Add FAIRyMAGs Taxonomic Binning Evaluation Workflow #923

SantaMcCloud · 2025-07-31T17:19:53Z

FOR CONTRIBUTOR:

I have read the Adding workflows guidelines
License permits unrestricted use (educational + commercial)
Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

.dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
Changelog contains appropriate entries
Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

mvdbeek

Hey @SantaMcCloud, this looks quite interesting! Here's a few things I noticed on a first pass through. Please also move all test data larger than 100KB to zenodo and delete the files from the test-data folder. Is binninge a typo in taxonomic-binninge-evaluation ? if so please also rename the folder.

@paulzierep @bebatut can you review the workflows ?

workflows/microbiome/taxonomic-binninge-evaluation/.dockstore.yml

workflows/microbiome/taxonomic-binninge-evaluation/FAIRyMAGs-GTDB-Tk-subworkflow.ga

...ws/microbiome/taxonomic-binninge-evaluation/FAIRyMAGs-taxonomic-binning-evaluation-tests.yml

workflows/microbiome/taxonomic-binninge-evaluation/FAIRyMAGs-taxonomic-binning-evaluation.ga

workflows/microbiome/taxonomic-binninge-evaluation/GTDB2NCBI-TaxID-Subworkflow.ga

github-actions · 2025-08-04T09:21:48Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	1
Error	2
Failure	0
Skipped	0

Errored Tests

❌ FAIRyMAGs-GTDB-Tk-subworkflow.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Sample Name and Number:
- step_state: scheduled
Step 2: Bins:
- step_state: scheduled

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"777443c8711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "@SampleID:", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "sample_0", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"777443c8711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "files": {"values": [{"id": 4, "src": "hdca"}]}, "is_select": "manually"}`
work	`"all"`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"777443c8711311f0a03a7c1e52196ae2"`
advanced	`{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gtdbtk_db	`"full_database_release_220_downloaded_2024-10-19"`

Step 6: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 37b67fa6fb2210c3
- history_state
  - ok
- invocation_id
  - 76808b45854391ef
- invocation_state
  - failed
- workflow_id
  - 6b943a1aa8392255

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"4":{"gtdbtk_db":"Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'."}}}

Passed Tests

✅ GTDB2NCBI-TaxID-Subworkflow.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: GTDB-Tk Summary:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

printf "Concatenating files:\n" && printf "gtdbtk.ar53.summary..." && cat '/tmp/tmpi_1r7evk/files/0/c/b/dataset_0cb1b611-2d9e-45b3-b941-0eb33c7cfe50.dat' >> '/tmp/tmpi_1r7evk/job_working_directory/000/15/outputs/dataset_b85e8906-e07f-4ea0-8291-dcc464d55e2a.dat' && printf "Done\n" && printf "gtdbtk.bac120.summary..." && cat '/tmp/tmpi_1r7evk/files/f/8/8/dataset_f88d79b4-bd3f-4d73-b75b-4bb9414fefb4.dat' >> '/tmp/tmpi_1r7evk/job_working_directory/000/15/outputs/dataset_b85e8906-e07f-4ea0-8291-dcc464d55e2a.dat' && printf "Done\n" && sleep 1

Exit Code:

```
0
```

Standard Output:

Concatenating files:
gtdbtk.ar53.summary...Done
gtdbtk.bac120.summary...Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dataset_names	`false`
dbkey	`"?"`
global_condition	`{"__current_case__": 0, "input_type": "singles", "inputs": {"values": [{"id": 9, "src": "hdca"}]}}`
headers	`"0"`

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ../home/.taxonkit &&  ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/names.dmp' 'names.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/merged.dmp' 'merged.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/nodes.dmp' 'nodes.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/delnodes.dmp' 'delnodes.dmp' &&  taxonkit name2taxid --data-dir '.' --name-field '1'   '/tmp/tmpi_1r7evk/files/b/2/6/dataset_b26fb29b-4326-4612-bc3b-4f0e496d5753.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/24/outputs/dataset_27147294-e2f7-42d7-8a7e-74aee536682f.dat'

Exit Code:

```
0
```

Standard Error:

09:19:22.829 �[33m[WARN]�[0m multiple TaxIds found for 'Planococcus'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
data	`{"__current_case__": 0, "is_select": "cached", "ncbi": "2024-06-05"}`
dbkey	`"?"`
name_field	`"1"`
sci_name	`false`
show_rank	`false`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpi_1r7evk/job_working_directory/000/25/configs/tmpc34mdyey' '/tmp/tmpi_1r7evk/files/2/7/1/dataset_27147294-e2f7-42d7-8a7e-74aee536682f.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/25/outputs/dataset_46e04b99-a013-4a7f-bfb2-2bcc7ca9885f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN {print \"NCBI_name\\tNCBI_TaxID\"} {print}"`
dbkey	`"?"`
variables	`[]`

Step 13: Paste1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpi_1r7evk/galaxy-dev/tools/filters/pasteWrapper.pl' '/tmp/tmpi_1r7evk/files/2/e/2/dataset_2e23a775-3888-4893-9daf-65debc82cfe3.dat' '/tmp/tmpi_1r7evk/files/4/6/e/dataset_46e04b99-a013-4a7f-bfb2-2bcc7ca9885f.dat' T '/tmp/tmpi_1r7evk/job_working_directory/000/26/outputs/dataset_de4c2728-ce75-44df-afe2-901b1e668a7b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /gtdb_taxonomy/, "classification", "g", $1 ) ; print $0 ; }' '/tmp/tmpi_1r7evk/files/d/e/4/dataset_de4c2728-ce75-44df-afe2-901b1e668a7b.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/27/outputs/dataset_61656c15-0f57-4325-a8b2-1230137c05d3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "gtdb_taxonomy", "replace_pattern": "classification"}]`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/sort-header' ./ && chmod +x sort-header && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/easyjoin'  -t $'\t' --header -e '-' -o auto -i -1 '2' -2 '1' '/tmp/tmpi_1r7evk/files/1/5/4/dataset_154e78e8-e4d1-4d4a-a0a7-b0d8d70b62cf.dat' '/tmp/tmpi_1r7evk/files/6/1/6/dataset_61656c15-0f57-4325-a8b2-1230137c05d3.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/28/outputs/dataset_01f8533a-09da-4401-ae85-7b28f1de8653.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column1	`"2"`
column2	`"1"`
dbkey	`"?"`
empty_string_filler	`"-"`
header	`true`
ignore_case	`true`
jointype	`" "`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpi_1r7evk/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpi_1r7evk/files/0/1/f/dataset_01f8533a-09da-4401-ae85-7b28f1de8653.dat' 'c2,c1,c25,c26' T '/tmp/tmpi_1r7evk/job_working_directory/000/29/outputs/dataset_3c3c1d80-130b-4c5b-9d22-53bf36bece2c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2,c1,c25,c26"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/sort-header' ./ && chmod +x sort-header && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/easyjoin'  -t $'\t' --header -e '-' -o auto -i -1 '1' -2 '1' '/tmp/tmpi_1r7evk/files/0/c/2/dataset_0c2427f9-9cb1-4bbc-ac48-c89cd6768b3a.dat' '/tmp/tmpi_1r7evk/files/3/c/3/dataset_3c3c1d80-130b-4c5b-9d22-53bf36bece2c.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/30/outputs/dataset_fb0ea397-2f92-4627-910e-35ca856ee97e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column1	`"1"`
column2	`"1"`
dbkey	`"?"`
empty_string_filler	`"-"`
header	`true`
ignore_case	`true`
jointype	`" "`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpi_1r7evk/job_working_directory/000/31/configs/tmpdrnlgbod' '/tmp/tmpi_1r7evk/files/3/c/3/dataset_3c3c1d80-130b-4c5b-9d22-53bf36bece2c.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/31/outputs/dataset_5031198c-21a8-4303-9a8b-1643893db334.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR == 1 { $0 = \"BinID\\tGTDB_name\\tNCBI_name\\tNCBI_TaxID\"; } { print }"`
dbkey	`"?"`
variables	`[]`

Step 19: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $21 = gensub( /classification/, "GTDB_name", "g", $21 ) ; print $0 ; }' '/tmp/tmpi_1r7evk/files/f/b/0/dataset_fb0ea397-2f92-4627-910e-35ca856ee97e.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/32/outputs/dataset_d4c24fee-9f08-4a0a-974a-9ab267bdd0e0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "21", "find_pattern": "classification", "replace_pattern": "GTDB_name"}]`

Step 3: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmpi_1r7evk/files/b/8/5/dataset_b85e8906-e07f-4ea0-8291-dcc464d55e2a.dat" ;   ) > /tmp/tmpi_1r7evk/job_working_directory/000/16/outputs/dataset_a185961b-b4a8-4136-a2fc-96afead85bfe.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpi_1r7evk/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpi_1r7evk/files/b/8/5/dataset_b85e8906-e07f-4ea0-8291-dcc464d55e2a.dat' 'c2' T '/tmp/tmpi_1r7evk/job_working_directory/000/17/outputs/dataset_5a482f2f-a8cc-4fbc-b965-df1f8308ee92.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpi_1r7evk/job_working_directory/000/18/configs/tmp25ygx7a7' '/tmp/tmpi_1r7evk/files/a/1/8/dataset_a185961b-b4a8-4136-a2fc-96afead85bfe.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/18/outputs/dataset_0c2427f9-9cb1-4bbc-ac48-c89cd6768b3a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	` "NR == 0
dbkey	`"?"`
variables	`[]`

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /^.*;/, "", "g", $1 ) ; print $0 ; }' '/tmp/tmpi_1r7evk/files/5/a/4/dataset_5a482f2f-a8cc-4fbc-b965-df1f8308ee92.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/19/outputs/dataset_8ffa348d-3f59-4a90-9918-fd7a1376839e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "^.*;", "replace_pattern": null}]`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $2 = gensub( /^.*;/, "", "g", $2 ) ; print $0 ; }' '/tmp/tmpi_1r7evk/files/0/c/2/dataset_0c2427f9-9cb1-4bbc-ac48-c89cd6768b3a.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/20/outputs/dataset_154e78e8-e4d1-4d4a-a0a7-b0d8d70b62cf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "2", "find_pattern": "^.*;", "replace_pattern": null}]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output &&  ln -s '/cvmfs/data.galaxyproject.org/byhand/gtdbtk_database_metadata_versioned/_release_220_downloaded_2024-09-10/bac'* 'bac_meta.tsv' && ln -s '/cvmfs/data.galaxyproject.org/byhand/gtdbtk_database_metadata_versioned/_release_220_downloaded_2024-09-10/ar'* 'ar_meta.tsv' &&  ncbi-gtdb_map.py -q gtdb_taxonomy '/tmp/tmpi_1r7evk/files/8/f/f/dataset_8ffa348d-3f59-4a90-9918-fd7a1376839e.dat' 'bac_meta.tsv' 'ar_meta.tsv' --completeness 50.0 --contamination 5.0 --fraction 0.9 --max-tips 100 --column 1   -o output --procs ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Standard Error:

2025-08-04 09:15:39,298 - Loading: bac_meta.tsv
2025-08-04 09:18:21,914 -   Entries lacking an NCBI taxonomy: 0
2025-08-04 09:18:21,914 -   Completeness-filtered entries: 17
2025-08-04 09:18:21,914 -   Contamination-filtered entries: 10353
2025-08-04 09:18:21,914 -   Entries used: 574012
2025-08-04 09:18:21,914 - Loading: ar_meta.tsv
2025-08-04 09:18:27,174 -   Entries lacking an NCBI taxonomy: 0
2025-08-04 09:18:27,174 -   Completeness-filtered entries: 1
2025-08-04 09:18:27,174 -   Contamination-filtered entries: 401
2025-08-04 09:18:27,174 -   Entries used: 12075
2025-08-04 09:18:27,174 - Reading in queries: /tmp/tmpi_1r7evk/files/8/f/f/dataset_8ffa348d-3f59-4a90-9918-fd7a1376839e.dat
2025-08-04 09:18:27,174 - No. of queries: 43
2025-08-04 09:18:27,174 - No. of de-rep queries: 36
2025-08-04 09:18:27,174 - Batching queries...
2025-08-04 09:18:27,175 -   No. of batches: 1
2025-08-04 09:18:27,175 -   Queries per batch: 36
2025-08-04 09:18:27,175 - Querying taxonomies...
2025-08-04 09:18:27,181 - PID10: Finished! Queries=36, Hits=32, No-Hits=4
2025-08-04 09:18:27,181 - File written: output/taxonomy_map_summary.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
add_prefix	`{"__current_case__": 1, "is_select": "n"}`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"1"`
completeness	`"50.0"`
contamination	`"5.0"`
data	`{"__current_case__": 0, "is_select": "cached", "metadata": "GTDB-Tk Database Version 220 Metadata from 09-10-2024 _release_220_downloaded_2024-09-10"}`
dbkey	`"?"`
fraction	`"0.9"`
header	`false`
max_tips	`"100"`
mode	`"gtdb"`
no_prefix	`false`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpi_1r7evk/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpi_1r7evk/files/2/e/2/dataset_2e23a775-3888-4893-9daf-65debc82cfe3.dat' 'c2' T '/tmp/tmpi_1r7evk/job_working_directory/000/22/outputs/dataset_80af1bb7-aa90-4503-96d6-1ca5ebea9e45.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /[a-z]__/, "", "g", $1 ) ; print $0 ; }' '/tmp/tmpi_1r7evk/files/8/0/a/dataset_80af1bb7-aa90-4503-96d6-1ca5ebea9e45.dat' > '/tmp/tmpi_1r7evk/job_working_directory/000/23/outputs/dataset_b26fb29b-4326-4612-bc3b-4f0e496d5753.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d74dd3c711311f0a03a7c1e52196ae2"`
chromInfo	`"/tmp/tmpi_1r7evk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "[a-z]__", "replace_pattern": null}]`

Other invocation details
- history_id
  - d7e1dc7cea7cf71f
- history_state
  - ok
- invocation_id
  - d7e1dc7cea7cf71f
- invocation_state
  - scheduled
- workflow_id
  - 254b5a19268a5b58

SantaMcCloud · 2025-08-04T09:59:29Z

@mvdbeek thank you for the review i will work on them later! I thought since all of the subworkflows are included in the main workflow they has to be submitted aswell. I can remove them if you want or keep it however you like. The second workflow can be used outside but i dont think this wf will be often used.

I only have 1 question and 1 Problem:

Q: When moveing the test-data to Zenodo can i still use them to compare since there are also outputs in the test-data dir?

Problem: When testing this WF i run into an error which might be because of the Galaxy logic. The first subworkflow runs GTDB-Tk and this outputs are provided for the second subworkflow. Since Galaxy start to create the jobs for the second subworfklow without wating till the inputs are done from GTDB-Tk the status of this run is marked as failed which will stop the test and let them fail.

I did try it out multiple times and always at this point its break and report me them as failed while on EU is runs normaly and after GTDB-Tk is done this subworkflow is running then. So i think it has to be something with this. Otherwise could you have a peek into the last test run here and could give me the reason why the test is failing?

The second subworkflow is the only one passing the test so this should be the problem.

mvdbeek · 2025-08-04T14:14:03Z

When moveing the test-data to Zenodo can i still use them to compare since there are also outputs in the test-data dir?

Please don't do that, you should write assertions against the data, e.g. for things you expect to be present in the outputs.
The files are huge and if in the future the slightest difference is detected we won't know if the results are valid.

Since Galaxy start to create the jobs for the second subworfklow without wating till the inputs are done from GTDB-Tk

So that would be an extremely sever bug that, while not impossible, is kind of unlikely to happen.
What I see in the test run is:

bioblend.ConnectionError: Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"4":{"gtdbtk_db":"Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'."}}}
╭─────────────────────── Invocation <76808b45854391ef> ────────────────────────╮
│ Steps ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━                ◆  62% ◆ 5/8 scheduled      │
│ Jobs  ◆                                          ◆   0% ◆ 0/3 terminal       │
│ Job States ◆ 🆕 3 ◆                                                          │
│ ╭─────────────── Subworkflow Invocation <37b67fa6fb2210c3> ────────────────╮ │
│ │ Steps ◆                                          ◆   0% ◆ Loading steps. │ │
│ │ Jobs  ◆                                          ◆   0% ◆                │ │
│ │ Job States ◆                                                             │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │

Can you use that database or do we need to update what is in CVMFS ?

SantaMcCloud · 2025-08-04T23:19:53Z

Please don't do that, you should write assertions against the data, e.g. for things you expect to be present in the outputs.
The files are huge and if in the future the slightest difference is detected we won't know if the results are valid.

Since the outputs are very small which are comapred (between 3 - 45 KB) i think this sould not be a problem since the delta is also very low (1500 bytes). I did remove all files over 100KB to Zenodo ( e21be0b) If you still dont want this for the test, the files size comparing, i will change it. I just didnt change it yet since if you dont want to have the subWFs uploaded here all of this kind of test will be deleted.

So that would be an extremely sever bug that, while not impossible, is kind of unlikely to happen.

Okay this is the only thing i could see other thing i couldnt explain but if these error are happening now you might can help me to find the error then to fix it since manually testing doesnt help me to find it.

Can you use that database or do we need to update what is in CVMFS ?

Yes this DB can used. The problem was the timestamp when the DB was created. I did change it (81c9fd6) now so it should not run into an error this time i hope. Thank you for the help!

github-actions · 2025-08-05T00:01:10Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	1
Error	2
Failure	0
Skipped	0

Errored Tests

❌ FAIRyMAGs-GTDB-Tk-subworkflow.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Sample Name and Number:
- step_state: scheduled
Step 2: Bins:
- step_state: scheduled

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3890a7f2718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "@SampleID:", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "sample_0", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3890a7f2718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "files": {"values": [{"id": 31, "src": "hdca"}]}, "is_select": "manually"}`
work	`"all"`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3890a7f2718e11f0a03a6045bdc83571"`
advanced	`{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gtdbtk_db	`"full_database_release_220_downloaded_2024-10-19"`

Step 6: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - faa8f04c24f8f32b
- history_state
  - ok
- invocation_id
  - ed2b968379c16054
- invocation_state
  - failed
- workflow_id
  - 8136d8c48809d3ab

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Biobox File(s):
- step_state: scheduled
Step 2: Assemblies:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
bedfile	__identifier__
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "", "input_bam": {"values": [{"id": 11, "src": "dce"}]}, "input_fasta": {"values": [{"id": 2, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 14: Unlabelled step:
- step_state: new

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
composition_file	__identifier__
coverage_file	__identifier__
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 18, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 18, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": false, "marker": false, "markers": false, "markerset": "107", "plotmarker": false}`

Step 19: Unlabelled step:
- step_state: new

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 3: Reads:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 27: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 28: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 29: Unlabelled step:
- step_state: new
Step 30: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mv '/tmp/tmpacu8ybli/job_working_directory/000/5/configs/tmpqt1vtddy' '/tmp/tmpacu8ybli/job_working_directory/000/5/outputs/dataset_2c9215ac-2f0d-4ef9-b8d3-5ef803720583.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 33: Unlabelled step:
- step_state: new
Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Unlabelled step:
- step_state: new
Step 38: Unlabelled step:
- step_state: new
Step 39: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 40: Unlabelled step:
- step_state: new

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpacu8ybli/files/b/2/4/dataset_b2452725-dfc4-4370-a044-4c1689dca1aa.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmpacu8ybli/job_working_directory/000/6/outputs/dataset_9af1c119-3308-445f-a6a7-58300fe87692.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/6/outputs/dataset_747f8fa0-2a33-44d0-9b05-c8ba3faf547b.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
bedfile	`true`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpacu8ybli/files/2/9/e/dataset_29e4632f-2502-4027-9852-454f85e0949c.dat' 'marine_pooled_gsb_trimmed' && ln -s '/tmp/tmpacu8ybli/files/b/2/4/dataset_b2452725-dfc4-4370-a044-4c1689dca1aa.dat' 'marine_pooled_gsa_trimmed' &&  add_length_column.py -g 'marine_pooled_gsb_trimmed' -f 'marine_pooled_gsa_trimmed' > gold_standard_file.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpacu8ybli/files/b/2/4/dataset_b2452725-dfc4-4370-a044-4c1689dca1aa.dat' genome && ln -s -f '/tmp/tmpacu8ybli/files/b/2/4/dataset_b2452725-dfc4-4370-a044-4c1689dca1aa.dat' genome.fa &&   ln -f -s '/tmp/tmpacu8ybli/files/f/3/1/dataset_f3109363-4fcc-417c-9d7f-a15931d61d11.dat' input_f.fastq &&  ln -f -s '/tmp/tmpacu8ybli/files/b/8/9/dataset_b8927309-5959-4e45-9f14-d3b21369daf3.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq'                2> >(tee '/tmp/tmpacu8ybli/job_working_directory/000/8/outputs/dataset_fbe96a12-6de4-4213-b3a7-a97df3951f12.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpacu8ybli/job_working_directory/000/8/outputs/dataset_ba277c52-78db-4b56-9208-23bbf4901936.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 2, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{gsub( $0 ,\"sample_\" (NR-1)); print}"`
dbkey	`"?"`
variables	`[]`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2537a746718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 10: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 9edaf5531db8d6d0
- history_state
  - ok
- invocation_id
  - 9edaf5531db8d6d0
- invocation_state
  - failed
- workflow_id
  - 4ae9d7f4a106bcf4

Passed Tests

✅ GTDB2NCBI-TaxID-Subworkflow.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: GTDB-Tk Summary:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

printf "Concatenating files:\n" && printf "gtdbtk.ar53.summary..." && cat '/tmp/tmpacu8ybli/files/c/7/6/dataset_c76f9f07-e7bc-4dcf-bb3a-571222092be8.dat' >> '/tmp/tmpacu8ybli/job_working_directory/000/29/outputs/dataset_01b1c4f9-954e-496e-ae57-012776f3bea1.dat' && printf "Done\n" && printf "gtdbtk.bac120.summary..." && cat '/tmp/tmpacu8ybli/files/3/2/d/dataset_32decbe5-694d-44a4-87bb-4e4c5e17ddcb.dat' >> '/tmp/tmpacu8ybli/job_working_directory/000/29/outputs/dataset_01b1c4f9-954e-496e-ae57-012776f3bea1.dat' && printf "Done\n" && sleep 1

Exit Code:

```
0
```

Standard Output:

Concatenating files:
gtdbtk.ar53.summary...Done
gtdbtk.bac120.summary...Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dataset_names	`false`
dbkey	`"?"`
global_condition	`{"__current_case__": 0, "input_type": "singles", "inputs": {"values": [{"id": 36, "src": "hdca"}]}}`
headers	`"0"`

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ../home/.taxonkit &&  ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/names.dmp' 'names.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/merged.dmp' 'merged.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/nodes.dmp' 'nodes.dmp' && ln -s '/cvmfs/data.galaxyproject.org/byhand/ncbi_taxonomy/2024-06-05/delnodes.dmp' 'delnodes.dmp' &&  taxonkit name2taxid --data-dir '.' --name-field '1'   '/tmp/tmpacu8ybli/files/a/6/0/dataset_a6047c65-f2cf-43c4-bbfe-e0be4c709b59.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/38/outputs/dataset_48ec0cb1-06ad-4bf3-9927-170026ac8685.dat'

Exit Code:

```
0
```

Standard Error:

23:58:52.377 �[33m[WARN]�[0m multiple TaxIds found for 'Planococcus'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
data	`{"__current_case__": 0, "is_select": "cached", "ncbi": "2024-06-05"}`
dbkey	`"?"`
name_field	`"1"`
sci_name	`false`
show_rank	`false`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpacu8ybli/job_working_directory/000/39/configs/tmp1_hihvcv' '/tmp/tmpacu8ybli/files/4/8/e/dataset_48ec0cb1-06ad-4bf3-9927-170026ac8685.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/39/outputs/dataset_2bdd95b2-a5c4-497e-add0-12a078300b15.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN {print \"NCBI_name\\tNCBI_TaxID\"} {print}"`
dbkey	`"?"`
variables	`[]`

Step 13: Paste1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpacu8ybli/galaxy-dev/tools/filters/pasteWrapper.pl' '/tmp/tmpacu8ybli/files/1/9/e/dataset_19e7a575-a729-460e-9443-052e792e360e.dat' '/tmp/tmpacu8ybli/files/2/b/d/dataset_2bdd95b2-a5c4-497e-add0-12a078300b15.dat' T '/tmp/tmpacu8ybli/job_working_directory/000/40/outputs/dataset_43068a74-b9f7-4ad4-ab81-b44073f13364.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /gtdb_taxonomy/, "classification", "g", $1 ) ; print $0 ; }' '/tmp/tmpacu8ybli/files/4/3/0/dataset_43068a74-b9f7-4ad4-ab81-b44073f13364.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/41/outputs/dataset_914fae7c-cf1a-4aa1-909b-63fd7d6bc457.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "gtdb_taxonomy", "replace_pattern": "classification"}]`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/sort-header' ./ && chmod +x sort-header && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/easyjoin'  -t $'\t' --header -e '-' -o auto -i -1 '2' -2 '1' '/tmp/tmpacu8ybli/files/2/8/7/dataset_287c3bd0-eea5-4e28-88b6-3cd79c6e7043.dat' '/tmp/tmpacu8ybli/files/9/1/4/dataset_914fae7c-cf1a-4aa1-909b-63fd7d6bc457.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/42/outputs/dataset_1658424a-63bd-4593-a6cb-f79256b0fcdd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column1	`"2"`
column2	`"1"`
dbkey	`"?"`
empty_string_filler	`"-"`
header	`true`
ignore_case	`true`
jointype	`" "`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpacu8ybli/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpacu8ybli/files/1/6/5/dataset_1658424a-63bd-4593-a6cb-f79256b0fcdd.dat' 'c2,c1,c25,c26' T '/tmp/tmpacu8ybli/job_working_directory/000/43/outputs/dataset_8e05e835-7c18-4085-87fc-e702d0cda548.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2,c1,c25,c26"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/sort-header' ./ && chmod +x sort-header && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/easyjoin'  -t $'\t' --header -e '-' -o auto -i -1 '1' -2 '1' '/tmp/tmpacu8ybli/files/b/4/7/dataset_b4779712-f44e-41bf-acd8-10ea9da7fc19.dat' '/tmp/tmpacu8ybli/files/8/e/0/dataset_8e05e835-7c18-4085-87fc-e702d0cda548.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/44/outputs/dataset_d0ee4ed3-cafe-4826-a456-29fa86ffbc5e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column1	`"1"`
column2	`"1"`
dbkey	`"?"`
empty_string_filler	`"-"`
header	`true`
ignore_case	`true`
jointype	`" "`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpacu8ybli/job_working_directory/000/45/configs/tmpksv1f339' '/tmp/tmpacu8ybli/files/8/e/0/dataset_8e05e835-7c18-4085-87fc-e702d0cda548.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/45/outputs/dataset_943e5060-11ca-4989-a307-802e71ffa079.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR == 1 { $0 = \"BinID\\tGTDB_name\\tNCBI_name\\tNCBI_TaxID\"; } { print }"`
dbkey	`"?"`
variables	`[]`

Step 19: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $21 = gensub( /classification/, "GTDB_name", "g", $21 ) ; print $0 ; }' '/tmp/tmpacu8ybli/files/d/0/e/dataset_d0ee4ed3-cafe-4826-a456-29fa86ffbc5e.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/46/outputs/dataset_d723ca5f-7469-4e94-ab45-9c3ad6dcd85e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "21", "find_pattern": "classification", "replace_pattern": "GTDB_name"}]`

Step 3: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmpacu8ybli/files/0/1/b/dataset_01b1c4f9-954e-496e-ae57-012776f3bea1.dat" ;   ) > /tmp/tmpacu8ybli/job_working_directory/000/30/outputs/dataset_3397dbe7-2a85-4595-943e-dda8492c5445.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpacu8ybli/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpacu8ybli/files/0/1/b/dataset_01b1c4f9-954e-496e-ae57-012776f3bea1.dat' 'c2' T '/tmp/tmpacu8ybli/job_working_directory/000/31/outputs/dataset_cd144f5e-0bbd-43ef-8421-7e82800b4906.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpacu8ybli/job_working_directory/000/32/configs/tmpc0x7cqyn' '/tmp/tmpacu8ybli/files/3/3/9/dataset_3397dbe7-2a85-4595-943e-dda8492c5445.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/32/outputs/dataset_b4779712-f44e-41bf-acd8-10ea9da7fc19.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	` "NR == 0
dbkey	`"?"`
variables	`[]`

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /^.*;/, "", "g", $1 ) ; print $0 ; }' '/tmp/tmpacu8ybli/files/c/d/1/dataset_cd144f5e-0bbd-43ef-8421-7e82800b4906.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/33/outputs/dataset_f1997edd-fbc0-43b6-945d-b67a262c9f2e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "^.*;", "replace_pattern": null}]`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $2 = gensub( /^.*;/, "", "g", $2 ) ; print $0 ; }' '/tmp/tmpacu8ybli/files/b/4/7/dataset_b4779712-f44e-41bf-acd8-10ea9da7fc19.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/34/outputs/dataset_287c3bd0-eea5-4e28-88b6-3cd79c6e7043.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "2", "find_pattern": "^.*;", "replace_pattern": null}]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output &&  ln -s '/cvmfs/data.galaxyproject.org/byhand/gtdbtk_database_metadata_versioned/_release_220_downloaded_2024-09-10/bac'* 'bac_meta.tsv' && ln -s '/cvmfs/data.galaxyproject.org/byhand/gtdbtk_database_metadata_versioned/_release_220_downloaded_2024-09-10/ar'* 'ar_meta.tsv' &&  ncbi-gtdb_map.py -q gtdb_taxonomy '/tmp/tmpacu8ybli/files/f/1/9/dataset_f1997edd-fbc0-43b6-945d-b67a262c9f2e.dat' 'bac_meta.tsv' 'ar_meta.tsv' --completeness 50.0 --contamination 5.0 --fraction 0.9 --max-tips 100 --column 1   -o output --procs ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Standard Error:

2025-08-04 23:55:41,305 - Loading: bac_meta.tsv
2025-08-04 23:57:59,523 -   Entries lacking an NCBI taxonomy: 0
2025-08-04 23:57:59,523 -   Completeness-filtered entries: 17
2025-08-04 23:57:59,523 -   Contamination-filtered entries: 10353
2025-08-04 23:57:59,523 -   Entries used: 574012
2025-08-04 23:57:59,523 - Loading: ar_meta.tsv
2025-08-04 23:58:04,516 -   Entries lacking an NCBI taxonomy: 0
2025-08-04 23:58:04,517 -   Completeness-filtered entries: 1
2025-08-04 23:58:04,517 -   Contamination-filtered entries: 401
2025-08-04 23:58:04,517 -   Entries used: 12075
2025-08-04 23:58:04,517 - Reading in queries: /tmp/tmpacu8ybli/files/f/1/9/dataset_f1997edd-fbc0-43b6-945d-b67a262c9f2e.dat
2025-08-04 23:58:04,517 - No. of queries: 43
2025-08-04 23:58:04,517 - No. of de-rep queries: 36
2025-08-04 23:58:04,517 - Batching queries...
2025-08-04 23:58:04,517 -   No. of batches: 1
2025-08-04 23:58:04,517 -   Queries per batch: 36
2025-08-04 23:58:04,517 - Querying taxonomies...
2025-08-04 23:58:04,525 - PID10: Finished! Queries=36, Hits=32, No-Hits=4
2025-08-04 23:58:04,525 - File written: output/taxonomy_map_summary.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
add_prefix	`{"__current_case__": 1, "is_select": "n"}`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"1"`
completeness	`"50.0"`
contamination	`"5.0"`
data	`{"__current_case__": 0, "is_select": "cached", "metadata": "GTDB-Tk Database Version 220 Metadata from 09-10-2024 _release_220_downloaded_2024-09-10"}`
dbkey	`"?"`
fraction	`"0.9"`
header	`false`
max_tips	`"100"`
mode	`"gtdb"`
no_prefix	`false`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpacu8ybli/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpacu8ybli/files/1/9/e/dataset_19e7a575-a729-460e-9443-052e792e360e.dat' 'c2' T '/tmp/tmpacu8ybli/job_working_directory/000/36/outputs/dataset_43f0e723-862b-4c8c-8053-ec8cc7ee08f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /[a-z]__/, "", "g", $1 ) ; print $0 ; }' '/tmp/tmpacu8ybli/files/4/3/f/dataset_43f0e723-862b-4c8c-8053-ec8cc7ee08f5.dat' > '/tmp/tmpacu8ybli/job_working_directory/000/37/outputs/dataset_a6047c65-f2cf-43c4-bbfe-e0be4c709b59.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3dff81ea718e11f0a03a6045bdc83571"`
chromInfo	`"/tmp/tmpacu8ybli/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "[a-z]__", "replace_pattern": null}]`

Other invocation details
- history_id
  - 6175c64f6158660f
- history_state
  - ok
- invocation_id
  - 4db2841fbe9f5df3
- invocation_state
  - scheduled
- workflow_id
  - 4db2841fbe9f5df3

SantaMcCloud · 2025-08-05T07:50:33Z

@mvdbeek could you check now why the test errored? I didnt found anything useful

github-actions · 2025-08-07T20:46:55Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Biobox File:
- step_state: scheduled
Step 2: Assemblies:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
bedfile	__identifier__
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "", "input_bam": {"values": [{"id": 11, "src": "dce"}]}, "input_fasta": {"values": [{"id": 2, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 14: Unlabelled step:
- step_state: new

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
composition_file	__identifier__
coverage_file	__identifier__
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 18, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 18, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": false, "marker": false, "markers": false, "markerset": "107", "plotmarker": false}`

Step 19: Unlabelled step:
- step_state: new

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 3: Reads:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 27: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 28: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 29: Unlabelled step:
- step_state: new
Step 30: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mv '/tmp/tmpyiw7ovbk/job_working_directory/000/5/configs/tmpnoa9fr8y' '/tmp/tmpyiw7ovbk/job_working_directory/000/5/outputs/dataset_101efeb4-b30f-4f00-810e-9350836432fd.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 33: Unlabelled step:
- step_state: new
Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Unlabelled step:
- step_state: new
Step 38: Unlabelled step:
- step_state: new
Step 39: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 40: Unlabelled step:
- step_state: new

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpyiw7ovbk/files/a/3/d/dataset_a3d67197-8fc4-4ea5-a27e-d727f216dc0f.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmpyiw7ovbk/job_working_directory/000/6/outputs/dataset_1bc8c141-1736-4804-8e8f-836933fc933b.dat' > '/tmp/tmpyiw7ovbk/job_working_directory/000/6/outputs/dataset_574e86f8-1f4e-44ae-8f28-53869d94f1ab.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
bedfile	`true`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpyiw7ovbk/files/d/c/5/dataset_dc507a1d-990b-4fb4-96f5-520d86315046.dat' 'marine_pooled_gsb_trimmed' && ln -s '/tmp/tmpyiw7ovbk/files/a/3/d/dataset_a3d67197-8fc4-4ea5-a27e-d727f216dc0f.dat' 'marine_pooled_gsa_trimmed' &&  add_length_column.py -g 'marine_pooled_gsb_trimmed' -f 'marine_pooled_gsa_trimmed' > gold_standard_file.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpyiw7ovbk/files/a/3/d/dataset_a3d67197-8fc4-4ea5-a27e-d727f216dc0f.dat' genome && ln -s -f '/tmp/tmpyiw7ovbk/files/a/3/d/dataset_a3d67197-8fc4-4ea5-a27e-d727f216dc0f.dat' genome.fa &&   ln -f -s '/tmp/tmpyiw7ovbk/files/8/5/3/dataset_8536e01a-74c7-44c0-a129-06ff131f1219.dat' input_f.fastq &&  ln -f -s '/tmp/tmpyiw7ovbk/files/3/9/2/dataset_39234ec2-fd16-4d48-afbf-3c3824574f7e.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq'                2> >(tee '/tmp/tmpyiw7ovbk/job_working_directory/000/8/outputs/dataset_cb2e3889-1dfd-4d50-9fa0-fe429a4b2cea.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpyiw7ovbk/job_working_directory/000/8/outputs/dataset_914512b5-445f-462f-8ada-a2fa265f72f8.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 2, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{gsub( $0 ,\"sample_\" (NR-1)); print}"`
dbkey	`"?"`
variables	`[]`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7443c50c73cf11f0a03a6045bd49bf37"`
chromInfo	`"/tmp/tmpyiw7ovbk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 10: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 3e27a4799429364c
- history_state
  - ok
- invocation_id
  - 3e27a4799429364c
- invocation_state
  - failed
- workflow_id
  - a2c464a6bb7e2db0

mvdbeek · 2025-08-18T10:35:46Z

could you check now why the test errored? I didnt found anything useful

that was likely bug in planemo, I've released a new version and re-triggered the tests 🤞!

github-actions · 2025-08-18T11:03:45Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Biobox File:
- step_state: scheduled
Step 2: Assemblies:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
bedfile	__identifier__
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "", "input_bam": {"values": [{"id": 11, "src": "dce"}]}, "input_fasta": {"values": [{"id": 2, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 14: Unlabelled step:
- step_state: new

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
composition_file	__identifier__
coverage_file	__identifier__
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 18, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 18, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": false, "marker": false, "markers": false, "markerset": "107", "plotmarker": false}`

Step 19: Unlabelled step:
- step_state: new

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 3: Reads:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 27: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 28: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 29: Unlabelled step:
- step_state: new
Step 30: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mv '/tmp/tmppcpfkab1/job_working_directory/000/5/configs/tmp3wqste5r' '/tmp/tmppcpfkab1/job_working_directory/000/5/outputs/dataset_f5b95f28-5b8c-4542-8fbd-4a06d2a82256.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 33: Unlabelled step:
- step_state: new
Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Unlabelled step:
- step_state: new
Step 38: Unlabelled step:
- step_state: new
Step 39: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 40: Unlabelled step:
- step_state: new

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmppcpfkab1/files/4/8/3/dataset_483da4e6-2935-4fbd-8775-97a9bfe9037d.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmppcpfkab1/job_working_directory/000/6/outputs/dataset_08663b13-6cc8-4e76-92e2-5e1926c5db16.dat' > '/tmp/tmppcpfkab1/job_working_directory/000/6/outputs/dataset_af111c2d-41b5-4b7c-bfec-8ea7c76ce236.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
bedfile	`true`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmppcpfkab1/files/3/1/0/dataset_31036fed-2a1d-46ee-bf69-e621ce1a9e19.dat' 'marine_pooled_gsb_trimmed' && ln -s '/tmp/tmppcpfkab1/files/4/8/3/dataset_483da4e6-2935-4fbd-8775-97a9bfe9037d.dat' 'marine_pooled_gsa_trimmed' &&  add_length_column.py -g 'marine_pooled_gsb_trimmed' -f 'marine_pooled_gsa_trimmed' > gold_standard_file.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmppcpfkab1/files/4/8/3/dataset_483da4e6-2935-4fbd-8775-97a9bfe9037d.dat' genome && ln -s -f '/tmp/tmppcpfkab1/files/4/8/3/dataset_483da4e6-2935-4fbd-8775-97a9bfe9037d.dat' genome.fa &&   ln -f -s '/tmp/tmppcpfkab1/files/f/5/3/dataset_f534ac30-b893-47fa-b5c8-f1f8744b34f8.dat' input_f.fastq &&  ln -f -s '/tmp/tmppcpfkab1/files/d/7/6/dataset_d768760c-69a6-462c-b672-ab4a780a9076.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq'                2> >(tee '/tmp/tmppcpfkab1/job_working_directory/000/8/outputs/dataset_dfc5897a-8245-4467-bb0b-f18ebb958fb6.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmppcpfkab1/job_working_directory/000/8/outputs/dataset_ca7b259e-20a2-469c-85c1-5fbb1703499a.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 2, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{gsub( $0 ,\"sample_\" (NR-1)); print}"`
dbkey	`"?"`
variables	`[]`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cd516ae07c2211f089926045bd313319"`
chromInfo	`"/tmp/tmppcpfkab1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 10: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 0cd7072898fea934
- history_state
  - ok
- invocation_id
  - 0cd7072898fea934
- invocation_state
  - failed
- workflow_id
  - 046c823641ec191e

github-actions · 2025-08-18T13:27:31Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Biobox File:
- step_state: scheduled
Step 2: Assemblies:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
bedfile	__identifier__
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "", "input_bam": {"values": [{"id": 11, "src": "dce"}]}, "input_fasta": {"values": [{"id": 2, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 14: Unlabelled step:
- step_state: new

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
composition_file	__identifier__
coverage_file	__identifier__
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 18, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 18, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": false, "marker": false, "markers": false, "markerset": "107", "plotmarker": false}`

Step 19: Unlabelled step:
- step_state: new

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 3: Reads:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 27: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 28: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 29: Unlabelled step:
- step_state: new
Step 30: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mv '/tmp/tmp9ai679av/job_working_directory/000/5/configs/tmp8clkvget' '/tmp/tmp9ai679av/job_working_directory/000/5/outputs/dataset_768490db-9642-4a7d-9da5-4c579e4023d3.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 33: Unlabelled step:
- step_state: new
Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Unlabelled step:
- step_state: new
Step 38: Unlabelled step:
- step_state: new
Step 39: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 40: Unlabelled step:
- step_state: new

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp9ai679av/files/a/7/a/dataset_a7a28303-1079-48c8-a2eb-bb92377b613a.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmp9ai679av/job_working_directory/000/6/outputs/dataset_e3dd6351-e867-4998-8bc9-04971ae4012e.dat' > '/tmp/tmp9ai679av/job_working_directory/000/6/outputs/dataset_bd440fd9-31da-43e5-8a1a-2a8b32841603.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
bedfile	`true`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
- Subworkflow Steps
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp9ai679av/files/e/8/a/dataset_e8ab5c46-6ded-4cd4-acd6-d019ae9b3ae8.dat' 'marine_pooled_gsb_trimmed' && ln -s '/tmp/tmp9ai679av/files/a/7/a/dataset_a7a28303-1079-48c8-a2eb-bb92377b613a.dat' 'marine_pooled_gsa_trimmed' &&  add_length_column.py -g 'marine_pooled_gsb_trimmed' -f 'marine_pooled_gsa_trimmed' > gold_standard_file.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmp9ai679av/files/a/7/a/dataset_a7a28303-1079-48c8-a2eb-bb92377b613a.dat' genome && ln -s -f '/tmp/tmp9ai679av/files/a/7/a/dataset_a7a28303-1079-48c8-a2eb-bb92377b613a.dat' genome.fa &&   ln -f -s '/tmp/tmp9ai679av/files/b/b/b/dataset_bbba9fd6-3c80-4006-befe-ef9a73577061.dat' input_f.fastq &&  ln -f -s '/tmp/tmp9ai679av/files/b/9/3/dataset_b938bed6-8eea-462d-ad9a-dda7b79decc6.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq'                2> >(tee '/tmp/tmp9ai679av/job_working_directory/000/8/outputs/dataset_e1b46da6-05d7-471f-868b-87d94e5e02b4.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmp9ai679av/job_working_directory/000/8/outputs/dataset_79a9982d-4287-4730-b050-be83fe7c30cc.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 2, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{gsub( $0 ,\"sample_\" (NR-1)); print}"`
dbkey	`"?"`
variables	`[]`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e3687c4c7c3611f089927ced8d2b2d15"`
chromInfo	`"/tmp/tmp9ai679av/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 10: Unlabelled step:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - b0fbf7ecaffb662f
- history_state
  - ok
- invocation_id
  - b0fbf7ecaffb662f
- invocation_state
  - failed
- workflow_id
  - e53f40e12475bf95

SantaMcCloud · 2025-08-18T21:53:25Z

could you check now why the test errored? I didnt found anything useful

that was likely bug in planemo, I've released a new version and re-triggered the tests 🤞!

still failing and i dont know where the log is now. Seems still be a bug since i runs normal on galaxy

mvdbeek · 2025-08-19T07:10:20Z

galaxyproject/galaxy#20784

SantaMcCloud · 2025-08-19T22:01:59Z

galaxyproject/galaxy#20784

Ah thank you thougt so there is a bug somewhere. The test is runnning and it seems that it works now. Thank you for the fix!

mvdbeek · 2025-08-20T08:46:11Z

2025-08-19T21:11:34.6697395Z ❌ Failed job 4a47ac78dc1c0398:
2025-08-19T21:11:34.6697814Z    Tool ID:
2025-08-19T21:11:34.6698137Z toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7
2025-08-19T21:11:34.6698481Z    Exit code: 1
2025-08-19T21:11:34.6698771Z    Command line: addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
2025-08-19T21:11:34.6699444Z addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&
2025-08-19T21:11:34.6700019Z samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}"
2025-08-19T21:11:34.6700884Z '/tmp/tmppvs1ohta/files/1/9/c/dataset_19c294a8-8d03-4f41-a849-28c23d768c7c.dat'
2025-08-19T21:11:34.6701549Z >
2025-08-19T21:11:34.6702095Z '/tmp/tmppvs1ohta/job_working_directory/000/10/outputs/dataset_f500fca9-b12b-446
2025-08-19T21:11:34.6702754Z 4-96ca-28b56dae1d0c.dat'
2025-08-19T21:11:34.6703198Z    Stderr:
2025-08-19T21:11:34.6703496Z       merging from 12 files and 1 in-memory blocks...
2025-08-19T21:11:34.6703841Z      [E::bgzf_flush] File write failed (wrong size)
2025-08-19T21:11:34.6704176Z      samtools sort: failed writing to "-": No space left on device
2025-08-19T21:11:34.6704484Z      [E::bgzf_close] File write failed

mvdbeek · 2025-08-20T08:48:11Z

...ows/microbiome/taxonomic-binning-evaluation/FAIRyMAGs-taxonomic-binning-evaluation-tests.yml

+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/16740696/files/Reads_forward.fastqsanger


This file is 3GB, that is far too large. I would suggest making this a megabyte or less.

this was the first test data which did run. I will minimize it but it will take time since only 1 tool need specific reads it seems to work. I will pick some and try it with it to see if it works better and faster

@mvdbeek i did change the file size now and i hope the current size is fine for it!

The i did test the WFs locally on the .EU serve via planemo and all test where fine i hope that there will no problem in github this time and if so could you help me to reolve them? Thank you in advance for this!!

github-actions · 2025-08-31T14:55:37Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ FAIRyMAGs-taxonomic-binning-evaluation.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"4":{"gtdbtk_db":"Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'."}}}

…/iwc into add_tax_binning_eva

SantaMcCloud · 2025-09-02T02:23:53Z

galaxyproject/usegalaxy-tools#1084

mvdbeek · 2025-09-04T14:16:17Z

The 143 status code indicates the github runner ran out of resources. If you have an invocation on usegalaxy.org you could look at what step consumes most memory or disk

SantaMcCloud · 2025-09-04T14:27:58Z

The 143 status code indicates the github runner ran out of resources. If you have an invocation on usegalaxy.org you could look at what step consumes most memory or disk

It didnt run on .org yet since some tools are not installed. I will start a run in the evinign to have the insider and based on this i will maybe try to cut some contigs from the input to have lower numbers

SantaMcCloud · 2025-09-12T18:22:17Z

https://usegalaxy.org/workflows/invocations/b5d824ddb9c13b12

https://usegalaxy.org/u/santinof/h/cwl-target-history-1

SantaMcCloud · 2025-09-16T11:06:30Z

This PR will be on hold since some adjustment has to be done since GTBD-Tk use to much memorey which make the test errors out always

SantaMcCloud added 6 commits July 31, 2025 19:17

Add FAIRyMAGs Taxonomic Binning Evaluation Workflow

4c3250a

fix linting

7f9e3a1

linting

1afafbd

fix linting now

e5ee6e6

fix some test

b304f5a

change file

2c43c74

mvdbeek reviewed Aug 4, 2025

View reviewed changes

mvdbeek mentioned this pull request Aug 4, 2025

Add FAIRyMAGs Binning Evaluation Workflow #924

Open

12 tasks

SantaMcCloud added 4 commits August 4, 2025 23:27

review changes

81c9fd6

labels

69fc68b

update zanodo data

e21be0b

wrong url

a36de90

typo

951988b

review changes and remove subworkflow

534f508

mvdbeek reviewed Aug 20, 2025

View reviewed changes

update WF and test

423031d

add release tag

f539a88

SantaMcCloud and others added 5 commits August 31, 2025 16:57

add the correct DB version for iwc

29c901a

Restart test

2b427f5

update test

4d77517

Merge branch 'add_tax_binning_eva' of https://github.com/SantaMcCloud…

bf78a66

…/iwc into add_tax_binning_eva

Restart test

17e90e7

SantaMcCloud added 3 commits September 10, 2025 01:26

Change input data

f1ae9b4

change input to shorter version

8ff3648

change output

3f3bb98

SantaMcCloud closed this Sep 18, 2025

Add FAIRyMAGs Taxonomic Binning Evaluation Workflow #923

Add FAIRyMAGs Taxonomic Binning Evaluation Workflow #923

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