Copying experiment: The potential link between inflammatory protein markers in stool samples of children with Autism Spectrum Disorder and their sibling

EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP

Job Status

Created: 2024-10-01 15:48:38
Modified: 2024-10-01 15:49:19
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: The potential link between inflammatory protein markers in stool samples of children with Autism Spectrum Disorder and their sibling
File Path: /data/labkey/files/Panorama Public/2024/EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP/@files/Experiment_2006.log
Files: Experiment_2006.log
Completed Runs: Osredkar IJHPP QC peptides.sky.zip
Osredkar IJHPP proteomics.sky.zip

Log File


01 Oct 2024 15:48:38,658 INFO : Copying experiment "The potential link between inflammatory protein markers in stool samples of children with Autism Spectrum Disorder and their sibling" from folder /EIRENE-CZ - Biomarker Analytical Laboratories/AJS 6495A/Osredkar J. et al. IJHPP to /Panorama Public/2024/EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP
01 Oct 2024 15:48:38,658 INFO : =======================================
01 Oct 2024 15:48:38,695 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
01 Oct 2024 15:48:38,695 INFO :
01 Oct 2024 15:48:38,695 INFO : Exporting experiment.
01 Oct 2024 15:48:56,701 INFO : Exporting files metadata.
01 Oct 2024 15:48:56,708 INFO :
01 Oct 2024 15:48:56,708 INFO : Experiment export completed successfully.
01 Oct 2024 15:48:56,708 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
01 Oct 2024 15:48:56,731 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
01 Oct 2024 15:48:56,731 INFO :
01 Oct 2024 15:48:56,731 INFO : Importing experiment.
01 Oct 2024 15:48:56,734 INFO : Loading folder properties (folder type, settings and active modules)
01 Oct 2024 15:48:56,813 INFO : Done importing folder properties (folder type, settings and active modules)
01 Oct 2024 15:48:56,814 INFO : Loading container specific module properties
01 Oct 2024 15:48:56,817 INFO : Done importing container specific module properties
01 Oct 2024 15:48:56,818 INFO : Loading queries
01 Oct 2024 15:48:56,821 INFO : 1 query imported
01 Oct 2024 15:48:56,821 INFO : Done importing queries
01 Oct 2024 15:48:56,822 INFO : Loading etl definitions
01 Oct 2024 15:48:56,823 INFO : Loading wikis
01 Oct 2024 15:48:56,825 INFO : 0 wikis imported
01 Oct 2024 15:48:56,825 INFO : Done importing wikis
01 Oct 2024 15:48:56,826 INFO : Starting Data Class Importer
01 Oct 2024 15:48:56,827 INFO : No types XAR file to process.
01 Oct 2024 15:48:56,827 INFO : Finished Data Class Importer
01 Oct 2024 15:48:56,827 INFO : Starting to copy files
01 Oct 2024 15:48:56,827 INFO : Copied 0 files
01 Oct 2024 15:48:56,827 INFO : Ensuring exp.data rows exist for imported files
01 Oct 2024 15:48:56,896 INFO : Starting Sample Type Importer
01 Oct 2024 15:48:56,896 INFO : No types XAR file to process.
01 Oct 2024 15:48:56,896 INFO : Finished Sample Type Importer
01 Oct 2024 15:48:56,898 INFO : Loading xar
01 Oct 2024 15:49:00,277 INFO : Starting import from Osredkar IJHPP QC peptides.sky.zip
01 Oct 2024 15:49:00,280 INFO : Starting to import Skyline document from Osredkar IJHPP QC peptides.sky.zip
01 Oct 2024 15:49:00,281 INFO : Expanding QC.skyd
01 Oct 2024 15:49:00,335 INFO : Expanding QC.sky.view
01 Oct 2024 15:49:00,336 INFO : Expanding QC.sky
01 Oct 2024 15:49:00,337 INFO : Reading Skyline file, QC.sky, to determine if the TransitionChromInfos in the document should be stored...
01 Oct 2024 15:49:00,339 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
01 Oct 2024 15:49:00,341 INFO : 8% Done
01 Oct 2024 15:49:00,509 INFO : Inserting P01009
01 Oct 2024 15:49:00,513 INFO : 20% Done
01 Oct 2024 15:49:00,525 INFO : 29% Done
01 Oct 2024 15:49:00,532 INFO : Inserting P0DJI8
01 Oct 2024 15:49:00,534 INFO : 38% Done
01 Oct 2024 15:49:00,543 INFO : 48% Done
01 Oct 2024 15:49:00,552 INFO : 58% Done
01 Oct 2024 15:49:00,559 INFO : Inserting P0DJI9
01 Oct 2024 15:49:00,561 INFO : 71% Done
01 Oct 2024 15:49:00,569 INFO : Inserting P19652
01 Oct 2024 15:49:00,571 INFO : 80% Done
01 Oct 2024 15:49:00,578 INFO : Inserting P35542
01 Oct 2024 15:49:00,580 INFO : 90% Done
01 Oct 2024 15:49:00,588 INFO : 98% Done
01 Oct 2024 15:49:00,595 INFO : Done parsing Skyline document.
01 Oct 2024 15:49:00,596 INFO : Creating and populating temp tables for Proportion values
01 Oct 2024 15:49:00,602 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
01 Oct 2024 15:49:00,607 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
01 Oct 2024 15:49:00,610 INFO : Cleaning up temp tables
01 Oct 2024 15:49:00,928 INFO : Completed import of Skyline document from Osredkar IJHPP QC peptides.sky.zip
01 Oct 2024 15:49:00,930 INFO : 100% Done
01 Oct 2024 15:49:00,936 INFO : Starting import from Osredkar IJHPP proteomics.sky.zip
01 Oct 2024 15:49:00,938 INFO : Starting to import Skyline document from Osredkar IJHPP proteomics.sky.zip
01 Oct 2024 15:49:00,939 INFO : Expanding Josko patients.skyd
01 Oct 2024 15:49:02,861 INFO : Expanding Josko patients.sky.view
01 Oct 2024 15:49:02,863 INFO : Expanding Josko patients.sky
01 Oct 2024 15:49:02,913 INFO : Reading Skyline file, Josko patients.sky, to determine if the TransitionChromInfos in the document should be stored...
01 Oct 2024 15:49:02,987 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
01 Oct 2024 15:49:02,992 INFO : 1% Done
01 Oct 2024 15:49:04,147 INFO : Inserting P69905 hemoglobin
01 Oct 2024 15:49:04,174 INFO : 6% Done
01 Oct 2024 15:49:04,589 INFO : 10% Done
01 Oct 2024 15:49:04,999 INFO : 14% Done
01 Oct 2024 15:49:05,401 INFO : 18% Done
01 Oct 2024 15:49:05,783 INFO : Inserting P01876
01 Oct 2024 15:49:05,809 INFO : 22% Done
01 Oct 2024 15:49:06,181 INFO : Inserting P01877
01 Oct 2024 15:49:06,207 INFO : 25% Done
01 Oct 2024 15:49:06,585 INFO : Inserting P01876/P01877
01 Oct 2024 15:49:06,612 INFO : 29% Done
01 Oct 2024 15:49:07,018 INFO : 33% Done
01 Oct 2024 15:49:07,398 INFO : Inserting P01009
01 Oct 2024 15:49:07,425 INFO : 37% Done
01 Oct 2024 15:49:07,829 INFO : Inserting P05109
01 Oct 2024 15:49:07,862 INFO : 41% Done
01 Oct 2024 15:49:08,286 INFO : 45% Done
01 Oct 2024 15:49:08,660 INFO : Inserting P12724
01 Oct 2024 15:49:08,689 INFO : 49% Done
01 Oct 2024 15:49:09,086 INFO : Inserting P06702
01 Oct 2024 15:49:09,114 INFO : 53% Done
01 Oct 2024 15:49:09,531 INFO : 57% Done
01 Oct 2024 15:49:09,910 INFO : Inserting P10153
01 Oct 2024 15:49:09,937 INFO : 61% Done
01 Oct 2024 15:49:10,337 INFO : Inserting P05164
01 Oct 2024 15:49:10,365 INFO : 65% Done
01 Oct 2024 15:49:10,787 INFO : 69% Done
01 Oct 2024 15:49:11,171 INFO : Inserting zonulin
01 Oct 2024 15:49:11,198 INFO : 74% Done
01 Oct 2024 15:49:11,615 INFO : 77% Done
01 Oct 2024 15:49:12,006 INFO : Inserting iFABP
01 Oct 2024 15:49:12,035 INFO : 81% Done
01 Oct 2024 15:49:12,456 INFO : 85% Done
01 Oct 2024 15:49:12,838 INFO : Inserting occludin
01 Oct 2024 15:49:12,865 INFO : 90% Done
01 Oct 2024 15:49:13,279 INFO : 94% Done
01 Oct 2024 15:49:13,690 INFO : 98% Done
01 Oct 2024 15:49:14,083 INFO : Done parsing Skyline document.
01 Oct 2024 15:49:14,085 INFO : Creating and populating temp tables for Proportion values
01 Oct 2024 15:49:14,113 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
01 Oct 2024 15:49:14,578 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
01 Oct 2024 15:49:14,744 INFO : Cleaning up temp tables
01 Oct 2024 15:49:15,132 INFO : Completed import of Skyline document from Osredkar IJHPP proteomics.sky.zip
01 Oct 2024 15:49:15,135 INFO : 100% Done
01 Oct 2024 15:49:15,149 INFO : Done importing xar
01 Oct 2024 15:49:15,151 INFO : Loading pages and webpart properties
01 Oct 2024 15:49:15,218 INFO : Done importing 3 page(s) with 4 webpart(s)
01 Oct 2024 15:49:15,218 INFO : Loading File Browser config
01 Oct 2024 15:49:15,218 INFO : Done importing File Browser config
01 Oct 2024 15:49:15,219 INFO : Starting Sample Status Data import
01 Oct 2024 15:49:15,220 INFO : No sample types XAR file to process.
01 Oct 2024 15:49:15,220 INFO : Finished importing Sample Status Data
01 Oct 2024 15:49:15,225 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
01 Oct 2024 15:49:15,228 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
01 Oct 2024 15:49:15,228 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
01 Oct 2024 15:49:15,229 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
01 Oct 2024 15:49:15,229 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
01 Oct 2024 15:49:15,229 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
01 Oct 2024 15:49:15,232 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
01 Oct 2024 15:49:15,240 INFO : Moving files to folder /Panorama Public/2024/EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP and creating symlinks
01 Oct 2024 15:49:15,873 INFO : Aligning data files urls in folder: /Panorama Public/2024/EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP
01 Oct 2024 15:49:15,884 INFO : Importing files metadata.
01 Oct 2024 15:49:15,886 INFO :
01 Oct 2024 15:49:15,886 INFO : Experiment import completed successfully.
01 Oct 2024 15:49:15,886 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
01 Oct 2024 15:49:15,912 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
01 Oct 2024 15:49:15,912 INFO :
01 Oct 2024 15:49:15,912 INFO : Checking for library folders.
01 Oct 2024 15:49:15,914 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
01 Oct 2024 15:49:15,933 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
01 Oct 2024 15:49:15,933 INFO :
01 Oct 2024 15:49:15,933 INFO : Finishing up experiment copy.
01 Oct 2024 15:49:15,935 INFO : Updating TargetedMS experiment entry in target folder /Panorama Public/2024/EIRENE-CZ Biomarker Analytical Laboratories - Osredkar J. et al. IJHPP
01 Oct 2024 15:49:15,936 INFO : Setting version on new experiment to 1
01 Oct 2024 15:49:15,938 INFO : Updating permanent link to point to the new copy of the data.
01 Oct 2024 15:49:15,966 INFO : Removing copy permissions given to Panorama Public
01 Oct 2024 15:49:15,969 INFO : Adding read permissions to all users that are folder admins in the source folder.
01 Oct 2024 15:49:15,970 INFO : Assigning ReaderRole to eliska.benesova@recetox.muni.cz
01 Oct 2024 15:49:15,970 INFO : Assigning ReaderRole to elliott.james.price@gmail.com
01 Oct 2024 15:49:15,970 INFO : Assigning ReaderRole to veronika.vidova@recetox.muni.cz
01 Oct 2024 15:49:15,970 INFO : Assigning ReaderRole to stepan.koudelka@recetox.muni.cz
01 Oct 2024 15:49:15,970 INFO : Assigning PanoramaPublicSubmitterRole to elliott.james.price@gmail.com
01 Oct 2024 15:49:15,970 INFO : Assigning PanoramaPublicSubmitterRole to veronika.vidova@recetox.muni.cz
01 Oct 2024 15:49:15,979 INFO : User elliott.james.price@gmail.com is already a member of group Panorama Public Submitters
01 Oct 2024 15:49:15,979 INFO : Adding user veronika.vidova@recetox.muni.cz to group Panorama Public Submitters
01 Oct 2024 15:49:15,980 INFO : Updating the 'Raw Data' tab configuration
01 Oct 2024 15:49:15,982 INFO : Creating a reviewer account.
01 Oct 2024 15:49:16,052 INFO : Created reviewer with email: panorama+reviewer293@proteinms.net
01 Oct 2024 15:49:16,052 INFO : Generating password.
01 Oct 2024 15:49:16,186 INFO : Set reviewer password successfully.
01 Oct 2024 15:49:16,195 INFO : Adding user panorama+reviewer293@proteinms.net to group Reviewers
01 Oct 2024 15:49:16,196 INFO : Hiding the Data Pipeline tab.
01 Oct 2024 15:49:16,201 INFO : Updating Submission. Setting copiedExperimentId to 1917
01 Oct 2024 15:49:18,392 INFO : Assigning a ProteomeXchange ID.
01 Oct 2024 15:49:18,612 INFO : Assigned ProteomeXchange ID: PXD056435
01 Oct 2024 15:49:18,612 INFO : Assigning a DOI.
01 Oct 2024 15:49:19,174 INFO : Assigned DOI: 10.6069/y9hr-js96
01 Oct 2024 15:49:19,294 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'