Add Metaproteomics GTN workflow #626

clsiguret · 2024-12-10T10:42:54Z

We followed the recommendation to publish the workflow (licence, author list and email, steps annotations...)

Workflow imported from usegalaxy.eu using planemo workflow_test_init to use a valid invocation
Workflow tests passed using planemo test command on the usegalaxy.eu server
Readme.md written
CHANGELOG.md written
.dockstore.yml written

Thanks 😃

github-actions · 2024-12-10T10:58:46Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Sixgill generated protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpp964t5zu/files/e/a/0/dataset_ea0a36ec-becd-4138-b63f-2ec6f774a195.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:96c9812ccf4bdab6)'; ln -s -f '/tmp/tmpp964t5zu/files/c/4/d/dataset_c4d86015-7af8-4004-b4e6-d3b87678387d.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:e62c2b51b352002d)'; ln -s -f '/tmp/tmpp964t5zu/files/4/a/f/dataset_4afc4524-d832-40e1-be0e-f5caf14e7d11.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:206590f6173e4ca0)'; cp "/tmp/tmpp964t5zu/files/7/7/4/dataset_774f07cc-9d41-4884-8be8-711d274e45d6.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:96c9812ccf4bdab6)
Spectrums:2016_Jan_12_QE2_46.mgf(API:e62c2b51b352002d)
Spectrums:2016_Jan_12_QE2_47.mgf(API:206590f6173e4ca0)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpp964t5zu/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 10.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Tue Dec 10 10:56:38 GMT 2024
Size: 17038 sequences


Tue Dec 10 10:56:41 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpp964t5zu/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 10.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Tue Dec 10 10:56:42 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpp964t5zu/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Tue Dec 10 10:56:49 GMT 2024 Validating MGF file: /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 10:56:51 GMT 2024 Validating MGF file: /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 10:56:51 GMT 2024 Validating MGF file: /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Tue Dec 10 10:56:52 GMT 2024 Indexing spectrum files.
Tue Dec 10 10:56:52 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 10:56:52 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 10:56:52 GMT 2024 X!Tandem finished for /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (86.0 milliseconds).

Tue Dec 10 10:56:52 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Tue Dec 10 10:56:52 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 10:56:52 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 10:56:52 GMT 2024 X!Tandem finished for /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (2.0 milliseconds).

Tue Dec 10 10:56:52 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Tue Dec 10 10:56:52 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 10:56:52 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 10:56:52 GMT 2024 X!Tandem finished for /tmp/tmpp964t5zu/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Tue Dec 10 10:56:52 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Tue Dec 10 10:56:52 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Tue Dec 10 10:56:52 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 10:56:53 GMT 2024 Search Completed (1.4 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpp964t5zu/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpp964t5zu/files/c/5/3/dataset_c53c8b9d-eddf-43f6-8cd7-422fa3ac523f.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121010561733828218' -sample 'Sample_2024121010561733828218' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,0,9,3  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Tue Dec 10 10:57:17 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Tue Dec 10 10:57:17 GMT 2024 Import process for Galaxy_Experiment_2024121010561733828218 (Sample: Sample_2024121010561733828218, Replicate: 1)

Tue Dec 10 10:57:17 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Tue Dec 10 10:57:23 GMT 2024 FASTA file import completed.
Tue Dec 10 10:57:23 GMT 2024 Establishing local database connection.
Tue Dec 10 10:57:25 GMT 2024 Reading identification files.
Tue Dec 10 10:57:25 GMT 2024 No identifications retained.
Tue Dec 10 10:57:25 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpp964t5zu/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5349bab6e511ef84db6045bdc8410a"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpp964t5zu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 33dafe9fc98b3957
- history_state
  - error
- invocation_id
  - 33dafe9fc98b3957
- invocation_state
  - scheduled
- workflow_id
  - 33dafe9fc98b3957

mvdbeek · 2024-12-10T11:04:52Z

Tue Dec 10 10:57:25 GMT 2024 Reading identification files.
Tue Dec 10 10:57:25 GMT 2024 No identifications retained.
Tue Dec 10 10:57:25 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpp964t5zu/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

That seems to be a problem ?

workflows/proteomics/metaproteomics-gtn/README.md

workflows/proteomics/metaproteomics-gtn/metaproteomics_gtn_wf.ga

wm75 · 2024-12-11T16:00:42Z

Currently, nearly all tool outputs are marked also as WF outputs. Can't judge whether that's useful or not.

workflows/proteomics/metaproteomics-gtn/README.md

"Sixgill" part removed

Name changed from "Metaproteomics workflow" to "Identification of expressed proteins in complex bacterial community samples - Metaproteomics data analysis"

github-actions · 2024-12-12T20:49:59Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '11' (Protein FASTA File) is not optional and no input provided.","err_code":0}

github-actions · 2024-12-12T20:54:13Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmp6ivr7kgm/files/9/7/d/dataset_97dda944-9a50-4e92-b380-a75b3df6cd99.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:fe3d5373ed3b9396)'; ln -s -f '/tmp/tmp6ivr7kgm/files/2/b/f/dataset_2bf86b38-a4ee-4231-894e-20871bf7ab07.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:98441d9c441f133f)'; ln -s -f '/tmp/tmp6ivr7kgm/files/c/f/0/dataset_cf0c4abe-802f-4954-b1bd-7a6ba990c8c0.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:99d8b91a5dc52d7b)'; cp "/tmp/tmp6ivr7kgm/files/1/f/0/dataset_1f06eeef-3c4f-4bad-bc39-ace1fb89cd6e.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:fe3d5373ed3b9396)
Spectrums:2016_Jan_12_QE2_46.mgf(API:98441d9c441f133f)
Spectrums:2016_Jan_12_QE2_47.mgf(API:99d8b91a5dc52d7b)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 12.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Thu Dec 12 20:52:12 GMT 2024
Size: 17038 sequences


Thu Dec 12 20:52:15 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 12.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Thu Dec 12 20:52:17 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Thu Dec 12 20:52:23 GMT 2024 Validating MGF file: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:52:24 GMT 2024 Validating MGF file: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:52:25 GMT 2024 Validating MGF file: /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Thu Dec 12 20:52:26 GMT 2024 Indexing spectrum files.
Thu Dec 12 20:52:26 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:52:26 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:52:26 GMT 2024 X!Tandem finished for /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (85.0 milliseconds).

Thu Dec 12 20:52:26 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Thu Dec 12 20:52:26 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:52:26 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:52:26 GMT 2024 X!Tandem finished for /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Thu Dec 12 20:52:26 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Thu Dec 12 20:52:26 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:52:26 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:52:26 GMT 2024 X!Tandem finished for /tmp/tmp6ivr7kgm/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Thu Dec 12 20:52:26 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 20:52:26 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 20:52:26 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:52:27 GMT 2024 Search Completed (1.3 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp6ivr7kgm/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmp6ivr7kgm/files/6/7/5/dataset_6758dec1-8b20-4a4a-8d35-87ca78111887.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121220521734036752' -sample 'Sample_2024121220521734036752' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 9,3,0,6  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Thu Dec 12 20:52:50 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Thu Dec 12 20:52:51 GMT 2024 Import process for Galaxy_Experiment_2024121220521734036752 (Sample: Sample_2024121220521734036752, Replicate: 1)

Thu Dec 12 20:52:51 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Thu Dec 12 20:52:56 GMT 2024 FASTA file import completed.
Thu Dec 12 20:52:56 GMT 2024 Establishing local database connection.
Thu Dec 12 20:52:59 GMT 2024 Reading identification files.
Thu Dec 12 20:52:59 GMT 2024 No identifications retained.
Thu Dec 12 20:52:59 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmp6ivr7kgm/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e01cc348b8ca11ef899e6045bdb3d275"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp6ivr7kgm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - b45fc0984011367e
- history_state
  - error
- invocation_id
  - b45fc0984011367e
- invocation_state
  - scheduled
- workflow_id
  - b45fc0984011367e

github-actions · 2024-12-12T20:56:31Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpd74p11hw/files/7/8/5/dataset_7853b257-908c-4f87-8b32-74bc45f15da3.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:d1ffae44b656747d)'; ln -s -f '/tmp/tmpd74p11hw/files/f/7/f/dataset_f7f4abcd-f2b3-4c3d-be9d-ae2ef326094a.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:063aad979baf56fe)'; ln -s -f '/tmp/tmpd74p11hw/files/1/3/d/dataset_13da586d-dcc2-4f00-b797-bca1493d10f6.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:42d4540568a406e6)'; cp "/tmp/tmpd74p11hw/files/e/5/5/dataset_e550b499-5682-4062-bda7-267cf5fef8d7.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:d1ffae44b656747d)
Spectrums:2016_Jan_12_QE2_46.mgf(API:063aad979baf56fe)
Spectrums:2016_Jan_12_QE2_47.mgf(API:42d4540568a406e6)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpd74p11hw/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 12.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Thu Dec 12 20:54:28 GMT 2024
Size: 17038 sequences


Thu Dec 12 20:54:31 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpd74p11hw/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 12.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Thu Dec 12 20:54:32 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpd74p11hw/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Thu Dec 12 20:54:39 GMT 2024 Validating MGF file: /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:54:40 GMT 2024 Validating MGF file: /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:54:41 GMT 2024 Validating MGF file: /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Thu Dec 12 20:54:41 GMT 2024 Indexing spectrum files.
Thu Dec 12 20:54:41 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:54:41 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:54:42 GMT 2024 X!Tandem finished for /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (84.0 milliseconds).

Thu Dec 12 20:54:42 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Thu Dec 12 20:54:42 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:54:42 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:54:42 GMT 2024 X!Tandem finished for /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Thu Dec 12 20:54:42 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Thu Dec 12 20:54:42 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 20:54:42 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 20:54:42 GMT 2024 X!Tandem finished for /tmp/tmpd74p11hw/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Thu Dec 12 20:54:42 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 20:54:42 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 20:54:42 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 20:54:42 GMT 2024 Search Completed (1.2 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpd74p11hw/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpd74p11hw/files/3/a/2/dataset_3a24537d-ce6b-4735-8bdd-643ad4f3d779.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121220541734036887' -sample 'Sample_2024121220541734036887' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 0,6,9,3  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Thu Dec 12 20:55:03 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Thu Dec 12 20:55:03 GMT 2024 Import process for Galaxy_Experiment_2024121220541734036887 (Sample: Sample_2024121220541734036887, Replicate: 1)

Thu Dec 12 20:55:03 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Thu Dec 12 20:55:08 GMT 2024 FASTA file import completed.
Thu Dec 12 20:55:08 GMT 2024 Establishing local database connection.
Thu Dec 12 20:55:10 GMT 2024 Reading identification files.
Thu Dec 12 20:55:10 GMT 2024 No identifications retained.
Thu Dec 12 20:55:10 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpd74p11hw/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2c75b68cb8cb11ef899e6045bd4ac6af"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpd74p11hw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 7547131503f3cf67
- history_state
  - error
- invocation_id
  - 7547131503f3cf67
- invocation_state
  - scheduled
- workflow_id
  - 7547131503f3cf67

github-actions · 2024-12-12T21:05:38Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmp03dqyshl/files/a/e/8/dataset_ae839210-1894-4952-abc9-c00159164ac0.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:d7ac2e1263ee1828)'; ln -s -f '/tmp/tmp03dqyshl/files/b/d/f/dataset_bdfdd8ec-f7b9-44df-937c-17f3f8cf19e4.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:5eef2ccbb6ea1f32)'; ln -s -f '/tmp/tmp03dqyshl/files/f/0/5/dataset_f059ea1c-fde3-42c2-b41d-01caa12e5eb3.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:91204767666a5902)'; cp "/tmp/tmp03dqyshl/files/d/3/7/dataset_d37c8847-dcc6-4cd5-bbcd-812aece5fc82.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:d7ac2e1263ee1828)
Spectrums:2016_Jan_12_QE2_46.mgf(API:5eef2ccbb6ea1f32)
Spectrums:2016_Jan_12_QE2_47.mgf(API:91204767666a5902)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmp03dqyshl/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 12.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Thu Dec 12 21:03:27 GMT 2024
Size: 17038 sequences


Thu Dec 12 21:03:30 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmp03dqyshl/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 12.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Thu Dec 12 21:03:31 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmp03dqyshl/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Thu Dec 12 21:03:38 GMT 2024 Validating MGF file: /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:03:39 GMT 2024 Validating MGF file: /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:03:40 GMT 2024 Validating MGF file: /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Thu Dec 12 21:03:41 GMT 2024 Indexing spectrum files.
Thu Dec 12 21:03:41 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:03:41 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:03:41 GMT 2024 X!Tandem finished for /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (83.0 milliseconds).

Thu Dec 12 21:03:41 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Thu Dec 12 21:03:41 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:03:41 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:03:41 GMT 2024 X!Tandem finished for /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Thu Dec 12 21:03:41 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Thu Dec 12 21:03:41 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:03:41 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:03:41 GMT 2024 X!Tandem finished for /tmp/tmp03dqyshl/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Thu Dec 12 21:03:41 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 21:03:41 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 21:03:41 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:03:42 GMT 2024 Search Completed (1.2 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp03dqyshl/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmp03dqyshl/files/1/1/7/dataset_11707f0a-b1b1-4ecb-acf7-8b2d1b5beb97.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121221031734037427' -sample 'Sample_2024121221031734037427' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 0,9,6,3  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Thu Dec 12 21:04:04 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Thu Dec 12 21:04:05 GMT 2024 Import process for Galaxy_Experiment_2024121221031734037427 (Sample: Sample_2024121221031734037427, Replicate: 1)

Thu Dec 12 21:04:05 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Thu Dec 12 21:04:10 GMT 2024 FASTA file import completed.
Thu Dec 12 21:04:10 GMT 2024 Establishing local database connection.
Thu Dec 12 21:04:12 GMT 2024 Reading identification files.
Thu Dec 12 21:04:12 GMT 2024 No identifications retained.
Thu Dec 12 21:04:12 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmp03dqyshl/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5c644d08b8cc11ef899e000d3a5c74d9"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp03dqyshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 076f88813b60c151
- history_state
  - error
- invocation_id
  - 076f88813b60c151
- invocation_state
  - scheduled
- workflow_id
  - 076f88813b60c151

github-actions · 2024-12-12T21:26:05Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [paused] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Sixgill generated protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmp7aze6fi3/files/2/4/a/dataset_24adbd99-ae4c-4a6a-b961-a07d14a786d3.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:a31fc01692cc390a)'; ln -s -f '/tmp/tmp7aze6fi3/files/0/1/5/dataset_0159c94a-e0ea-48c0-b866-138cff04599c.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:adb1ad40a1bba611)'; ln -s -f '/tmp/tmp7aze6fi3/files/8/0/c/dataset_80c1a3d3-e3aa-48e0-826d-5503c3a55a21.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:8a20e1db0100afbd)'; cp "/tmp/tmp7aze6fi3/files/5/4/6/dataset_5468d3ab-b24a-48d5-9c78-7ec17844c9f2.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:a31fc01692cc390a)
Spectrums:2016_Jan_12_QE2_46.mgf(API:adb1ad40a1bba611)
Spectrums:2016_Jan_12_QE2_47.mgf(API:8a20e1db0100afbd)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 12.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Thu Dec 12 21:23:49 GMT 2024
Size: 17038 sequences


Thu Dec 12 21:23:52 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 12.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Thu Dec 12 21:23:53 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Thu Dec 12 21:24:01 GMT 2024 Validating MGF file: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:24:02 GMT 2024 Validating MGF file: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:24:02 GMT 2024 Validating MGF file: /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Thu Dec 12 21:24:03 GMT 2024 Indexing spectrum files.
Thu Dec 12 21:24:03 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:24:03 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:24:03 GMT 2024 X!Tandem finished for /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (83.0 milliseconds).

Thu Dec 12 21:24:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Thu Dec 12 21:24:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:24:03 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:24:03 GMT 2024 X!Tandem finished for /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Thu Dec 12 21:24:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Thu Dec 12 21:24:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 12 21:24:03 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 12 21:24:03 GMT 2024 X!Tandem finished for /tmp/tmp7aze6fi3/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Thu Dec 12 21:24:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 21:24:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Thu Dec 12 21:24:03 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 12 21:24:04 GMT 2024 Search Completed (1.3 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp7aze6fi3/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmp7aze6fi3/files/0/d/b/dataset_0db13c8e-d708-44fe-90fb-e4d7e25f4cd2.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121221241734038650' -sample 'Sample_2024121221241734038650' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 9,0,3,6  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Thu Dec 12 21:24:30 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Thu Dec 12 21:24:30 GMT 2024 Import process for Galaxy_Experiment_2024121221241734038650 (Sample: Sample_2024121221241734038650, Replicate: 1)

Thu Dec 12 21:24:30 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Thu Dec 12 21:24:35 GMT 2024 FASTA file import completed.
Thu Dec 12 21:24:35 GMT 2024 Establishing local database connection.
Thu Dec 12 21:24:38 GMT 2024 Reading identification files.
Thu Dec 12 21:24:38 GMT 2024 No identifications retained.
Thu Dec 12 21:24:38 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmp7aze6fi3/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9e1d0508b8c911ef899e6045bdc804e3"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp7aze6fi3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [paused] state.
- history_id
  - 697a9cdf38bca60b
- history_state
  - paused
- invocation_id
  - 697a9cdf38bca60b
- invocation_state
  - scheduled
- workflow_id
  - 697a9cdf38bca60b

github-actions · 2024-12-19T08:53:02Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpailhdwii/files/d/2/3/dataset_d2393248-2c47-441d-8648-f550b24351d0.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:ec16f1e5f3be8f6a)'; ln -s -f '/tmp/tmpailhdwii/files/1/a/7/dataset_1a721929-87d3-4e7a-a585-9ddbc3939a87.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:71e8bf67d38a5f89)'; ln -s -f '/tmp/tmpailhdwii/files/6/2/5/dataset_6250f5c9-bdf9-4055-af14-5e35e401cf31.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:3b7304eedfbdf7ff)'; cp "/tmp/tmpailhdwii/files/f/a/4/dataset_fa4391eb-e8eb-45c6-883e-2f4af8c6de09.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:ec16f1e5f3be8f6a)
Spectrums:2016_Jan_12_QE2_46.mgf(API:71e8bf67d38a5f89)
Spectrums:2016_Jan_12_QE2_47.mgf(API:3b7304eedfbdf7ff)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpailhdwii/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 19.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Thu Dec 19 08:50:53 GMT 2024
Size: 17038 sequences


Thu Dec 19 08:50:56 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpailhdwii/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 19.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Thu Dec 19 08:50:57 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpailhdwii/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Thu Dec 19 08:51:04 GMT 2024 Validating MGF file: /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 19 08:51:05 GMT 2024 Validating MGF file: /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 19 08:51:06 GMT 2024 Validating MGF file: /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Thu Dec 19 08:51:07 GMT 2024 Indexing spectrum files.
Thu Dec 19 08:51:07 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 19 08:51:07 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 19 08:51:07 GMT 2024 X!Tandem finished for /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (12.0 milliseconds).

Thu Dec 19 08:51:07 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Thu Dec 19 08:51:07 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 19 08:51:07 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 19 08:51:07 GMT 2024 X!Tandem finished for /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (2.0 milliseconds).

Thu Dec 19 08:51:07 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Thu Dec 19 08:51:07 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Thu Dec 19 08:51:07 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Thu Dec 19 08:51:07 GMT 2024 X!Tandem finished for /tmp/tmpailhdwii/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Thu Dec 19 08:51:07 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Thu Dec 19 08:51:07 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Thu Dec 19 08:51:07 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Thu Dec 19 08:51:08 GMT 2024 Search Completed (1.2 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpailhdwii/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpailhdwii/files/b/f/9/dataset_bf947d80-5027-400c-9eae-600c319059ad.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121908511734598273' -sample 'Sample_2024121908511734598273' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,9,3,0  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Thu Dec 19 08:51:27 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Thu Dec 19 08:51:27 GMT 2024 Import process for Galaxy_Experiment_2024121908511734598273 (Sample: Sample_2024121908511734598273, Replicate: 1)

Thu Dec 19 08:51:27 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Thu Dec 19 08:51:33 GMT 2024 FASTA file import completed.
Thu Dec 19 08:51:33 GMT 2024 Establishing local database connection.
Thu Dec 19 08:51:36 GMT 2024 Reading identification files.
Thu Dec 19 08:51:36 GMT 2024 No identifications retained.
Thu Dec 19 08:51:36 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpailhdwii/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"45bc8628bde611ef8af66045bdd4c394"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpailhdwii/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 6bcdd20665b8b12f
- history_state
  - error
- invocation_id
  - 6bcdd20665b8b12f
- invocation_state
  - scheduled
- workflow_id
  - 6bcdd20665b8b12f

github-actions · 2024-12-22T03:42:49Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpqbga3ngd/files/2/0/5/dataset_20594a18-eb48-4c6b-a972-19aacadee1c6.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:06c54de68df560c7)'; ln -s -f '/tmp/tmpqbga3ngd/files/c/c/5/dataset_cc52a70e-bc85-4f69-893d-649d19c8b095.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:d16d5486fe26e837)'; ln -s -f '/tmp/tmpqbga3ngd/files/3/6/2/dataset_362b10fb-a382-44c8-8746-9bd6cc5fa7d6.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:31c5d38ab4ea6e6b)'; cp "/tmp/tmpqbga3ngd/files/5/8/1/dataset_581ef212-9a12-4acc-8868-82e9b67eee35.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:06c54de68df560c7)
Spectrums:2016_Jan_12_QE2_46.mgf(API:d16d5486fe26e837)
Spectrums:2016_Jan_12_QE2_47.mgf(API:31c5d38ab4ea6e6b)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 22.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Sun Dec 22 03:40:49 GMT 2024
Size: 17038 sequences


Sun Dec 22 03:40:52 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 22.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Sun Dec 22 03:40:53 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Sun Dec 22 03:41:00 GMT 2024 Validating MGF file: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:41:01 GMT 2024 Validating MGF file: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:41:02 GMT 2024 Validating MGF file: /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Sun Dec 22 03:41:03 GMT 2024 Indexing spectrum files.
Sun Dec 22 03:41:03 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:41:03 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:41:03 GMT 2024 X!Tandem finished for /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (10.0 milliseconds).

Sun Dec 22 03:41:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Sun Dec 22 03:41:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:41:03 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:41:03 GMT 2024 X!Tandem finished for /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Sun Dec 22 03:41:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Sun Dec 22 03:41:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:41:03 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:41:03 GMT 2024 X!Tandem finished for /tmp/tmpqbga3ngd/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Sun Dec 22 03:41:03 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 03:41:03 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 03:41:03 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:41:04 GMT 2024 Search Completed (1.4 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpqbga3ngd/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpqbga3ngd/files/2/a/2/dataset_2a2bcdc7-8e32-4217-9a27-db166f03ff0d.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024122203411734838869' -sample 'Sample_2024122203411734838869' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,0,9,3  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Sun Dec 22 03:41:23 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Sun Dec 22 03:41:23 GMT 2024 Import process for Galaxy_Experiment_2024122203411734838869 (Sample: Sample_2024122203411734838869, Replicate: 1)

Sun Dec 22 03:41:23 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Sun Dec 22 03:41:29 GMT 2024 FASTA file import completed.
Sun Dec 22 03:41:29 GMT 2024 Establishing local database connection.
Sun Dec 22 03:41:31 GMT 2024 Reading identification files.
Sun Dec 22 03:41:31 GMT 2024 No identifications retained.
Sun Dec 22 03:41:31 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpqbga3ngd/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"723e371ec01611ef8af66045bdb94edd"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpqbga3ngd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 00eeea23ad5f0fa1
- history_state
  - error
- invocation_id
  - 00eeea23ad5f0fa1
- invocation_state
  - scheduled
- workflow_id
  - 00eeea23ad5f0fa1

github-actions · 2024-12-22T03:57:42Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmp167hk_83/files/d/9/3/dataset_d934b0ee-6d1d-464a-b15c-d08c8190f195.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:fbbc2fdabbe4faa3)'; ln -s -f '/tmp/tmp167hk_83/files/9/1/3/dataset_9131e818-4cd9-4043-b49e-610ef11fd6ab.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:6fd0b6257cbeef48)'; ln -s -f '/tmp/tmp167hk_83/files/e/b/e/dataset_ebe0b64a-0565-4d6a-aed3-e9d766aa3127.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:a0a6b14fe512b8f5)'; cp "/tmp/tmp167hk_83/files/b/0/5/dataset_b058bdef-bee9-4a21-92f4-662af29dad05.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:fbbc2fdabbe4faa3)
Spectrums:2016_Jan_12_QE2_46.mgf(API:6fd0b6257cbeef48)
Spectrums:2016_Jan_12_QE2_47.mgf(API:a0a6b14fe512b8f5)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmp167hk_83/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 22.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Sun Dec 22 03:54:08 GMT 2024
Size: 17038 sequences


Sun Dec 22 03:54:11 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmp167hk_83/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 22.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Sun Dec 22 03:54:12 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmp167hk_83/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Sun Dec 22 03:54:19 GMT 2024 Validating MGF file: /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:54:31 GMT 2024 Validating MGF file: /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:54:38 GMT 2024 Validating MGF file: /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Sun Dec 22 03:54:45 GMT 2024 Indexing spectrum files.
Sun Dec 22 03:54:46 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:54:46 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:54:46 GMT 2024 X!Tandem finished for /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (81.0 milliseconds).

Sun Dec 22 03:54:46 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Sun Dec 22 03:54:46 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:54:46 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:54:46 GMT 2024 X!Tandem finished for /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (0.0 milliseconds).

Sun Dec 22 03:54:46 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Sun Dec 22 03:54:46 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 03:54:46 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 03:54:46 GMT 2024 X!Tandem finished for /tmp/tmp167hk_83/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Sun Dec 22 03:54:46 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 03:54:46 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 03:54:46 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 03:55:49 GMT 2024 Search Completed (1 minute 4.0 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp167hk_83/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmp167hk_83/files/a/8/b/dataset_a8bd3735-6b82-42a3-93e3-ff6f82678ff6.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024122203551734839755' -sample 'Sample_2024122203551734839755' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,3,0,9  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Sun Dec 22 03:56:07 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Sun Dec 22 03:56:15 GMT 2024 Import process for Galaxy_Experiment_2024122203551734839755 (Sample: Sample_2024122203551734839755, Replicate: 1)

Sun Dec 22 03:56:15 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Sun Dec 22 03:56:21 GMT 2024 FASTA file import completed.
Sun Dec 22 03:56:21 GMT 2024 Establishing local database connection.
Sun Dec 22 03:56:23 GMT 2024 Reading identification files.
Sun Dec 22 03:56:23 GMT 2024 No identifications retained.
Sun Dec 22 03:56:23 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmp167hk_83/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5259d2f8c01811ef8af66045bdb0b7ee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp167hk_83/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 00eaddba0f9edda6
- history_state
  - error
- invocation_id
  - 00eaddba0f9edda6
- invocation_state
  - scheduled
- workflow_id
  - 00eaddba0f9edda6

github-actions · 2024-12-22T04:07:27Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpjaknl2m8/files/8/e/c/dataset_8ec1d6a5-a7d7-480c-8a94-ddae324eb2a9.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:81160b2801c264d5)'; ln -s -f '/tmp/tmpjaknl2m8/files/3/b/7/dataset_3b7ddcb2-ff4e-414e-bda3-4bae0591b39b.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:ef6b79e6a34456e4)'; ln -s -f '/tmp/tmpjaknl2m8/files/a/5/c/dataset_a5c784ae-258d-47eb-aca6-c3476715c5f4.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:a0c5ef1f66a4b4e8)'; cp "/tmp/tmpjaknl2m8/files/2/d/d/dataset_2dd90594-bfc5-4357-ad25-994769eab218.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:81160b2801c264d5)
Spectrums:2016_Jan_12_QE2_46.mgf(API:ef6b79e6a34456e4)
Spectrums:2016_Jan_12_QE2_47.mgf(API:a0c5ef1f66a4b4e8)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 22.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Sun Dec 22 04:03:43 GMT 2024
Size: 17038 sequences


Sun Dec 22 04:03:45 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 22.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Sun Dec 22 04:03:46 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Sun Dec 22 04:03:53 GMT 2024 Validating MGF file: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:04:05 GMT 2024 Validating MGF file: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:04:12 GMT 2024 Validating MGF file: /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Sun Dec 22 04:04:19 GMT 2024 Indexing spectrum files.
Sun Dec 22 04:04:20 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:04:20 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:04:20 GMT 2024 X!Tandem finished for /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (10.0 milliseconds).

Sun Dec 22 04:04:20 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Sun Dec 22 04:04:20 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:04:20 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:04:20 GMT 2024 X!Tandem finished for /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (61.0 milliseconds).

Sun Dec 22 04:04:20 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Sun Dec 22 04:04:20 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:04:20 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:04:20 GMT 2024 X!Tandem finished for /tmp/tmpjaknl2m8/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Sun Dec 22 04:04:20 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 04:04:20 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 04:04:20 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:05:23 GMT 2024 Search Completed (1 minute 4.0 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpjaknl2m8/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpjaknl2m8/files/3/0/e/dataset_30e00515-94c2-4928-88c7-074d96f05eea.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024122204051734840329' -sample 'Sample_2024122204051734840329' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,3,9,0  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Sun Dec 22 04:05:46 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Sun Dec 22 04:05:54 GMT 2024 Import process for Galaxy_Experiment_2024122204051734840329 (Sample: Sample_2024122204051734840329, Replicate: 1)

Sun Dec 22 04:05:55 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Sun Dec 22 04:05:59 GMT 2024 FASTA file import completed.
Sun Dec 22 04:05:59 GMT 2024 Establishing local database connection.
Sun Dec 22 04:06:02 GMT 2024 Reading identification files.
Sun Dec 22 04:06:02 GMT 2024 No identifications retained.
Sun Dec 22 04:06:02 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpjaknl2m8/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2f8618dac01911ef8af6000d3a5d5557"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpjaknl2m8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 001a89ab2b027fc8
- history_state
  - error
- invocation_id
  - 001a89ab2b027fc8
- invocation_state
  - scheduled
- workflow_id
  - 001a89ab2b027fc8

github-actions · 2024-12-22T04:44:33Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpnehc3v7g/files/8/4/a/dataset_84aaaf52-fafd-44fc-8349-9ba4255d50e9.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:c659c7b88b105a29)'; ln -s -f '/tmp/tmpnehc3v7g/files/6/1/5/dataset_6159921f-b659-45e3-86ff-5a6caa59263f.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:2d2172a9dec8ede9)'; ln -s -f '/tmp/tmpnehc3v7g/files/c/2/d/dataset_c2d67ead-3370-43eb-b725-f7e096127429.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:b0708c6e5e6f9755)'; cp "/tmp/tmpnehc3v7g/files/4/2/3/dataset_423ae693-0f72-4c4b-81b7-0e38dc9ae5cd.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:c659c7b88b105a29)
Spectrums:2016_Jan_12_QE2_46.mgf(API:2d2172a9dec8ede9)
Spectrums:2016_Jan_12_QE2_47.mgf(API:b0708c6e5e6f9755)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 22.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Sun Dec 22 04:40:56 GMT 2024
Size: 17038 sequences


Sun Dec 22 04:40:58 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 22.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Sun Dec 22 04:40:59 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Sun Dec 22 04:41:06 GMT 2024 Validating MGF file: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:41:18 GMT 2024 Validating MGF file: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:41:25 GMT 2024 Validating MGF file: /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Sun Dec 22 04:41:32 GMT 2024 Indexing spectrum files.
Sun Dec 22 04:41:32 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:41:33 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:41:33 GMT 2024 X!Tandem finished for /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (9.0 milliseconds).

Sun Dec 22 04:41:33 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Sun Dec 22 04:41:33 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:41:33 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:41:33 GMT 2024 X!Tandem finished for /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Sun Dec 22 04:41:33 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Sun Dec 22 04:41:33 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 04:41:33 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 04:41:33 GMT 2024 X!Tandem finished for /tmp/tmpnehc3v7g/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (0.0 milliseconds).

Sun Dec 22 04:41:33 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 04:41:33 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 04:41:33 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 04:42:35 GMT 2024 Search Completed (1 minute 4.0 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpnehc3v7g/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpnehc3v7g/files/6/5/5/dataset_6556e9e2-b1ed-4576-9836-5f7ce077bb0d.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024122204421734842562' -sample 'Sample_2024122204421734842562' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 6,3,9,0  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Sun Dec 22 04:43:03 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Sun Dec 22 04:43:12 GMT 2024 Import process for Galaxy_Experiment_2024122204421734842562 (Sample: Sample_2024122204421734842562, Replicate: 1)

Sun Dec 22 04:43:12 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Sun Dec 22 04:43:17 GMT 2024 FASTA file import completed.
Sun Dec 22 04:43:17 GMT 2024 Establishing local database connection.
Sun Dec 22 04:43:20 GMT 2024 Reading identification files.
Sun Dec 22 04:43:20 GMT 2024 No identifications retained.
Sun Dec 22 04:43:20 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpnehc3v7g/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ba0f8cd4c01e11ef8af67c1e520596d5"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpnehc3v7g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - b923e8893ff3210e
- history_state
  - error
- invocation_id
  - b923e8893ff3210e
- invocation_state
  - scheduled
- workflow_id
  - b923e8893ff3210e

github-actions · 2024-12-22T19:42:04Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metaproteomics_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
sqlquery	`"SELECT go.description, \ncount(distinct psms.sequence) as \"peptides\", count(distinct psms.id) as \"psms\" \nFROM go JOIN prot_go ON go.go_id = prot_go.go_reference JOIN prot on prot_go.id = prot.id JOIN psms ON prot.peptide = psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY peptides desc,psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmp05cyqyaa/files/5/f/4/dataset_5f426967-904b-43e2-b5de-429339d69b23.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:21f3807248954c03)'; ln -s -f '/tmp/tmp05cyqyaa/files/6/9/d/dataset_69d123a2-2bab-4365-969e-633ed24aba0c.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:838663e32bf94f57)'; ln -s -f '/tmp/tmp05cyqyaa/files/c/b/8/dataset_cb85d54c-7a54-4c02-b13b-9b75d40d7057.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:538ea64578d8fa73)'; cp "/tmp/tmp05cyqyaa/files/3/8/b/dataset_38b7e5d2-283c-44e6-a824-6db427e4404b.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:21f3807248954c03)
Spectrums:2016_Jan_12_QE2_46.mgf(API:838663e32bf94f57)
Spectrums:2016_Jan_12_QE2_47.mgf(API:538ea64578d8fa73)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 22.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Sun Dec 22 19:38:29 GMT 2024
Size: 17038 sequences


Sun Dec 22 19:38:31 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 22.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Sun Dec 22 19:38:32 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Sun Dec 22 19:38:39 GMT 2024 Validating MGF file: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 19:38:51 GMT 2024 Validating MGF file: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 19:38:59 GMT 2024 Validating MGF file: /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Sun Dec 22 19:39:05 GMT 2024 Indexing spectrum files.
Sun Dec 22 19:39:06 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 19:39:06 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 19:39:06 GMT 2024 X!Tandem finished for /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (14.0 milliseconds).

Sun Dec 22 19:39:06 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Sun Dec 22 19:39:06 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 19:39:06 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 19:39:06 GMT 2024 X!Tandem finished for /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Sun Dec 22 19:39:06 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Sun Dec 22 19:39:06 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Sun Dec 22 19:39:06 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Sun Dec 22 19:39:06 GMT 2024 X!Tandem finished for /tmp/tmp05cyqyaa/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Sun Dec 22 19:39:06 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 19:39:06 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Sun Dec 22 19:39:06 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Sun Dec 22 19:40:09 GMT 2024 Search Completed (1 minute 4.0 seconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmp05cyqyaa/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmp05cyqyaa/files/a/8/c/dataset_a8c25776-55f1-495c-9cf7-ecb9fd195dd7.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024122219401734896416' -sample 'Sample_2024122219401734896416' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 9,3,0,6  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Sun Dec 22 19:40:30 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Sun Dec 22 19:40:38 GMT 2024 Import process for Galaxy_Experiment_2024122219401734896416 (Sample: Sample_2024122219401734896416, Replicate: 1)

Sun Dec 22 19:40:38 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Sun Dec 22 19:40:43 GMT 2024 FASTA file import completed.
Sun Dec 22 19:40:43 GMT 2024 Establishing local database connection.
Sun Dec 22 19:40:45 GMT 2024 Reading identification files.
Sun Dec 22 19:40:45 GMT 2024 No identifications retained.
Sun Dec 22 19:40:46 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmp05cyqyaa/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2a76b54cc09c11ef8af6000d3a358eee"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmp05cyqyaa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": null}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 3e354b5ba0235d04
- history_state
  - error
- invocation_id
  - 3e354b5ba0235d04
- invocation_state
  - scheduled
- workflow_id
  - 3e354b5ba0235d04

Init metaproteomics-gtn

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