21 Jun 2021 20:37:19,863 INFO : Copying experiment "Targeted Detection of SARS-CoV-2 Protein Variants by Mass Spectrometry" from folder /Mayo Clinic - Pandey Lab/Targeted Detection of SARS-CoV-2 Protein Variants to /Panorama Public/2021/Mayo Clinic Pandey Lab - Targeted Detection of SARS-CoV-2 Protein Variants
21 Jun 2021 20:37:19,863 INFO : =======================================
21 Jun 2021 20:37:19,950 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
21 Jun 2021 20:37:19,950 INFO : 
21 Jun 2021 20:37:19,950 INFO : Exporting experiment.
21 Jun 2021 20:37:21,395 INFO : 
21 Jun 2021 20:37:21,395 INFO : Experiment export completed successfully.
21 Jun 2021 20:37:21,396 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
21 Jun 2021 20:37:21,433 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
21 Jun 2021 20:37:21,433 INFO : 
21 Jun 2021 20:37:21,433 INFO : Importing experiment.
21 Jun 2021 20:37:21,437 INFO : Loading folder properties (folder type, settings and active modules)
21 Jun 2021 20:37:21,514 INFO : Done importing folder properties (folder type, settings and active modules)
21 Jun 2021 20:37:21,520 INFO : Loading etl definitions
21 Jun 2021 20:37:21,522 INFO : Loading wikis
21 Jun 2021 20:37:21,529 INFO : 1 wiki imported
21 Jun 2021 20:37:21,529 INFO : Done importing wikis
21 Jun 2021 20:37:21,529 INFO : Starting to copy files
21 Jun 2021 20:37:21,903 INFO : Copied 13 files
21 Jun 2021 20:37:21,903 INFO : Ensuring exp.data rows exist for imported files
21 Jun 2021 20:37:22,121 INFO : Starting Sample Type and Data Class import
21 Jun 2021 20:37:22,122 INFO : No types XAR file to process.
21 Jun 2021 20:37:22,122 INFO : Finished importing Sample Types and Data Classes
21 Jun 2021 20:37:22,124 INFO : Loading xar
21 Jun 2021 20:37:22,188 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip'
21 Jun 2021 20:37:22,190 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Core'
21 Jun 2021 20:37:22,192 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Output'
21 Jun 2021 20:37:22,193 DEBUG: Protocol import complete
21 Jun 2021 20:37:22,194 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8745:Targeted+Detection+of+SARS-CoV-2+Protein+Variants+by+Mass+Spectrometry'
21 Jun 2021 20:37:22,194 DEBUG: Experiment/Run group import complete
21 Jun 2021 20:37:22,203 DEBUG: Protocol action set import complete
21 Jun 2021 20:37:22,227 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip'
21 Jun 2021 20:37:22,241 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8745:9a4a6637-b4dc-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,246 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8745:d22820cb-b4de-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,246 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Core'
21 Jun 2021 20:37:22,248 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Output'
21 Jun 2021 20:37:22,249 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8745:d2282381-b4de-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,264 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip'
21 Jun 2021 20:37:22,270 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8745:9a4a669c-b4dc-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,274 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8745:d22823a5-b4de-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,275 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Core'
21 Jun 2021 20:37:22,277 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8745:TargetedMS.ImportSkyZip.Output'
21 Jun 2021 20:37:22,277 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8745:d2282508-b4de-1039-be5b-fea6ddf5138a'
21 Jun 2021 20:37:22,278 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants.sky.zip into the system
21 Jun 2021 20:37:22,280 INFO : Starting import from Mutants.sky.zip
21 Jun 2021 20:37:22,285 INFO : Starting to import Skyline document from Mutants.sky.zip
21 Jun 2021 20:37:22,286 INFO : Expanding Mutants.skyd
21 Jun 2021 20:37:22,300 INFO : Expanding Mutants.sky.view
21 Jun 2021 20:37:22,301 INFO : Expanding Mutants.sky
21 Jun 2021 20:37:22,309 INFO : Expanding Mutants.skyl
21 Jun 2021 20:37:22,358 WARN : The version of this Skyline document is 20.22. This is newer than the highest supported version 20.2
21 Jun 2021 20:37:22,366 INFO : 2% Done
21 Jun 2021 20:37:22,397 DEBUG: Starting to load chromatogram headers
21 Jun 2021 20:37:22,398 DEBUG: Done loading chromatogram headers
21 Jun 2021 20:37:22,475 INFO : Inserting peptides1
21 Jun 2021 20:37:22,532 INFO : 18% Done
21 Jun 2021 20:37:23,088 INFO : 45% Done
21 Jun 2021 20:37:23,827 INFO : 62% Done
21 Jun 2021 20:37:24,222 INFO : 80% Done
21 Jun 2021 20:37:24,508 DEBUG: Total peptides inserted: 4
21 Jun 2021 20:37:24,509 INFO : Done parsing Skyline document.
21 Jun 2021 20:37:24,516 INFO : No group comparisons found.
21 Jun 2021 20:37:24,516 INFO : Calculating calibration curves
21 Jun 2021 20:37:24,516 DEBUG: Calculating calibration curve for peptides1, 1 of 1
21 Jun 2021 20:37:25,087 INFO : 98% Done
21 Jun 2021 20:37:25,090 INFO : Done calculating calibration curves.
21 Jun 2021 20:37:54,598 INFO : Creating and populating temp tables for Proportion values
21 Jun 2021 20:37:54,610 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
21 Jun 2021 20:37:54,625 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
21 Jun 2021 20:37:54,632 INFO : Cleaning up temp tables
21 Jun 2021 20:37:54,853 INFO : Completed import of Skyline document from Mutants.sky.zip
21 Jun 2021 20:37:54,856 INFO : 100% Done
21 Jun 2021 20:37:54,860 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants.sky.zip into the system
21 Jun 2021 20:37:54,860 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants/Mutants.skyd into the system
21 Jun 2021 20:37:54,861 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants/Mutants.skyd into the system
21 Jun 2021 20:37:54,861 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221.sky.zip into the system
21 Jun 2021 20:37:54,862 INFO : Starting import from Mutant040221.sky.zip
21 Jun 2021 20:37:54,864 INFO : Starting to import Skyline document from Mutant040221.sky.zip
21 Jun 2021 20:37:54,865 INFO : Expanding Mutant040221.skyd
21 Jun 2021 20:37:54,879 INFO : Expanding Mutant040221.sky.view
21 Jun 2021 20:37:54,880 INFO : Expanding Mutant040221.sky
21 Jun 2021 20:37:54,887 INFO : Expanding Mutant040221.skyl
21 Jun 2021 20:37:54,927 INFO : 2% Done
21 Jun 2021 20:37:54,996 DEBUG: Starting to load chromatogram headers
21 Jun 2021 20:37:54,996 DEBUG: Done loading chromatogram headers
21 Jun 2021 20:37:55,107 INFO : Inserting peptides1
21 Jun 2021 20:37:55,164 INFO : 18% Done
21 Jun 2021 20:37:55,764 INFO : 43% Done
21 Jun 2021 20:37:56,621 INFO : 62% Done
21 Jun 2021 20:37:57,014 INFO : 80% Done
21 Jun 2021 20:37:57,319 DEBUG: Total peptides inserted: 4
21 Jun 2021 20:37:57,319 INFO : Done parsing Skyline document.
21 Jun 2021 20:37:57,323 INFO : No group comparisons found.
21 Jun 2021 20:37:57,323 INFO : Calculating calibration curves
21 Jun 2021 20:37:57,324 DEBUG: Calculating calibration curve for peptides1, 1 of 1
21 Jun 2021 20:37:57,921 INFO : 98% Done
21 Jun 2021 20:37:57,923 INFO : Done calculating calibration curves.
21 Jun 2021 20:38:20,597 INFO : Creating and populating temp tables for Proportion values
21 Jun 2021 20:38:20,608 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
21 Jun 2021 20:38:20,625 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
21 Jun 2021 20:38:20,633 INFO : Cleaning up temp tables
21 Jun 2021 20:38:20,845 INFO : Completed import of Skyline document from Mutant040221.sky.zip
21 Jun 2021 20:38:20,848 INFO : 100% Done
21 Jun 2021 20:38:20,851 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221.sky.zip into the system
21 Jun 2021 20:38:20,851 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221/Mutant040221.skyd into the system
21 Jun 2021 20:38:20,852 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221/Mutant040221.skyd into the system
21 Jun 2021 20:38:20,862 INFO : Done importing xar
21 Jun 2021 20:38:20,864 INFO : Loading pages and webpart properties
21 Jun 2021 20:38:20,928 INFO : Done importing pages and webpart properties
21 Jun 2021 20:38:20,928 INFO : 
21 Jun 2021 20:38:20,928 INFO : Experiment import completed successfully.
21 Jun 2021 20:38:20,928 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
21 Jun 2021 20:38:20,965 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
21 Jun 2021 20:38:20,965 INFO : 
21 Jun 2021 20:38:20,965 INFO : Finishing up experiment copy.
21 Jun 2021 20:38:20,967 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
21 Jun 2021 20:38:20,970 INFO : Assigning a DOI.
21 Jun 2021 20:38:22,646 INFO : Assigned DOI: 10.6069/v57r-fk13
21 Jun 2021 20:38:22,650 INFO : Updating access URL to point to the new copy of the data.
21 Jun 2021 20:38:22,654 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
21 Jun 2021 20:38:22,655 INFO : Removing copy permissions given to journal.
21 Jun 2021 20:38:22,667 INFO : Adding read permissions to all users that are folder admins in the source container.
21 Jun 2021 20:38:22,674 INFO : Setting the TargetedMS folder type to 'Experimental Data'
21 Jun 2021 20:38:22,682 INFO : Updating the 'Raw Data' tab configuration
21 Jun 2021 20:38:22,684 INFO : Updating dataFileUrls for run Mutants.sky.zip; targetedms run ID 114175
21 Jun 2021 20:38:22,685 INFO : Updating dataFileUrl...
21 Jun 2021 20:38:22,685 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants.sky.zip
21 Jun 2021 20:38:22,686 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants/@files/Mutants.sky.zip
21 Jun 2021 20:38:22,688 INFO : Updating dataFileUrl...
21 Jun 2021 20:38:22,689 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111933/Mutants/Mutants.skyd
21 Jun 2021 20:38:22,690 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants/@files/Mutants/Mutants.skyd
21 Jun 2021 20:38:22,695 INFO : Updating dataFileUrls for run Mutant040221.sky.zip; targetedms run ID 114176
21 Jun 2021 20:38:22,695 INFO : Updating dataFileUrl...
21 Jun 2021 20:38:22,695 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221/Mutant040221.skyd
21 Jun 2021 20:38:22,695 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants/@files/Mutant040221/Mutant040221.skyd
21 Jun 2021 20:38:22,697 INFO : Updating dataFileUrl...
21 Jun 2021 20:38:22,697 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants_ab59f92a-b537-1039-be5b-fea6ddf5138a/_temp__2021-06-21_20-37-19/export/xar/experiments_and_runs.xar.exploded/Run111934/Mutant040221.sky.zip
21 Jun 2021 20:38:22,697 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Mayo%20Clinic%20Pandey%20Lab%20-%20Targeted%20Detection%20of%20SARS-CoV-2%20Protein%20Variants/@files/Mutant040221.sky.zip
21 Jun 2021 20:38:22,699 INFO : Creating a reviewer account.
21 Jun 2021 20:38:22,905 INFO : Created reviewer with email: User panorama+reviewer41@proteinms.net
21 Jun 2021 20:38:22,913 INFO : Hiding the Data Pipeline tab.
21 Jun 2021 20:38:23,013 INFO : Emailing submitter.
21 Jun 2021 20:38:23,130 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'