01 Jul 2021 16:03:20,773 INFO : Copying experiment "Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification" from folder /Ehime HBFP/ALACAT to /Panorama Public/2021/Ehime HBFP - ALACAT

01 Jul 2021 16:03:20,773 INFO : =======================================

01 Jul 2021 16:03:21,011 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

01 Jul 2021 16:03:21,011 INFO : 

01 Jul 2021 16:03:21,011 INFO : Exporting experiment.

01 Jul 2021 16:03:21,362 INFO : 

01 Jul 2021 16:03:21,362 INFO : Experiment export completed successfully.

01 Jul 2021 16:03:21,362 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

01 Jul 2021 16:03:21,435 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

01 Jul 2021 16:03:21,435 INFO : 

01 Jul 2021 16:03:21,435 INFO : Importing experiment.

01 Jul 2021 16:03:21,440 INFO : Loading folder properties (folder type, settings and active modules)

01 Jul 2021 16:03:21,522 INFO : Done importing folder properties (folder type, settings and active modules)

01 Jul 2021 16:03:21,525 INFO : Loading etl definitions

01 Jul 2021 16:03:21,528 INFO : Loading wikis

01 Jul 2021 16:03:21,529 INFO : 0 wikis imported

01 Jul 2021 16:03:21,529 INFO : Done importing wikis

01 Jul 2021 16:03:21,529 INFO : Starting to copy files

01 Jul 2021 16:03:21,584 INFO : Copied 9 files

01 Jul 2021 16:03:21,585 INFO : Ensuring exp.data rows exist for imported files

01 Jul 2021 16:03:21,672 INFO : Starting Sample Type and Data Class import

01 Jul 2021 16:03:21,673 INFO : No types XAR file to process.

01 Jul 2021 16:03:21,673 INFO : Finished importing Sample Types and Data Classes

01 Jul 2021 16:03:21,676 INFO : Loading xar

01 Jul 2021 16:03:21,704 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip'

01 Jul 2021 16:03:21,707 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip.Core'

01 Jul 2021 16:03:21,710 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip.Output'

01 Jul 2021 16:03:21,710 DEBUG: Protocol import complete

01 Jul 2021 16:03:21,713 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8803:Synthetic+biology+meets+proteomics%3A+Construction+of+%C3%A0+la+carte+QconCATs+for+absolute+protein+quantification'

01 Jul 2021 16:03:21,713 DEBUG: Experiment/Run group import complete

01 Jul 2021 16:03:21,726 DEBUG: Protocol action set import complete

01 Jul 2021 16:03:21,740 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip'

01 Jul 2021 16:03:21,752 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8803:904d3dbb-bb87-1039-b76f-fea6ddf5767a'

01 Jul 2021 16:03:21,759 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8803:904d3ee2-bb87-1039-b76f-fea6ddf5767a'

01 Jul 2021 16:03:21,759 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip.Core'

01 Jul 2021 16:03:21,763 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8803:TargetedMS.ImportSkyZip.Output'

01 Jul 2021 16:03:21,764 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8803:904d3eec-bb87-1039-b76f-fea6ddf5767a'

01 Jul 2021 16:03:21,766 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT.sky.zip into the system

01 Jul 2021 16:03:21,767 INFO : Starting import from ALACAT.sky.zip

01 Jul 2021 16:03:21,772 INFO : Starting to import Skyline document from ALACAT.sky.zip

01 Jul 2021 16:03:21,773 INFO : Expanding ALA201.blib

01 Jul 2021 16:03:21,774 INFO : Expanding ALACAT.skyd

01 Jul 2021 16:03:21,777 INFO : Expanding ALACAT.sky.view

01 Jul 2021 16:03:21,777 INFO : Expanding ALACAT.sky

01 Jul 2021 16:03:21,788 INFO : 18% Done

01 Jul 2021 16:03:21,789 DEBUG: Starting to load chromatogram headers

01 Jul 2021 16:03:21,790 DEBUG: Done loading chromatogram headers

01 Jul 2021 16:03:21,811 INFO : 45% Done

01 Jul 2021 16:03:21,813 INFO : Inserting ALACAT B1

01 Jul 2021 16:03:21,823 INFO : 68% Done

01 Jul 2021 16:03:21,849 INFO : 98% Done

01 Jul 2021 16:03:21,864 DEBUG: Total peptides inserted: 2

01 Jul 2021 16:03:21,865 INFO : Done parsing Skyline document.

01 Jul 2021 16:03:21,867 INFO : Creating and populating temp tables for Proportion values

01 Jul 2021 16:03:21,881 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

01 Jul 2021 16:03:21,883 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

01 Jul 2021 16:03:21,884 INFO : Cleaning up temp tables

01 Jul 2021 16:03:22,108 INFO : Completed import of Skyline document from ALACAT.sky.zip

01 Jul 2021 16:03:22,112 INFO : 100% Done

01 Jul 2021 16:03:22,116 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT.sky.zip into the system

01 Jul 2021 16:03:22,116 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT/ALACAT.skyd into the system

01 Jul 2021 16:03:22,116 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT/ALACAT.skyd into the system

01 Jul 2021 16:03:22,124 INFO : Done importing xar

01 Jul 2021 16:03:22,126 INFO : Loading pages and webpart properties

01 Jul 2021 16:03:22,214 INFO : Done importing pages and webpart properties

01 Jul 2021 16:03:22,215 INFO : 

01 Jul 2021 16:03:22,215 INFO : Experiment import completed successfully.

01 Jul 2021 16:03:22,215 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

01 Jul 2021 16:03:22,276 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

01 Jul 2021 16:03:22,276 INFO : 

01 Jul 2021 16:03:22,276 INFO : Finishing up experiment copy.

01 Jul 2021 16:03:22,277 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

01 Jul 2021 16:03:22,279 INFO : Assigning a ProteomeXchange ID.

01 Jul 2021 16:03:24,356 INFO : Assigning a DOI.

01 Jul 2021 16:03:25,584 INFO : Assigned DOI: 10.6069/gsa8-dw81

01 Jul 2021 16:03:25,589 INFO : Updating access URL to point to the new copy of the data.

01 Jul 2021 16:03:25,595 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.

01 Jul 2021 16:03:25,597 INFO : Removing copy permissions given to journal.

01 Jul 2021 16:03:25,604 INFO : Adding read permissions to all users that are folder admins in the source container.

01 Jul 2021 16:03:25,610 INFO : Setting the TargetedMS folder type to 'Experimental Data'

01 Jul 2021 16:03:25,612 INFO : Updating the 'Raw Data' tab configuration

01 Jul 2021 16:03:25,614 INFO : Updating dataFileUrls for run ALACAT.sky.zip; targetedms run ID 115000

01 Jul 2021 16:03:25,615 INFO : Updating dataFileUrl...

01 Jul 2021 16:03:25,615 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT.sky.zip

01 Jul 2021 16:03:25,615 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Ehime%20HBFP%20-%20ALACAT/@files/ALACAT.sky.zip

01 Jul 2021 16:03:25,617 INFO : Updating dataFileUrl...

01 Jul 2021 16:03:25,617 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Ehime%20HBFP%20-%20ALACAT_dc7f8e7c-bced-1039-b76f-fea6ddf5767a/_temp__2021-07-01_16-03-20/export/xar/experiments_and_runs.xar.exploded/Run112310/ALACAT/ALACAT.skyd

01 Jul 2021 16:03:25,617 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Ehime%20HBFP%20-%20ALACAT/@files/ALACAT/ALACAT.skyd

01 Jul 2021 16:03:25,620 INFO : Creating a reviewer account.

01 Jul 2021 16:03:25,847 INFO : Created reviewer with email: User panorama+reviewer44@proteinms.net

01 Jul 2021 16:03:25,854 INFO : Hiding the Data Pipeline tab.

01 Jul 2021 16:03:25,997 INFO : Emailing submitter.

01 Jul 2021 16:03:26,101 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'