-qo4kiqau

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d7f85415-b209-4481-84b1-4a73b88547ce/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-f54zab0_

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/1f08105b-2217-472d-badb-e8e23240977f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-y78cy41v

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/50eff916-0d05-4e75-819c-a7ba7e76713f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-1nm324as

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8d597482-f088-409a-934b-ac044dfc5819/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-vysyydlb

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b48d4044-77e8-484d-96b8-3c95f2d016d0/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-7_eq9gmv

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/e7dd2d80-37c2-423f-8910-2ed9d1de51a1/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-3btds340

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/f45a3714-0166-4d83-9e5b-d2446bdb0f3a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ge_h0l98

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/87c63edf-4af7-48c7-8850-0c90fc51f8db/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-rtfglcr2

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/ecb55268-e108-485f-89aa-cc4518568504/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-mzjtyarf

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d365d40c-5c8f-4c6a-8263-88a7de4c7aec/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-mk7e2zol

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0df9ed3f-942e-4108-932d-ce4558eed2bb/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ekvr8mvf

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a8cdd16d-f64d-4a47-a4f9-1249ca58cd30/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-sl6czoyh

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/20dc38eb-8471-4f37-9265-b562f6354fde/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2y8kpbx1

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/807f5957-f953-40a8-90a1-ad0ecc3f6d68/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2gvxbx4s

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/e7dabbc1-a2d7-4700-bcf8-4683246209d3/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-kxhbybv_

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d430cf20-8dcf-4707-9e90-70c1b0565530/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-9xlt_o15

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/47f3781f-4908-495a-9dc0-f5386785662e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-nwz3z0bp

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/be47f70d-398e-4d5a-8433-1f0a0d65535a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-en4ih810

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/6c74a2e0-c8b0-499f-93a5-ae3807765053/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-9__a9fdw

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/e156d1fb-c29e-4cdc-8c1a-2663d15bacad/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-jyjmorub

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5b3b077e-3d05-4293-a44c-867e54d9c558/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ukswmlwr

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0e8dd22b-a05c-4024-bdb2-b3b5ab6094f9/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-u6gh1u7b

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/3bb24c89-d37d-4efd-bb5f-967f3a59aec2/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-4bdwk0ro

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/9e61b948-32be-4fb2-a52b-6de6f0ef2284/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-8s08ma83

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/30d50cfe-a963-48cd-bf3d-917e913d9675/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-0hkf0h5f

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/89c0bb6b-5d7f-4855-bbc5-791867c548a5/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-v5l_7ox9

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/3867d2b0-8be8-49b6-b72e-219dcaf29612/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-bhxapk8f

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/954f9bc7-0d40-4e81-825f-979ffaf3e14e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-om007826

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2e4ac41c-b60c-4bb9-887d-1590f5f2480c/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-mqzebhfe

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/6df6d3ff-f44c-43b4-9025-1dc9c0a210a2/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-3pwo2qun

                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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8b66ecd1-380b-4a39-8e49-e4952fb8eb20/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2895ccf2-f0a1-4356-b1d9-459192b06e41/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-yu9yi_1f

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "6d6f163df8b211eea1c979b956b379de" ` |
                  | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * 78f7a0c1305ac35c - **history_state** * ok - **invocation_id** * 78f7a0c1305ac35c - **invocation_state** * scheduled - **workflow_id** * 3a4f3be35aa588e3

  • ✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
    Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp91xuue3w/job_working_directory/000/13/configs/tmpqo805k7w' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [10:17:53] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_47/pplacer.backbone.gn_nrl7i.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_47/pplacer.tree.4sh2zhd_.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_47/pplacer.extended.0.yky5wp8_.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_47/pplacer.extended.0.yky5wp8_.jplace [10:17:59] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_48/pplacer.backbone.70_hf3a4.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_48/pplacer.tree.gx3f5mq_.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_48/pplacer.extended.0.2m8mwy6g.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_48/pplacer.extended.0.2m8mwy6g.jplace [10:18:05] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_49/pplacer.backbone.phixlb47.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_49/pplacer.tree._or1u70a.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_49/pplacer.extended.0.2aj86puo.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_49/pplacer.extended.0.2aj86puo.jplace [10:18:09] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_50/pplacer.backbone.yltcggx_.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_50/pplacer.tree.1fghlhov.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_50/pplacer.extended.0.ur32qt2j.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_50/pplacer.extended.0.ur32qt2j.jplace [10:18:12] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_54/pplacer.backbone.qpynh4dc.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_54/pplacer.tree.sl6f1i88.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_54/pplacer.extended.0.8zxn8ymw.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_54/pplacer.extended.0.8zxn8ymw.jplace [10:18:15] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_60/pplacer.backbone.ylfz4_fx.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_60/pplacer.tree.esl7yzym.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_60/pplacer.extended.0.fuz30kva.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_60/pplacer.extended.0.fuz30kva.jplace [10:18:18] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_61/pplacer.backbone.k_mwxl8o.fasta, tree_file:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_61/pplacer.tree.u3i38vvs.tre, info_file:/tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_61/pplacer.extended.0.1c5s_s24.fasta, output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tempssd-Gsb73wq5ny/q2-fragment-insertion.2y1pj20n/root/P_61/pplacer.extended.0.1c5s_s24.jplace [10:18:59] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tmp-J6LnIlkxLw/q2-fragment-insertion_placement.json [10:19:00] algorithm.py (line 195): INFO: Current execution Finished in 602 seconds [10:19:00] algorithm.py (line 197): INFO: All checkpointed executions Finished in 602 cumulative time ==> 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/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tmp-J6LnIlkxLw . Consider removing /tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tmp-J6LnIlkxLw if its files are not needed. Removing /tmp/tmp91xuue3w/tmp/tmp.xHbvpdoX6w/sepp-tmp-J6LnIlkxLw Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "93aa5cb8f8b411eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • Other invocation details - **history_id** * 4eae33e487ee6423 - **history_state** * ok - **invocation_id** * a17337272d3860a4 - **invocation_state** * scheduled - **workflow_id** * a17337272d3860a4

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmp91xuue3w/job_working_directory/000/17/configs/tmp_5auhafj' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c6555559-f454-444e-9f41-ce060942576e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-i0owprfy 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5c4ef498-9095-45c3-b218-9f0534ce6967/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-egezju02 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/4d56f957-d0a6-4a68-a8bb-358dccd08754/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-iis06q1_ 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b3d7a1be-762f-461e-897c-c7996f00ca84/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-xyg73op6 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5ee68681-9e78-438c-a085-a9d24a4e9e1a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-63oou6cy 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/7830a7cb-b082-4883-b9f2-261dd903f006/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5y8ca8ei 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/2756a15f-90bc-494c-8128-7d0bdc31a4a8/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-nnzdawxj 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b99ede61-d35e-40a2-b39a-83495f2eac6b/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ihxxdzjy 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/bfe3e26a-b355-4039-878f-719ef4110c53/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5voaka98 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a686655d-5958-46b3-baf0-8ac248fc5b1f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-lisxyra1 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/150b58ed-ffe4-4812-8ac7-843266815c6d/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-bp5k630i 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8c4ae5c8-e43c-4eff-b81e-96899556a915/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-enb4f5o1 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/920e11e7-bccd-4b7d-806d-8ea6e99b7f96/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-e719eouo 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0f1b94c0-e15c-4298-9278-caf907694d16/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-tnjr5fuz 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/131bcef2-e648-4a44-ac2d-78c4f04ef188/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-42t8vugf 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/30761a9a-1bc6-404e-b4f4-e7912d60bfbb/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2btijl4o 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/4b293c35-476e-40da-b7ae-9bdbc7e69539/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-in5xh2y_ 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/9db0b66a-7085-4e37-84b3-c8f0254e7c84/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-c8o_37vv 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/be70a8e6-09f3-45e5-9918-0cd95bc6c82c/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-cc6g8jyy 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d7f7dc22-b7f1-4c0f-b629-12afd8ac1c6c/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-zjzryi1t 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/db241476-cd59-4e80-aff2-b071c65505a4/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-nj21rvyw 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/fe5d5bb0-73cb-4434-9cb8-e92a184e0e68/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-p2thagpb 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5c3c6ea2-02ed-499d-85ef-ea540bdf6b34/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-gci9dury 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/7f0b94d5-a414-43fe-a4c7-e1a99a7452ab/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-dor4wbrm 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d9884964-90bf-4471-9592-f19baeb04964/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-rdpcl4yk 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b894a348-78d7-4526-ab78-2e93068905d9/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-_ojspoy3 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/daee8249-f49e-4a19-976d-ff8f5eb87c49/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-qsifkvtb 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c9397aad-49de-46b7-817e-976d65cacf70/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ga5ugtet 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/56a8a8cf-ac3b-47d6-90bf-5f03e6619d9f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5mccvu6s 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/43d4c6d1-7c43-49ef-b936-853404ec82fa/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-zq213jyl 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/6fca6eb1-4432-425e-b894-604c60c5a378/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-zf17rr66 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/7a479ba7-0cd8-42a .. w/tmp/qiime2/uid=#1001/data/88965fc4-ea0b-46e1-8e3c-20c4eb20c266/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-mk7jj6qm 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/9f76e24b-b09a-4fad-b20b-224c0b1b53b7/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-g87egs0i 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/81f263b1-609f-426b-8724-4966702217d4/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-e27v2yz8 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/79106de2-7379-4130-91c2-6064c203e5dd/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-faxq6ll6 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/464bb848-d0e7-4579-bf0b-5cde1693e199/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-zaak_y7a 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/66b49e61-a5e0-42d9-917f-0799e65724aa/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-sryfoskt 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0fc72a8f-e3bb-43bd-9adf-3b818613b38e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2qyv0o6k 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b5d4600c-3149-45a8-972b-a060869cdc64/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-pu_msuvr 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/94888a53-f750-4b17-85ed-f1ee2c5800fd/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-68aamgxy 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b883abbf-f642-4368-831e-12fa1441981e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-4su75vxt 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c6b71186-5e79-4137-b69b-86cd2932a9f6/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-l6hckw7c 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/cc5279f0-91be-49e9-b964-e470b21daa6b/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-r6bq14ok 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/b36eac00-89af-4c45-b148-c773edc989ef/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-d1qzi1kw 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/e370e2e6-2552-4eed-ae54-71f91a73acaf/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-n90wo663 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d53a22ca-d086-4479-8cad-bbc796daa2ca/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-2bw7zv3g 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/f627c583-52ea-4a13-96da-dbb4b431952f/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-prth_z1o 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/68e7b19c-9426-4330-95ef-6a339b69c783/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-eldcuem_ 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/185dc2c9-364e-4cda-8048-6d530abf9600/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-n6ez2vq2 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/492d40c2-e309-4e51-a8e8-1a16df476675/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-6tzs3b7s 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/0d26f80a-ffd1-4785-83db-6e24db89759a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-hi8g5z6j 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/5a845d5d-924b-4001-aa0a-500bde51761a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-muuo1oh7 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/d2f2a563-1c31-4b02-9270-2499b71fd560/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-mudt9ptm 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/7b7dd64d-0c03-420e-8ace-8e552794a412/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-finzr7tr 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/a69391cf-36d5-43ab-a76a-e50dcfd413a6/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5n8ffp2t 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c09186ef-9fe5-4ca1-b545-6b6c23246513/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-v0vjif05 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/c687d139-cab4-4371-a4b2-6e0a5309176e/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-bxa5qbv1 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/ea1bf344-4864-4b05-b4c5-e8f98ded66e6/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-ps5v9h_b 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/df69ac0f-560f-4574-a517-013a12bbdc30/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-uh0pe02_ 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/6d2a3b11-6ecc-4870-9b23-9f64791a97a1/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-4he019o_ 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/8016693b-7ebc-4a87-b76e-06c2363f60f1/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-aqht_juf 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/ded1f7e7-3917-4484-bca8-ca02ed200b61/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-e6e9cdgh 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/df169412-9b34-448d-b02f-0e49a7f649ca/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-5j8iyt0m 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/tmp91xuue3w/tmp/qiime2/uid=#1001/data/cfc64296-533a-4ec7-90bb-77b08843644a/data/feature-table.biom -t /tmp/tmp91xuue3w/tmp/qiime2/uid=#1001/data/11643ff9-c72b-40f9-863f-5695eaa20c25/data/tree.nwk -o /tmp/tmp91xuue3w/tmp/q2-AlphaDiversityFormat-7vlii4p7 Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 16, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 18, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "50ad2682f8b611eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * a44a835a395d4172 - **history_state** * ok - **invocation_id** * f395e6dec20084ee - **invocation_state** * scheduled - **workflow_id** * f395e6dec20084ee

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmp91xuue3w/job_working_directory/000/22/configs/tmpe72mdf2y' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "92a4e980f8b611eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/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:** * ```console q2galaxy run taxa barplot '/tmp/tmp91xuue3w/job_working_directory/000/23/configs/tmphsp5r0gk' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: 98fd1ae9-10c0-4a3f-8636-f567d3b9cd65｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 20, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 24, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "92a4e980f8b611eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmp91xuue3w/job_working_directory/000/24/configs/tmp0btc8dj1' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "92a4e980f8b611eea1c979b956b379de" ` | | chromInfo | ` "/tmp/tmp91xuue3w/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 24, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * 3a4f3be35aa588e3 - **history_state** * ok - **invocation_id** * 732f54bfa1bf7ea7 - **invocation_state** * scheduled - **workflow_id** * 732f54bfa1bf7ea7

github-actions[bot] commented 3 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Unlabelled step**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpotj7yt48/job_working_directory/000/6/configs/tmp7jft1ovy' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [18:02:23] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_47/pplacer.backbone.mxd729ab.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_47/pplacer.tree.7q3x58mf.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_47/pplacer.extended.0.l5xypn89.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_47/pplacer.extended.0.l5xypn89.jplace [18:02:29] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_48/pplacer.backbone.9yrrcxe6.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_48/pplacer.tree.7ilulqlt.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_48/pplacer.extended.0.z0y718kk.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_48/pplacer.extended.0.z0y718kk.jplace [18:02:35] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_49/pplacer.backbone.limt5nil.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_49/pplacer.tree.n5kf5g0o.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_49/pplacer.extended.0.itur4_d8.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_49/pplacer.extended.0.itur4_d8.jplace [18:02:39] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_50/pplacer.backbone.4chsm_j3.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_50/pplacer.tree.oixsjgeg.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_50/pplacer.extended.0.g0nonzp6.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_50/pplacer.extended.0.g0nonzp6.jplace [18:02:42] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_54/pplacer.backbone.nlhxbcg7.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_54/pplacer.tree.jvj2r3zn.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_54/pplacer.extended.0.jxb4uc10.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_54/pplacer.extended.0.jxb4uc10.jplace [18:02:45] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_60/pplacer.backbone.qi035tcn.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_60/pplacer.tree.h2yd0z2u.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_60/pplacer.extended.0.52o8ijal.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_60/pplacer.extended.0.52o8ijal.jplace [18:02:48] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_61/pplacer.backbone.yam8ucid.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_61/pplacer.tree.r7jy7jph.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_61/pplacer.extended.0.d9q4najn.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tempssd-kKLqsQZPwu/q2-fragment-insertion.jf278rbj/root/P_61/pplacer.extended.0.d9q4najn.jplace [18:03:30] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tmp-S7DznWMl17/q2-fragment-insertion_placement.json [18:03:32] algorithm.py (line 195): INFO: Current execution Finished in 617 seconds [18:03:32] algorithm.py (line 197): INFO: All checkpointed executions Finished in 617 cumulative time ==> 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/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tmp-S7DznWMl17 . Consider removing /tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tmp-S7DznWMl17 if its files are not needed. Removing /tmp/tmpotj7yt48/tmp/tmp.A303dEzq5C/sepp-tmp-S7DznWMl17 Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "1cfb579d1ead11efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Unlabelled step**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmpotj7yt48/job_working_directory/000/7/configs/tmp2sh8dhfy'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "1cfb579e1ead11efa1ee2507fc704a63" ` |
                  | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmpotj7yt48/job_working_directory/000/8/configs/tmpuitstf_j'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: 2e91764c-f55b-4bf9-a34a-86488436e280｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "1cfb579e1ead11efa1ee2507fc704a63" ` |
                  | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmpotj7yt48/job_working_directory/000/9/configs/tmpbamggnwo'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "1cfb579e1ead11efa1ee2507fc704a63" ` |
                  | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Unlabelled step**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmpotj7yt48/job_working_directory/000/10/configs/tmpbhof3ge4'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: 557cb162-664b-437e-b8a5-ea601b864849｣
                ｢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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/030eebe7-c64d-4204-9b52-157789adfea3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-noyt1ypo

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/6d6c1637-8750-4ebf-8cab-104277cbd9f3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-55b8pkxz

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a2b83b79-9e22-4f75-8a1b-afd3be59bf34/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-5j62nh5f

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/e55ef7f2-483c-40e1-818e-4ca0cd5aa13b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-2qjbww1v

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/04dd4344-7f82-4ced-a155-762fbe1e47ed/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-nawv1xyy

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c0a4b3c2-bce4-420a-999a-7618d4337224/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-nlab42v5

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/88a94743-21bd-4db2-b89e-23794fd19120/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-3wac0lhs

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c673a787-a24f-4791-ae12-3af9ed15e2b9/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-n16t65iv

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/fcd5aa6c-0b18-44e6-8ae7-49e3a9ac40c5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-okdawz04

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/940fb147-96c0-479f-be7c-7110a634dd21/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-4xpp9w2v

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/11d0ce9e-4f36-4c0a-af9a-09bf75cde21d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0ssw32rc

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/ae896bc6-6625-4c32-acd4-d7892f80c63b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-jqy319en

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/0e90a808-7e4c-422e-9089-4b106598df58/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-tdikeljf

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/924aa9af-8a96-4ea1-ac15-422d523cd037/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-3fe7keqr

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/bfc5f576-a16f-47dd-967c-ac2418ea7b86/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-owos9ki4

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/7bfdb1cc-625c-4232-a383-932815806bee/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-oiznyhso

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/58f6956e-ecbd-496a-8b35-5d1581e0df95/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-em6c5_tx

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/5d2f4429-2c68-4223-aa2b-0310f76bb08b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-_n4r61ji

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d63a6940-f521-4d3a-b681-fd3f7d92a04b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-w1ohglhg

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/da34e8d1-d262-45fe-afe4-477ea486e83c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-t_sviy01

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/77b4336b-2362-4b08-95f0-cadc82381384/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-kwacw95l

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/688267b3-e94f-45c6-8ffd-1b4df0ec7598/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-hlq5c0im

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/5a4801e9-b082-42ce-b953-c6a4d873ddb5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-3gjez1h4

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d7b74e3f-8e13-4f1e-906b-a643fa2179a3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-on5nhd79

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2bc9faa1-c4b8-4039-b044-f45fb268a6b6/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-vij73188

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c03735bd-109c-4700-84d6-ef7bbc4687b5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-wnu7lp9c

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/6495fda4-fe31-4f09-b6e1-f244f72c5ddc/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-d4pqzido

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/7d804526-729b-452d-b68f-81f49fca9181/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-no_h3t6e

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/8a2a9a7a-7fd8-4917-9e07-0d6d3eb26c64/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-_chkci4l

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/78d0dd3e-e9c6-4f4c-af16-3c14973352a1/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-b__x4m4f

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2c3a25ba-9397-4c1a-8223-5404fd0fa980/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-3ztxwcw8

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d2da0a3b-8482-460
                ..
                8/tmp/qiime2/uid=#1001/data/e5f75713-6910-4ab2-87d6-0c9d5b0abece/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-a5egfnbz

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/7af407ee-ccff-4d10-9418-4959a8cc2d2b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-c53v71w4

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2d3a4a3e-fc8a-463e-ab6f-6f700d9424e8/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-50lyyv4m

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/65faa03a-fecb-4437-ac52-a73402eb6467/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-e6qbd7b6

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a2bcad01-d604-40a4-bc12-2f5b683426cb/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-czi8zc7d

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c9638427-8e5f-45e7-9ea5-98cdc8437553/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-rjarz2t4

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/092658cc-1302-4aab-a894-cd8f7d2b76ff/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-r5zk_mhv

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/bf316883-c014-40ee-9af1-0312f8747616/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-cj8zrl8o

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/8a037dc3-2716-451c-99f3-045a90ea7f55/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-u53c75gy

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/6b47d93c-4ecb-41fb-9943-6a8c95915e96/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-1i43qbr0

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/56cd7dd7-4864-4248-bf7a-1534bbebef5b/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-q8y6fy56

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/785981a0-536e-4d78-b99e-2921f7a3632c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-aw4s_f9k

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/eac90758-8851-4d0e-bdc7-aa68ece4c4cf/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-stcmvfog

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/f6ef2d37-a9a5-4ca5-a5a6-bb24300be3bd/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-u0938q4z

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/b3923e16-67a8-470d-9064-b483b5f87d23/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-o9wqaojv

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/65d0de34-36af-4cde-b218-4b1812ca81b3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-qekjq4e_

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/6318263d-753d-4fa5-9404-27f23e33c51d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-tomj50lu

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d41ab9ee-1993-4f94-95fd-c91874066caf/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-l1u9r_we

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/03e753b1-5e63-4c6c-b334-c3fab41574a3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-06cu2lzb

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c90064e4-d75b-41de-9207-8c9d3f3b763f/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-q8g3ts__

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/884b21a5-1558-4bf1-9165-9a9ccbd3ded8/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-v6al2v51

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/362d7efb-21fb-4ce7-a59d-84e7971e4657/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-k8v_whyl

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a8734e63-19e6-4c4d-96ed-d57d43af96f9/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-70bisxvo

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/19dc9436-e8e9-4e7e-9f6c-79fd7cfc002d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-cr96vskv

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2375e143-3270-4453-b30e-c51872570793/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-quf33rs0

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d66c6515-f931-419f-8b89-f08c3554e729/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0pqko63u

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/dfa2f82e-74c1-4435-b16b-124e345d3aa8/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-pckvty18

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d5e785b0-42f2-40ed-aef4-2d3c12fec534/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-52fd9es8

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/e615caa6-e4f3-4e17-8e15-20c013780a46/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-bhnyb81o

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4fd9e499-a67b-4eb8-a1d4-7652353ffbff/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-4petu4qo

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d3c7978f-c304-4bd1-844e-a9aa60bbdab0/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-_v2375ne

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/8a74db7e-ac95-4b54-b4bd-63c6f0122430/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-s4qshvrw

                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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/9c0d20a1-d85f-4347-8278-c31de9bcdb75/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4c1523e3-a6b5-4566-8772-c5c206687f00/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0t8_kmc5

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "1cfb579f1ead11efa1ee2507fc704a63" ` |
                  | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * 46f1f506123eca11 - **history_state** * ok - **invocation_id** * 46f1f506123eca11 - **invocation_state** * scheduled - **workflow_id** * ce267ab5978d7745

  • ✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
    Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpotj7yt48/job_working_directory/000/13/configs/tmpnbm4aek6' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [18:16:01] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_47/pplacer.backbone.pypgznvw.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_47/pplacer.tree.vvs5tzc8.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_47/pplacer.extended.0.gd3e_egm.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_47/pplacer.extended.0.gd3e_egm.jplace [18:16:07] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_48/pplacer.backbone.g91b_hih.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_48/pplacer.tree.49m_ctbq.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_48/pplacer.extended.0.nsaq68y9.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_48/pplacer.extended.0.nsaq68y9.jplace [18:16:13] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_49/pplacer.backbone.iawrnybk.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_49/pplacer.tree.xdzjiuoy.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_49/pplacer.extended.0.ltvfx6jt.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_49/pplacer.extended.0.ltvfx6jt.jplace [18:16:16] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_50/pplacer.backbone.8orohee2.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_50/pplacer.tree.z21eyo85.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_50/pplacer.extended.0.s_lzvlcw.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_50/pplacer.extended.0.s_lzvlcw.jplace [18:16:19] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_54/pplacer.backbone.vw1u86yd.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_54/pplacer.tree.1as6939y.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_54/pplacer.extended.0.ulj9qsbw.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_54/pplacer.extended.0.ulj9qsbw.jplace [18:16:22] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_60/pplacer.backbone.1lymzgkn.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_60/pplacer.tree.cslhaltw.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_60/pplacer.extended.0.p2tdno8x.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_60/pplacer.extended.0.p2tdno8x.jplace [18:16:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_61/pplacer.backbone.303gd4ad.fasta, tree_file:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_61/pplacer.tree.v4q176ke.tre, info_file:/tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_61/pplacer.extended.0.gc_7mhds.fasta, output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tempssd-UfdaWdIb8c/q2-fragment-insertion.9n5jbkm6/root/P_61/pplacer.extended.0.gc_7mhds.jplace [18:17:06] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tmp-fX5cZke5qk/q2-fragment-insertion_placement.json [18:17:08] algorithm.py (line 195): INFO: Current execution Finished in 601 seconds [18:17:08] algorithm.py (line 197): INFO: All checkpointed executions Finished in 601 cumulative time ==> 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/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tmp-fX5cZke5qk . Consider removing /tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tmp-fX5cZke5qk if its files are not needed. Removing /tmp/tmpotj7yt48/tmp/tmp.9HS7wYdzxj/sepp-tmp-fX5cZke5qk Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "52544e6a1eaf11efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • Other invocation details - **history_id** * e9b3b430df46ce12 - **history_state** * ok - **invocation_id** * a369d4fbda309ba8 - **invocation_state** * scheduled - **workflow_id** * a369d4fbda309ba8

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmpotj7yt48/job_working_directory/000/17/configs/tmpqqxf0t26' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4eafa141-1079-4086-889e-25cc4d105e24/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-gkawkin0 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/1e88b55f-3909-42bf-ae49-d03b5dd9a8cb/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-z90p8qiu 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/206d9d38-c526-423f-92d9-669a8a9bd926/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-ge7yvhef 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/ede5e52d-ebc9-4c32-a5bd-fb576f9480b2/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-jmcjknze 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/97966d38-006c-488d-b27e-5d0b0a1a6840/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0k2ffqmr 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/6bd981c0-2aeb-4692-acf3-4b96f64bc23f/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-tzzjse_i Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. Command: faithpd -i /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/17a3fde6-745c-498d-b747-063db23d1c74/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-8i72hzsi 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/0d7c36f0-9992-4c40-a6c4-9e4627ef62fb/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-nbm8mtdk 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/ec52f61b-dd2f-4a7f-a5e4-2c5c700b3293/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-k2lhvulk 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/9bc83ea0-43df-425d-b2e1-fadf76ee4061/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-pcgxlzv2 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/280ad570-cab4-4a02-a403-30c46f8fe628/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-hjh67m56 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/88d979e9-3387-4fbc-b8d6-0811579a2aa3/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-o8cbdyrl 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a328c330-a6f0-4896-8c52-05b2aa0d42da/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-vwwslp65 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d5af91a9-10a7-4f4e-a492-4808fc1952ec/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-ahly_2z2 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2d177e48-5ebf-47b6-bcf1-8288334a84d8/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-5enacajr 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/9780a709-091d-4c6f-91f0-1f20778df9d5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-wv0fmv5z 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/e3b85665-a8b4-4474-88ae-4da515e1cd2c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-rvvz9si9 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/576ddc15-086c-4bcf-814f-b2e0e9c6c745/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0e9i1hhe 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/ffcebce3-9984-4600-8a43-3b29b46a44bd/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0pp3vlm_ 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/54efab6b-f01d-4eef-ab94-7267012db51e/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-utscfjqe 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/1353be0d-7657-40ad-8a11-8a15b7f0cc6f/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-_0a0vubx 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c7279bf2-21ae-4c8a-90a5-93cd8329bdc0/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-ctc7hyfk 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/0ecbb45b-cc32-4974-a270-713abb6ab90c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-l6c_vu9z 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/e1053d22-15ae-491d-b252-3b8db64cc21e/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-knv4q9s1 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/693548c4-6507-4189-91f3-1c2288ed805d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-13oz6vqv 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/dcabd828-9fb2-47ec-b043-47b2dadf6007/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-6f8pi4y9 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/2d6b4cf3-9b0e-4831-8aae-9dca61d7361c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-c3fztkbq 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/4473c8bd-1a8f-4d2a-a179-bfba08605e6c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-fcxt61xp 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/7fe1ea1a-4870-4490-875b-3117e4b3a21e/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-qtwveyw2 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/61537834-bb3a-412f-a18a-c0b91961cf65/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-d7bxw61g 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/137f5f55-a062-404b-b2e1-2b7f1ae4d5c5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-dlhqrpca 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/10239241-eea6-433 .. 8/tmp/qiime2/uid=#1001/data/651f9237-a82a-42db-a09b-5f55b844037c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-9ktpiami 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c788e11b-02b7-4f5c-8ea0-85f4156cc53c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-66_2ot4i 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/e0e95588-cf5f-4d29-bfa0-bcce17cd79ae/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-e4wt75bu 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/000160a6-a79b-480d-9adc-91c00a0187a5/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-1yl301dt 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a8bfa144-19c8-45e7-a6e0-b768bae97dde/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-e_n8kzm4 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/d489b140-ca67-459c-a625-82be39a3eca9/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-ejuhmfdh 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/dbbb49cd-6b37-4fa4-8bc5-76cd75843a52/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-ycqd9ufw 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/5ed984ee-7b42-470b-a401-0d9850f2248d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-8ban9ph_ 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/8d67de99-7f22-4783-a533-f2bc4732c122/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-u052wm77 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/cf0628ea-8d92-40c6-a36e-5fcff00c48b8/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-57t0paki 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a50093f5-b105-4b46-88f8-7cdf155afb09/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-bn52cxxe 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/0124adf9-eba2-40af-ba69-0981164ed29d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-rnnqph4k 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/658a8cfd-89c3-4ea4-ac5e-1f4d392fd687/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-p4kmwwgg 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/b0fe9b8a-6db4-4393-987a-388313e31641/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-5fnaq81z 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/77624869-4f7a-4ecb-82e4-c908b6c02581/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-i4wmvy5c 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/10f5c04c-05e3-46a5-9997-30ee400904b6/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-p1wegnze 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/c5dab925-64ee-45bd-9a8f-8d173e60b482/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-szvs6xz2 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/29e08c76-34ad-445c-9a3a-d6a164469c93/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-k58vtobk 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/1b9a757d-295d-4396-9b51-807984335b52/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-lai1v0na 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/5f071ada-afa6-435c-bdb8-32e810064dcc/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-2zp_x_5r 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/bfab6217-b6f8-4146-9e13-046e6f0d7be6/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-u6lmomm0 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/5abcf18a-1282-4f1f-ad64-94152364079e/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-uv872fvb 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/bc755dab-3b16-4e44-abb0-5847894e2685/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-1yx32cep 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/f5cad3da-f1c2-4af7-af70-ad33054a2ae4/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-z4303u7b 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/3689c45f-399d-406e-b4bb-e773bbb34a36/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-rni3nc_8 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/846aec0c-919f-4df8-a7a5-cba3c79df94f/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-g1l3_w8x 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/12cb0d6a-41aa-48d7-aa1e-2cde1dab1ddf/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-2jy6a10d 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/ad914eb2-7e2b-4fce-a998-9fcb330a0d23/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-0y56o8sh 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/04ad02f6-8ea3-4344-a5e3-284794ee80bc/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-hkubu2ar 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/393d6a81-5b9f-48dc-8df4-318840468751/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-tcwrwq9z 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/41ad0c74-206f-4df7-b6d7-507d24461a79/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-44zr6t4_ 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a1b56be9-e483-4ba0-8fc1-063f14af435c/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-c8y_mzti 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/tmpotj7yt48/tmp/qiime2/uid=#1001/data/a1c894a3-e962-49af-a122-062e5874ef4d/data/feature-table.biom -t /tmp/tmpotj7yt48/tmp/qiime2/uid=#1001/data/392dd29e-607a-46ec-95df-d12ac3cdcb39/data/tree.nwk -o /tmp/tmpotj7yt48/tmp/q2-AlphaDiversityFormat-a4gm2j5j Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 16, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 18, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "0fe3958e1eb111efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 4aaba6f769f0256a - **history_state** * ok - **invocation_id** * 333436a2362fd44a - **invocation_state** * scheduled - **workflow_id** * 333436a2362fd44a

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmpotj7yt48/job_working_directory/000/22/configs/tmp3hczi6_e' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "544a12481eb111efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/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:** * ```console q2galaxy run taxa barplot '/tmp/tmpotj7yt48/job_working_directory/000/23/configs/tmpquy4log5' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: 0021c260-3cf8-4375-870c-9fdaaf06ac65｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 20, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 24, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "544a12481eb111efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmpotj7yt48/job_working_directory/000/24/configs/tmp38yuio9r' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "544a12481eb111efa1ee2507fc704a63" ` | | chromInfo | ` "/tmp/tmpotj7yt48/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 24, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * ce267ab5978d7745 - **history_state** * ok - **invocation_id** * f722e62e6b38d2c6 - **invocation_state** * scheduled - **workflow_id** * f722e62e6b38d2c6

github-actions[bot] commented 3 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Phylogenetic tree for diversity analysis**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp30t15fe8/job_working_directory/000/6/configs/tmpqszwsa1w' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [09:03:26] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_47/pplacer.backbone.uwvuxapu.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_47/pplacer.tree.nvr4vo4n.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_47/pplacer.extended.0.mr0z7r8d.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_47/pplacer.extended.0.mr0z7r8d.jplace [09:03:32] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_48/pplacer.backbone.ekwbbk_5.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_48/pplacer.tree.z5pkkon9.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_48/pplacer.extended.0.htyg_g7n.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_48/pplacer.extended.0.htyg_g7n.jplace [09:03:38] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_49/pplacer.backbone.iq9ovx8z.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_49/pplacer.tree.q73blp4t.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_49/pplacer.extended.0.c6s3by00.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_49/pplacer.extended.0.c6s3by00.jplace [09:03:42] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_50/pplacer.backbone.8k8c_53g.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_50/pplacer.tree.llw1rr0m.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_50/pplacer.extended.0.l_wjm_ly.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_50/pplacer.extended.0.l_wjm_ly.jplace [09:03:45] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_54/pplacer.backbone.zny05fyk.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_54/pplacer.tree.5t89pqkf.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_54/pplacer.extended.0._5jf461i.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_54/pplacer.extended.0._5jf461i.jplace [09:03:48] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_60/pplacer.backbone.pbvyf0w9.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_60/pplacer.tree.p_phktsw.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_60/pplacer.extended.0.8djw1c7b.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_60/pplacer.extended.0.8djw1c7b.jplace [09:03:51] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_61/pplacer.backbone.wikca_5w.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_61/pplacer.tree.7bbt72x5.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_61/pplacer.extended.0._0h8kxvp.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tempssd-pLVnttnYgY/q2-fragment-insertion.j7oay7lv/root/P_61/pplacer.extended.0._0h8kxvp.jplace [09:04:34] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tmp-eRwEzAFF7W/q2-fragment-insertion_placement.json [09:04:35] algorithm.py (line 195): INFO: Current execution Finished in 625 seconds [09:04:35] algorithm.py (line 197): INFO: All checkpointed executions Finished in 625 cumulative time ==> 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/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tmp-eRwEzAFF7W . Consider removing /tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tmp-eRwEzAFF7W if its files are not needed. Removing /tmp/tmp30t15fe8/tmp/tmp.wUpVa4mkwm/sepp-tmp-eRwEzAFF7W Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "02b7b5cd2d5011efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmp30t15fe8/job_working_directory/000/7/configs/tmp6r3a7rqt'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "02b7b5ce2d5011efb6ec37d80a8de170" ` |
                  | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmp30t15fe8/job_working_directory/000/8/configs/tmp6d4fctxu'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: 988c4284-054b-4ca9-8e67-48aa89b1d73e｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "02b7b5ce2d5011efb6ec37d80a8de170" ` |
                  | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmp30t15fe8/job_working_directory/000/9/configs/tmpclw7r0v2'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "02b7b5ce2d5011efb6ec37d80a8de170" ` |
                  | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmp30t15fe8/job_working_directory/000/10/configs/tmptr9m3unt'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: 36bc2632-d41a-4069-9e56-5915916848cf｣
                ｢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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/491e9488-d301-44c5-8766-cab051f312d5/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-hmlsdywr

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/d6cb6264-ca3c-45d5-836d-4138f895fb19/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-lx79o39f

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3dcfc57b-3195-433d-a9d3-45b1df4a9692/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-qn6brur7

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e8aeb7f6-75ec-4c68-b4f5-f23f2a65369c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-tb4m6xkc

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/24ba196f-60f7-4aa7-a20a-c8209c6a6303/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-osmtsv5b

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/469cc36c-8f38-411f-a724-7347097fd479/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-k1djdzt1

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cced3d92-0470-4a0c-baf0-f7a40c0ff54d/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-hwx9qhf4

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/53c1bad5-95b9-48ce-b8f5-303f9c302fff/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-lggsry91

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/83deb288-df13-49de-850d-82ac38e69737/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ewai9ury

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/62291367-ea09-4547-b399-d026c8733a2e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ohj6is_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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/81c5ff70-64d6-4651-a434-718dc4c00191/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-vbfe983t

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b074e08b-eefe-4bc6-80a5-89f2f9ce48b8/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-u86brhmw

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e3cfa164-d235-45b4-a2df-4f0aea1c634f/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-vy9gtbaw

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/06a3d167-ecc3-482a-812e-9e5c2b692911/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-lr8hr3k9

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/68c75e34-be1e-4236-abbd-dfa31a89ffaa/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-20y36gzo

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/fd2c97ae-9b4d-40da-85b3-a58864daa41e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-w5spbzqd

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/8f0b5de8-2df0-433a-9c74-dc035f1cc0cf/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ljx0gfyg

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/ec37dc49-df89-4e27-b50b-b7948010c598/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-t3vsmrmp

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/4126456c-1b12-48e9-886c-b6361bb22615/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-pawrxknp

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/4be9ece5-771d-46a6-8853-ec8e5a2f2abf/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-p7k4act3

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/009ecdaa-c96e-435a-a3ff-e40305d499ce/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-q70khpoq

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/74b10946-e59f-45f8-895e-f3a95fb4e5ca/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-yel5ziok

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/034fd08e-8f3b-4ae3-883b-210fd0ea7654/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-__myqdll

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/6d5747ee-3e82-418d-ad8b-181f2f1f1ad3/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-zms23etr

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a4c8f3a4-d5f3-431b-b719-508cea5515b2/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-xmk1owfb

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/feeee11f-4037-46b4-8292-986c4ae3196b/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-p5tde2bi

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7f59e813-16c2-46be-b6bc-ae29b3803b07/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-0lhinm28

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cdff059c-8bc9-4a6e-8276-7c26ca4c0e88/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ia2lisup

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/ed552d93-bf35-4495-9f5f-fe849ed8154c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-1p8nrnsy

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/92ec24bf-2e62-4580-8cdb-ac7cc1f628a8/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-c87w6snm

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/191879ec-6a71-4664-8e06-7cd93d1be732/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-v81qgc85

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7e1a575a-4650-462
                ..
                8/tmp/qiime2/uid=#1001/data/75e085d0-db75-4d03-b17d-ceafab0459d1/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ey_5t3bf

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/370ee681-5f70-450c-bc2b-a781fbc3b2dc/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-vnnqdk9x

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b8111b4a-4a53-4f9b-8d97-f37de78c67d9/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-9e67zf8x

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/4b811ee1-9283-4173-90c3-919ee64bdac2/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-fgntcds0

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/98f1039f-1ed9-48be-9bdc-56967f6db8ca/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-9d4i89qo

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/bae5947c-6a8a-4201-8637-1a4bd63c4281/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-e0jqbisp

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7d323ba8-fb36-4cf6-872a-a33bcd0821b4/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-mtiqvuzt

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/d0126bdb-4f15-40a5-a34a-4a9c65a80006/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-qah2yip4

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/331d32b7-1146-4190-b495-22d93a7414b9/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-nmhnr88m

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/84fdf860-78ad-4737-819c-59cdb7ccb36e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-96ieaxqo

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3fc80b7d-fea9-4699-8c1f-6046d3357c8c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-vegznszs

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/c291a4f1-2f6d-4241-8ebe-8e265c529cca/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-9jyylfo4

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/5e3ddafb-f254-4529-8ff9-ad05e70a82a2/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-7u7hyxwf

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/5e3f6a12-36c8-4997-8d2a-e0ea39a2ff94/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ywjtm6ov

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/f12baf12-1117-4c13-8548-86f164fa37d0/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-x9xh964m

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7fc65b2f-d003-4202-8417-951799631dbc/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-pm52f4m3

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/1514ad52-14dd-4693-89e8-55962b716f24/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-u5wh3pqu

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/aebdff7f-f506-4373-a7b3-6c462331419a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-qo4mnvnm

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/9f6a111e-09c0-4df9-80d3-7806cfddaad9/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-bu6irrzv

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/404af3fc-0181-4ba2-86b4-1b9ea5b5f381/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ut5rf97o

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/23c5f8c8-3ebd-465f-abf6-3b2556867eff/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ga8gzgk4

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/15352a5d-83f7-47cc-bc14-7120ffd4bcfd/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-wv5pu94h

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/69f80651-2ace-4d74-b628-337f2b10bad7/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-48qtt5j4

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b752a21a-b5d9-447d-a20f-40e1c343fb36/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-wiurj5h9

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/33b752f9-a868-436d-af98-4ccb62830438/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ocg5bgib

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/275dc0f9-b90e-4be0-8ae2-48a664be8d66/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-449mtknp

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cc879ebf-a508-4ad8-ac0a-f71ba7a3f08c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-xk4jnffq

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/17683fb5-b475-4b63-aa77-d05a053316dd/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-v9tozb88

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/abdacdc5-355f-473d-9921-232b83d6b8ee/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-m_g4b7jz

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/21e3cba1-cbde-4c1e-98b0-9a8c4fc2df39/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-v1ut93sr

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/1d04e704-7210-446a-b27f-9014d5a19ad0/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-npl7ayeq

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cd686980-9c05-4d50-8540-6b10cf711ac1/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-784cerjo

                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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3c5dcede-1942-4fe5-82ee-d1bd36b17989/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/945e23ae-d6d1-4852-894f-9f3ed863c41e/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ii2tdfg6

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "02b7b5cf2d5011efb6ec37d80a8de170" ` |
                  | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * 0a8bc4e02d5cb071 - **history_state** * ok - **invocation_id** * 0a8bc4e02d5cb071 - **invocation_state** * scheduled - **workflow_id** * ecb8bb60c4382f2e

  • ✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
    Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp30t15fe8/job_working_directory/000/13/configs/tmpucoq63_q' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [09:17:03] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_47/pplacer.backbone.vfhjsxgo.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_47/pplacer.tree.xlr_nsnk.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_47/pplacer.extended.0.eu85h45x.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_47/pplacer.extended.0.eu85h45x.jplace [09:17:09] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_48/pplacer.backbone.oqmllg1m.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_48/pplacer.tree.rb4_1m59.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_48/pplacer.extended.0.d7oz8aso.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_48/pplacer.extended.0.d7oz8aso.jplace [09:17:15] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_49/pplacer.backbone.6smptr91.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_49/pplacer.tree.u8nuzd55.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_49/pplacer.extended.0.awds1dtl.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_49/pplacer.extended.0.awds1dtl.jplace [09:17:19] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_50/pplacer.backbone.jvpenwmf.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_50/pplacer.tree.gtr8x145.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_50/pplacer.extended.0.1hyciol_.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_50/pplacer.extended.0.1hyciol_.jplace [09:17:22] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_54/pplacer.backbone.d4likfjt.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_54/pplacer.tree.fj6ygkmv.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_54/pplacer.extended.0.jlt4jnfv.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_54/pplacer.extended.0.jlt4jnfv.jplace [09:17:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_60/pplacer.backbone.b8n3qvs1.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_60/pplacer.tree.yvs4ohve.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_60/pplacer.extended.0.6lnry1d_.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_60/pplacer.extended.0.6lnry1d_.jplace [09:17:28] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_61/pplacer.backbone.xsr6bvvt.fasta, tree_file:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_61/pplacer.tree.odu3a2ml.tre, info_file:/tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_61/pplacer.extended.0.y_f63kj3.fasta, output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tempssd-q2IMks7daX/q2-fragment-insertion.5fdhgdk1/root/P_61/pplacer.extended.0.y_f63kj3.jplace [09:18:09] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tmp-7jguIWONEq/q2-fragment-insertion_placement.json [09:18:10] algorithm.py (line 195): INFO: Current execution Finished in 604 seconds [09:18:10] algorithm.py (line 197): INFO: All checkpointed executions Finished in 604 cumulative time ==> 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/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tmp-7jguIWONEq . Consider removing /tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tmp-7jguIWONEq if its files are not needed. Removing /tmp/tmp30t15fe8/tmp/tmp.kkbKV3sszW/sepp-tmp-7jguIWONEq Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2cbeb5942d5211efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • Other invocation details - **history_id** * 26bca79d5c782664 - **history_state** * ok - **invocation_id** * 9a4eb007548fc2d5 - **invocation_state** * scheduled - **workflow_id** * 9a4eb007548fc2d5

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmp30t15fe8/job_working_directory/000/17/configs/tmphusntjw0' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/af468750-5c7b-445d-9b85-f7e36c35d2f5/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-u_8ft8pz 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7a01b0f9-3bf7-488c-99da-7b30b060c5c2/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-pz2_zklb 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/2c4995e4-4e0d-4d67-a2ee-acf09b5fb448/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-wxopcfky 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/c09b3787-c9dd-4741-853e-483f34e63e26/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-41a36i84 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/c5320b37-236c-426c-a1f3-9523e109c26e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-dejegq4t 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/4b6b0941-b1da-4061-a74c-65952845cfeb/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-mmpk011c 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a55f0440-17b8-4ea9-ac58-252f03f2c57d/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-d4gekmnh 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e0af4d02-cae1-46aa-a7af-2a8f887d90c1/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-8cpjlrqz 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/1a77cf8d-bc8b-457e-9fe1-95e3251aeb4a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-nh8woymj 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b3156f20-71b6-458d-b102-78d23110058e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-96bwuq6n 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/5234b144-d98d-4c98-9977-b9034a02c092/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-phjlh9m5 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/fdcd237b-07de-463b-899d-a6ddeaac0200/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ryzdc5__ 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/79ea3063-4365-47b7-8857-e427dedecae3/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-3j673zqu 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/31fc47ec-3f8b-4a10-b6a5-f723536d6e70/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-s_5z_4ib 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/08d93c39-08dd-48bf-8d2b-3c522d02b23a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-_mlzj6gn 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/ad3981f9-c55d-469c-a222-4e4e5c4d9d2e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-8h3vqy7y 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e188725f-4105-4a01-af3b-93b5bce6d976/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-qhsc3kxp 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/23b04b73-321d-46f0-ac89-a97813ce64da/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-kenv4rys 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/16cbdfcc-f7a8-40b1-9bc3-d47e99854029/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-unk0a6h1 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/d6b18465-bd3a-4214-9abe-cbe27b101b54/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-krckje5q 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/83ef295f-6f12-4c2c-a144-6d3ebd4ba6c7/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-v9011ezm 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/216c0c9f-d3aa-4bc4-9859-04bac4597e8a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-t8zthmrb 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/991ddbf4-1142-45a1-8558-346305e2a8b0/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-7zi0tjay 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/06f7a6b6-fd35-4e04-8a37-39275dfea2d7/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-zfbwe5ln 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b41031f8-13e7-4455-93af-183d8bfeb1af/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-8lj0e2wq 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/30ad7a7d-72b0-4541-ab09-c426e5fde972/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-o16jh_4j 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/51aa2ef1-c675-44b9-bd49-a48dcd0d328c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-4olly_9d 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/ecdada0c-031f-4b59-8032-0302dce90679/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-6y0nj8xr 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e1f73ad6-7db8-4fa2-bb96-5dea27175b7a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-5on6wel2 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cc969b07-5a41-43dd-9884-e3708aaf8a35/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-cu_7erbf 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a4c8236e-d2c8-460d-92cc-7ca5125190cb/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-v0calww0 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/0e901226-6b48-45a .. 8/tmp/qiime2/uid=#1001/data/9ea14c56-5c88-490f-b1b1-0c0aa7dabce8/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-edvfy38y 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/833d55a8-74a6-45af-b7f3-fb9f925f560f/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-78x6pli8 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/fa6411b7-6428-4da8-be89-2dda8279c361/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-8dcsty9o 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/bffc4594-3583-453d-b643-0375e18354f8/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-eyybwl7v 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e714681a-c761-4d0b-9405-757dc8c09770/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-akt5lsbd 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/079e1f47-001a-4d5d-8894-8f27619fbca6/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-rjth2raj 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a9925f9d-112d-4c13-a04b-e277e7d58c38/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-r_to3fp3 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/85964927-32b0-4774-85e1-d0104e36024e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-c5dgvckc 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b7ea5890-3695-45af-aa4d-65589b1b469e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-3ustjdk7 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/96e29494-6263-440f-b90b-35a737ffda54/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-1mbijr39 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/16e6f9cf-1bb2-44d8-b79f-dba9edf8422b/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-7djx5r45 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/95423e40-cf8a-493a-9912-a346f200de8c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-1qfi6_xf 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/dadcadd3-b378-4e94-91df-e746f6e35d4a/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-t_e8hboh 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/d768bd2a-c226-4348-9854-4ac1958dfa9b/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-0vcsfngc 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/831e87f4-af0c-4e22-8807-95112c803781/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-5ur9jshm 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7e6fa35f-d326-4855-96e3-44066a155aca/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-5p747g45 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b4428d4a-92b8-4e00-b2b8-4649df099031/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-yzzhbbvq 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/5f7b793e-150d-46a6-be7f-91cd7f256177/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-k4bxm0b9 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/a5039d9c-cfe0-47e3-b7d4-40ebc589aacd/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-dxdb13c3 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/2dcc3ae0-1cf3-41a0-a974-fce851c5737f/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-qf6fts7o 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/e07572c2-337c-4fbf-aa7d-4680a34cd01f/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-g407oybu 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/07f88d9c-040a-4458-a1be-71a855cd4c9f/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-9im2b7tq 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/c144f317-97a1-4048-bdf8-766f6bd60519/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-ap1uwk11 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b402467c-eddb-46d8-bda3-7900bc417533/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-d10ycjk8 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b667c341-b9bf-4c08-b628-6695c5cb9e5d/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-nirjm2ur 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/5c590a8f-db41-462a-a720-0be9965c704c/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-xslo6m4h 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/c81c0c9c-3e42-4e19-9437-a71311b64985/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-arrj3xi_ 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/68a9aa0f-bc1c-48a2-b62b-1bb8617ccdff/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-o581fxzf 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3a439568-a557-42c6-8c70-f27d0a31a1f4/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-gij70a4j 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3d237244-9f94-45c9-a7ff-52f58e309157/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-g2vchiz8 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/7381f521-a6f9-4a27-a1b1-229ca8335462/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-g8m28nyy 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/cf2bafd4-fc93-4f19-bc05-2491e4346c7e/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-g_snu5_m 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/tmp30t15fe8/tmp/qiime2/uid=#1001/data/b1bf465c-f2b5-4285-9e10-bad09362b1f0/data/feature-table.biom -t /tmp/tmp30t15fe8/tmp/qiime2/uid=#1001/data/3548145e-088c-4db1-8de0-20e2931fb2ff/data/tree.nwk -o /tmp/tmp30t15fe8/tmp/q2-AlphaDiversityFormat-synr6vnh Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 16, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 18, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "ec9a67f42d5311efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 55440a29039a69b6 - **history_state** * ok - **invocation_id** * f509b3e15481247c - **invocation_state** * scheduled - **workflow_id** * f509b3e15481247c

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmp30t15fe8/job_working_directory/000/22/configs/tmp70r_8sv3' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2f0f40782d5411efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/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:** * ```console q2galaxy run taxa barplot '/tmp/tmp30t15fe8/job_working_directory/000/23/configs/tmpd3v9ln74' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: 62836df1-5bb6-456e-8e7a-441a9e1d2e7e｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 20, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 24, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2f0f40782d5411efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmp30t15fe8/job_working_directory/000/24/configs/tmpnztatp8v' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2f0f40782d5411efb6ec37d80a8de170" ` | | chromInfo | ` "/tmp/tmp30t15fe8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 24, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * ecb8bb60c4382f2e - **history_state** * ok - **invocation_id** * ee6a9b3bfd9f1d71 - **invocation_state** * scheduled - **workflow_id** * ee6a9b3bfd9f1d71

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Phylogenetic tree for diversity analysis**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp4ht6r3zq/job_working_directory/000/6/configs/tmp7kc8aeoi' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [11:40:18] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_47/pplacer.backbone.n14t8zhk.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_47/pplacer.tree.f4tf_sr6.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_47/pplacer.extended.0.945qt4q3.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_47/pplacer.extended.0.945qt4q3.jplace [11:40:24] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_48/pplacer.backbone.s2h6_p2r.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_48/pplacer.tree.epwsuxfa.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_48/pplacer.extended.0.p96xz50i.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_48/pplacer.extended.0.p96xz50i.jplace [11:40:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_49/pplacer.backbone.3_ma77ze.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_49/pplacer.tree.609cq94g.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_49/pplacer.extended.0.2n5qozzo.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_49/pplacer.extended.0.2n5qozzo.jplace [11:40:34] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_50/pplacer.backbone.ysfstx60.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_50/pplacer.tree.dkcvqu5e.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_50/pplacer.extended.0.8ko9h9lh.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_50/pplacer.extended.0.8ko9h9lh.jplace [11:40:37] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_54/pplacer.backbone.pmya5a6j.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_54/pplacer.tree.w18ez6m6.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_54/pplacer.extended.0.u8l9sipc.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_54/pplacer.extended.0.u8l9sipc.jplace [11:40:40] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_60/pplacer.backbone.pybdqwms.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_60/pplacer.tree.aim3mjdj.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_60/pplacer.extended.0.g36yu2o0.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_60/pplacer.extended.0.g36yu2o0.jplace [11:40:43] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_61/pplacer.backbone.pap27i1z.fasta, tree_file:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_61/pplacer.tree.02lk6gky.tre, info_file:/tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_61/pplacer.extended.0.ugksj7zx.fasta, output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tempssd-bC99ezUa64/q2-fragment-insertion.614k5ncv/root/P_61/pplacer.extended.0.ugksj7zx.jplace [11:41:24] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tmp-HzLX0Kilb0/q2-fragment-insertion_placement.json [11:41:26] algorithm.py (line 195): INFO: Current execution Finished in 614 seconds [11:41:26] algorithm.py (line 197): INFO: All checkpointed executions Finished in 614 cumulative time ==> 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/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tmp-HzLX0Kilb0 . Consider removing /tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tmp-HzLX0Kilb0 if its files are not needed. Removing /tmp/tmp4ht6r3zq/tmp/tmp.anX6xGrpId/sepp-tmp-HzLX0Kilb0 Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9ee431ff308a11efa56439b9572c1a56" ` | | chromInfo | ` "/tmp/tmp4ht6r3zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmp4ht6r3zq/job_working_directory/000/7/configs/tmp2chj02aj'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "9ee43200308a11efa56439b9572c1a56" ` |
                  | chromInfo | ` "/tmp/tmp4ht6r3zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmp4ht6r3zq/job_working_directory/000/8/configs/tmpwxx5ji2u'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: b6142374-29fa-45fd-845c-539e6dd31a84｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "9ee43200308a11efa56439b9572c1a56" ` |
                  | chromInfo | ` "/tmp/tmp4ht6r3zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmp4ht6r3zq/job_working_directory/000/9/configs/tmprxvy67mg'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "9ee43200308a11efa56439b9572c1a56" ` |
                  | chromInfo | ` "/tmp/tmp4ht6r3zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmp4ht6r3zq/job_working_directory/000/10/configs/tmp3n6lne5h'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: bb52dc4e-f9d6-49e9-bf42-3aa42829dacb｣
                ｢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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/38103d95-c434-4819-b5f4-8693a44227bf/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-f1fy8umj

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/9d67b66e-9c4f-4e6a-bd08-34b6fdb2f638/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-mxondtje

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/c3edee96-d8b9-41b8-b453-7aa1f83c92a7/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-vd5jrwm1

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/12a460a8-6d29-48cd-a45b-5fda454c9342/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-231bx1k9

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/fe854e5a-7ab5-4c4c-b796-2925a6f2de97/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ungjhlkf

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d367d4b7-8ba3-4056-9025-dd22fd9ede00/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-zl119roa

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/1f95a058-5940-42af-8bcf-9e415803a38f/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-tz79ws09

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/b7966433-4091-4d8a-8dd3-46dcefefd914/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-sysi_sqn

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/06712f74-5c2a-4950-bcf0-18777ce076a6/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-77p_sx44

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/459e0a6c-22c0-401f-921c-b7f1b7714fed/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-82gt2fif

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/77c0ea9e-143a-4b22-bc59-73477892483a/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-c6_e29_p

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/fb8d9f61-d862-4ca3-a154-01ab6caa1245/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-xpvkh0i6

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/dfdde382-13eb-4026-92c7-7b3a40bcf5a7/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-b7h7uugt

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a9e57fc4-1cec-41c6-b32a-963b94a8602a/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-p2j0x9ye

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/014f16dd-7927-4d59-a4a4-9c16081e3342/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-bytquqc0

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/9215f18f-94e0-488d-a1c2-2a0e0a3f5ea4/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-tt6fa6me

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/8d9bb55a-a350-4faf-b4cf-944745be9501/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-jv1o5fc3

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/8c7a4c52-860e-4c9b-95ee-24a68f45ca2c/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-w55nyx2a

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/f26704d6-5867-4e3e-b06b-eec5ef282b19/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-fmn06iib

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/bbf57b42-9613-4da4-a314-f09786beadfa/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-gxgo5bq0

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/7986257a-b85a-4a25-b348-be34e0b62760/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-scgnf6j8

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/f80cec99-b1a3-4edc-b7f8-bcb73531a3c9/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-dznvqqio

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/35e51aac-e931-4442-8d5e-e53683dc82bd/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-xmdsa817

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/e423cc00-f644-4950-907d-4de494b1d563/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-g9wy46w9

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d250fd48-8f15-4474-94e2-ceeb0a19cfcf/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-z6gsr_zu

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/4d5f45fa-d96b-4b3e-b85b-c72da478e406/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-4j2t7s8d

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/ae483cf9-6afb-4d1e-bb82-761729f45034/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-83lripav

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/9bec53ba-c8fd-4515-9e29-8a1b12da6f9c/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-cd9gh4iw

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/e10ccbce-fa09-45b2-b10b-b412afc42c93/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ckdkhg_7

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/19087308-b40f-4632-8a7f-61a6e7fbbb64/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ns5c3ooa

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/91906dc5-0fa7-4125-ae7a-b6bbe7b008a7/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-o0btjpjz

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/7afd9f95-c5f5-489
                ..
                q/tmp/qiime2/uid=#1001/data/09213602-4f9f-415e-af8e-1c6728808b3a/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-xfm923g3

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/77c31069-f428-4310-afc3-2e6b5ddf84f4/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-l26eq1r1

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/0ab7ceed-9f0c-4b57-a682-221adf95cbcb/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ul7_5t0j

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/9c23c577-a5d0-42d3-9098-708f2787d505/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-01vuziea

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/10833dde-3825-4fd1-ae18-7bf3d89c136d/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-a8iabxqn

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/78d9144e-9ff8-4966-aec8-499c6bf25b56/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-p28kld18

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/e97281f0-48a9-4d04-ba1f-75adb244bbff/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-f013catd

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a1b74710-6f1c-4955-b6d7-84713f75c818/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-s2qmc7qe

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/49b81aa6-85e5-4eff-8df7-da67f77f8b2e/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-2yprjx5i

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/98ae2aed-5ae3-48dd-9171-003d39367e93/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-jlj44u_r

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/0dbef2f1-6dad-4ce9-bbc4-c7edea527d42/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-4j95xcr_

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/a70474c8-2e14-48fb-8118-af9052b56f4f/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-3k9kx9ft

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/ba9e6663-89a6-40da-8243-4cf10f93b6c1/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-tiawr47o

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/7532d282-819a-42fa-9bb7-5c5f499611a2/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-kllhuojg

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/c3d0004b-8ef9-45ee-bfa1-c5f2f83d89c7/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-53b6ykxa

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/6333355d-d989-4d6f-969a-4cbc1a6e333a/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-bob4tsyp

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/fc211501-37fe-4a41-b6f0-1173849db91c/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-9eypnu9z

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/56c6eb05-1d0f-4d2a-81da-b1e4c3195b8d/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-_9y7i0et

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/7ea1f580-87e0-48ee-8635-eea7a720e661/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-iglbb096

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/2d679c7b-b2fb-47b6-8e7c-8de76f7445d1/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-wedpbvna

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/65abecff-e0ed-48f6-aec4-c436a916d66e/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-5p6x8gse

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/ad4a366f-393b-45a2-8dbd-87c120b84213/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-abc6hged

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/5f354b11-fe15-4bd7-bc9b-291210810c94/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ewsu41y3

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/179bae81-b478-48f7-b2ab-1a9a52949830/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-m37ffbxw

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/f75ef69e-54b3-410f-a28e-08017b43ab65/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-mlitpap1

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/04b2814e-f5e8-4e80-bfb9-efad6d1ef5b9/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-rg2fpp3c

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/e41f0af6-1fa1-4b05-ba94-69cfbb0aee38/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-mxbjah0u

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/142bdc5f-ad6a-4165-83c1-39b164359c27/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-ekbgj4cz

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/996b4dc3-3f71-4473-9314-d0966d8d9dc7/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-117k4e__

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/8dfeffd0-e10b-4c8a-9487-13a77bf535c5/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-09p63_7o

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/22df7bc6-fdec-43b7-b588-d7d0ade2c2d3/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-lflonode

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/e1beb98f-4d1b-47ec-a3bf-614b10847c92/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-imtjkijp

                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/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/68cfe4ab-f484-44e2-8168-73a45e3a7877/data/feature-table.biom -t /tmp/tmp4ht6r3zq/tmp/qiime2/uid=#1001/data/d124681d-f619-4967-8fef-01a529b10112/data/tree.nwk -o /tmp/tmp4ht6r3zq/tmp/q2-AlphaDiversityFormat-yk3bfzx2

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "9ee43201308a11efa56439b9572c1a56" ` |
                  | chromInfo | ` "/tmp/tmp4ht6r3zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * 97c6d8516b8759f3 - **history_state** * ok - **invocation_id** * 97c6d8516b8759f3 - **invocation_state** * scheduled - **workflow_id** * 69e271bcb3e0b5cc

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Phylogenetic tree for diversity analysis**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmp9664o0ez/job_working_directory/000/6/configs/tmpl3iq_0sf' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [14:05:14] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_47/pplacer.backbone.g9wesztd.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_47/pplacer.tree.tgczkpm_.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_47/pplacer.extended.0.xcmje5vn.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_47/pplacer.extended.0.xcmje5vn.jplace [14:05:20] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_48/pplacer.backbone.q7ypgk4n.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_48/pplacer.tree.k4yyw669.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_48/pplacer.extended.0.c_xs05d9.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_48/pplacer.extended.0.c_xs05d9.jplace [14:05:26] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_49/pplacer.backbone.1gvj02x1.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_49/pplacer.tree.s1_eiygi.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_49/pplacer.extended.0.vs8lu8j6.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_49/pplacer.extended.0.vs8lu8j6.jplace [14:05:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_50/pplacer.backbone.cf0bc94n.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_50/pplacer.tree.6j5lmisa.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_50/pplacer.extended.0.2oyfrqie.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_50/pplacer.extended.0.2oyfrqie.jplace [14:05:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_54/pplacer.backbone.39q5mc94.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_54/pplacer.tree.ctbwffaz.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_54/pplacer.extended.0.sc725q9d.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_54/pplacer.extended.0.sc725q9d.jplace [14:05:36] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_60/pplacer.backbone.x4rrqetl.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_60/pplacer.tree.09yku4z4.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_60/pplacer.extended.0.zunu65cx.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_60/pplacer.extended.0.zunu65cx.jplace [14:05:39] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_61/pplacer.backbone.d_1szk6k.fasta, tree_file:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_61/pplacer.tree.0_ac4k0o.tre, info_file:/tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_61/pplacer.extended.0.7b6t3qcj.fasta, output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tempssd-GsbooO56wv/q2-fragment-insertion.ekxj_aw7/root/P_61/pplacer.extended.0.7b6t3qcj.jplace [14:06:20] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tmp-RPFqoJ0oGN/q2-fragment-insertion_placement.json [14:06:22] algorithm.py (line 195): INFO: Current execution Finished in 608 seconds [14:06:22] algorithm.py (line 197): INFO: All checkpointed executions Finished in 608 cumulative time ==> 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/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tmp-RPFqoJ0oGN . Consider removing /tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tmp-RPFqoJ0oGN if its files are not needed. Removing /tmp/tmp9664o0ez/tmp/tmp.RWIhlTrrFl/sepp-tmp-RPFqoJ0oGN Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "dfad7def309e11ef9562e5df34c94bba" ` | | chromInfo | ` "/tmp/tmp9664o0ez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmp9664o0ez/job_working_directory/000/7/configs/tmp4_joznrh'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "dfad7df0309e11ef9562e5df34c94bba" ` |
                  | chromInfo | ` "/tmp/tmp9664o0ez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmp9664o0ez/job_working_directory/000/8/configs/tmpnqu900a1'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: 85153256-8df1-4baf-b22a-94d8bf970f55｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "dfad7df0309e11ef9562e5df34c94bba" ` |
                  | chromInfo | ` "/tmp/tmp9664o0ez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmp9664o0ez/job_working_directory/000/9/configs/tmpall62rb3'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "dfad7df0309e11ef9562e5df34c94bba" ` |
                  | chromInfo | ` "/tmp/tmp9664o0ez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmp9664o0ez/job_working_directory/000/10/configs/tmp328nom3g'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: 576d7663-9f3a-4579-b021-3270e5935278｣
                ｢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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/d565443c-02e6-4d28-96c8-d50be96c2999/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-vh_cf55c

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5b8d39f5-9e21-42a7-aa18-b809c1087680/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-oa8l3ant

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/3d1099af-9e7a-4b31-a141-1f050408ae3c/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-vcx1fkan

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/922054bd-da84-4241-9c93-6f7e0eaff566/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-dwk2_4v_

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/31a7bd63-1e8d-41ee-867a-c75d3d2c353a/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-s8q7nuod

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/1b3af3b6-604a-4e03-a46b-9d5d54b70a6a/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-_zlhfh6n

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/77dd0359-9052-4d57-94bc-082aef1d9659/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-g92pi4o1

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/7b15b509-024f-4b2d-b58b-c1bacdb12482/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-4sbrv5tu

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/1e6b0069-1ae0-453e-a99f-bf8d2c1c387e/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-awconby6

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/9d2ac4eb-7a22-4ac5-81e9-eff4d006d602/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-910v7lbo

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5256cc9f-1c84-4670-8fa6-d40270145d84/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-ma8oxp43

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/3e73315e-611b-4cb4-b7cd-7930ace17bc4/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-wh6m6z7a

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/c5a8df02-8402-4665-bf52-2a95db2ec93e/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-f9ijh0pi

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/28542422-b675-43c8-bea3-0ed85d29c351/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-zup3xb8d

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/c6329d68-3aac-4b6c-833a-9c46273d2357/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-0ipn295i

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/6f3e8213-0e66-4ec3-a265-0dce248ade8d/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-9wlzcbfl

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/47f32edd-7aea-48cd-92d9-5043a61eaedc/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-qdwa53b5

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/0af04ce3-53de-4524-9c84-4db3c668cd76/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-0qxa7ao6

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/69881067-444b-4ec0-8f1c-d4d5ffca4a2a/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-rocbopz8

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/26f2d90d-7046-4d62-93cb-387d67011284/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-b_rtqdg3

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/3ff86e45-4789-4863-99c8-c024661afb14/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-gh_up3sa

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5a2220fa-f053-4fbb-bf65-c260442f4cff/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-4sk0ifme

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/17258eb2-c27f-4ae4-80a9-57161fbf56b2/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-z7kj6xl9

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/44ccf8f2-e4f7-43dd-b164-75224a43fc60/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-pcvrw12x

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/86d829f5-d316-4dd8-abdf-bfb1afd1d604/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-s8u2ien2

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/30019c0a-f717-40d3-90ee-9ace34f18352/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-ckffdc5g

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/71799b1d-56f7-465b-94d9-81523568efaf/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-x2talwed

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/0a77789c-f854-4ff0-847f-fad23f25ee7c/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-ki41jppo

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/93ffd50b-e1cf-4e21-9740-2ce01d1e749a/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-ras7tt7_

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/72261b76-a874-461b-bf62-83262b63ee67/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-d5fq_s0g

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/bb2fd340-81e2-4ed3-9eb9-8644387a72ae/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-dhnj0w6b

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/f55825a0-fb86-4ff
                ..
                z/tmp/qiime2/uid=#1001/data/8e5a2315-e6fd-41db-a39e-874b2b5ca748/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-dubu_zvi

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/2b9e7092-1138-446f-b554-3ae56c001bb4/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-8671ms17

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/7af7c11e-25c2-47a0-a358-5037da6d1787/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-pij6ba4f

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/bc08626c-c709-42b8-af62-ea2603014031/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-1rq6wxrf

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/43484516-b5e3-4a1f-892c-ce2a0147d511/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-_tg6ndhq

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/ceae9e03-955d-4107-a3e6-17ad6fea7473/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-pgzdksn9

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/9e759281-4e39-48ef-a754-5a7bec71bd35/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-skyz4hgb

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/1c4bf8ab-636b-4acd-a135-8d22af323eac/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-y96fjvxf

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/c5d543ec-14a3-4f6a-a421-384adff504cc/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-5f54u3u0

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/71d7a3de-344f-42c9-af1f-ec1db46d898c/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-37vvpt4y

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/0836255c-5711-4819-9e2a-7a48e25eb2e7/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-9853e48q

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/536cf780-18b5-4ef6-98bb-5779db7586b1/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-7lokqj0_

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/189391a5-d9a6-47c5-8aca-3061ae752640/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-yfxgbjoi

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/b66e3315-ede9-4de8-9c04-1f282602e183/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-w1hx7a8p

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/74f094d9-8b54-428a-81e4-17bfc2b22058/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-atputi2b

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/8bd013f7-51ce-4eb8-86ce-32502dae6e37/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-_ohk7_em

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/e8efe588-820e-46ba-b989-f13613001786/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-9fyzj4zx

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/b8f22191-8dbf-4940-8a0d-ddbb0c33ca1d/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-e_n_a73z

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/97ad6cc6-196a-47e2-8e20-c0374b802f5b/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-7o2p6j9w

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/744c9b9b-9524-4124-98e4-ee4a035ac749/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-rhpfnzyh

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/41e85200-dc8e-47a0-88b8-4dfe0143968f/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-398pa99h

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/e040d48e-a390-4852-938a-02a85cd80801/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-a9ktr0v7

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5d1ef6ef-b8fb-4dd8-9e70-44f824958baf/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-fpjhp6ji

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/379817b7-9aa3-4af0-a261-5f3fd75cb7c7/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-ojgcu9ig

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/7a46b501-8909-44eb-8362-bb216485f67e/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-8b1v1683

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/dfd69d5e-73b0-487f-a186-122fd36b10b0/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-xc_sy9wh

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/44658337-60c5-4e73-82c7-f98d60e883b3/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-5x46e2u5

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/dd60ce9e-a3a0-4c95-a721-8dec1f8e0a68/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-y39da32u

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/30146b57-fc71-4aba-a9fc-c271515bd185/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-k7yq87rs

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/dc36117f-14a6-4cff-8e9c-96deefee6083/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-cm22eq92

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/51269e90-a384-4a51-bb41-e115a9be7eb6/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-egluxgs4

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/23756425-7c69-4a8a-9ae1-3154a5d511c1/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-bzrqrrdu

                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/tmp9664o0ez/tmp/qiime2/uid=#1001/data/9a562dc0-59a9-44d7-a48d-f6191708a759/data/feature-table.biom -t /tmp/tmp9664o0ez/tmp/qiime2/uid=#1001/data/5445cd51-f500-4afb-8653-d66aee47c3a9/data/tree.nwk -o /tmp/tmp9664o0ez/tmp/q2-AlphaDiversityFormat-3fh8ojqc

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "dfad7df1309e11ef9562e5df34c94bba" ` |
                  | chromInfo | ` "/tmp/tmp9664o0ez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * 7fcb0d74dc0b6553 - **history_state** * ok - **invocation_id** * 7fcb0d74dc0b6553 - **invocation_state** * scheduled - **workflow_id** * f29dfd511f7afb60

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
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 error **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpe18gwman/job_working_directory/000/6/configs/tmps8xxzo43' ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console This plugin encountered an error: /tmp/tmpe18gwman/tmp/qiime2/uid=#1001 /data/455eda14-0d01-4a9b-98af-d3eaa0c 0d79a/data/dna-sequences.fasta is not a file. :( Traceback (most recent call last): File "/opt/conda/envs/qiime2-2023.5/bin/q2galaxy", line 11, in sys.exit(root()) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/__main__.py", line 98, in run action_runner(plugin, action, config) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 30, in action_runner results = _execute_action(action, action_kwargs, File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped return function(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 115, in _execute_action return action(**action_kwargs) File "", line 2, in sepp File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable outputs = self._callable_executor_( File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in _callable_executor_ output_views = self._callable(**view_args) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp _run(str(representative_sequences.file.view(DNAFASTAFormat)), File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 82, in view return transformation(self.path_maker()) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view, level=validate_level) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/transform.py", line 143, in validate view.validate(level) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 22, in validate raise ValidationError("%s is not a file." % self.path) qiime2.core.exceptions.ValidationError: /tmp/tmpe18gwman/tmp/qiime2/uid=#1001/data/455eda14-0d01-4a9b-98af-d3eaa0c0d79a/data/dna-sequences.fasta is not a file. ``` **Standard Output:** * ```console This plugin encountered an error: /tmp/tmpe18gwman/tmp/qiime2/uid=#1001 /data/455eda14-0d01-4a9b-98af-d3eaa0c 0d79a/data/dna-sequences.fasta is not a file. :( ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "0eab86d730a411ef94833378726b6132" ` | | chromInfo | ` "/tmp/tmpe18gwman/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmpe18gwman/job_working_directory/000/7/configs/tmpgfhzlz_k'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "0eab86d830a411ef94833378726b6132" ` |
                  | chromInfo | ` "/tmp/tmpe18gwman/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is running

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmpe18gwman/job_working_directory/000/8/configs/tmpf824mq9b'
                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "0eab86d830a411ef94833378726b6132" ` |
                  | chromInfo | ` "/tmp/tmpe18gwman/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is running

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmpe18gwman/job_working_directory/000/9/configs/tmpe4r3uv6w'
                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "0eab86d830a411ef94833378726b6132" ` |
                  | chromInfo | ` "/tmp/tmpe18gwman/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is paused

             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "0eab86d930a411ef94833378726b6132" ` |
                  | chromInfo | ` "/tmp/tmpe18gwman/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * f0416fbf8890f106 - **history_state** * error - **invocation_id** * f0416fbf8890f106 - **invocation_state** * scheduled - **workflow_id** * e3829475a2b58ad4

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 3
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 error **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpd8wf3q41/job_working_directory/000/6/configs/tmp7bydeayi' ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console This plugin encountered an error: /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001 /data/455eda14-0d01-4a9b-98af-d3eaa0c 0d79a/data/dna-sequences.fasta is not a file. :( Traceback (most recent call last): File "/opt/conda/envs/qiime2-2023.5/bin/q2galaxy", line 11, in sys.exit(root()) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/__main__.py", line 98, in run action_runner(plugin, action, config) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 30, in action_runner results = _execute_action(action, action_kwargs, File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped return function(*args, **kwargs) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2galaxy/core/drivers/action.py", line 115, in _execute_action return action(**action_kwargs) File "", line 2, in sepp File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable outputs = self._callable_executor_( File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in _callable_executor_ output_views = self._callable(**view_args) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp _run(str(representative_sequences.file.view(DNAFASTAFormat)), File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 82, in view return transformation(self.path_maker()) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view, level=validate_level) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/transform.py", line 143, in validate view.validate(level) File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 22, in validate raise ValidationError("%s is not a file." % self.path) qiime2.core.exceptions.ValidationError: /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/455eda14-0d01-4a9b-98af-d3eaa0c0d79a/data/dna-sequences.fasta is not a file. ``` **Standard Output:** * ```console This plugin encountered an error: /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001 /data/455eda14-0d01-4a9b-98af-d3eaa0c 0d79a/data/dna-sequences.fasta is not a file. :( ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "268c7bbd30a811efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmpd8wf3q41/job_working_directory/000/7/configs/tmpaxzjs0n0'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "268c7bbe30a811efaf0a7d68e481b0dd" ` |
                  | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is running

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmpd8wf3q41/job_working_directory/000/8/configs/tmppy0do1es'
                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "268c7bbe30a811efaf0a7d68e481b0dd" ` |
                  | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is running

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmpd8wf3q41/job_working_directory/000/9/configs/tmpat0tzm12'
                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "268c7bbe30a811efaf0a7d68e481b0dd" ` |
                  | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is paused

             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "268c7bbf30a811efaf0a7d68e481b0dd" ` |
                  | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 52f701f390b1fbf2 - **history_state** * error - **invocation_id** * 52f701f390b1fbf2 - **invocation_state** * scheduled - **workflow_id** * 4f390845dac9a20e

Passed Tests *
✅ QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpd8wf3q41/job_working_directory/000/13/configs/tmp4n3s0p44' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [15:13:00] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_47/pplacer.backbone.jymxid_l.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_47/pplacer.tree.pgkr1owq.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_47/pplacer.extended.0._fw7rfbx.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_47/pplacer.extended.0._fw7rfbx.jplace [15:13:05] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_48/pplacer.backbone.h7zgfkgv.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_48/pplacer.tree.0ny0wjqv.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_48/pplacer.extended.0.xthrxi59.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_48/pplacer.extended.0.xthrxi59.jplace [15:13:11] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_49/pplacer.backbone.u5x3heo3.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_49/pplacer.tree.otn440j7.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_49/pplacer.extended.0.ri1dtwr5.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_49/pplacer.extended.0.ri1dtwr5.jplace [15:13:15] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_50/pplacer.backbone.pdjquves.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_50/pplacer.tree.loj072xv.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_50/pplacer.extended.0.zwsjb1ah.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_50/pplacer.extended.0.zwsjb1ah.jplace [15:13:18] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_54/pplacer.backbone.rknc9coj.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_54/pplacer.tree.t3gxt_wz.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_54/pplacer.extended.0.9l_wwm_x.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_54/pplacer.extended.0.9l_wwm_x.jplace [15:13:21] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_60/pplacer.backbone.qduq58i9.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_60/pplacer.tree.22f2qul5.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_60/pplacer.extended.0.ee_2i7a4.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_60/pplacer.extended.0.ee_2i7a4.jplace [15:13:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_61/pplacer.backbone.ogvf54f6.fasta, tree_file:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_61/pplacer.tree.jm6q48xf.tre, info_file:/tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_61/pplacer.extended.0.5jy9ms9s.fasta, output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tempssd-mAFauVCJjG/q2-fragment-insertion.tas0jnsc/root/P_61/pplacer.extended.0.5jy9ms9s.jplace [15:14:06] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tmp-H3wNu0laNA/q2-fragment-insertion_placement.json [15:14:08] algorithm.py (line 195): INFO: Current execution Finished in 602 seconds [15:14:08] algorithm.py (line 197): INFO: All checkpointed executions Finished in 602 cumulative time ==> 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/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tmp-H3wNu0laNA . Consider removing /tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tmp-H3wNu0laNA if its files are not needed. Removing /tmp/tmpd8wf3q41/tmp/tmp.32hqrwcwGI/sepp-tmp-H3wNu0laNA Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "91bfc98e30a811efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
  </details>
  • Other invocation details - **history_id** * f5eea06ee3d0ad40 - **history_state** * ok - **invocation_id** * 6d7538a3aa5c82ab - **invocation_state** * scheduled - **workflow_id** * 6d7538a3aa5c82ab

  • ✅ QIIME2-IV-rarefaction.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run diversity alpha_rarefaction '/tmp/tmpd8wf3q41/job_working_directory/000/17/configs/tmpbhpmzf_m' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. median_ = grouped.median() ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢max_depth: 2019｣ ｢phylogeny: b37f57aa-ce89-466a-82e7-14a9417b8cd0｣ ｢metrics: None｣ ｢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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e03d3c35-02b2-4879-9b55-03a6a3266333/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-rg75n3m9 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/da855269-df47-4383-a983-549701df850e/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-gnv6todr 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/4beda408-aeae-4789-874c-1bd35762ab71/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-6tkkblws 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/5a634e3f-3a59-4301-82cf-15f94c39cea5/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-g190e951 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/46281755-30c2-4d37-8ba7-f23534322eae/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-euyi9j0s 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/7cb959ff-e03c-461a-b80d-33f51194b08d/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-zs9xk8yx 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/3df6e0ca-428d-458e-91cc-00d13ca41d19/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-oacetwoi 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/720a92b3-2fb5-4ef4-8545-c63fbdfc9bd5/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-j99y88k1 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/1612299f-a3ca-4b12-ba5e-30ae92a4b2df/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-2zxxlids 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/6765f48c-9b5a-45e8-8a26-75c5056d3e63/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-oh8i68sn 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/19bfc448-984a-4904-978e-35baa85bdccc/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-9vzs5rk5 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/54452879-bd07-4b09-be36-499f3ca14f98/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-wp1sn3_j 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e210622d-4024-45e6-ae25-d49197469d33/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-4jqold56 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/41b81405-edbb-4cb5-b363-cd3afcfb8a50/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-s_6vjgv3 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/146a32b3-7768-4d7b-9a41-4dfb957561f4/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-3qnd2sm6 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/6d35336c-e0dd-47d4-8dcc-cecaa52c4064/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-3msecjtl 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/878e9625-7b6f-4878-86ea-2dc3069e4fd9/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-90qiro5j 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/582e58b1-912e-42a8-bcc5-724b390c69db/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-gn066qnz 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/1ec78e07-56db-4fdc-b514-6353f68d30b4/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-iyw7pmc5 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/09b79238-2864-4991-acc0-92a6e95e9421/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-2xgruco4 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/dd23f3bb-9da0-4bc3-aecc-eb7a3769f037/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-t5hp4ctn 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8c016d5-41a5-41e3-a176-66f42ece9574/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-j3zbzzpi 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/c33135d7-06ad-4410-9380-c05060fd4cb7/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-poid90a2 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/82500e6d-c8ab-4148-8f2a-4092491c55f9/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-96ng7ldx 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/dc4b1b3a-c02f-4d85-8156-d8279e3fb2f0/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-koj3_zh0 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/461a2b2d-4c79-46d4-a53a-c09f0a0d758b/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-xy26wqsp 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/b31c6390-1520-4d8a-aecb-2d33357bf583/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-t5wccip3 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/ec9f0105-1ebc-4e9b-a4ad-9f39eab35216/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-2j66czgf 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/480be4f0-288e-48a0-8c48-5cb11614cd5f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-e380au8v 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/3e778905-4246-4784-b466-ac2e1f47cc4c/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-pgozj6qg 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/b116362c-8f6e-46bf-849a-6c2bbba1eafb/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-cms16vls 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/09873c85-7683-424 .. 1/tmp/qiime2/uid=#1001/data/f6ecb98a-112d-4a57-bcae-18ed8b1ea966/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-w_i_abna 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/ddb1d37f-acb3-4e64-8b54-85264c6dd03b/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-rc2hsmv0 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/bb246cd3-2072-410d-8782-d39ac91aaf09/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-e1bqtu28 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/c93d9788-a9a3-433e-929f-9bce6139c49d/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-h5rclmbg 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/cc18b6f3-4d41-459d-bf8d-ac8d4c83678e/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-y64rrlyk 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/fc55be01-3916-4cc3-8375-6c4fbb7b248a/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-_n_vysi3 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/b1eab275-09d3-4fb2-acc4-626381845054/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-obk60rhn 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/26a62557-1ba0-4fb8-ab8a-710406e45b18/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-tl7izgyl 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e7460151-1758-48ae-88c2-55fb13f0a6d1/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-kaejthzd 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/8eb4cdb3-4c30-4e3a-a4d7-fa4204646688/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-8f93924z 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a1a48b44-da31-4070-97b5-c2f813852c6f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-_s34w_ik 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/c69e964a-04f7-455c-933c-8ea9108166b3/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-wwcj2p9y 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/eb8fa411-2812-4d90-b7e8-1f14a2102068/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-9xgpxkhp 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/a25b59ec-c293-4ea3-b736-5cd0f64e5f26/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-lx0v7jrp 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/9c2dd04a-d42c-42be-89c3-f4a501977f02/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-x4wo4x1g 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/2a72ac08-385d-46e6-ab73-8c30eb2d1c53/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-eqa76jag 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/34edf7a9-deb5-47e4-9a15-3e9c63dc3e20/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-bv52l3fz 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/d389e29b-80b1-4ba3-a04a-93c7b012f162/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-_ss2wwgq 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/ba09127b-17db-45a0-bb89-050e48f7622f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-if2w0gnh 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/5df428bd-ebce-4059-a6bf-2e0e2a024f47/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-u_8qk7iw 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/c766b4d2-23e3-434c-8f23-47d071e5f226/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-oqrf0pro 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e3c0bbe2-ceda-4d47-9753-60c787312ea2/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-lgw4jlst 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/b0bdb82a-3f24-4670-9d8f-5b4661e28342/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-wcp4sna3 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/fee57503-50e3-4480-afae-47c04abe306b/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-47tqud06 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/d6dd09e4-4c23-4ddc-9349-86f7f039619f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-z00xchka 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/d8c60cdb-fccc-496d-95c1-86424bfd5353/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-u7ejt9ng 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/8bb98714-eafc-4131-a962-8c63fd0badc8/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-ccvv5n4i 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/94cf8284-434f-4a54-81ca-756ffb182200/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-71v5vidd 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/4500dd69-2f42-4a1f-a35e-0c7b1a3fbd03/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-vrl78yp9 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/c1769c31-56a8-47c1-b5f2-83243b3a3ab5/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-anlvabb5 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/ff4d203d-70be-4273-bec7-75946a79e62f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-l2ks_p0h 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/47224717-5ba5-4ce2-9691-faf58d0b490f/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-ltrgh4fz 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/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/3545ead3-7fda-4360-94fa-07f457ccf922/data/feature-table.biom -t /tmp/tmpd8wf3q41/tmp/qiime2/uid=#1001/data/e8a98352-8895-468e-af52-f4ba70d85422/data/tree.nwk -o /tmp/tmpd8wf3q41/tmp/q2-AlphaDiversityFormat-ud8rjm9_ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 16, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 18, "src": "hda"}]}, "steps": "10"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "4e8191b430aa11efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | max\_depth | ` "2019" ` |

    • Other invocation details - **history_id** * 7f630553609e2376 - **history_state** * ok - **invocation_id** * 7d70134bf071dbdc - **invocation_state** * scheduled - **workflow_id** * 7d70134bf071dbdc

  • ✅ QIIME2-V-taxonomic-analysis.ga_0
    #### Workflow invocation details * Invocation Messages *
    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:** * ```console q2galaxy run feature_classifier classify_sklearn '/tmp/tmpd8wf3q41/job_working_directory/000/22/configs/tmp005gfof8' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣ ｢reads_per_batch: 'auto'｣ ｢n_jobs: 1｣ ｢pre_dispatch: '2*n_jobs'｣ ｢confidence: 0.7｣ ｢read_orientation: 'auto'｣ Saved FeatureData[Taxonomy] to: classification.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9154ecd430aa11efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/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:** * ```console q2galaxy run taxa barplot '/tmp/tmpd8wf3q41/job_working_directory/000/23/configs/tmp4iv1hj8k' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣ ｢taxonomy: d86bd131-16ca-418e-b7db-8687b0e7fdea｣ ｢metadata: ｣ ｢level_delimiter: None｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 20, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 24, "src": "hda"}]}} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9154ecd430aa11efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/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:** * ```console q2galaxy run metadata tabulate '/tmp/tmpd8wf3q41/job_working_directory/000/24/configs/tmpcsvs3geb' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢input: ｣ ｢page_size: 100｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9154ecd430aa11efaf0a7d68e481b0dd" ` | | chromInfo | ` "/tmp/tmpd8wf3q41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 24, "src": "hda"}]}, "type": "qza"}}] ` |

  • Other invocation details - **history_id** * 4f390845dac9a20e - **history_state** * ok - **invocation_id** * 0a829197f41eaad5 - **invocation_state** * scheduled - **workflow_id** * 0a829197f41eaad5

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests *
✅ QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Representative sequences**: * step_state: scheduled - **Step 2: Feature table**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Minimum depth**: * step_state: scheduled - **Step 5: Maximum depth**: * step_state: scheduled - **Step 6: SEPP fragment insertion reference**: * step_state: scheduled - **Step 7: Taxonomic classifier**: * step_state: scheduled - **Step 8: Phylogenetic tree for diversity analysis**: * step_state: scheduled *
Subworkflow Steps - **Step 1: DADA2 representative sequences**: * step_state: scheduled - **Step 2: SEPP fragment insertion source file**: * step_state: scheduled - **Step 3: Phylogenetic tree generation**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run fragment_insertion sepp '/tmp/tmpcwm07jtv/job_working_directory/000/6/configs/tmpmy5o7eqq' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢representative_sequences: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣ ｢reference_database: a14c6180-506b-4ecb-bacb-9cb30bc3044b｣ ｢alignment_subset_size: 1000｣ ｢placement_subset_size: 5000｣ ｢threads: 1｣ ｢debug: False｣ ==> sepp-q2-fragment-insertion-err.log <== [15:38:41] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_47/pplacer.backbone.6m4xcbtp.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_47/pplacer.tree.k5mshbgs.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_47/pplacer.extended.0.ei7rkbir.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_47/pplacer.extended.0.ei7rkbir.jplace [15:38:47] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_48/pplacer.backbone.a0ni2k5n.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_48/pplacer.tree.5k952fj7.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_48/pplacer.extended.0.j_oao0im.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_48/pplacer.extended.0.j_oao0im.jplace [15:38:53] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_49/pplacer.backbone.syhrjffr.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_49/pplacer.tree.i2kg_frm.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_49/pplacer.extended.0.v_7diy3p.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_49/pplacer.extended.0.v_7diy3p.jplace [15:38:57] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_50/pplacer.backbone.chk9gqjj.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_50/pplacer.tree.2nti1fgt.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_50/pplacer.extended.0.d0tp3l8q.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_50/pplacer.extended.0.d0tp3l8q.jplace [15:39:00] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_54/pplacer.backbone.u1vhrknp.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_54/pplacer.tree.yi2u7wo3.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_54/pplacer.extended.0.oto28nuz.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_54/pplacer.extended.0.oto28nuz.jplace [15:39:03] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_60/pplacer.backbone.1lndkxym.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_60/pplacer.tree.5m_b2x4w.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_60/pplacer.extended.0.x57rshgh.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_60/pplacer.extended.0.x57rshgh.jplace [15:39:06] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_61/pplacer.backbone.5g3a_te_.fasta, tree_file:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_61/pplacer.tree.34qmiged.tre, info_file:/tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt, extended alignment:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_61/pplacer.extended.0.xppo97f1.fasta, output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tempssd-LdYx4xFMKA/q2-fragment-insertion.lnzbxmqp/root/P_61/pplacer.extended.0.xppo97f1.jplace [15:39:48] jobs.py (line 131): INFO: Finished jsonmerger Job with input: input:pipe output:/tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tmp-cW0ybsAJEQ/q2-fragment-insertion_placement.json [15:39:50] algorithm.py (line 195): INFO: Current execution Finished in 619 seconds [15:39:50] algorithm.py (line 197): INFO: All checkpointed executions Finished in 619 cumulative time ==> 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/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tmp-cW0ybsAJEQ . Consider removing /tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tmp-cW0ybsAJEQ if its files are not needed. Removing /tmp/tmpcwm07jtv/tmp/tmp.LF0WvALTIa/sepp-tmp-cW0ybsAJEQ Saved Phylogeny[Rooted] to: tree.qza Saved Placements to: placements.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"alignment_subset_size": "1000", "debug": false, "placement_subset_size": "5000", "threads": "1"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "e82114a730ab11ef9a6413ee71a649e7" ` | | chromInfo | ` "/tmp/tmpcwm07jtv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | 
       </details>

 - **Step 9: Taxonomic analysis**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 representative sequences**:

         * step_state: scheduled

      - **Step 3: Taxonomic classifier**:

         * step_state: scheduled

      - **Step 4: DADA2 feature table**:

         * step_state: scheduled

      - **Step 5: Taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run feature_classifier classify_sklearn '/tmp/tmpcwm07jtv/job_working_directory/000/7/configs/tmpxe_m68bv'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢reads: 455eda14-0d01-4a9b-98af-d3eaa0c0d79a｣
                ｢classifier: 4b2a57b7-1e5a-4a4d-8201-99551ab50858｣
                ｢reads_per_batch: 'auto'｣
                ｢n_jobs: 1｣
                ｢pre_dispatch: '2*n_jobs'｣
                ｢confidence: 0.7｣
                ｢read_orientation: 'auto'｣

                Saved FeatureData[Taxonomy] to: classification.qza

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__confidence__": {"__current_case__": 1, "__q2galaxy__GUI__select__": "__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)", "confidence": "0.7"}, "__q2galaxy__GUI__conditional__reads_per_batch__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "auto", "reads_per_batch": "auto"}, "n_jobs": "1", "pre_dispatch": "2*n_jobs", "read_orientation": "auto"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "e82114a830ab11ef9a6413ee71a649e7" ` |
                  | chromInfo | ` "/tmp/tmpcwm07jtv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 6: Taxonomy barplot**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run taxa barplot '/tmp/tmpcwm07jtv/job_working_directory/000/8/configs/tmpbmlzl2ch'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢taxonomy: 59fcda76-86e6-4799-b180-a2d65e8c947c｣
                ｢metadata: <Metadata>｣
                ｢level_delimiter: None｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"__q2galaxy__GUI__conditional__level_delimiter__": {"__current_case__": 0, "__q2galaxy__GUI__select__": "__q2galaxy__::control::default", "level_delimiter": "__q2galaxy__::literal::None"}, "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "taxonomy": {"values": [{"id": 8, "src": "hda"}]}} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "e82114a830ab11ef9a6413ee71a649e7" ` |
                  | chromInfo | ` "/tmp/tmpcwm07jtv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |

           </details>

      - **Step 7: Tabulate taxonomy classification**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run metadata tabulate '/tmp/tmpcwm07jtv/job_working_directory/000/9/configs/tmpnsrnirv5'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Output:**

              * ```console
                ｢input: <Metadata>｣
                ｢page_size: 100｣

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"page_size": "100"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "e82114a830ab11ef9a6413ee71a649e7" ` |
                  | chromInfo | ` "/tmp/tmpcwm07jtv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | input | ` [{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 8, "src": "hda"}]}, "type": "qza"}}] ` |

           </details>
       </details>

 - **Step 10: Rarefaction**:

    * step_state: scheduled

    * <details><summary>Subworkflow Steps</summary>

      - **Step 1: Metadata**:

         * step_state: scheduled

      - **Step 2: DADA2 feature table**:

         * step_state: scheduled

      - **Step 3: Rooted tree**:

         * step_state: scheduled

      - **Step 4: Minimum depth**:

         * step_state: scheduled

      - **Step 5: Maximum depth**:

         * step_state: scheduled

      - **Step 6: Alpha rarefaction**:

         * step_state: scheduled

         * <details><summary>Jobs</summary>

           - **Job 1:**

             * Job state is ok

             **Command Line:**

              * ```console
                q2galaxy run diversity alpha_rarefaction '/tmp/tmpcwm07jtv/job_working_directory/000/10/configs/tmpj0vz2ia2'
                ```
             **Exit Code:**

              * ```console
                0
                ```
             **Standard Error:**

              * ```console
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()
                /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py:245: FutureWarning: The default value of numeric_only in DataFrameGroupBy.median is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
                  median_ = grouped.median()

                ```
             **Standard Output:**

              * ```console
                ｢table: 07913ecd-c005-4f93-b52c-50dcde5b2e13｣
                ｢max_depth: 2019｣
                ｢phylogeny: 0a23e8c8-94d6-4782-8bee-00a67919c7b1｣
                ｢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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a02dc7b8-5efe-4f73-8149-c9d15d28c657/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-9thho178

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/b4fb33c5-a09b-49b8-bffc-ce5a5d4dbedd/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-x2pcrh08

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/23fbda3d-f9a5-45c3-960c-2bc8cd80ea39/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-vw3bs8sj

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/0eac25ad-a9f3-4017-8e6d-c79e9a448c82/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-en9cw05h

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/fb20250a-9eef-4d35-b292-ecc65c3936ef/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-jy5bu_hx

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/28d100b5-2ad7-44e9-b7c9-4a5eb011d068/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-poe2mdr4

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/0c7c3425-e2d3-426f-b5a7-f8a860fffd26/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-syexk9k0

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/0a865dc0-7865-4554-862a-defd3e26fcd6/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-2n02styk

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/4e2ba2bb-a7c3-4af4-bcf4-4a04b1b5654f/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-tyawg9xl

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/31e0c552-b79b-4aab-9afa-d5d2a36a7870/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-xwlz13ms

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/8f6e3085-77ca-4e6b-bc07-5f350ecef8f5/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-ynm1j_ds

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/8feac4f6-c659-4458-b10a-8eb031dc10cf/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-_onfv5r6

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/9ad4fc75-9e67-4a79-81e3-a741f96304b4/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-dada1gf7

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/5fce1bce-4eee-4f42-be81-1e81a952aa54/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-mydzwaq9

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/10de00d8-6af7-4e9c-a93e-4708833c7384/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-_17jmxg7

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/9356cbe5-a9d5-4a10-9afa-caadb2959353/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-phveyecu

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/ef9475f7-3b43-4649-9138-39a0ed7a0f9d/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-l5kapo_o

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/d5dee14b-aa18-422c-9edb-590158fdf5ee/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-tir7e3ii

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/86500b0b-a03f-4a33-ab07-c2a973fd9810/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-75sq85zd

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/4d1b661e-b493-4a4d-a191-227de81c2056/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-bo7kk1lu

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/59e98761-60c4-4248-abe2-c6267ceffdb8/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-vu41pbkh

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a4ea504c-536a-488f-845f-f9abc36d7be3/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-4p4dxbyi

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/69d192e5-3a8a-404c-af69-0c45c55a82c5/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-_6rlz36q

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/dedf557e-af6e-4be9-92de-2fbc81ea001f/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-quz4gd5p

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/d7b05ba5-0d52-4fd3-b606-3b249964c985/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-q3pj9zh6

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/bf893475-fa87-4259-91d1-7e8122319dd6/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-7ol5tjk0

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/57e6d944-e3f1-40e1-aa19-1a673ee20a87/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-v1c8yjl7

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/b0a96c20-8990-4ad4-943e-45bb88d8162e/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-sl8a20__

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/21f59c14-fb22-473f-af90-adc80f076777/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-9461rgu7

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/35444698-e6b2-4343-83c3-14275c122b2f/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-mszrjogv

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a1946fb6-0eff-4eed-af21-610f8a2a8bdb/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-m88f6ull

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6e5379d-8d6e-4ab
                ..
                v/tmp/qiime2/uid=#1001/data/c841ae47-b615-48e4-81ec-08b2c8fc6eea/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-ab8wn7_2

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/412c00e5-0e70-43db-b87d-df1f648025f1/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-u5tjcti5

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/a8960fb3-8ed9-45f7-937d-4859b19d900c/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-dly8bq0z

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/7f164299-2b3e-4d79-b59f-71d6112ce8fe/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-__7wjfc1

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c1d7ccd7-4a13-469a-ab57-719a45f7da28/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-sjk4flwk

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/35976cea-7148-4960-b3b0-e542cbcd6976/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-r3ny876z

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/76f544f8-f676-4b5b-ba53-c29a076f5cf5/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-4rdwoprl

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/2b4fd402-7036-480f-b943-49e930902edd/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-747r9whp

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/325d09aa-4d3f-4ae0-b6b0-0cdd1fb2c5bf/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-h58xxxzs

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/3f95bb4e-e96f-45f3-b036-c54b26a28db1/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-kli039he

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/9d894c7c-dc00-4992-ada4-3c3a2b5d09dc/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-uch7p1rw

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/4dbcccef-1ab6-4b75-acfd-678e0f610ff1/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-6efmorsc

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/9982380e-3567-497f-b2c6-1524f4bc35ed/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-21zoywht

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/8e04ed33-085d-4e59-a394-757250926c72/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-9i8boihf

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/935dbece-f7a3-47ec-b4ba-48978eef92f5/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-abw4p815

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/3f8659d0-1141-4231-b18d-7a433946668d/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-wzhk3ukx

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/42140b49-7519-44cd-a7f3-6e450fbecd73/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-b7atgmke

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/4c352988-06bf-4718-8da2-c1b71ec5d032/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-nrimwrac

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/28c46a36-e1ca-4dab-89ed-936686d36f38/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-h7uo1_dc

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/b504b717-cf83-488d-bada-d3d86e82e24d/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-ppatollf

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/e9846cea-6659-48a5-acdc-7a18144bb03c/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-s12rk64n

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/085eb373-c208-4cec-b8f5-97e1724892ae/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-7ztamev9

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/7cd46cc1-e15f-4cfe-a931-472b978e42fa/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-d9cvtumi

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/f44b06da-b2ea-48e7-ba20-8d70687dd086/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-es81dcek

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/ec5b1935-51f5-4aec-8762-b6cbe2cd48f3/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-q3oyavd4

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/029e5c74-e533-4a89-bfb9-ecadb40e3f83/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-2jniqmei

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/49fef4e0-27b0-4057-8746-66a090215de9/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-ucdfj4oi

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/df88603b-6d7c-4478-856b-de212148768f/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-f_1g2qdy

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/2126aba1-b78a-4daf-bb3b-1c8468d472b9/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-6qcfkmqq

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/6756c575-e8e5-4b29-b89c-c30af1375b64/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-w8r966ah

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/bb406d85-6bba-4d38-8e59-c0c760df3149/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-ustqnma3

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/6a02ba08-8c61-4ada-acf3-64b296ed1b0f/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-5x5r85fp

                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/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/76ee76d0-df45-4054-879f-4554294b5c85/data/feature-table.biom -t /tmp/tmpcwm07jtv/tmp/qiime2/uid=#1001/data/c6cf9e98-74bc-4a0a-a7b1-cf8e3d18bbd8/data/tree.nwk -o /tmp/tmpcwm07jtv/tmp/q2-AlphaDiversityFormat-80h2cjt5

                Saved Visualization to: visualization.qzv

                ```
             **Traceback:**

              * ```console

                ```
             **Job Parameters:**

              *   | Job parameter | Parameter value |
                  | ------------- | --------------- |
                  | \_\_input\_ext | ` "input" ` |
                  | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"iterations": "10", "metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}], "metrics": [], "min_depth": "1", "phylogeny": {"values": [{"id": 6, "src": "hda"}]}, "steps": "10"} ` |
                  | \_\_workflow\_invocation\_uuid\_\_ | ` "e82114a930ab11ef9a6413ee71a649e7" ` |
                  | chromInfo | ` "/tmp/tmpcwm07jtv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
                  | dbkey | ` "?" ` |
                  | max\_depth | ` "2019" ` |

           </details>
       </details>

  </details>
  • Other invocation details - **history_id** * d5636e0550167e05 - **history_state** * ok - **invocation_id** * d5636e0550167e05 - **invocation_state** * scheduled - **workflow_id** * 15540516d0fcbe16