Galaxy Tool Error Report
Error Localization
| Dataset | 128537196 (f9cad7b01a47213591554cf62bef75f3) |
|---|---|
| History | 11033459 (bbd44e69cb8906b5610647652733cf85) |
| Failed Job | 104: Peptide Shaker on data 84, data 85, and others: mzidentML file (f9cad7b01a4721356cc5399fe311e3dc) |
User Provided Information
The user ‘lliburd23@email.mmc.edu’ provided the following information:
So I have 12 proteomic samples that I processed on SearchGUI using the ommsa, ms-gf+, xtandem, and myrimatch. This generated .xml, .omx, and .mzid files for each sample. I then uploaded my SearchGUI identification files with the .par file so the software knows the parameters I did the search on. Originally it was a zip file that I converted to a searchgui_archive type file by editing the datatype. I then uploaded the corresponding fasta file used and the mzmL files associated with all samples. Can I get some help of how to get this software to successfully process my files? Below are the details of my issues. Details Execution resulted in the following messages: Fatal error: Exit code 2 (Job Failed) Tool generated the following standard error: error: End-of-centdir-64 signature not where expected (prepended bytes?) (attempting to process anyway) warning [searchgui_input.zip]: 270608575 extra bytes at beginning or within zipfile (attempting to process anyway) file #1: bad zipfile offset (local header sig): 270608657 (attempting to re-compensate) Detected Common Potential Problems The tool was started with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices.
Detailed Job Information
Job environment and execution information is available at the job info page.
| Job ID | 68499136 (bbd44e69cb8906b514b459e63f71a340) |
|---|---|
| Tool ID | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1 |
| Tool Version | 2.0.33+galaxy1 |
| Job PID or DRM id | 68499136 |
| Job Tool Version |
Job Execution and Failure Information
Command Line
mkdir output_reports && cwd=pwd && export HOME=$cwd && ln -s ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_c427e7c8-a996-4f3c-a46a-ce90335aa977.dat’ searchgui_input.zip && unzip -o searchgui_input.zip *.par && mv *.par SEARCHGUI_IdentificationParameters.par && cp ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_32cdddeb-c4d1-4bc4-9d62-a530cb327271.dat’ ‘./input_fasta_file.fasta’ && mkdir peaklist_input_files && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_5b18fc95-bae4-4a46-90dd-12dfb174262d.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_04-09-2025_Hum-gel_LNCaP_E1.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_c480c2d1-a000-42ae-ab75-5b5a8c62eff4.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_04-09-2025_Hum-gel_LNCaP_E2.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_3940733b-088f-4b8c-b349-e129cb66a80f.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_04-09-2025_Hum-gel_LNCaP_E3.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_c0a31644-715e-40de-8cf0-a1b055ca394f.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s1.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_8fec7268-ac92-461c-bf9e-bdd7db93ad65.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s2.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_0c4f635a-282c-4ff1-a80c-3253f62a833c.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s3.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_0e5bf74b-3448-4e9e-9f33-45dc130566a5.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s4.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_83ede142-0dd3-41de-9341-b19fd2c128dc.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s5.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_c99cc7a8-07f2-4c89-9365-f47a1bb77da4.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s6.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_50d8eb93-1358-4d7f-99a2-70795ee22d1c.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s10.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_5475190f-377d-4b43-98f2-e8ab097438cb.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s11.mzML.mzml’ && ln -s -f ‘/jetstream2/scratch/main/jobs/68499136/inputs/dataset_6607d6ae-21b4-4516-97df-07364b901a90.dat’ ‘peaklist_input_files/SPratap-Lincoln_SG_08-21-2024_Hum-gel_ex2-s12.mzML.mzml’ && peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI -gui 0 -temp_folder $cwd/PeptideShakerCLI -use_log_folder 0 -reference ‘Galaxy_Experiment_2025061710151750173347’ -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -fasta_file ‘./input_fasta_file.fasta’ -spectrum_files $cwd/peaklist_input_files -threads “${GALAXY_SLOTS:-12}” -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name “Proteomics” -contact_last_name “Galaxy” -contact_email “galaxyp@umn.edu” -contact_address “galaxyp@umn.edu” -organization_name “University of Minnesota” -organization_email “galaxyp@umn.edu” -organization_address “Minneapolis, MN 55455, Vereinigte Staaten” -out_reports $cwd/output_reports -reports 6,9,1 | grep -v “resources/conf/paths.txt (Permission denied)” && find $cwd/output_reports -name ‘*Default_Hierarchical_Report.txt’ -exec bash -c ‘mv “$0” “hierarchical.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”’ {} ; && true
stderr
error: End-of-centdir-64 signature not where expected (prepended bytes?) (attempting to process anyway) warning [searchgui_input.zip]: 270608575 extra bytes at beginning or within zipfile (attempting to process anyway) file #1: bad zipfile offset (local header sig): 270608657 (attempting to re-compensate)
stdout
Archive: searchgui_input.zip inflating: LNCaP_searchgui_out/PEAKS Settings.par
Job Information
None
Job Traceback
None
