Updating workflows/proteomics/clinicalmp/clinicalmp-discovery from 0.1 to 0.2

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/proteomics/clinicalmp/clinicalmp-discovery. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 should be updated to toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.4
• toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
• toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1
• toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1

The workflow release number has been updated from 0.1 to 0.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ iwc-clinicalmp-discovery-workflow.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Human UniProt Microbial Proteins from MetaNovo and cRAP:

      • step_state: scheduled

    • Step 2: IdentificationParameters:PAR file:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mkdir output; cwd=`pwd`; export HOME=$cwd;    echo 'running Identification Parameters CLI' && searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="./bin/" -use_log_folder 0 -out './IdentificationParametersOutput.par'  -frag_tol '0.6' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -enzyme "Trypsin" -mc "2" -specificity "0"   -fixed_mods "Carbamidomethylation of C,TMT 11-plex of K+4,TMT 11-plex of peptide N-term" -variable_mods "Oxidation of M"   -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1     -xtandem_output_spectra 1   -myrimatch_output mzIdentML                                   -annotation_level 0.75   -annotation_high_resolution 1   -sequence_matching_type 2 -sequence_matching_x 0.25 -sequence_matching_enzymatic_tags 0 -sequence_matching_max_ptms_per_tag 3 -sequence_matching_min_amino_acid_score 30 -sequence_matching_min_tag_length 3    -import_peptide_length_min '8' -import_peptide_length_max '30' -import_precursor_mz '10.0' -import_precursor_mz_ppm '1' -exclude_unknown_ptms '1'    -ptm_score '1' -ptm_alignment '1' -ptm_sequence_matching_type '1'    -useGeneMapping 0 -updateGeneMapping 0    -simplify_groups 1 -simplify_evidence 1 -simplify_confidence 1 -simplify_confidence_threshold 0.05 -simplify_enzymaticity 1 -simplify_variant 1 -pi_modifications 1      -protein_fdr '1.0' -peptide_fdr '1.0' -psm_fdr '1.0'    -protein_fraction_mw_confidence '95.0'     -fasta_target_decoy 1 -fasta_decoy_tag _REVERSED -fasta_decoy_type 1 -fasta_target_decoy 0 -fasta_decoy_file_tag _concatenated_target_decoy

          Exit Code:

          • 0

          Standard Output:

          • running Identification Parameters CLI
            Path configuration completed.
            
            Identification parameters file created: /tmp/tmp5hs96cwg/job_working_directory/000/4/working/./IdentificationParametersOutput.par
            
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            advanced_options	{"database_processing_options": {"decoy_conditional": {"__current_case__": 1, "create_decoy_selector": "yes", "decoy_tag": "_REVERSED", "decoy_type": "1"}, "decoy_file_tag": "_concatenated_target_decoy"}, "fraction_analysis_options": {"protein_fraction_mw_confidence": "95.0"}, "gene_annotation_options": {"update_gene_mapping": false, "use_gene_mapping": false}, "import_filters_options": {"exclude_unknown_ptms": true, "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "1", "min_peptide_length": "8", "missed_cleavages_max": null, "missed_cleavages_min": null}, "protein_inference_options": {"simplify_protein_groups_conditional": {"__current_case__": 1, "simplify_protein_groups_confidence": true, "simplify_protein_groups_confidence_threshold": "0.05", "simplify_protein_groups_enzymaticity": true, "simplify_protein_groups_evidence": true, "simplify_protein_groups_selector": "yes", "simplify_protein_groups_variant": true}, "simplify_protein_pi_modifications": true}, "ptm_localization_options": {"ptm_alignment": true, "ptm_score": {"__current_case__": 0, "ptm_score_selector": "1", "ptm_threshold": "95.0", "score_neutral_losses": false}, "ptm_sequence_matching_type": "1"}, "sequence_matching_options": {"sequence_matching_enzymatic_tags": false, "sequence_matching_max_ptms_per_tag": "3", "sequence_matching_min_amino_acid_score": "30", "sequence_matching_min_tag_length": "3", "sequence_matching_type": "2", "sequence_matching_x": "0.25"}, "spectrum_annotation_options": {"annotation_high_resolution": true, "annotation_level": "0.75", "annotation_mz_tolerance": "0.5"}, "validation_levels_options": {"peptide_fdr": "1.0", "protein_fdr": "1.0", "psm_fdr": "1.0"}}
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            searchengines_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "metamorpheus": {"__current_case__": 0, "metamorpheus_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"}, "pepnovo": {"__current_case__": 0, "pepnovo_advanced": "no"}, "pnovo": {"__current_case__": 0, "pnovo_advanced": "no"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 0, "xtandem_advanced": "no"}}
            spectrum_matching_options	{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2", "specificity": "0"}]}, "fixed_modifications": ["Carbamidomethylation of C", "TMT 11-plex of K+4", "TMT 11-plex of peptide N-term"], "forward_ion": "b", "fragment_tol": "0.6", "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", "variable_modifications": ["Oxidation of M"]}

    • Step 11: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            peak_lists_files	None
            search_engines_options	{"engines": ["X!Tandem", "MSGF"]}
            searchgui_advanced	{"__current_case__": 0, "searchgui_advanced_selector": "basic"}

    • Step 12: FASTA to Tabular:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            descr_columns	"1"
            keep_first	"0"

    • Step 13: Select microbial peptides MQ:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            invert	"-v"
            keep_header	true
            pattern	` "(_HUMAN)

    • Step 14: Peptide Shaker:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            exporting_options	{"followup_conditional": {"__current_case__": 0, "followup_conditional_selector": "no"}, "mzidentml_conditional": {"__current_case__": 0, "contact_options": {"__current_case__": 0, "contact_options_selector": "no"}, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_psdb": false, "zip_output_boolean": false}}
            optional_main_parameters	{"input_fasta_file": null, "input_optional_identification_parameters": null, "input_optional_spectrum_files": null}

    • Step 15: Filtering Accesions:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment_char	true
            dbkey	"?"
            linefilters	` [{"index": 0, "filter": {"current_case": 9, "columns": "1", "filter_type": "select_columns"}}, {"index": 1, "filter": {"current_case": 11, "add": null, "column": "1", "filter_type": "replace", "regex_pattern": "^[^

    • Step 16: MQ Peptide Sequences:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c1"
            dbkey	"?"
            delimiter	"T"

    • Step 17: Select microbial peptides SGPS:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            invert	"-v"
            keep_header	true
            pattern	` "(_HUMAN)

    • Step 18: Select microbial PSMs SGPS:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            invert	"-v"
            keep_header	true
            pattern	` "(_HUMAN)

    • Step 19: Remove beginning from MQ Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            num_lines	"1"

    • Step 20: Filter confident microbial Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"c17=='Confident'"
            dbkey	"?"
            header_lines	"1"

    • Step 3: Tandem Mass Spectrometry MSMS files:

      • step_state: scheduled

    • Step 21: Filter confident microbial PSMs:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"c24=='Confident'"
            dbkey	"?"
            header_lines	"1"

    • Step 22: MQ Distinct Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            groupcol	"1"
            ignorecase	false
            ignorelines	None
            operations	[]

    • Step 23: Extracting peptides SGPS from PSM:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            add_to_database	{"withdb": null}
            addqueries	{"queries": []}
            chromInfo	"/tmp/tmp5hs96cwg/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 id,Proteins,Sequence\nFROM psms \nWHERE psms.ln NOT IN\n(SELECT distinct prots.ln\nFROM prots JOIN Uniprot ON prots.prot = Uniprot.prot)\nORDER BY psms.ln"
            tables	[{"__index__": 0, "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": 31, "src": "hda"}]}, "tbl_opts": {"col_names": "ln,id,Proteins,Sequence", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "ln", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psms"}}, {"__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"}}, {"__index__": 2, "filter": {"__current_case__": 12, "columns": "3", "filter_type": "normalize", "separator": ","}}]}, "table": {"values": [{"id": 31, "src": "hda"}]}, "tbl_opts": {"col_names": "ln,id,prot", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "prot,ln", "unique": true}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "prots"}}, {"__index__": 2, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 25, "src": "hda"}]}, "tbl_opts": {"col_names": "prot", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "prot", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "Uniprot"}}]
            workdb	"workdb.sqlite"

    • Step 24: Cut Peptide column:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 25: SGPS Distinct Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            groupcol	"1"
            ignorecase	false
            ignorelines	None
            operations	[]

    • Step 26: SGPS MQ Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 27: Distinct Peptides:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            groupcol	"1"
            ignorecase	false
            ignorelines	None
            operations	[]

    • Step 4: Human SwissProt:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/983bf725dfc2/dbbuilder/uniprotkb.py' --url 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=(taxonomy_id:9606)+AND+(reviewed:true)+AND+(keyword:KW-1185)' -o 'tmp.gz' && gzip -dc 'tmp.gz' > '/tmp/tmp5hs96cwg/job_working_directory/000/5/outputs/dataset_bb3a4aed-6129-47a2-a200-ba334989d19d.dat'

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"data"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            source	{"__current_case__": 0, "from": "uniprot", "include_isoform": false, "reviewed": "reviewed:true", "set": "keyword:KW-1185", "taxon": "9606", "taxon_id": null}

    • Step 5: Contaminants:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • wget -nv 'https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta' -O '/tmp/tmp5hs96cwg/job_working_directory/000/6/outputs/dataset_3f8251ef-4d7b-4101-99c8-ed3b7de4f907.dat' --no-check-certificate

          Exit Code:

          • 0

          Standard Error:

          • 2024-12-16 05:45:23 URL:https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta [43362/43362] -> "/tmp/tmp5hs96cwg/job_working_directory/000/6/outputs/dataset_3f8251ef-4d7b-4101-99c8-ed3b7de4f907.dat" [1]
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"data"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            source	{"__current_case__": 1, "from": "cRAP"}

    • Step 6: Experimental Design Discovery MaxQuant:

      • step_state: scheduled

    • Step 7: FastaCLI_ MetaNovo Human SwissProt cRAP with decoys:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mkdir output && cwd=`pwd` &&  echo 'DB: Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta sequences: 21289' && cp '/tmp/tmp5hs96cwg/files/0/4/8/dataset_048d422b-a065-4078-9c44-2d933569c4ca.dat' 'Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta' &&   echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -use_log_folder 0 -temp_folder `pwd` -in 'Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta' -decoy -decoy_flag _REVERSED -suffix 2 -decoy_suffix _concatenated_target_decoy && mv 'Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP_concatenated_target_decoy.fasta' output

          Exit Code:

          • 0

          Standard Output:

          • DB: Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta sequences: 21289
            Creating decoy database.
            Path configuration completed.
            10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
            Input: /tmp/tmp5hs96cwg/job_working_directory/000/7/working/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta
            
            Extracting FASTA summary. Please wait...
            
            10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
            
            Name: Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP
            Description: /tmp/tmp5hs96cwg/job_working_directory/000/7/working/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta
            Version: Mon Dec 16 05:43:22 GMT 2024
            Decoy Flag: _REVERSED (Suffix)
            Type: Generic Split Header (0.0%), UniProtKB (1.0%)
            Last modified: Mon Dec 16 05:43:22 GMT 2024
            Size: 21289 sequences (21289 target)
            
            Mon Dec 16 05:43:27 GMT 2024 Appending Decoy Sequences. Please Wait...
            10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
            
            Decoy file successfully created.
            
            Output: /tmp/tmp5hs96cwg/job_working_directory/000/7/working/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP_concatenated_target_decoy.fasta
            Name: Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP (target-decoy)
            Description: /tmp/tmp5hs96cwg/job_working_directory/000/7/working/Human_UniProt_Microbial_Proteins_(from_MetaNovo)_and_cRAP.fasta
            Version: Mon Dec 16 05:43:22 GMT 2024
            Decoy Flag: _REVERSED (Suffix)
            Type: Generic Split Header (0.0%), UniProtKB (1.0%)
            Last modified: Mon Dec 16 05:43:28 GMT 2024
            Size: 42578 sequences (21289 target)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database_processing_options	{"decoy_file_tag": "_concatenated_target_decoy", "decoy_tag": "_REVERSED", "decoy_type": "2"}
            dbkey	"?"

    • Step 8: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.4:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • ln -s '/tmp/tmp5hs96cwg/files/8/7/6/dataset_87615b30-3f27-47fc-91da-0aa55b97992f.dat' 'PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw' &&   CAN_SUDO=$(sudo -n -l > /dev/null 2> /dev/null; echo $?) && if [ "$CAN_SUDO" -eq "0" ]; then uid=`id -u` && gid=`id -g` && WINE="wine64_anyuser"; else WINE="wine64" && export WINEPREFIX=$(mktemp -d) && (cp -a /wineprefix64/* $WINEPREFIX 2> /dev/null || true); fi && $WINE msconvert 'PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw'  --outdir outputs --mgf       --filter "scanSumming precursorTol=0.05 scanTimeTol=10.0 ionMobilityTol=0.01"   --stripLocationFromSourceFiles  --filter "peakPicking vendor msLevel=1-"     --filter "mzWindow [0.0,0.0]"  --filter "ETDFilter true true true true 3.1MZ"  --filter "MS2Denoise 6 30.0 true"   --filter "demultiplex massError=10.0PPM nnlsMaxIter=50 nnlsEps=1e-10 noWeighting=false demuxBlockExtra=0.0 variableFill=false noSumNormalize=false optimization=none interpolateRT=true minWindowSize=0.2"      --filter "msLevel [0, 0]"    --mz64 --inten32  --zlib   && if [ "$CAN_SUDO" -eq "0" ]; then sudo chown -R $uid:$gid './'; fi

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"thermo.raw"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            data_processing	{"charge_state_calculation": {"__current_case__": 0, "charge_state_calculation_method": "false"}, "demultiplex": {"__current_case__": 0, "demultiplex_on": "true", "demuxBlockExtra": "0.0", "interpolateRT": true, "massError": "10.0", "massErrorUnits": "PPM", "minWindowSize": "0.2", "nnlsEps": "1e-10", "nnlsMaxIter": "50", "noSumNormalize": false, "noWeighting": false, "optimization": "none", "variableFill": false}, "etd_filtering": {"__current_case__": 1, "blanket_removal": "true", "do_etd_filtering": "true", "matching_tolerance": "3.1", "matching_tolerance_units": "MZ", "remove_charge_reduced": "true", "remove_neutral_loss": "true", "remove_precursor": "true"}, "filter_mz_windows": {"__current_case__": 1, "do_mzwindow_filter": "true", "mz_window_from": "0.0", "mz_window_to": "0.0"}, "ms2deisotope": false, "ms2denoise": {"__current_case__": 0, "denoise": "true", "num_peaks": "6", "relax": true, "window_width": "30.0"}, "peak_picking": {"__current_case__": 1, "pick_peaks": "true", "pick_peaks_algorithm": "vendor", "pick_peaks_ms_levels": "1-"}, "precursor_refinement": {"__current_case__": 0, "use_mzrefinement": "false"}, "thresholds": []}
            dbkey	"?"
            filtering	{"activation": "false", "analyzer": "false", "filter_ms_levels": {"__current_case__": 1, "do_ms_level_filter": "true", "ms_level_from": "0", "ms_level_to": "0"}, "indices": [], "polarity": "false", "scan_numbers": [], "strip_it": false}
            general_options	{"acceptZeroLengthSpectra": false, "combineIonMobilitySpectra": false, "ignoreUnknownInstrumentError": false, "multi_run_output": {"__current_case__": 1, "do_multi_run_output": "true", "run_index_set": []}, "scan_summing": {"__current_case__": 1, "do_scan_summing": "true", "ionMobilityTol": "0.01", "precursorTol": "0.05", "scanTimeTol": "10.0"}, "simAsSpectra": false, "srmAsSpectra": false}
            license_agreement	true
            output_type	"mgf"
            settings	{"binary_compression": "zlib", "gzip_compression": false, "intensity_encoding": "32", "mz_encoding": "64"}

    • Step 9: Human SwissProt+cRAP:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            accession_parser	"^>([^ ]+).*$"
            batchmode	{"__current_case__": 0, "input_fastas": [{"__index__": 0, "input_fasta": {"values": [{"id": 5, "src": "hda"}]}}, {"__index__": 1, "input_fasta": {"values": [{"id": 6, "src": "hda"}]}}], "processmode": "individual"}
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            uniqueness_criterion	"sequence"

    • Step 10: toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • export COMPlus_EnableDiagnostics=0 && maxquant -c mqpar.xml 2>/dev/null  && cp '/tmp/tmp5hs96cwg/job_working_directory/000/10/configs/tmpgjjlf1m7' '/tmp/tmp5hs96cwg/job_working_directory/000/10/outputs/dataset_e7d3199e-fd21-4201-a824-733481339c44.dat' && cp '/tmp/tmp5hs96cwg/files/8/7/6/dataset_87615b30-3f27-47fc-91da-0aa55b97992f.dat' 'PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.raw.thermo.raw' && python3 '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/9c52362ae7bb/maxquant/create_mqpar.py' --exp_design='/tmp/tmp5hs96cwg/files/a/4/9/dataset_a4956edc-c749-4bee-a9f7-dc160663be3c.dat' --version=2.0.3.0 --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w\-\s\.]' --yaml='/tmp/tmp5hs96cwg/job_working_directory/000/10/configs/tmpgjjlf1m7' mqpar.xml  && maxquant mqpar.xml > '/tmp/tmp5hs96cwg/job_working_directory/000/10/outputs/dataset_e10c1885-25fc-483c-8f6e-466a24fe31ba.dat' && mv mqpar.xml combined/txt/mqpar.xml

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"89b31284bb7011ef899e7c1e52169168"
            chromInfo	"/tmp/tmp5hs96cwg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_opts	{"description_parse_rule": ">(.*)", "fasta_files": {"values": [{"id": 1, "src": "hda"}]}, "ftype": ".thermo.raw", "identifier_parse_rule": ">([^\\s]*)"}
            output_opts	{"dry_run": false, "output": ["proteinGroups", "mqpar", "peptides", "msms", "msmsScans", "summary", "log", "config"]}
            paramGroups	[{"__index__": 0, "digestion_mode": "0", "enzymes": ["Trypsin/P"], "files": {"values": [{"id": 1, "src": "hdca"}]}, "fixedModifications": ["Carbamidomethyl (C)"], "maxMissedCleavages": "2", "quant_method": {"__current_case__": 3, "filter_by_pif": {"__current_case__": 0, "filter_pif": "True", "reporter_pif": "0.75"}, "iso_labels": {"__current_case__": 4, "labeling": "tmt11plex"}, "select_quant_method": "reporter_ion_ms2"}, "variableModifications": ["Oxidation (M)"]}]
            protein_quant	{"lfq_opts": {"advancedSiteIntensities": true, "do_ibaq": {"__current_case__": 1, "ibaq": "False"}, "lfqRequireMsms": true, "lfqStabilizeLargeRatios": true, "separateLfq": false}, "only_unmod_prot": {"__current_case__": 0, "discard_unmod_cpart_peptides": true, "mods_used_prot_quant": ["Oxidation (M)"], "unmod_prot": "True"}, "peptides_for_quantification": "1"}
            qc	{"__current_case__": 1, "do_it": "false"}
            search_opts	{"calc_peak_properties": false, "decoy_mode": "revert", "incl_contaminants": false, "max_pep_length": "50", "max_peptide_mass": "4600", "mbr": {"__current_case__": 1, "alignment_ion_mobility_window": "1", "alignment_time_window": "20", "match_between_runs": "True", "match_unidentified_features": false, "matching_ion_mobility_window": "0.05", "matching_time_window": "0.7"}, "min_pep_length": "8", "min_peptide_len": "8", "min_unique_pep": "0", "protein_fdr": "0.01", "psm_fdr": "0.01", "template": {"values": [{"id": 2, "src": "hda"}]}}

  • Other invocation details

    • error_message

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

    • history_id

      • 4b795d26518fb5c6

    • history_state

      • error

    • invocation_id

      • 4b795d26518fb5c6

    • invocation_state

      • scheduled

    • workflow_id

      • 4b795d26518fb5c6