Add clinicalmp-quantitation workflow #505

subinamehta · 2024-08-14T15:35:19Z

WIP-Adding a workflow under IWC

github-actions · 2024-08-14T20:05:06Z

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:

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:

```
127
```

Traceback:

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

Jobs

Job 1:

Job state is paused

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

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	`[]`

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

mvdbeek

Nice, this looks very promising so far, thanks a lot @subinamehta!

.DS_Store

workflows/proteomics/clinicalmp/clinicalmp-quantitation/README.md

workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga

github-actions · 2024-08-30T02:02:33Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - 2cd21e5d1fd8fd52
- history_state
  - ok
- invocation_id
  - 2cd21e5d1fd8fd52
- invocation_state
  - scheduled
- workflow_id
  - 2cd21e5d1fd8fd52

subinamehta · 2024-08-30T16:52:20Z

Could we please take a look at this pull request?

mvdbeek · 2024-08-30T17:15:37Z

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 · 2024-08-30T17:17:01Z

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

mvdbeek

This looks super nice. Let me know if it's not feasible to reduce the test runtime, it would be better if we can test this quicker but if not this is also OK.

workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga

workflows/proteomics/encyclopedia/encyclopedia.ga

subinamehta · 2024-08-30T17:38:14Z

I think I resolved all the issues now!

github-actions · 2024-08-30T20:55:31Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - e77dabd5ae0a2b50
- history_state
  - ok
- invocation_id
  - e77dabd5ae0a2b50
- invocation_state
  - scheduled
- workflow_id
  - e77dabd5ae0a2b50

github-actions · 2024-08-30T20:55:46Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - 45b3fa7bf4eb8286
- history_state
  - ok
- invocation_id
  - 45b3fa7bf4eb8286
- invocation_state
  - scheduled
- workflow_id
  - 45b3fa7bf4eb8286

github-actions · 2024-08-30T21:11:52Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - af1c595670eb209b
- history_state
  - ok
- invocation_id
  - af1c595670eb209b
- invocation_state
  - scheduled
- workflow_id
  - af1c595670eb209b

github-actions · 2024-08-30T21:34:26Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - af5507def4945622
- history_state
  - ok
- invocation_id
  - af5507def4945622
- invocation_state
  - scheduled
- workflow_id
  - af5507def4945622

subinamehta · 2024-08-31T01:23:15Z

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

mvdbeek · 2024-09-02T14:36:02Z

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

mvdbeek · 2024-09-02T14:41:15Z

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

subinamehta · 2024-09-02T14:42:39Z

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 <#505 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGP3A7LLYP6Z2PCUNXLJAHLZUR2KFAVCNFSM6AAAAABMQTLKYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRUHEYDKMBTGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

.gitignore

workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga

mvdbeek · 2024-09-02T14:46:49Z

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 · 2024-09-03T12:42:41Z

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:

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:

```
0
```

Standard Output:

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:

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

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 6: extracting microbial Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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)

Step 7: extract proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 8: extract peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Traceback:

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"`

Step 9: Quantified-Proteins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Step 10: Quantified-Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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:

```
0
```

Standard Output:

```
--Group by c1: 
```

Traceback:

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	`[]`

Other invocation details
- history_id
  - 9be721e34a966909
- history_state
  - ok
- invocation_id
  - 9be721e34a966909
- invocation_state
  - scheduled
- workflow_id
  - 9be721e34a966909

subinamehta · 2024-09-26T21:00:43Z

could we please merge this?

subinamehta · 2024-09-27T13:54:06Z

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

mvdbeek

Thank you! I would still suggest to improve the step labels a little, but we can do that in a followup.

mvdbeek reviewed Aug 15, 2024

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subinamehta requested a review from mvdbeek August 15, 2024 20:49

mvdbeek reviewed Aug 30, 2024

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mvdbeek reviewed Sep 2, 2024

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Create README.md

710b24f

mvdbeek force-pushed the patch-1 branch from 83e46a0 to 710b24f Compare September 3, 2024 09:16

mvdbeek changed the title ~~Create README.md~~ Add clinicalmp-quantitation and encyclopedia workflows Sep 3, 2024

subinamehta added 2 commits September 26, 2024 12:34

Delete workflows/proteomics/encyclopedia directory

3210086

Merge branch 'galaxyproject:main' into patch-1

164e033

mvdbeek approved these changes Sep 27, 2024

View reviewed changes

mvdbeek merged commit e200678 into galaxyproject:main Sep 27, 2024
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mvdbeek changed the title ~~Add clinicalmp-quantitation and encyclopedia workflows~~ Add clinicalmp-quantitation workflow Sep 27, 2024

subinamehta deleted the patch-1 branch September 27, 2024 14:21

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