galaxyproject / iwc

Galaxy Workflows maintained by the Intergalactic Workflow Commission
https://dockstore.org/organizations/iwc
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Add clinicalmp-quantitation workflow #505

Closed subinamehta closed 1 month ago

subinamehta commented 2 months ago

WIP-Adding a workflow under IWC

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

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmpud2a43j_/files/4/4/7/dataset_4472d544-dda4-4f89-96e2-611ddfe50c4a.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpud2a43j_/files/a/e/a/dataset_aeac6a5e-5abe-45f5-aa5e-429760462dd4.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpud2a43j_/files/e/5/c/dataset_e5c68587-d84b-4a1d-aad2-5514488b0cdb.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpud2a43j_/files/0/b/e/dataset_0beb2355-9f08-4155-93ba-52e6682831cf.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/tmpud2a43j_/files/e/c/6/dataset_ec6b095f-16e6-4cab-b632-b70ca4e63d55.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmpud2a43j_/job_working_directory/000/7/configs/tmpkijs8dbe' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` | | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmpud2a43j_/files/3/3/0/dataset_330d7f05-b821-4e8d-801f-063bb834d9ee.dat' | grep -P -f '/tmp/tmpud2a43j_/job_working_directory/000/8/configs/tmp9rhlzkqe' -v >> '/tmp/tmpud2a43j_/job_working_directory/000/8/outputs/dataset_6377ccb2-9eb7-4bee-9f51-af06aab7b342.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmpud2a43j_/files/c/d/4/dataset_cd463bed-5256-47a0-9c16-00477c072f04.dat' | grep -P -f '/tmp/tmpud2a43j_/job_working_directory/000/9/configs/tmpp4jyc7yw' -v >> '/tmp/tmpud2a43j_/job_working_directory/000/9/outputs/dataset_0644b31b-468f-48e8-939e-3330f4a8899f.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmpud2a43j_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpud2a43j_/files/6/3/7/dataset_6377ccb2-9eb7-4bee-9f51-af06aab7b342.dat' 'c1' T '/tmp/tmpud2a43j_/job_working_directory/000/10/outputs/dataset_de339c15-bfad-4cbe-adbc-ae5214269e12.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmpud2a43j_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpud2a43j_/files/0/6/4/dataset_0644b31b-468f-48e8-939e-3330f4a8899f.dat' 'c1' T '/tmp/tmpud2a43j_/job_working_directory/000/11/outputs/dataset_80453254-958a-49fb-b0a8-fe3550c1e825.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmpud2a43j_/galaxy-dev/tools/stats/grouping.py' '/tmp/tmpud2a43j_/job_working_directory/000/12/outputs/dataset_e831b453-59ff-43b4-9467-0c0c8eb6ed4f.dat' '/tmp/tmpud2a43j_/files/d/e/3/dataset_de339c15-bfad-4cbe-adbc-ae5214269e12.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmpud2a43j_/galaxy-dev/tools/stats/grouping.py' '/tmp/tmpud2a43j_/job_working_directory/000/13/outputs/dataset_7a574fbb-ca34-4089-831d-f6e305e36507.dat' '/tmp/tmpud2a43j_/files/8/0/4/dataset_80453254-958a-49fb-b0a8-fe3550c1e825.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "75f58388665911efbb823de578656872" ` |
             | chromInfo | ` "/tmp/tmpud2a43j_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * 2cd21e5d1fd8fd52 - **history_state** * ok - **invocation_id** * 2cd21e5d1fd8fd52 - **invocation_state** * scheduled - **workflow_id** * 2cd21e5d1fd8fd52

subinamehta commented 2 months ago

Could we please take a look at this pull request?

mvdbeek commented 2 months ago

Sure, could you delete the .DS_Store files and move the test data to zenodo ? The test run took 3 hours, do you see a way to make the tests run a little faster ? Perhaps by reducing the input data size ?

mvdbeek commented 2 months ago

I see you've moved the test data to zenodo, but it's still included here, can you also delete those files ?

subinamehta commented 2 months ago

I think I resolved all the issues now!

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmpfx5y6akr/files/8/9/b/dataset_89be8c8d-2abe-4c1f-b658-83fab4a69fd6.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpfx5y6akr/files/5/4/e/dataset_54e9aed5-4e52-45f5-bebf-557ce08c1c45.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpfx5y6akr/files/b/1/3/dataset_b13699ea-e09b-4330-8241-6445ad3f82af.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmpfx5y6akr/files/a/9/3/dataset_a93e211b-e4b7-4b36-b6ab-6d176c393765.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/tmpfx5y6akr/files/9/2/c/dataset_92c9b353-91a3-4fc9-b92b-2cfc93999b31.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmpfx5y6akr/job_working_directory/000/7/configs/tmpyodulw9a' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` | | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmpfx5y6akr/files/b/4/f/dataset_b4f086b5-302d-4020-9731-bfd6ed8c20dd.dat' | grep -P -f '/tmp/tmpfx5y6akr/job_working_directory/000/8/configs/tmpf7napmyi' -v >> '/tmp/tmpfx5y6akr/job_working_directory/000/8/outputs/dataset_a419b74d-78b3-4d3f-bdec-902d02341cca.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmpfx5y6akr/files/6/f/a/dataset_6fa542fa-5c62-4547-90bc-4fb0885d17a4.dat' | grep -P -f '/tmp/tmpfx5y6akr/job_working_directory/000/9/configs/tmpi_7rjo6n' -v >> '/tmp/tmpfx5y6akr/job_working_directory/000/9/outputs/dataset_006a5cfb-eecc-490c-8bfa-705098ba7e06.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmpfx5y6akr/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpfx5y6akr/files/a/4/1/dataset_a419b74d-78b3-4d3f-bdec-902d02341cca.dat' 'c1' T '/tmp/tmpfx5y6akr/job_working_directory/000/10/outputs/dataset_cf818483-649f-4d41-8b2c-c8bde0b680c8.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmpfx5y6akr/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpfx5y6akr/files/0/0/6/dataset_006a5cfb-eecc-490c-8bfa-705098ba7e06.dat' 'c1' T '/tmp/tmpfx5y6akr/job_working_directory/000/11/outputs/dataset_6381c5e6-cfc1-491f-ab1b-2e5c1bd1fdea.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmpfx5y6akr/galaxy-dev/tools/stats/grouping.py' '/tmp/tmpfx5y6akr/job_working_directory/000/12/outputs/dataset_64782f97-70b0-4ad2-943c-ec9659317895.dat' '/tmp/tmpfx5y6akr/files/c/f/8/dataset_cf818483-649f-4d41-8b2c-c8bde0b680c8.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmpfx5y6akr/galaxy-dev/tools/stats/grouping.py' '/tmp/tmpfx5y6akr/job_working_directory/000/13/outputs/dataset_a13e6241-a6ed-4034-896e-1e05c035b9f3.dat' '/tmp/tmpfx5y6akr/files/6/3/8/dataset_6381c5e6-cfc1-491f-ab1b-2e5c1bd1fdea.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "b7cf187066f711efb6da519872425259" ` |
             | chromInfo | ` "/tmp/tmpfx5y6akr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * e77dabd5ae0a2b50 - **history_state** * ok - **invocation_id** * e77dabd5ae0a2b50 - **invocation_state** * scheduled - **workflow_id** * e77dabd5ae0a2b50

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmp5sk6ay8c/files/a/9/3/dataset_a9301a80-2e98-401c-b7ed-38c90a004950.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp5sk6ay8c/files/f/1/7/dataset_f17976a5-3af9-48d2-a47a-8d02df27e2bc.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp5sk6ay8c/files/5/4/f/dataset_54f1683b-6201-4537-b89b-822a92a963a3.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp5sk6ay8c/files/b/6/0/dataset_b60930ea-0ff9-4424-aeca-0cc8d8dc3db0.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/tmp5sk6ay8c/files/2/8/c/dataset_28ca916a-4d76-4c1e-9cf0-3c9e098113c4.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmp5sk6ay8c/job_working_directory/000/7/configs/tmpml6ckfoc' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` | | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp5sk6ay8c/files/3/6/0/dataset_360be324-b683-4cea-bc7c-62cfc484e4ea.dat' | grep -P -f '/tmp/tmp5sk6ay8c/job_working_directory/000/8/configs/tmppdrgnysk' -v >> '/tmp/tmp5sk6ay8c/job_working_directory/000/8/outputs/dataset_8cc88bee-a213-4039-9c77-f156f1b20963.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp5sk6ay8c/files/d/7/e/dataset_d7e524fa-b389-4c7f-b02f-9d9b503333eb.dat' | grep -P -f '/tmp/tmp5sk6ay8c/job_working_directory/000/9/configs/tmp6mhok38_' -v >> '/tmp/tmp5sk6ay8c/job_working_directory/000/9/outputs/dataset_8d25359a-820c-403d-9f4e-e0c388bc5702.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp5sk6ay8c/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5sk6ay8c/files/8/c/c/dataset_8cc88bee-a213-4039-9c77-f156f1b20963.dat' 'c1' T '/tmp/tmp5sk6ay8c/job_working_directory/000/10/outputs/dataset_f57d75dd-3997-44ef-bbc1-f5faba40ad64.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp5sk6ay8c/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp5sk6ay8c/files/8/d/2/dataset_8d25359a-820c-403d-9f4e-e0c388bc5702.dat' 'c1' T '/tmp/tmp5sk6ay8c/job_working_directory/000/11/outputs/dataset_74e55f4c-91b5-4048-9036-be7de97d6f0d.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp5sk6ay8c/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp5sk6ay8c/job_working_directory/000/12/outputs/dataset_ce7ed719-a99a-4839-bc9e-657d8327ba38.dat' '/tmp/tmp5sk6ay8c/files/f/5/7/dataset_f57d75dd-3997-44ef-bbc1-f5faba40ad64.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp5sk6ay8c/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp5sk6ay8c/job_working_directory/000/13/outputs/dataset_e1aea269-b511-40e7-95cb-02bbf71a1578.dat' '/tmp/tmp5sk6ay8c/files/7/4/e/dataset_74e55f4c-91b5-4048-9036-be7de97d6f0d.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "4192256c66f711efa3795503bf425ce2" ` |
             | chromInfo | ` "/tmp/tmp5sk6ay8c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * 45b3fa7bf4eb8286 - **history_state** * ok - **invocation_id** * 45b3fa7bf4eb8286 - **invocation_state** * scheduled - **workflow_id** * 45b3fa7bf4eb8286

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmp8r9rclca/files/2/3/b/dataset_23bce435-8406-45f3-bb6b-925d3fa99864.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp8r9rclca/files/5/e/e/dataset_5ee5ea3e-a484-4403-ac7c-379f7e57bc1d.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp8r9rclca/files/4/e/b/dataset_4ebbad87-5557-4191-b323-076f6cb5393c.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp8r9rclca/files/9/f/5/dataset_9f5122ca-8616-4bdb-9df7-32baf3178411.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/tmp8r9rclca/files/a/5/0/dataset_a5029a62-ef7e-4374-8abc-d93891b874ee.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmp8r9rclca/job_working_directory/000/7/configs/tmpexsil470' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` | | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp8r9rclca/files/4/b/d/dataset_4bdf410a-4c33-4913-89e7-71ec718fefb0.dat' | grep -P -f '/tmp/tmp8r9rclca/job_working_directory/000/8/configs/tmp93msti5r' -v >> '/tmp/tmp8r9rclca/job_working_directory/000/8/outputs/dataset_5b7a86c3-4cdf-4d33-a4c3-839bd872f35f.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp8r9rclca/files/6/6/5/dataset_6653538a-cf46-447c-ad55-67abfbb136f5.dat' | grep -P -f '/tmp/tmp8r9rclca/job_working_directory/000/9/configs/tmpp2ixucjv' -v >> '/tmp/tmp8r9rclca/job_working_directory/000/9/outputs/dataset_96283d00-212f-4d29-a7c4-f962bbbf016e.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp8r9rclca/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8r9rclca/files/5/b/7/dataset_5b7a86c3-4cdf-4d33-a4c3-839bd872f35f.dat' 'c1' T '/tmp/tmp8r9rclca/job_working_directory/000/10/outputs/dataset_377823e7-ddfc-46a3-bbfa-e65b8ac37a9a.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp8r9rclca/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8r9rclca/files/9/6/2/dataset_96283d00-212f-4d29-a7c4-f962bbbf016e.dat' 'c1' T '/tmp/tmp8r9rclca/job_working_directory/000/11/outputs/dataset_6049b22a-c80e-45aa-80ee-e22b782e2638.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp8r9rclca/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp8r9rclca/job_working_directory/000/12/outputs/dataset_77e228dd-9170-487c-bcda-576335e06044.dat' '/tmp/tmp8r9rclca/files/3/7/7/dataset_377823e7-ddfc-46a3-bbfa-e65b8ac37a9a.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp8r9rclca/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp8r9rclca/job_working_directory/000/13/outputs/dataset_f03b10a4-b659-482a-8fec-43f0268c85b4.dat' '/tmp/tmp8r9rclca/files/6/0/4/dataset_6049b22a-c80e-45aa-80ee-e22b782e2638.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0f28880266fa11efba1bed903e2e3d7c" ` |
             | chromInfo | ` "/tmp/tmp8r9rclca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * af1c595670eb209b - **history_state** * ok - **invocation_id** * af1c595670eb209b - **invocation_state** * scheduled - **workflow_id** * af1c595670eb209b

github-actions[bot] commented 2 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmp_embqg8_/files/a/0/e/dataset_a0e1c55e-5a0c-4b73-91ce-c1991aa5b3ac.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp_embqg8_/files/d/9/1/dataset_d917a892-1a56-4a39-bff0-811c2b0dfede.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp_embqg8_/files/1/b/7/dataset_1b78b425-1d5e-42d5-95f4-abb4d0092138.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmp_embqg8_/files/1/5/f/dataset_15f62ae2-89ca-4689-a508-75c8443ade5f.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/tmp_embqg8_/files/7/9/7/dataset_79763768-d6e1-40d8-86cc-6ff740af013f.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmp_embqg8_/job_working_directory/000/7/configs/tmpsygwowhy' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` | | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp_embqg8_/files/2/d/b/dataset_2dbad038-d634-4cc4-9640-77b5f20ed1d1.dat' | grep -P -f '/tmp/tmp_embqg8_/job_working_directory/000/8/configs/tmp39quqsej' -v >> '/tmp/tmp_embqg8_/job_working_directory/000/8/outputs/dataset_6e9d66b9-6b5b-485d-8685-ef14b3306625.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmp_embqg8_/files/3/3/6/dataset_336b0ea8-278f-4393-9992-a7598c48527a.dat' | grep -P -f '/tmp/tmp_embqg8_/job_working_directory/000/9/configs/tmpg40_6hbt' -v >> '/tmp/tmp_embqg8_/job_working_directory/000/9/outputs/dataset_5245fe27-3197-48b9-82bf-5cf81d71bf54.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp_embqg8_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp_embqg8_/files/6/e/9/dataset_6e9d66b9-6b5b-485d-8685-ef14b3306625.dat' 'c1' T '/tmp/tmp_embqg8_/job_working_directory/000/10/outputs/dataset_e895c82b-61c5-4f45-b976-a3151345f389.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmp_embqg8_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp_embqg8_/files/5/2/4/dataset_5245fe27-3197-48b9-82bf-5cf81d71bf54.dat' 'c1' T '/tmp/tmp_embqg8_/job_working_directory/000/11/outputs/dataset_d2f1b496-1c6f-45a1-bb7d-695ea85b30b6.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp_embqg8_/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp_embqg8_/job_working_directory/000/12/outputs/dataset_73287013-ac52-4723-b620-e706a77af461.dat' '/tmp/tmp_embqg8_/files/e/8/9/dataset_e895c82b-61c5-4f45-b976-a3151345f389.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmp_embqg8_/galaxy-dev/tools/stats/grouping.py' '/tmp/tmp_embqg8_/job_working_directory/000/13/outputs/dataset_8e04a175-dbd8-40ac-bb00-38dd8428692c.dat' '/tmp/tmp_embqg8_/files/d/2/f/dataset_d2f1b496-1c6f-45a1-bb7d-695ea85b30b6.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "9d46f79866fc11efba4003068345a63c" ` |
             | chromInfo | ` "/tmp/tmp_embqg8_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * af5507def4945622 - **history_state** * ok - **invocation_id** * af5507def4945622 - **invocation_state** * scheduled - **workflow_id** * af5507def4945622

subinamehta commented 2 months ago

Could you tell me what this chunked test error is saying?

mvdbeek commented 1 month ago

The error is saying that your uploads didn't work. I see that zenodo seems to be down currently ?

Screenshot 2024-09-02 at 16 35 56
mvdbeek commented 1 month ago

We're also running out of disk space, is there any way those test files could be made smaller ?

subinamehta commented 1 month ago

Let me see if for the workflow purpose to use just one file. Will that work?

Subina Mehta Researcher, Dept. of Biochemistry, Molecular Biology and Biophysics Bioinformatics Specialist, Proteogenomics Shared Resource, Masonic Cancer Center University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: @. @.> www.galaxyp.org* http://www.galaxyp.org/ http://z.umn.edu/itcrgalaxyvideo

On Mon, Sep 2, 2024 at 10:41 AM Marius van den Beek < @.***> wrote:

We're also running out of disk space, is there any way those test files could be made smaller ?

— Reply to this email directly, view it on GitHub https://github.com/galaxyproject/iwc/pull/505#issuecomment-2324905036, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGP3A7LLYP6Z2PCUNXLJAHLZUR2KFAVCNFSM6AAAAABMQTLKYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRUHEYDKMBTGY . You are receiving this because you were mentioned.Message ID: @.***>

mvdbeek commented 1 month ago

I think the number of files doesn't matter, it's the total size that is the limit currently. This is the error message:

galaxy.tool_util.provided_metadata DEBUG 2024-08-30 18:27:42,131 [pN:main.1,p:5367,tN:LocalRunner.work_thread-1] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': '191023JAT11_3_Mix_1_1ug_pOT_30k_390_1010_12_20.raw', 'dbkey': '?', 'ext': 'thermo.raw', 'link_data_only': False, 'sources': [{'source_uri': 'https://zenodo.org/records/13505774/files/191023JAT11_3_Mix_1_1ug_pOT_30k_390_1010_12_20.raw'}], 'hashes': [], 'info': 'uploaded thermo.raw file', 'state': 'ok', 'filename': '/tmp/tmp13s1901f/job_working_directory/000/11/working/gx_file_stream9a1oqtlw', 'object_id': 11}]}]}]

galaxy.objectstore CRITICAL 2024-08-30 18:27:45,928 [pN:main.1,p:5367,tN:LocalRunner.work_thread-1] Error copying /tmp/tmp13s1901f/job_working_directory/000/11/working/gx_file_stream9a1oqtlw to /tmp/tmp13s1901f/files/0/b/2/dataset_0b2689fd-6b6a-4f86-bfc2-a9cec8ce309b.dat: [Errno 28] No space left on 

The file causing it is https://zenodo.org/records/13505774/files/191023JAT11_3_Mix_1_1ug_pOT_30k_390_1010_12_20.raw which is 1.6GB in size.

github-actions[bot] commented 1 month ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 2
Passed 1
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ encyclopedia.ga_0
**Execution Problem:** * ``` Failed to upload data, upload state is [error]. ```

Passed Tests *
✅ iwc-clinicalmp-quantitation.ga_0
#### 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 ok **Command Line:** * ```console export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null && cp '/tmp/tmplwc7bb8o/files/b/b/a/dataset_bba9b9d6-fb2a-45d6-bd11-f796d361fe0d.dat' 'PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmplwc7bb8o/files/1/d/b/dataset_1db4446b-441b-4c43-8379-3b13f2f3fa4e.dat' 'PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmplwc7bb8o/files/0/0/1/dataset_00149037-1d70-4aac-b984-8a3b956114c9.dat' 'PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && cp '/tmp/tmplwc7bb8o/files/c/e/9/dataset_ce9b5011-be1f-4e56-a4ac-04d9e9533b02.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/tmplwc7bb8o/files/c/3/2/dataset_c3202b7c-0a24-45e7-96c8-d49e168a92fd.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmplwc7bb8o/job_working_directory/000/7/configs/tmpkv4d07z7' mqpar.xml && maxquant mqpar.xml && mv mqpar.xml combined/txt/mqpar.xml ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Configuring Assemble run info Finish run info Testing fasta files Testing raw files Feature detection Deisotoping MS/MS preparation Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration Calculating masses MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Calculating PEP Copying identifications Applying FDR Assembling second peptide MS/MS Combining second peptide files Second peptide search Reading search engine results (SP) Finish search engine results (SP) Filtering identifications (SP) Applying FDR (SP) Re-quantification Reporter quantification Retention time alignment Matching between runs 1 Matching between runs 2 Matching between runs 3 Matching between runs 4 Prepare protein assembly Assembling proteins Assembling unidentified peptides Finish protein assembly Updating identifications Estimating complexity Prepare writing tables Writing tables Finish writing tables ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` | | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmplwc7bb8o/files/b/e/3/dataset_be3b1fe3-3723-45d3-8be3-e2fe6293988e.dat' | grep -P -f '/tmp/tmplwc7bb8o/job_working_directory/000/8/configs/tmp38ei6eji' -v >> '/tmp/tmplwc7bb8o/job_working_directory/000/8/outputs/dataset_dabf7088-9a9f-4a92-98b3-4d03772d5e3a.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           set -eo pipefail; cat '/tmp/tmplwc7bb8o/files/e/d/6/dataset_ed66e046-239b-4854-95eb-69c0712f0c0b.dat' | grep -P -f '/tmp/tmplwc7bb8o/job_working_directory/000/9/configs/tmp5j65jxzg' -v >> '/tmp/tmplwc7bb8o/job_working_directory/000/9/outputs/dataset_79e95fc7-33a9-4373-8c5c-9d5fe55f9a6f.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmplwc7bb8o/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmplwc7bb8o/files/d/a/b/dataset_dabf7088-9a9f-4a92-98b3-4d03772d5e3a.dat' 'c1' T '/tmp/tmplwc7bb8o/job_working_directory/000/10/outputs/dataset_73b5ee4a-43d4-4dbf-bacb-fc55871336ed.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           perl '/tmp/tmplwc7bb8o/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmplwc7bb8o/files/7/9/e/dataset_79e95fc7-33a9-4373-8c5c-9d5fe55f9a6f.dat' 'c1' T '/tmp/tmplwc7bb8o/job_working_directory/000/11/outputs/dataset_89aae2d5-3ec6-4eea-8c07-f798bac8d149.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmplwc7bb8o/galaxy-dev/tools/stats/grouping.py' '/tmp/tmplwc7bb8o/job_working_directory/000/12/outputs/dataset_c630a815-7960-4ea4-8a5f-790c87ea413c.dat' '/tmp/tmplwc7bb8o/files/7/3/b/dataset_73b5ee4a-43d4-4dbf-bacb-fc55871336ed.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/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 ok

        **Command Line:**

         * ```console
           python '/tmp/tmplwc7bb8o/galaxy-dev/tools/stats/grouping.py' '/tmp/tmplwc7bb8o/job_working_directory/000/13/outputs/dataset_376cc2d5-6ca6-4f7a-9ec8-f55b0656e80c.dat' '/tmp/tmplwc7bb8o/files/8/9/a/dataset_89aae2d5-3ec6-4eea-8c07-f798bac8d149.dat' '1' '0' 'None'
           ```
        **Exit Code:**

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

         * ```console
           --Group by c1: 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "2c5b770269d611ef91906bdd1d6688f5" ` |
             | chromInfo | ` "/tmp/tmplwc7bb8o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | groupcol | ` "1" ` |
             | ignorecase | ` false ` |
             | ignorelines | ` None ` |
             | operations | ` [] ` |

      </details>
  </details>
  • Other invocation details - **history_id** * 9be721e34a966909 - **history_state** * ok - **invocation_id** * 9be721e34a966909 - **invocation_state** * scheduled - **workflow_id** * 9be721e34a966909

subinamehta commented 1 month ago

could we please merge this?

subinamehta commented 1 month ago

@mvdbeek : could we merge this into the IWC, we have a workshop coming up next week and we would like to portray this.