QIIME2 workflows #354

debjyoti197 · 2024-03-07T14:32:21Z

Input
- Input demultiplexed data single and paired end
- Input multiplexed data single and paired end
- Other imports https://forum.qiime2.org/t/importing-and-demultiplexing-sequence-data-quick-reference/14002
Denoising
Phylogeny
Diversity Analysis
Taxonomic Classification

bernt-matthias · 2024-03-07T21:21:35Z

Let me add my own TODO list :)

for the input workflows the sample data should be limited fastq.gz .. or better fastqsanger.gz (since the tool doesn't do this yet)
the Vizualisations should be workflow outputs (I guess), other wise we can not test them.
Finish tests for Ia and Ib (test data?)
Finish tests for II* (use output from Ic and Id)
double check that tags have been removed
split into separate directories

- finish tests for 1c,d - make viz a workflow output - allow only fastq.gz input

for easier handling on the command line

start README

bernt-matthias · 2024-04-08T10:26:13Z

Hi @mvdbeek. Besides the inputs in the workflows this should be ready for review. All other (downstream) workflows will be in #372

mvdbeek · 2024-04-08T10:37:14Z

workflows/amplicon/qiime2/qiime2-I-import/.dockstore.yml

+  - name: "Helmholtz-Zentrum f\xFCr Umweltforschung - UFZ"
+    address: "Permoserstra\xDFe 15, 04318 Leipzig"


That's interesting, can you fix the umlaut here ? Seems like a bug we should fix.

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end.ga

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga

...con/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga

...con/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga

workflows/amplicon/qiime2/qiime2-II-denoising/README.md

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

…sing-and-feature-table-creation-paired-end.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

mvdbeek · 2024-04-08T11:27:11Z

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga

@@ -15,6 +15,7 @@
    ],
    "format-version": "0.1",
    "license": "MIT",
+    "release" "0.1",


Oops, missing colon here :(

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

github-actions · 2024-04-08T13:01:25Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	6
Passed	6
Error	0
Failure	0
Skipped	0

Passed Tests

✅ QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: Demultiplexed sequences:
- step_state: scheduled
Step 3: Truncation length:
- step_state: scheduled
Step 4: Trimming length:
- step_state: scheduled

Step 5: Denoising the datasets:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run dada2 denoise_single '/tmp/tmpbwmxk3t9/job_working_directory/000/3/configs/tmp8e2tnqqq'

Exit Code:

```
0
```

Standard Error:

```
Loading required package: Rcpp
```

Standard Output:

｢demultiplexed_seqs: 2e0c55c9-a797-42b0-9df7-72632e01b862｣
｢trunc_len: 120｣
｢trim_left: 0｣
｢max_ee: 2.0｣
｢trunc_q: 2｣
｢pooling_method: 'independent'｣
｢chimera_method: 'consensus'｣
｢min_fold_parent_over_abundance: 1.0｣
｢allow_one_off: False｣
｢n_threads: 1｣
｢n_reads_learn: 1000000｣
｢hashed_feature_ids: True｣
                                                                                                                                                                                                                                                               
R version 4.2.3 (2023-03-15) 
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6 
2) Filtering ..................................
3) Learning Error Rates
19539480 total bases in 162829 reads from 34 samples will be used for learning the error rates.
4) Denoise samples 
..................................
5) Remove chimeras (method = consensus)
6) Report read numbers through the pipeline
7) Write output
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmpbwmxk3t9/tmp/qiime2/uid=#1001/data/2e0c55c9-a797-42b0-9df7-72632e01b862/data --output_path /tmp/tmpbwmxk3t9/tmp/tmpv4c7ljqz/output.tsv.biom --output_track /tmp/tmpbwmxk3t9/tmp/tmpv4c7ljqz/track.tsv --filtered_directory /tmp/tmpbwmxk3t9/tmp/tmpv4c7ljqz --truncation_length 120 --trim_left 0 --max_expected_errors 2.0 --truncation_quality_score 2 --max_length Inf --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000 --homopolymer_gap_penalty NULL --band_size 16

Saved FeatureTable[Frequency] to: table.qza
Saved FeatureData[Sequence] to: representative_sequences.qza
Saved SampleData[DADA2Stats] to: denoising_stats.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"allow_one_off": false, "chimera_method": "consensus", "hashed_feature_ids": true, "max_ee": "2.0", "min_fold_parent_over_abundance": "1.0", "n_reads_learn": "1000000", "n_threads": "1", "pooling_method": "independent", "trim_left": "0", "trunc_q": "2"}`
__workflow_invocation_uuid__	`"1d287672f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
trunc_len	`"120"`

Step 6: Tabulate DADA2 denoised representative sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table tabulate_seqs '/tmp/tmpbwmxk3t9/job_working_directory/000/4/configs/tmpte3zbudt'

Exit Code:

```
0
```

Standard Output:

｢data: 9164231d-4014-4fd1-98fc-53f65adffd02｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1d287672f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

**Step 7: Tabulate DADA2 statistical metadata **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmpbwmxk3t9/job_working_directory/000/5/configs/tmps9nug1uz'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"1d287672f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`[{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}}]`

Step 8: Summing up the dada2 output table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table summarize '/tmp/tmpbwmxk3t9/job_working_directory/000/6/configs/tmpz45ds91c'

Exit Code:

```
0
```

Standard Output:

｢table: 476d5a20-f844-4fa3-8372-9ae2a4f531cb｣
｢sample_metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"sample_metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__sample_metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}]}`
__workflow_invocation_uuid__	`"1d287672f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 5b36cfcbf0ee1c21
- history_state
  - ok
- invocation_id
  - 5b36cfcbf0ee1c21
- invocation_state
  - scheduled
- workflow_id
  - 5b36cfcbf0ee1c21

✅ QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: Demultiplexed sequences:
- step_state: scheduled
Step 3: Truncation length (forward):
- step_state: scheduled
Step 4: Truncation length (reverse):
- step_state: scheduled
Step 5: Trimming length (forward):
- step_state: scheduled
Step 6: Trimming length (reverse):
- step_state: scheduled

Step 7: Denoising the datasets:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run dada2 denoise_paired '/tmp/tmpbwmxk3t9/job_working_directory/000/9/configs/tmpcd1vrgww'

Exit Code:

```
0
```

Standard Error:

```
Loading required package: Rcpp
```

Standard Output:

｢demultiplexed_seqs: 072825e7-549d-4f68-b037-769149d7120a｣
｢trunc_len_f: 204｣
｢trunc_len_r: 205｣
｢trim_left_f: 1｣
｢trim_left_r: 1｣
｢max_ee_f: 2.0｣
｢max_ee_r: 2.0｣
｢trunc_q: 2｣
｢min_overlap: 12｣
｢pooling_method: 'independent'｣
｢chimera_method: 'consensus'｣
｢min_fold_parent_over_abundance: 1.0｣
｢allow_one_off: False｣
｢n_threads: 1｣
｢n_reads_learn: 1000000｣
｢hashed_feature_ids: True｣
                                                                                                                                                                                                                                                               
R version 4.2.3 (2023-03-15) 
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6 
2) Filtering .........................................
3) Learning Error Rates
209797658 total bases in 1033486 reads from 24 samples will be used for learning the error rates.
210831144 total bases in 1033486 reads from 24 samples will be used for learning the error rates.
3) Denoise samples .........................................
.........................................
5) Remove chimeras (method = consensus)
6) Report read numbers through the pipeline
7) Write output
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/forward --input_directory_reverse /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/reverse --output_path /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/output.tsv.biom --output_track /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/track.tsv --filtered_directory /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/filt_f --filtered_directory_reverse /tmp/tmpbwmxk3t9/tmp/tmpbihnz5g8/filt_r --truncation_length 204 --truncation_length_reverse 205 --trim_left 1 --trim_left_reverse 1 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000

Saved FeatureTable[Frequency] to: table.qza
Saved FeatureData[Sequence] to: representative_sequences.qza
Saved SampleData[DADA2Stats] to: denoising_stats.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"allow_one_off": false, "chimera_method": "consensus", "hashed_feature_ids": true, "max_ee_f": "2.0", "max_ee_r": "2.0", "min_fold_parent_over_abundance": "1.0", "min_overlap": "12", "n_reads_learn": "1000000", "n_threads": "1", "pooling_method": "independent", "trim_left_f": "1", "trim_left_r": "1", "trunc_q": "2"}`
__workflow_invocation_uuid__	`"a1d146c4f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
trunc_len_f	`"204"`
trunc_len_r	`"205"`

Step 8: Tabulate DADA2 denoised representative sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table tabulate_seqs '/tmp/tmpbwmxk3t9/job_working_directory/000/10/configs/tmp4g031hj2'

Exit Code:

```
0
```

Standard Output:

｢data: 8bbed231-ef99-4f81-bb8f-9ff5cb3242bf｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a1d146c4f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

**Step 9: Tabulate DADA2 statistical metadata **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmpbwmxk3t9/job_working_directory/000/11/configs/tmpm7t_9exx'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"a1d146c4f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/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"}}]`

Step 10: Summing up the dada2 output table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table summarize '/tmp/tmpbwmxk3t9/job_working_directory/000/12/configs/tmp0bqt_32l'

Exit Code:

```
0
```

Standard Output:

｢table: eb6407a0-f2a8-4624-9496-5d6b3609134e｣
｢sample_metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"sample_metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__sample_metadata__": {"__current_case__": 0, "source": {"values": [{"id": 9, "src": "hda"}]}, "type": "tsv"}}]}`
__workflow_invocation_uuid__	`"a1d146c4f5a511ee92b6937f47487261"`
chromInfo	`"/tmp/tmpbwmxk3t9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - e0a644de8dff26b8
- history_state
  - ok
- invocation_id
  - e0a644de8dff26b8
- invocation_state
  - scheduled
- workflow_id
  - e0a644de8dff26b8

✅ QIIME2-Ia-multiplexed-data-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequences:
- step_state: scheduled
Step 2: Barcodes:
- step_state: scheduled
Step 3: Metadata:
- step_state: scheduled
Step 4: Metadata parameter:
- step_state: scheduled
Step 5: Reverse complement barcodes:
- step_state: scheduled

Step 6: Input files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/4/configs/tmpvylpsnc3'

Exit Code:

```
0
```

Standard Output:

｢type: EMPSingleEndSequences｣
｢format: EMPSingleEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b59216aef59e11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 5, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPSingleEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 2, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_sequences": {"data": {"values": [{"id": 1, "src": "hda"}]}, "name": "sequences.fastq.gz"}}, "type": "EMPSingleEndSequences"}`

Step 7: Metadata as artifact:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/5/configs/tmpeq0wo2hm'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b59216aef59e11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 3, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 8: Demultiplex single-end data:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux emp_single '/tmp/tmp47bks9je/job_working_directory/000/6/configs/tmpsvnr_y0t'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for sample_id, barcode in barcodes.to_series().iteritems():

Standard Output:

｢seqs: 0953a9d9-6f58-446c-9b11-4e9c6276a7d7｣
｢barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=34>｣
｢golay_error_correction: True｣
｢rev_comp_barcodes: False｣
｢rev_comp_mapping_barcodes: False｣
｢ignore_description_mismatch: False｣
                                                                                                                                                                                                                                                               
Saved SampleData[SequencesWithQuality] to: per_sample_sequences.qza
Saved ErrorCorrectionDetails to: error_correction_details.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": false}`
__workflow_invocation_uuid__	`"b59216aef59e11ee822b0dbb2fabbbda"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Summarize demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmp47bks9je/job_working_directory/000/7/configs/tmplyq81cxl'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: c30cc82e-2594-448c-86b3-3676fb4d6a80｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"b59216aef59e11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 302e522032afd342
- history_state
  - ok
- invocation_id
  - 302e522032afd342
- invocation_state
  - scheduled
- workflow_id
  - 302e522032afd342

✅ QIIME2-Ib-multiplexed-data-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Forward sequences:
- step_state: scheduled
Step 2: Reverse sequences:
- step_state: scheduled
Step 3: Barcodes:
- step_state: scheduled
Step 4: Metadata:
- step_state: scheduled
Step 5: Metadata parameter:
- step_state: scheduled
Step 6: Reverse complement of barcodes needed?:
- step_state: scheduled

Step 7: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/12/configs/tmpuv7e7zf5'

Exit Code:

```
0
```

Standard Output:

｢type: EMPPairedEndSequences｣
｢format: EMPPairedEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e0fe4a6f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 4, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPPairedEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 11, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_forward": {"data": {"values": [{"id": 9, "src": "hda"}]}, "name": "forward.fastq.gz"}, "import_reverse": {"data": {"values": [{"id": 10, "src": "hda"}]}, "name": "reverse.fastq.gz"}}, "type": "EMPPairedEndSequences"}`

Step 8: Metadata as artifact:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/13/configs/tmph0z7zziw'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e0fe4a6f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 9: Demultiplex paired-end sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux emp_paired '/tmp/tmp47bks9je/job_working_directory/000/14/configs/tmpz58qew7i'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for sample_id, barcode in barcodes.to_series().iteritems():

Standard Output:

｢seqs: adb3d158-8d73-4a90-a452-fcb669c13970｣
｢barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=75>｣
｢golay_error_correction: True｣
｢rev_comp_barcodes: False｣
｢rev_comp_mapping_barcodes: True｣
｢ignore_description_mismatch: False｣
                                                                                                                                                                                                                                                               
Saved SampleData[PairedEndSequencesWithQuality] to: per_sample_sequences.qza
Saved ErrorCorrectionDetails to: error_correction_details.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": true}`
__workflow_invocation_uuid__	`"4e0fe4a6f59f11ee822b0dbb2fabbbda"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 14, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 10: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmp47bks9je/job_working_directory/000/15/configs/tmp8m8v7mgx'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)
/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: 224da326-6605-4976-9582-13e288ee05d8｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"4e0fe4a6f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 7bc9c4acc08ca712
- history_state
  - ok
- invocation_id
  - 7bc9c4acc08ca712
- invocation_state
  - scheduled
- workflow_id
  - 7bc9c4acc08ca712

✅ QIIME2-Ic-demultiplexed-data-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequence collection:
- step_state: scheduled

Step 2: Extract element identifiers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp47bks9je/job_working_directory/000/19/configs/tmp4psckqhx' '/tmp/tmp47bks9je/job_working_directory/000/19/outputs/dataset_7c00804c-5888-442d-86dd-2af6b9e446fb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"ebf35432f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: Screening laneless and single-lane:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmp47bks9je/files/7/c/0/dataset_7c00804c-5888-442d-86dd-2af6b9e446fb.dat' --output '/tmp/tmp47bks9je/job_working_directory/000/20/outputs/dataset_f11d6b35-1fcf-45ab-8807-d23167aaa311.dat' --input_display_name 'Extract element identifiers on data 3, data 2, and data 1' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ebf35432f59f11ee822b0dbb2fabbbda"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: Relabel sequence files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ebf35432f59f11ee822b0dbb2fabbbda"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 22, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 5: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/22/configs/tmpa60p_22g'

Exit Code:

```
0
```

Standard Output:

｢type: SampleData[SequencesWithQuality]｣
｢format: CasavaOneEightLanelessPerSampleDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ebf35432f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 49, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 2, "src": "hdca"}]}}}}, "type": "SampleData__ob__SequencesWithQuality__cb__"}`

Step 6: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmp47bks9je/job_working_directory/000/23/configs/tmppu4j2drn'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: 1f8d67ef-21c2-4d50-98aa-fe0a722c1d30｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"ebf35432f59f11ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - c9929213f44ee9d5
- history_state
  - ok
- invocation_id
  - c9929213f44ee9d5
- invocation_state
  - scheduled
- workflow_id
  - c9929213f44ee9d5

✅ QIIME2-Id-demultiplexed-data-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequence collection:
- step_state: scheduled

Step 2: Extract element identifiers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp47bks9je/job_working_directory/000/30/configs/tmpszdkqjz6' '/tmp/tmp47bks9je/job_working_directory/000/30/outputs/dataset_69f54938-1b68-4194-916d-4400670de171.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"57f30c54f5a011ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 3, "src": "hdca"}]}`

Step 3: Screening laneless and single-lane:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmp47bks9je/files/6/9/f/dataset_69f54938-1b68-4194-916d-4400670de171.dat' --output '/tmp/tmp47bks9je/job_working_directory/000/31/outputs/dataset_909a74da-ffe6-4e87-91ff-20729d26a6d0.dat' --input_display_name 'Extract element identifiers on data 6, data 5, and others' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"57f30c54f5a011ee822b0dbb2fabbbda"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: Relabel sequence files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"57f30c54f5a011ee822b0dbb2fabbbda"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 35, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 3, "src": "hdca"}]}`

Step 5: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmp47bks9je/job_working_directory/000/33/configs/tmpr3odikh3'

Exit Code:

```
0
```

Standard Output:

｢type: SampleData[PairedEndSequencesWithQuality]｣
｢format: CasavaOneEightLanelessPerSampleDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"57f30c54f5a011ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 46, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 4, "src": "hdca"}]}}}}, "type": "SampleData__ob__PairedEndSequencesWithQuality__cb__"}`

Step 6: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmp47bks9je/job_working_directory/000/34/configs/tmpzmxfp389'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)
/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: 5e474a5e-2da1-49c9-aed3-dcb82368696a｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"57f30c54f5a011ee822b0dbb2fabbbda"`
chromInfo	`"/tmp/tmp47bks9je/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 13cbd55e2b6a6a05
- history_state
  - ok
- invocation_id
  - 13cbd55e2b6a6a05
- invocation_state
  - scheduled
- workflow_id
  - 13cbd55e2b6a6a05

github-actions · 2024-04-08T13:50:38Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	6
Passed	6
Error	0
Failure	0
Skipped	0

Passed Tests

✅ QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: Demultiplexed sequences:
- step_state: scheduled
Step 3: Truncation length:
- step_state: scheduled
Step 4: Trimming length:
- step_state: scheduled

Step 5: Denoising the datasets:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run dada2 denoise_single '/tmp/tmp1811dfta/job_working_directory/000/3/configs/tmp_gc7f9_1'

Exit Code:

```
0
```

Standard Error:

```
Loading required package: Rcpp
```

Standard Output:

｢demultiplexed_seqs: 2e0c55c9-a797-42b0-9df7-72632e01b862｣
｢trunc_len: 120｣
｢trim_left: 0｣
｢max_ee: 2.0｣
｢trunc_q: 2｣
｢pooling_method: 'independent'｣
｢chimera_method: 'consensus'｣
｢min_fold_parent_over_abundance: 1.0｣
｢allow_one_off: False｣
｢n_threads: 1｣
｢n_reads_learn: 1000000｣
｢hashed_feature_ids: True｣
                                                                                                                                                                                                                                                               
R version 4.2.3 (2023-03-15) 
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6 
2) Filtering ..................................
3) Learning Error Rates
19539480 total bases in 162829 reads from 34 samples will be used for learning the error rates.
4) Denoise samples 
..................................
5) Remove chimeras (method = consensus)
6) Report read numbers through the pipeline
7) Write output
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmp1811dfta/tmp/qiime2/uid=#1001/data/2e0c55c9-a797-42b0-9df7-72632e01b862/data --output_path /tmp/tmp1811dfta/tmp/tmprqb4j2g8/output.tsv.biom --output_track /tmp/tmp1811dfta/tmp/tmprqb4j2g8/track.tsv --filtered_directory /tmp/tmp1811dfta/tmp/tmprqb4j2g8 --truncation_length 120 --trim_left 0 --max_expected_errors 2.0 --truncation_quality_score 2 --max_length Inf --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000 --homopolymer_gap_penalty NULL --band_size 16

Saved FeatureTable[Frequency] to: table.qza
Saved FeatureData[Sequence] to: representative_sequences.qza
Saved SampleData[DADA2Stats] to: denoising_stats.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"allow_one_off": false, "chimera_method": "consensus", "hashed_feature_ids": true, "max_ee": "2.0", "min_fold_parent_over_abundance": "1.0", "n_reads_learn": "1000000", "n_threads": "1", "pooling_method": "independent", "trim_left": "0", "trunc_q": "2"}`
__workflow_invocation_uuid__	`"fdae9da6f5ab11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
trunc_len	`"120"`

Step 6: Tabulate DADA2 denoised representative sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table tabulate_seqs '/tmp/tmp1811dfta/job_working_directory/000/4/configs/tmpgxu0rqxq'

Exit Code:

```
0
```

Standard Output:

｢data: 7f66d64d-cd19-41a6-a167-27c8911845f9｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fdae9da6f5ab11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

**Step 7: Tabulate DADA2 statistical metadata **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmp1811dfta/job_working_directory/000/5/configs/tmp8d787yim'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"fdae9da6f5ab11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`[{"__index__": 0, "__q2galaxy__GUI__conditional__input__": {"__current_case__": 1, "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}}]`

Step 8: Summing up the dada2 output table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table summarize '/tmp/tmp1811dfta/job_working_directory/000/6/configs/tmpm5_mo2e5'

Exit Code:

```
0
```

Standard Output:

｢table: 389b4d32-2e65-4616-8e0c-6a4e1de7a811｣
｢sample_metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"sample_metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__sample_metadata__": {"__current_case__": 0, "source": {"values": [{"id": 1, "src": "hda"}]}, "type": "tsv"}}]}`
__workflow_invocation_uuid__	`"fdae9da6f5ab11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 6b77f7e58747de08
- history_state
  - ok
- invocation_id
  - 6b77f7e58747de08
- invocation_state
  - scheduled
- workflow_id
  - 6b77f7e58747de08

✅ QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Metadata:
- step_state: scheduled
Step 2: Demultiplexed sequences:
- step_state: scheduled
Step 3: Truncation length (forward):
- step_state: scheduled
Step 4: Truncation length (reverse):
- step_state: scheduled
Step 5: Trimming length (forward):
- step_state: scheduled
Step 6: Trimming length (reverse):
- step_state: scheduled

Step 7: Denoising the datasets:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run dada2 denoise_paired '/tmp/tmp1811dfta/job_working_directory/000/9/configs/tmpl0msmnjq'

Exit Code:

```
0
```

Standard Error:

```
Loading required package: Rcpp
```

Standard Output:

｢demultiplexed_seqs: 072825e7-549d-4f68-b037-769149d7120a｣
｢trunc_len_f: 204｣
｢trunc_len_r: 205｣
｢trim_left_f: 1｣
｢trim_left_r: 1｣
｢max_ee_f: 2.0｣
｢max_ee_r: 2.0｣
｢trunc_q: 2｣
｢min_overlap: 12｣
｢pooling_method: 'independent'｣
｢chimera_method: 'consensus'｣
｢min_fold_parent_over_abundance: 1.0｣
｢allow_one_off: False｣
｢n_threads: 1｣
｢n_reads_learn: 1000000｣
｢hashed_feature_ids: True｣
                                                                                                                                                                                                                                                               
R version 4.2.3 (2023-03-15) 
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6 
2) Filtering .........................................
3) Learning Error Rates
209797658 total bases in 1033486 reads from 24 samples will be used for learning the error rates.
210831144 total bases in 1033486 reads from 24 samples will be used for learning the error rates.
3) Denoise samples .........................................
.........................................
5) Remove chimeras (method = consensus)
6) Report read numbers through the pipeline
7) Write output
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmp1811dfta/tmp/tmpp8qmfj61/forward --input_directory_reverse /tmp/tmp1811dfta/tmp/tmpp8qmfj61/reverse --output_path /tmp/tmp1811dfta/tmp/tmpp8qmfj61/output.tsv.biom --output_track /tmp/tmp1811dfta/tmp/tmpp8qmfj61/track.tsv --filtered_directory /tmp/tmp1811dfta/tmp/tmpp8qmfj61/filt_f --filtered_directory_reverse /tmp/tmp1811dfta/tmp/tmpp8qmfj61/filt_r --truncation_length 204 --truncation_length_reverse 205 --trim_left 1 --trim_left_reverse 1 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000

Saved FeatureTable[Frequency] to: table.qza
Saved FeatureData[Sequence] to: representative_sequences.qza
Saved SampleData[DADA2Stats] to: denoising_stats.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"allow_one_off": false, "chimera_method": "consensus", "hashed_feature_ids": true, "max_ee_f": "2.0", "max_ee_r": "2.0", "min_fold_parent_over_abundance": "1.0", "min_overlap": "12", "n_reads_learn": "1000000", "n_threads": "1", "pooling_method": "independent", "trim_left_f": "1", "trim_left_r": "1", "trunc_q": "2"}`
__workflow_invocation_uuid__	`"8497fd9ef5ac11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
trunc_len_f	`"204"`
trunc_len_r	`"205"`

Step 8: Tabulate DADA2 denoised representative sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table tabulate_seqs '/tmp/tmp1811dfta/job_working_directory/000/10/configs/tmpfib6fb41'

Exit Code:

```
0
```

Standard Output:

｢data: 8e4dc316-0c55-4600-baca-02a5d24180f4｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8497fd9ef5ac11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

**Step 9: Tabulate DADA2 statistical metadata **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run metadata tabulate '/tmp/tmp1811dfta/job_working_directory/000/11/configs/tmpsoy4j7op'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"page_size": "100"}`
__workflow_invocation_uuid__	`"8497fd9ef5ac11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/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"}}]`

Step 10: Summing up the dada2 output table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run feature_table summarize '/tmp/tmp1811dfta/job_working_directory/000/12/configs/tmpaou4pjd9'

Exit Code:

```
0
```

Standard Output:

｢table: 25fd121e-1938-4a1a-909d-1ebc089ee48f｣
｢sample_metadata: <Metadata>｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"sample_metadata": [{"__index__": 0, "__q2galaxy__GUI__conditional__sample_metadata__": {"__current_case__": 0, "source": {"values": [{"id": 9, "src": "hda"}]}, "type": "tsv"}}]}`
__workflow_invocation_uuid__	`"8497fd9ef5ac11eebc67d7f2bf5cdb5d"`
chromInfo	`"/tmp/tmp1811dfta/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - e371ccb6596ff499
- history_state
  - ok
- invocation_id
  - e371ccb6596ff499
- invocation_state
  - scheduled
- workflow_id
  - e371ccb6596ff499

✅ QIIME2-Ia-multiplexed-data-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequences:
- step_state: scheduled
Step 2: Barcodes:
- step_state: scheduled
Step 3: Metadata:
- step_state: scheduled
Step 4: Metadata parameter:
- step_state: scheduled
Step 5: Reverse complement barcodes:
- step_state: scheduled

Step 6: Input files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/4/configs/tmp_xxsbh7r'

Exit Code:

```
0
```

Standard Output:

｢type: EMPSingleEndSequences｣
｢format: EMPSingleEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37e0c0a8f5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 5, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPSingleEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 2, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_sequences": {"data": {"values": [{"id": 1, "src": "hda"}]}, "name": "sequences.fastq.gz"}}, "type": "EMPSingleEndSequences"}`

Step 7: Metadata as artifact:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/5/configs/tmpx99bggq7'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37e0c0a8f5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 3, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 8: Demultiplex single-end data:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux emp_single '/tmp/tmpr42do8f2/job_working_directory/000/6/configs/tmpra6ocwsu'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for sample_id, barcode in barcodes.to_series().iteritems():

Standard Output:

｢seqs: 9e64891e-6006-4512-8aee-41f8668f5021｣
｢barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=34>｣
｢golay_error_correction: True｣
｢rev_comp_barcodes: False｣
｢rev_comp_mapping_barcodes: False｣
｢ignore_description_mismatch: False｣
                                                                                                                                                                                                                                                               
Saved SampleData[SequencesWithQuality] to: per_sample_sequences.qza
Saved ErrorCorrectionDetails to: error_correction_details.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": false}`
__workflow_invocation_uuid__	`"37e0c0a8f5ac11ee85fe0fe49cb854e5"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Summarize demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmpr42do8f2/job_working_directory/000/7/configs/tmpqkc5qjow'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: f83c0935-f70c-4899-9add-716dc30e3dd9｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"37e0c0a8f5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 9b21a5d7a6731a29
- history_state
  - ok
- invocation_id
  - 9b21a5d7a6731a29
- invocation_state
  - scheduled
- workflow_id
  - 9b21a5d7a6731a29

✅ QIIME2-Ib-multiplexed-data-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Forward sequences:
- step_state: scheduled
Step 2: Reverse sequences:
- step_state: scheduled
Step 3: Barcodes:
- step_state: scheduled
Step 4: Metadata:
- step_state: scheduled
Step 5: Metadata parameter:
- step_state: scheduled
Step 6: Reverse complement of barcodes needed?:
- step_state: scheduled

Step 7: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/12/configs/tmp2fzrd0t7'

Exit Code:

```
0
```

Standard Output:

｢type: EMPPairedEndSequences｣
｢format: EMPPairedEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c933328ef5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 4, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPPairedEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 11, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_forward": {"data": {"values": [{"id": 9, "src": "hda"}]}, "name": "forward.fastq.gz"}, "import_reverse": {"data": {"values": [{"id": 10, "src": "hda"}]}, "name": "reverse.fastq.gz"}}, "type": "EMPPairedEndSequences"}`

Step 8: Metadata as artifact:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/13/configs/tmpz5m4vdnu'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c933328ef5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}`

Step 9: Demultiplex paired-end sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux emp_paired '/tmp/tmpr42do8f2/job_working_directory/000/14/configs/tmpt4331a3_'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for sample_id, barcode in barcodes.to_series().iteritems():

Standard Output:

｢seqs: 1d351c02-b328-47ba-afd8-42aaeb2be608｣
｢barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=75>｣
｢golay_error_correction: True｣
｢rev_comp_barcodes: False｣
｢rev_comp_mapping_barcodes: True｣
｢ignore_description_mismatch: False｣
                                                                                                                                                                                                                                                               
Saved SampleData[PairedEndSequencesWithQuality] to: per_sample_sequences.qza
Saved ErrorCorrectionDetails to: error_correction_details.qza

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": true}`
__workflow_invocation_uuid__	`"c933328ef5ac11ee85fe0fe49cb854e5"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 14, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 10: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmpr42do8f2/job_working_directory/000/15/configs/tmpz9peiw5h'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)
/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: 9b03842a-db5e-43e1-9ba6-4323ba83258f｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"c933328ef5ac11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 479c64a9c04e8638
- history_state
  - ok
- invocation_id
  - 479c64a9c04e8638
- invocation_state
  - scheduled
- workflow_id
  - 479c64a9c04e8638

✅ QIIME2-Ic-demultiplexed-data-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequence collection:
- step_state: scheduled

Step 2: Extract element identifiers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpr42do8f2/job_working_directory/000/19/configs/tmpa7mj7rtn' '/tmp/tmpr42do8f2/job_working_directory/000/19/outputs/dataset_40399713-c4ef-4a8c-b8ab-01e9611d0b79.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5e3e4224f5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: Screening laneless and single-lane:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpr42do8f2/files/4/0/3/dataset_40399713-c4ef-4a8c-b8ab-01e9611d0b79.dat' --output '/tmp/tmpr42do8f2/job_working_directory/000/20/outputs/dataset_56c34d60-538f-46b3-8445-519d79c2597a.dat' --input_display_name 'Extract element identifiers on data 3, data 2, and data 1' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5e3e4224f5ad11ee85fe0fe49cb854e5"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: Relabel sequence files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"5e3e4224f5ad11ee85fe0fe49cb854e5"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 22, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 5: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/22/configs/tmpi4z_3vm_'

Exit Code:

```
0
```

Standard Output:

｢type: SampleData[SequencesWithQuality]｣
｢format: CasavaOneEightLanelessPerSampleDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5e3e4224f5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 49, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 2, "src": "hdca"}]}}}}, "type": "SampleData__ob__SequencesWithQuality__cb__"}`

Step 6: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmpr42do8f2/job_working_directory/000/23/configs/tmph84rr4bx'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: df4255cc-1e93-49eb-98c2-2bffa3f02e8c｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"5e3e4224f5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - a051e378060e00bd
- history_state
  - ok
- invocation_id
  - a051e378060e00bd
- invocation_state
  - scheduled
- workflow_id
  - a051e378060e00bd

✅ QIIME2-Id-demultiplexed-data-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Sequence collection:
- step_state: scheduled

Step 2: Extract element identifiers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpr42do8f2/job_working_directory/000/30/configs/tmp29egrzb4' '/tmp/tmpr42do8f2/job_working_directory/000/30/outputs/dataset_9390b839-2cbf-432d-8ba2-61d023a5845c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4a2b5eaf5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 3, "src": "hdca"}]}`

Step 3: Screening laneless and single-lane:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpr42do8f2/files/9/3/9/dataset_9390b839-2cbf-432d-8ba2-61d023a5845c.dat' --output '/tmp/tmpr42do8f2/job_working_directory/000/31/outputs/dataset_b434af05-4881-4f8e-8224-d73c976f95f6.dat' --input_display_name 'Extract element identifiers on data 6, data 5, and others' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4a2b5eaf5ad11ee85fe0fe49cb854e5"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: Relabel sequence files:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c4a2b5eaf5ad11ee85fe0fe49cb854e5"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 35, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 3, "src": "hdca"}]}`

Step 5: Import data into the pipeline:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run tools import '/tmp/tmpr42do8f2/job_working_directory/000/33/configs/tmpowda0jno'

Exit Code:

```
0
```

Standard Output:

｢type: SampleData[PairedEndSequencesWithQuality]｣
｢format: CasavaOneEightLanelessPerSampleDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4a2b5eaf5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 46, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 4, "src": "hdca"}]}}}}, "type": "SampleData__ob__PairedEndSequencesWithQuality__cb__"}`

Step 6: Summarising the demultiplexed output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

q2galaxy run demux summarize '/tmp/tmpr42do8f2/job_working_directory/000/34/configs/tmppz83o0_i'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)
/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  context['result_data'] = context['result_data'].append(df)

Standard Output:

｢data: 50a7d466-5a5b-4b03-ade7-818539c7318d｣
｢n: 10000｣
                                                                                                                                                                                                                                                               
Saved Visualization to: visualization.qzv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"c4a2b5eaf5ad11ee85fe0fe49cb854e5"`
chromInfo	`"/tmp/tmpr42do8f2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - e682a7b8c3879c46
- history_state
  - ok
- invocation_id
  - e682a7b8c3879c46
- invocation_state
  - scheduled
- workflow_id
  - e682a7b8c3879c46

mvdbeek

Thanks a lot, looks great!

workflows/amplicon/qiime2/README.md

initial commit of 1st qiime2 workflows

c882f83

debjyoti197 marked this pull request as draft March 7, 2024 14:34

bernt-matthias added 2 commits March 9, 2024 17:28

finishing 1c and 1d

18bef05

- finish tests for 1c,d - make viz a workflow output - allow only fastq.gz input

rename files

0307855

for easier handling on the command line

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2 more import and denoising workflows

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bernt-matthias added 2 commits March 18, 2024 16:09

rename files

a56ab53

finish import workflow tests

6071024

start README

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add workflowhub file

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update dockstore

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dockstore fix

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bernt-matthias mentioned this pull request Mar 26, 2024

Fix markdown template: add missing closing details tag galaxyproject/planemo#1440

Merged

bernt-matthias added 2 commits March 27, 2024 18:19

fix tests for II

72a15d2

some fixes for denoising workflows and tests

eeb2931

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restructure and finalize

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bernt-matthias marked this pull request as ready for review April 8, 2024 10:23