23 Jul 2021 06:10:11,033 INFO : Copying experiment "Quantification of the ratio between the two PsbO protein isoforms in the thylakoids lumen of Arabidopsis thaliana" from folder /University of Turku - Plant Biology/PsbO to /Panorama Public/2021/University of Turku Plant Biology - PsbO
23 Jul 2021 06:10:11,033 INFO : =======================================
23 Jul 2021 06:10:11,095 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
23 Jul 2021 06:10:11,095 INFO : 
23 Jul 2021 06:10:11,095 INFO : Exporting experiment.
23 Jul 2021 06:10:24,426 INFO : 
23 Jul 2021 06:10:24,426 INFO : Experiment export completed successfully.
23 Jul 2021 06:10:24,426 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
23 Jul 2021 06:10:24,461 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
23 Jul 2021 06:10:24,462 INFO : 
23 Jul 2021 06:10:24,462 INFO : Importing experiment.
23 Jul 2021 06:10:24,468 INFO : Loading folder properties (folder type, settings and active modules)
23 Jul 2021 06:10:24,532 INFO : Done importing folder properties (folder type, settings and active modules)
23 Jul 2021 06:10:24,536 INFO : Loading etl definitions
23 Jul 2021 06:10:24,541 INFO : Loading wikis
23 Jul 2021 06:10:24,543 INFO : 0 wikis imported
23 Jul 2021 06:10:24,544 INFO : Done importing wikis
23 Jul 2021 06:10:24,544 INFO : Starting to copy files
23 Jul 2021 06:10:36,485 INFO : Copied 38 files
23 Jul 2021 06:10:36,485 INFO : Ensuring exp.data rows exist for imported files
23 Jul 2021 06:10:36,714 INFO : Starting Sample Type and Data Class import
23 Jul 2021 06:10:36,715 INFO : No types XAR file to process.
23 Jul 2021 06:10:36,715 INFO : Finished importing Sample Types and Data Classes
23 Jul 2021 06:10:36,718 INFO : Loading xar
23 Jul 2021 06:10:36,733 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip'
23 Jul 2021 06:10:36,738 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip.Core'
23 Jul 2021 06:10:36,742 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip.Output'
23 Jul 2021 06:10:36,742 DEBUG: Protocol import complete
23 Jul 2021 06:10:36,743 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8893:Quantification+of+the+ratio+between+the+two+PsbO+protein+isoforms+in+the+thylakoids+lumen+of+Arabidopsis+thaliana'
23 Jul 2021 06:10:36,743 DEBUG: Experiment/Run group import complete
23 Jul 2021 06:10:36,752 DEBUG: Protocol action set import complete
23 Jul 2021 06:10:36,771 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip'
23 Jul 2021 06:10:36,780 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8893:d12f303f-cdac-1039-b76f-fea6ddf5767a'
23 Jul 2021 06:10:36,786 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8893:d12f3147-cdac-1039-b76f-fea6ddf5767a'
23 Jul 2021 06:10:36,786 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip.Core'
23 Jul 2021 06:10:36,789 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8893:TargetedMS.ImportSkyZip.Output'
23 Jul 2021 06:10:36,790 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8893:d12f316d-cdac-1039-b76f-fea6ddf5767a'
23 Jul 2021 06:10:36,791 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4.sky.zip into the system
23 Jul 2021 06:10:36,793 INFO : Starting import from FL_MAL_PsbO_band_SRM_v4.sky.zip
23 Jul 2021 06:10:36,797 INFO : Starting to import Skyline document from FL_MAL_PsbO_band_SRM_v4.sky.zip
23 Jul 2021 06:10:36,799 INFO : Expanding PsbO_iRT.irtdb
23 Jul 2021 06:10:36,800 INFO : Expanding PsbO_band_min.blib
23 Jul 2021 06:10:36,801 INFO : Expanding PsbO_band_min.redundant.blib
23 Jul 2021 06:10:36,803 INFO : Expanding FL_MAL_PsbO_band_SRM_v4.skyd
23 Jul 2021 06:10:36,806 INFO : Expanding FL_MAL_PsbO_band_SRM_v4.sky.view
23 Jul 2021 06:10:36,807 INFO : Expanding FL_MAL_PsbO_band_SRM_v4.sky
23 Jul 2021 06:10:36,809 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.2
23 Jul 2021 06:10:36,815 INFO : 2% Done
23 Jul 2021 06:10:36,820 DEBUG: Starting to load chromatogram headers
23 Jul 2021 06:10:36,820 DEBUG: Done loading chromatogram headers
23 Jul 2021 06:10:36,869 INFO : 3% Done
23 Jul 2021 06:10:36,872 INFO : Inserting PSBO1
23 Jul 2021 06:10:36,877 INFO : 6% Done
23 Jul 2021 06:10:36,891 INFO : 12% Done
23 Jul 2021 06:10:36,909 INFO : 17% Done
23 Jul 2021 06:10:36,927 INFO : 19% Done
23 Jul 2021 06:10:36,938 INFO : 22% Done
23 Jul 2021 06:10:36,947 INFO : 26% Done
23 Jul 2021 06:10:36,961 INFO : 28% Done
23 Jul 2021 06:10:36,973 INFO : 33% Done
23 Jul 2021 06:10:36,989 INFO : 36% Done
23 Jul 2021 06:10:37,000 INFO : 41% Done
23 Jul 2021 06:10:37,012 DEBUG: Total peptides inserted: 10
23 Jul 2021 06:10:37,015 INFO : Inserting PSBO2
23 Jul 2021 06:10:37,019 INFO : 44% Done
23 Jul 2021 06:10:37,031 INFO : 46% Done
23 Jul 2021 06:10:37,042 INFO : 50% Done
23 Jul 2021 06:10:37,055 INFO : 57% Done
23 Jul 2021 06:10:37,081 INFO : 64% Done
23 Jul 2021 06:10:37,101 INFO : 67% Done
23 Jul 2021 06:10:37,112 INFO : 71% Done
23 Jul 2021 06:10:37,130 INFO : 75% Done
23 Jul 2021 06:10:37,150 INFO : 79% Done
23 Jul 2021 06:10:37,158 DEBUG: Total peptides inserted: 9
23 Jul 2021 06:10:37,160 INFO : Inserting Biognosys|iRT
23 Jul 2021 06:10:37,163 INFO : 81% Done
23 Jul 2021 06:10:37,170 INFO : 83% Done
23 Jul 2021 06:10:37,178 INFO : 85% Done
23 Jul 2021 06:10:37,186 INFO : 87% Done
23 Jul 2021 06:10:37,196 INFO : 91% Done
23 Jul 2021 06:10:37,204 INFO : 93% Done
23 Jul 2021 06:10:37,212 INFO : 95% Done
23 Jul 2021 06:10:37,222 INFO : 97% Done
23 Jul 2021 06:10:37,231 INFO : 98% Done
23 Jul 2021 06:10:37,236 DEBUG: Total peptides inserted: 9
23 Jul 2021 06:10:37,237 INFO : Done parsing Skyline document.
23 Jul 2021 06:10:37,238 INFO : Creating and populating temp tables for Proportion values
23 Jul 2021 06:10:37,248 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
23 Jul 2021 06:10:37,265 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
23 Jul 2021 06:10:37,275 INFO : Cleaning up temp tables
23 Jul 2021 06:10:37,489 INFO : Completed import of Skyline document from FL_MAL_PsbO_band_SRM_v4.sky.zip
23 Jul 2021 06:10:37,492 INFO : 100% Done
23 Jul 2021 06:10:37,496 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4.sky.zip into the system
23 Jul 2021 06:10:37,496 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4/FL_MAL_PsbO_band_SRM_v4.skyd into the system
23 Jul 2021 06:10:37,496 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4/FL_MAL_PsbO_band_SRM_v4.skyd into the system
23 Jul 2021 06:10:37,502 INFO : Done importing xar
23 Jul 2021 06:10:37,504 INFO : Loading pages and webpart properties
23 Jul 2021 06:10:37,567 INFO : Done importing pages and webpart properties
23 Jul 2021 06:10:37,575 INFO : 
23 Jul 2021 06:10:37,575 INFO : Experiment import completed successfully.
23 Jul 2021 06:10:37,575 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
23 Jul 2021 06:10:37,609 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
23 Jul 2021 06:10:37,609 INFO : 
23 Jul 2021 06:10:37,609 INFO : Finishing up experiment copy.
23 Jul 2021 06:10:37,611 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
23 Jul 2021 06:10:37,612 INFO : Assigning a ProteomeXchange ID.
23 Jul 2021 06:10:37,800 INFO : Assigning a DOI.
23 Jul 2021 06:10:39,071 INFO : Assigned DOI: 10.6069/0m11-n039
23 Jul 2021 06:10:39,075 INFO : Updating access URL to point to the new copy of the data.
23 Jul 2021 06:10:39,079 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
23 Jul 2021 06:10:39,080 INFO : Removing copy permissions given to journal.
23 Jul 2021 06:10:39,090 INFO : Adding read permissions to all users that are folder admins in the source container.
23 Jul 2021 06:10:39,097 INFO : Setting the TargetedMS folder type to 'Experimental Data'
23 Jul 2021 06:10:39,103 INFO : Updating the 'Raw Data' tab configuration
23 Jul 2021 06:10:39,105 INFO : Updating dataFileUrls for run FL_MAL_PsbO_band_SRM_v4.sky.zip; targetedms run ID 116790
23 Jul 2021 06:10:39,107 INFO : Updating dataFileUrl...
23 Jul 2021 06:10:39,107 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4.sky.zip
23 Jul 2021 06:10:39,107 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/University%20of%20Turku%20Plant%20Biology%20-%20PsbO/@files/FL_MAL_PsbO_band_SRM_v4.sky.zip
23 Jul 2021 06:10:39,109 INFO : Updating dataFileUrl...
23 Jul 2021 06:10:39,109 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/University%20of%20Turku%20Plant%20Biology%20-%20PsbO_4bdee977-cde4-1039-b76f-fea6ddf5767a/_temp__2021-07-23_06-10-10/export/xar/experiments_and_runs.xar.exploded/Run114266/FL_MAL_PsbO_band_SRM_v4/FL_MAL_PsbO_band_SRM_v4.skyd
23 Jul 2021 06:10:39,109 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/University%20of%20Turku%20Plant%20Biology%20-%20PsbO/@files/FL_MAL_PsbO_band_SRM_v4/FL_MAL_PsbO_band_SRM_v4.skyd
23 Jul 2021 06:10:39,112 INFO : Creating a reviewer account.
23 Jul 2021 06:10:39,351 INFO : Created reviewer with email: User panorama+reviewer50@proteinms.net
23 Jul 2021 06:10:39,359 INFO : Hiding the Data Pipeline tab.
23 Jul 2021 06:10:39,481 INFO : Emailing submitter.
23 Jul 2021 06:10:39,663 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'