github-actions[bot]
commented
2 months ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 0 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
*❌ iwc-clinicalmp-quantitation.ga_0
**Execution Problem:**
* ```
Failed to run workflow, at least one job is in [error] state.
```
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: Quantitation_Database-For-MaxQuant**: * step_state: scheduled - **Step 2: Experimental-Design Discovery MaxQuant**: * step_state: scheduled - **Step 3: Input Raw-files**: * step_state: scheduled - **Step 4: MaxQuant**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is error **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmpf111aja0/files/b/d/0/dataset_bd09f8ad-71f8-4a08-81ef-1e86da069a63.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpf111aja0/files/6/0/5/dataset_605b5ec8-a8a8-43e8-b55e-9c294cc7d61d.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpf111aja0/files/9/0/3/dataset_90341914-43db-49ee-878e-d75b610a3b54.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpf111aja0/files/a/5/1/dataset_a5164c0a-dcfd-42c2-8526-eef865d4b4f7.dat' 'PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && python3 '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/9c52362ae7bb/maxquant/create_mqpar.py' --exp_design='/tmp/tmpf111aja0/files/5/f/b/dataset_5fbcbac3-98f3-4ddf-9d62-46b9aea4f0f5.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmpf111aja0/job_working_directory/000/7/configs/tmpzz2dvou6' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` | | chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input\_opts | ` {"description_parse_rule": ">(.*)", "fasta_files": {"values": [{"id": 1, "src": "hda"}]}, "ftype": ".thermo.raw", "identifier_parse_rule": ">([^\\s]*)"} ` | | output\_opts | ` {"dry_run": false, "output": ["proteinGroups", "mqpar", "peptides", "msms", "evidence"]} ` | | paramGroups | ` [{"__index__": 0, "digestion_mode": "0", "enzymes": ["Trypsin/P"], "files": {"values": [{"id": 1, "src": "hdca"}]}, "fixedModifications": ["Carbamidomethyl (C)"], "maxMissedCleavages": "2", "quant_method": {"__current_case__": 3, "filter_by_pif": {"__current_case__": 1, "filter_pif": "False"}, "iso_labels": {"__current_case__": 4, "labeling": "tmt11plex"}, "select_quant_method": "reporter_ion_ms2"}, "variableModifications": ["Oxidation (M)"]}] ` | | protein\_quant | ` {"lfq_opts": {"advancedSiteIntensities": true, "do_ibaq": {"__current_case__": 1, "ibaq": "False"}, "lfqRequireMsms": true, "lfqStabilizeLargeRatios": true, "separateLfq": false}, "only_unmod_prot": {"__current_case__": 0, "discard_unmod_cpart_peptides": true, "mods_used_prot_quant": ["Oxidation (M)"], "unmod_prot": "True"}, "peptides_for_quantification": "1"} ` | | qc | ` {"__current_case__": 1, "do_it": "false"} ` | | search\_opts | ` {"calc_peak_properties": false, "decoy_mode": "revert", "incl_contaminants": false, "max_pep_length": "50", "max_peptide_mass": "4600", "mbr": {"__current_case__": 1, "alignment_ion_mobility_window": "1", "alignment_time_window": "20", "match_between_runs": "True", "match_unidentified_features": false, "matching_ion_mobility_window": "0.05", "matching_time_window": "0.7"}, "min_pep_length": "8", "min_peptide_len": "8", "min_unique_pep": "0", "protein_fdr": "0.01", "psm_fdr": "0.01", "template": {"values": [{"id": 2, "src": "hda"}]}} ` | - **Step 5: extracting microbial Proteins**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| invert | ` "-v" ` |
| keep\_header | ` false ` |
| pattern | ` "(_HUMAN)|(_REVERSED)|(CON)|(con)" ` |
</details>
- **Step 6: extracting microbial Peptides**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| invert | ` "-v" ` |
| keep\_header | ` false ` |
| pattern | ` "(_HUMAN)|(_REVERSED)|(CON)|(con)" ` |
</details>
- **Step 7: extract proteins**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c1" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 8: extract peptides**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c1" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 9: Quantified-Proteins**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| groupcol | ` "1" ` |
| ignorecase | ` false ` |
| ignorelines | ` None ` |
| operations | ` [] ` |
</details>
- **Step 10: Quantified-Peptides**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "48111f5a5a7811ef9f9cc3d1f5a260ab" ` |
| chromInfo | ` "/tmp/tmpf111aja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| groupcol | ` "1" ` |
| ignorecase | ` false ` |
| ignorelines | ` None ` |
| operations | ` [] ` |
</details>
</details>-
Other invocation details
- **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 975d33cb637714a4 - **history_state** * error - **invocation_id** * 975d33cb637714a4 - **invocation_state** * scheduled - **workflow_id** * 975d33cb637714a4
subinamehta
mvdbeek
WIP-Adding a workflow under IWC