19 Jul 2021 20:02:28,235 INFO : Copying experiment "The metabolome as a biomarker of aging in Drosophila melanogaster" from folder /MacCoss/Collaborations/Promislow lab/The metabolome as a biomarker of aging in Drosophila melanogaster/SRM_Data-The metabolome as a biomarker of aging in Drosophila melanogaster to /Panorama Public/2021/MacCoss - SRM_Data-The metabolome as a biomarker of aging in Drosophila melanogaster
19 Jul 2021 20:02:28,236 INFO : =======================================
19 Jul 2021 20:02:28,590 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
19 Jul 2021 20:02:28,590 INFO :
19 Jul 2021 20:02:28,590 INFO : Exporting experiment.
19 Jul 2021 20:11:30,737 INFO :
19 Jul 2021 20:11:30,737 INFO : Experiment export completed successfully.
19 Jul 2021 20:11:30,737 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
19 Jul 2021 20:11:30,823 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
19 Jul 2021 20:11:30,823 INFO :
19 Jul 2021 20:11:30,824 INFO : Importing experiment.
19 Jul 2021 20:11:30,831 INFO : Loading folder properties (folder type, settings and active modules)
19 Jul 2021 20:11:30,951 INFO : Done importing folder properties (folder type, settings and active modules)
19 Jul 2021 20:11:30,956 INFO : Loading grid views
19 Jul 2021 20:11:30,962 INFO : 1 custom view imported
19 Jul 2021 20:11:30,962 INFO : Done importing grid views
19 Jul 2021 20:11:30,966 INFO : Loading etl definitions
19 Jul 2021 20:11:30,969 INFO : Loading wikis
19 Jul 2021 20:11:30,981 INFO : 1 wiki imported
19 Jul 2021 20:11:30,981 INFO : Done importing wikis
19 Jul 2021 20:11:30,982 INFO : Starting to copy files
19 Jul 2021 20:12:21,835 INFO : Copied 632 files
19 Jul 2021 20:12:21,835 INFO : Ensuring exp.data rows exist for imported files
19 Jul 2021 20:12:26,593 INFO : Starting Sample Type and Data Class import
19 Jul 2021 20:12:26,593 INFO : No types XAR file to process.
19 Jul 2021 20:12:26,594 INFO : Finished importing Sample Types and Data Classes
19 Jul 2021 20:12:26,596 INFO : Loading xar
19 Jul 2021 20:12:29,147 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip'
19 Jul 2021 20:12:29,151 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Core'
19 Jul 2021 20:12:29,154 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Output'
19 Jul 2021 20:12:29,155 DEBUG: Protocol import complete
19 Jul 2021 20:12:29,158 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8877:The+metabolome+as+a+biomarker+of+aging+in+Drosophila+melanogaster'
19 Jul 2021 20:12:29,158 DEBUG: Experiment/Run group import complete
19 Jul 2021 20:12:29,174 DEBUG: Protocol action set import complete
19 Jul 2021 20:12:29,201 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip'
19 Jul 2021 20:12:29,213 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8877:8c306bb7-c8ab-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,219 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8877:8c306b77-c8ab-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,219 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Core'
19 Jul 2021 20:12:29,223 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Output'
19 Jul 2021 20:12:29,224 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8877:8c308352-c8ab-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,241 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip'
19 Jul 2021 20:12:29,247 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8877:24e6ab1c-c8b4-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,251 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8877:24e6ab0d-c8b4-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,251 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Core'
19 Jul 2021 20:12:29,254 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8877:TargetedMS.ImportSkyZip.Output'
19 Jul 2021 20:12:29,254 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8877:24e6ab38-c8b4-1039-b76f-fea6ddf5767a'
19 Jul 2021 20:12:29,258 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13/Promislow_Xiaqing_2019_07.skyd into the system
19 Jul 2021 20:12:29,258 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13/Promislow_Xiaqing_2019_07.skyd into the system
19 Jul 2021 20:12:29,258 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip into the system
19 Jul 2021 20:12:29,260 INFO : Starting import from Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip
19 Jul 2021 20:12:29,265 INFO : Starting to import Skyline document from Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip
19 Jul 2021 20:12:29,316 INFO : Expanding iroa_pos_rp.blib
19 Jul 2021 20:12:29,317 INFO : Expanding Promislow_Xiaqing_2019_07.skyd
19 Jul 2021 20:12:30,663 INFO : Expanding Promislow_Xiaqing_2019_07.sky.view
19 Jul 2021 20:12:30,664 INFO : Expanding Promislow_Xiaqing_2019_07.sky
19 Jul 2021 20:12:30,861 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.2
19 Jul 2021 20:12:30,896 INFO : 1% Done
19 Jul 2021 20:12:32,115 DEBUG: Starting to load chromatogram headers
19 Jul 2021 20:12:32,193 DEBUG: Done loading chromatogram headers
19 Jul 2021 20:12:32,473 INFO : Inserting all_rpPos_iroa
19 Jul 2021 20:12:32,749 INFO : 2% Done
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19 Jul 2021 20:12:39,304 INFO : 23% Done
19 Jul 2021 20:12:39,304 DEBUG: Inserted 50 molecules
19 Jul 2021 20:12:39,596 INFO : 24% Done
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19 Jul 2021 20:12:40,447 INFO : 26% Done
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19 Jul 2021 20:12:45,570 INFO : 45% Done
19 Jul 2021 20:12:45,741 INFO : 46% Done
19 Jul 2021 20:12:45,741 DEBUG: Inserted 100 molecules
19 Jul 2021 20:12:46,066 INFO : 47% Done
19 Jul 2021 20:12:46,205 INFO : 48% Done
19 Jul 2021 20:12:46,824 INFO : 49% Done
19 Jul 2021 20:12:47,054 INFO : 50% Done
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19 Jul 2021 20:12:52,996 INFO : 72% Done
19 Jul 2021 20:12:53,178 INFO : 73% Done
19 Jul 2021 20:12:53,178 DEBUG: Inserted 150 molecules
19 Jul 2021 20:12:53,458 INFO : 74% Done
19 Jul 2021 20:12:54,103 INFO : 75% Done
19 Jul 2021 20:12:54,256 INFO : 76% Done
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19 Jul 2021 20:13:00,051 INFO : 96% Done
19 Jul 2021 20:13:00,143 INFO : 97% Done
19 Jul 2021 20:13:00,277 INFO : 98% Done
19 Jul 2021 20:13:00,544 DEBUG: Total molecules inserted: 199
19 Jul 2021 20:13:00,544 INFO : None of the 103425 TransitionChromInfos in the file were imported because they exceed the limit of 100000
19 Jul 2021 20:15:56,588 INFO : Updated 54766 PrecursorChromInfos with transition chromatogram index information
19 Jul 2021 20:15:56,590 INFO : Done parsing Skyline document.
19 Jul 2021 20:15:56,591 INFO : Creating and populating temp tables for Proportion values
19 Jul 2021 20:15:56,984 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
19 Jul 2021 20:15:59,054 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
19 Jul 2021 20:16:00,257 INFO : Cleaning up temp tables
19 Jul 2021 20:16:00,262 INFO : Completed import of Skyline document from Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip
19 Jul 2021 20:16:00,266 INFO : 100% Done
19 Jul 2021 20:16:00,272 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip into the system
19 Jul 2021 20:16:00,272 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42/TSQ2_2019_0623_RJ.skyd into the system
19 Jul 2021 20:16:00,272 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42/TSQ2_2019_0623_RJ.skyd into the system
19 Jul 2021 20:16:00,273 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip into the system
19 Jul 2021 20:16:00,274 INFO : Starting import from TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip
19 Jul 2021 20:16:00,277 INFO : Starting to import Skyline document from TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip
19 Jul 2021 20:16:00,278 INFO : Expanding TSQ2_2019_0623_RJ.skyd
19 Jul 2021 20:16:00,303 INFO : Expanding TSQ2_2019_0623_RJ.sky.view
19 Jul 2021 20:16:00,303 INFO : Expanding TSQ2_2019_0623_RJ.sky
19 Jul 2021 20:16:00,307 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.2
19 Jul 2021 20:16:00,316 INFO : 4% Done
19 Jul 2021 20:16:00,323 DEBUG: Starting to load chromatogram headers
19 Jul 2021 20:16:00,325 DEBUG: Done loading chromatogram headers
19 Jul 2021 20:16:00,352 INFO : Inserting CIL_aa_pos
19 Jul 2021 20:16:00,357 INFO : 8% Done
19 Jul 2021 20:16:00,374 INFO : 14% Done
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19 Jul 2021 20:16:00,633 INFO : 86% Done
19 Jul 2021 20:16:00,652 INFO : 91% Done
19 Jul 2021 20:16:00,666 DEBUG: Total molecules inserted: 18
19 Jul 2021 20:16:00,666 INFO : Inserting contaminant
19 Jul 2021 20:16:00,671 INFO : 94% Done
19 Jul 2021 20:16:00,685 INFO : 98% Done
19 Jul 2021 20:16:00,697 DEBUG: Total molecules inserted: 2
19 Jul 2021 20:16:00,698 INFO : Done parsing Skyline document.
19 Jul 2021 20:16:00,699 INFO : Creating and populating temp tables for Proportion values
19 Jul 2021 20:16:00,711 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
19 Jul 2021 20:16:00,733 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
19 Jul 2021 20:16:00,748 INFO : Cleaning up temp tables
19 Jul 2021 20:16:00,951 INFO : Completed import of Skyline document from TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip
19 Jul 2021 20:16:00,967 INFO : 100% Done
19 Jul 2021 20:16:00,974 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip into the system
19 Jul 2021 20:16:00,995 INFO : Done importing xar
19 Jul 2021 20:16:00,997 INFO : Loading pages and webpart properties
19 Jul 2021 20:16:01,131 INFO : Done importing pages and webpart properties
19 Jul 2021 20:16:01,132 INFO :
19 Jul 2021 20:16:01,132 INFO : Experiment import completed successfully.
19 Jul 2021 20:16:01,132 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
19 Jul 2021 20:16:01,316 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
19 Jul 2021 20:16:01,316 INFO :
19 Jul 2021 20:16:01,316 INFO : Finishing up experiment copy.
19 Jul 2021 20:16:01,318 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
19 Jul 2021 20:16:01,321 INFO : Assigning a DOI.
19 Jul 2021 20:16:02,356 INFO : Assigned DOI: 10.6069/783p-hz10
19 Jul 2021 20:16:02,361 INFO : Updating access URL to point to the new copy of the data.
19 Jul 2021 20:16:02,368 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
19 Jul 2021 20:16:02,370 INFO : Removing copy permissions given to journal.
19 Jul 2021 20:16:02,380 INFO : Adding read permissions to all users that are folder admins in the source container.
19 Jul 2021 20:16:02,389 INFO : Setting the TargetedMS folder type to 'Experimental Data'
19 Jul 2021 20:16:02,398 INFO : Updating the 'Raw Data' tab configuration
19 Jul 2021 20:16:02,400 INFO : Updating dataFileUrls for run Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip; targetedms run ID 116452
19 Jul 2021 20:16:02,400 INFO : Updating dataFileUrl...
19 Jul 2021 20:16:02,401 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip
19 Jul 2021 20:16:02,401 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster/@files/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13.sky.zip
19 Jul 2021 20:16:02,404 INFO : Updating dataFileUrl...
19 Jul 2021 20:16:02,404 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113770/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13/Promislow_Xiaqing_2019_07.skyd
19 Jul 2021 20:16:02,404 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster/@files/Promislow_Xiaqing_2019_07_2021-07-16_14-35-13/Promislow_Xiaqing_2019_07.skyd
19 Jul 2021 20:16:02,409 INFO : Updating dataFileUrls for run TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip; targetedms run ID 116453
19 Jul 2021 20:16:02,409 INFO : Updating dataFileUrl...
19 Jul 2021 20:16:02,410 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42/TSQ2_2019_0623_RJ.skyd
19 Jul 2021 20:16:02,410 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster/@files/TSQ2_2019_0623_RJ_2021-07-16_15-37-42/TSQ2_2019_0623_RJ.skyd
19 Jul 2021 20:16:02,411 INFO : Updating dataFileUrl...
19 Jul 2021 20:16:02,412 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster_a85237f8-cb34-1039-b76f-fea6ddf5767a/_temp__2021-07-19_20-02-27/export/xar/experiments_and_runs.xar.exploded/Run113774/TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip
19 Jul 2021 20:16:02,412 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SRM_Data-The%20metabolome%20as%20a%20biomarker%20of%20aging%20in%20Drosophila%20melanogaster/@files/TSQ2_2019_0623_RJ_2021-07-16_15-37-42.sky.zip
19 Jul 2021 20:16:02,415 INFO : Creating a reviewer account.
19 Jul 2021 20:16:02,653 INFO : Created reviewer with email: User panorama+reviewer48@proteinms.net
19 Jul 2021 20:16:02,662 INFO : Hiding the Data Pipeline tab.
19 Jul 2021 20:16:02,804 INFO : Emailing submitter.
19 Jul 2021 20:16:02,952 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'