09 Jul 2021 07:13:44,822 INFO : Copying experiment "Optimized liquid and gas phase fractionations increase HLA-peptidome coverage for primary cell and tissue samples" from folder /Carr/HLA_Melanoma_TSQQuantiva to /Panorama Public/2021/Carr - HLA_Melanoma_TSQQuantiva
09 Jul 2021 07:13:44,823 INFO : =======================================
09 Jul 2021 07:13:44,914 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
09 Jul 2021 07:13:44,914 INFO :
09 Jul 2021 07:13:44,915 INFO : Exporting experiment.
09 Jul 2021 07:13:46,633 INFO :
09 Jul 2021 07:13:46,633 INFO : Experiment export completed successfully.
09 Jul 2021 07:13:46,633 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
09 Jul 2021 07:13:46,680 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
09 Jul 2021 07:13:46,680 INFO :
09 Jul 2021 07:13:46,680 INFO : Importing experiment.
09 Jul 2021 07:13:46,685 INFO : Loading folder properties (folder type, settings and active modules)
09 Jul 2021 07:13:46,751 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jul 2021 07:13:46,753 INFO : Loading etl definitions
09 Jul 2021 07:13:46,755 INFO : Loading wikis
09 Jul 2021 07:13:46,758 INFO : 0 wikis imported
09 Jul 2021 07:13:46,758 INFO : Done importing wikis
09 Jul 2021 07:13:46,758 INFO : Starting to copy files
09 Jul 2021 07:13:47,519 INFO : Copied 26 files
09 Jul 2021 07:13:47,519 INFO : Ensuring exp.data rows exist for imported files
09 Jul 2021 07:13:47,704 INFO : Starting Sample Type and Data Class import
09 Jul 2021 07:13:47,705 INFO : No types XAR file to process.
09 Jul 2021 07:13:47,705 INFO : Finished importing Sample Types and Data Classes
09 Jul 2021 07:13:47,708 INFO : Loading xar
09 Jul 2021 07:13:47,740 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip'
09 Jul 2021 07:13:47,743 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip.Core'
09 Jul 2021 07:13:47,745 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip.Output'
09 Jul 2021 07:13:47,745 DEBUG: Protocol import complete
09 Jul 2021 07:13:47,747 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8844:Optimized+liquid+and+gas+phase+fractionations+increase+HLA-peptidome+coverage+for+primary+cell+and+tissue+samples'
09 Jul 2021 07:13:47,747 DEBUG: Experiment/Run group import complete
09 Jul 2021 07:13:47,757 DEBUG: Protocol action set import complete
09 Jul 2021 07:13:47,784 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip'
09 Jul 2021 07:13:47,793 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8844:84c4b3d2-c260-1039-b76f-fea6ddf5767a'
09 Jul 2021 07:13:47,797 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8844:84c4b3c3-c260-1039-b76f-fea6ddf5767a'
09 Jul 2021 07:13:47,798 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip.Core'
09 Jul 2021 07:13:47,801 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8844:TargetedMS.ImportSkyZip.Output'
09 Jul 2021 07:13:47,801 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8844:84c4b3d6-c260-1039-b76f-fea6ddf5767a'
09 Jul 2021 07:13:47,802 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20/HLA_NeoAntg_HL_Mel6_PeptideYIH.skyd into the system
09 Jul 2021 07:13:47,803 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20/HLA_NeoAntg_HL_Mel6_PeptideYIH.skyd into the system
09 Jul 2021 07:13:47,803 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip into the system
09 Jul 2021 07:13:47,805 INFO : Starting import from HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip
09 Jul 2021 07:13:47,808 INFO : Starting to import Skyline document from HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip
09 Jul 2021 07:13:47,810 INFO : Expanding HLA_NuOrfs.optdb
09 Jul 2021 07:13:47,810 INFO : Expanding HLA_NeoAntg_HL_Mel6_PeptideYIH.skyd
09 Jul 2021 07:13:47,818 INFO : Expanding HLA_NeoAntg_HL_Mel6_PeptideYIH.sky.view
09 Jul 2021 07:13:47,818 INFO : Expanding HLA_NeoAntg_HL_Mel6_PeptideYIH.sky
09 Jul 2021 07:13:47,829 INFO : 44% Done
09 Jul 2021 07:13:47,840 DEBUG: Starting to load chromatogram headers
09 Jul 2021 07:13:47,840 DEBUG: Done loading chromatogram headers
09 Jul 2021 07:13:47,857 INFO : Inserting 13240-011_NCEH1_p.G147R
09 Jul 2021 07:13:47,862 INFO : 80% Done
09 Jul 2021 07:13:47,887 DEBUG: Total peptides inserted: 1
09 Jul 2021 07:13:47,888 INFO : Done parsing Skyline document.
09 Jul 2021 07:13:47,890 INFO : No group comparisons found.
09 Jul 2021 07:13:47,890 INFO : Calculating calibration curves
09 Jul 2021 07:13:47,891 DEBUG: Calculating calibration curve for 13240-011_NCEH1_p.G147R, 1 of 1
09 Jul 2021 07:13:47,904 INFO : 98% Done
09 Jul 2021 07:13:47,905 INFO : Done calculating calibration curves.
09 Jul 2021 07:13:47,906 INFO : Creating and populating temp tables for Proportion values
09 Jul 2021 07:13:47,917 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jul 2021 07:13:47,918 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jul 2021 07:13:47,919 INFO : Cleaning up temp tables
09 Jul 2021 07:13:48,118 INFO : Completed import of Skyline document from HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip
09 Jul 2021 07:13:48,122 INFO : 100% Done
09 Jul 2021 07:13:48,126 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip into the system
09 Jul 2021 07:13:48,133 INFO : Done importing xar
09 Jul 2021 07:13:48,135 INFO : Loading pages and webpart properties
09 Jul 2021 07:13:48,198 INFO : Done importing pages and webpart properties
09 Jul 2021 07:13:48,198 INFO :
09 Jul 2021 07:13:48,198 INFO : Experiment import completed successfully.
09 Jul 2021 07:13:48,198 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
09 Jul 2021 07:13:48,227 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
09 Jul 2021 07:13:48,227 INFO :
09 Jul 2021 07:13:48,227 INFO : Finishing up experiment copy.
09 Jul 2021 07:13:48,229 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
09 Jul 2021 07:13:48,231 INFO : Copying ProteomeXchange ID from the previous copy of the data.
09 Jul 2021 07:13:48,231 INFO : Copying DOI from the previous copy of the data.
09 Jul 2021 07:13:48,234 INFO : Updating access URL to point to the new copy of the data.
09 Jul 2021 07:13:48,239 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
09 Jul 2021 07:13:48,240 INFO : Removing copy permissions given to journal.
09 Jul 2021 07:13:48,251 INFO : Adding read permissions to all users that are folder admins in the source container.
09 Jul 2021 07:13:48,252 INFO : Adding read permissions to all users that had read access to previous copy.
09 Jul 2021 07:13:48,260 INFO : Setting the TargetedMS folder type to 'Experimental Data'
09 Jul 2021 07:13:48,268 INFO : Updating the 'Raw Data' tab configuration
09 Jul 2021 07:13:48,270 INFO : Updating dataFileUrls for run HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip; targetedms run ID 115824
09 Jul 2021 07:13:48,270 INFO : Updating dataFileUrl...
09 Jul 2021 07:13:48,270 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip
09 Jul 2021 07:13:48,270 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Carr%20-%20HLA_Melanoma_TSQQuantiva/@files/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip
09 Jul 2021 07:13:48,274 INFO : Updating dataFileUrl...
09 Jul 2021 07:13:48,274 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Carr%20-%20HLA_Melanoma_TSQQuantiva_37160849-c2ec-1039-b76f-fea6ddf5767a/_temp__2021-07-09_07-13-44/export/xar/experiments_and_runs.xar.exploded/Run113277/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20/HLA_NeoAntg_HL_Mel6_PeptideYIH.skyd
09 Jul 2021 07:13:48,274 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Carr%20-%20HLA_Melanoma_TSQQuantiva/@files/HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20/HLA_NeoAntg_HL_Mel6_PeptideYIH.skyd
09 Jul 2021 07:13:48,277 INFO : Hiding the Data Pipeline tab.
09 Jul 2021 07:13:48,481 INFO : Emailing submitter.
09 Jul 2021 07:13:48,664 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'