07 Feb 2021 20:27:59,292 INFO : Copying experiment "Shadow ORFs illuminated:  long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection" from folder /BayBioMS/Kreitmeier_OLG_PSE to /Panorama Public/2021/BayBioMS - Kreitmeier_OLG_PSE
07 Feb 2021 20:27:59,292 INFO : =======================================
07 Feb 2021 20:27:59,522 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
07 Feb 2021 20:27:59,523 INFO : 
07 Feb 2021 20:27:59,523 INFO : Exporting experiment.
07 Feb 2021 20:35:50,674 INFO : 
07 Feb 2021 20:35:50,674 INFO : Experiment export completed successfully.
07 Feb 2021 20:35:50,674 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
07 Feb 2021 20:35:50,850 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
07 Feb 2021 20:35:50,850 INFO : 
07 Feb 2021 20:35:50,851 INFO : Importing experiment.
07 Feb 2021 20:35:50,898 INFO : Loading folder properties (folder type, settings and active modules)
07 Feb 2021 20:35:51,272 INFO : Done importing folder properties (folder type, settings and active modules)
07 Feb 2021 20:35:51,279 INFO : Loading etl definitions
07 Feb 2021 20:35:51,286 INFO : Loading wikis
07 Feb 2021 20:35:51,332 INFO : 0 wikis imported
07 Feb 2021 20:35:51,332 INFO : Done importing wikis
07 Feb 2021 20:35:51,333 INFO : Starting to copy files
07 Feb 2021 20:37:56,373 INFO : 25 files copied, now copying BBM_332_P110_C04_PRM_030.raw
07 Feb 2021 20:40:01,277 INFO : 35 files copied, now copying BBM_332_P110_C04_PRM_016.raw
07 Feb 2021 20:42:03,241 INFO : 44 files copied, now copying BBM_332_P110_C04_PRM_005.raw
07 Feb 2021 20:42:58,178 INFO : Copied 49 files
07 Feb 2021 20:42:58,178 INFO : Ensuring exp.data rows exist for imported files
07 Feb 2021 20:42:59,543 INFO : Loading xar
07 Feb 2021 20:43:06,045 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip'
07 Feb 2021 20:43:06,048 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip.Core'
07 Feb 2021 20:43:06,051 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip.Output'
07 Feb 2021 20:43:06,051 DEBUG: Protocol import complete
07 Feb 2021 20:43:06,090 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8200:Shadow+ORFs+illuminated%3A++long+overlapping+genes+in+Pseudomonas+aeruginosa+are+translated+and+under+purifying+selection'
07 Feb 2021 20:43:06,090 DEBUG: Experiment/Run group import complete
07 Feb 2021 20:43:06,140 DEBUG: Protocol action set import complete
07 Feb 2021 20:43:06,153 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip'
07 Feb 2021 20:43:06,360 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8200:32e4b6d3-4b71-1039-9674-3013bb9b91fd'
07 Feb 2021 20:43:06,372 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8200:32e4b62d-4b71-1039-9674-3013bb9b91fd'
07 Feb 2021 20:43:06,372 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip.Core'
07 Feb 2021 20:43:06,379 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8200:TargetedMS.ImportSkyZip.Output'
07 Feb 2021 20:43:06,381 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8200:32e4b7ae-4b71-1039-9674-3013bb9b91fd'
07 Feb 2021 20:43:06,384 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40/OLG_PSE_PRM.skyd into the system
07 Feb 2021 20:43:06,385 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40/OLG_PSE_PRM.skyd into the system
07 Feb 2021 20:43:06,385 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip into the system
07 Feb 2021 20:43:06,388 INFO : Starting import from OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip
07 Feb 2021 20:43:06,415 INFO : Starting to import Skyline document from OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip
07 Feb 2021 20:43:06,430 INFO : Expanding Background_proteome_OLG_PAO1.protdb
07 Feb 2021 20:43:07,390 INFO : Expanding OLG_publication.blib
07 Feb 2021 20:43:07,521 INFO : Expanding OLG_publication.redundant.blib
07 Feb 2021 20:43:13,186 INFO : Expanding OLG_PSE_PRM.skyd
07 Feb 2021 20:43:13,327 INFO : Expanding OLG_PSE_PRM.sky.view
07 Feb 2021 20:43:13,328 INFO : Expanding OLG_PSE_PRM.sky
07 Feb 2021 20:43:13,339 INFO : Expanding OLG_PSE_PRM.skyl
07 Feb 2021 20:43:13,539 INFO : 4% Done
07 Feb 2021 20:43:13,690 DEBUG: Starting to load chromatogram headers
07 Feb 2021 20:43:13,693 DEBUG: Done loading chromatogram headers
07 Feb 2021 20:43:14,180 INFO : Inserting OLG1
07 Feb 2021 20:43:14,226 INFO : 10% Done
07 Feb 2021 20:43:15,531 INFO : 15% Done
07 Feb 2021 20:43:16,229 INFO : 20% Done
07 Feb 2021 20:43:16,749 INFO : 25% Done
07 Feb 2021 20:43:17,458 DEBUG: Total peptides inserted: 4
07 Feb 2021 20:43:17,459 INFO : Inserting PA0260
07 Feb 2021 20:43:17,492 INFO : 29% Done
07 Feb 2021 20:43:18,067 INFO : 34% Done
07 Feb 2021 20:43:18,803 INFO : 39% Done
07 Feb 2021 20:43:19,319 INFO : 44% Done
07 Feb 2021 20:43:19,901 DEBUG: Total peptides inserted: 4
07 Feb 2021 20:43:19,902 INFO : Inserting OLG2
07 Feb 2021 20:43:19,915 INFO : 49% Done
07 Feb 2021 20:43:20,798 DEBUG: Total peptides inserted: 1
07 Feb 2021 20:43:20,798 INFO : Inserting PA1383
07 Feb 2021 20:43:20,813 INFO : 54% Done
07 Feb 2021 20:43:21,537 INFO : 58% Done
07 Feb 2021 20:43:21,884 INFO : 63% Done
07 Feb 2021 20:43:22,459 INFO : 68% Done
07 Feb 2021 20:43:22,942 INFO : 72% Done
07 Feb 2021 20:43:23,346 DEBUG: Total peptides inserted: 5
07 Feb 2021 20:43:23,346 INFO : Inserting Procal_iRT
07 Feb 2021 20:43:23,379 INFO : 74% Done
07 Feb 2021 20:43:23,523 INFO : 76% Done
07 Feb 2021 20:43:23,700 INFO : 78% Done
07 Feb 2021 20:43:23,883 INFO : 80% Done
07 Feb 2021 20:43:24,113 INFO : 82% Done
07 Feb 2021 20:43:24,321 INFO : 85% Done
07 Feb 2021 20:43:24,467 INFO : 87% Done
07 Feb 2021 20:43:24,628 INFO : 89% Done
07 Feb 2021 20:43:24,812 INFO : 91% Done
07 Feb 2021 20:43:25,029 INFO : 94% Done
07 Feb 2021 20:43:25,196 INFO : 96% Done
07 Feb 2021 20:43:25,370 INFO : 98% Done
07 Feb 2021 20:43:25,530 DEBUG: Total peptides inserted: 12
07 Feb 2021 20:43:25,541 INFO : Done parsing Skyline document.
07 Feb 2021 20:43:29,249 INFO : Creating and populating temp tables for Proportion values
07 Feb 2021 20:43:29,344 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
07 Feb 2021 20:43:30,324 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
07 Feb 2021 20:43:30,446 INFO : Cleaning up temp tables
07 Feb 2021 20:43:30,468 INFO : Completed import of Skyline document from OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip
07 Feb 2021 20:43:30,476 INFO : 100% Done
07 Feb 2021 20:43:30,486 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip into the system
07 Feb 2021 20:43:30,539 INFO : Done importing xar
07 Feb 2021 20:43:30,545 INFO : Loading pages and webpart properties
07 Feb 2021 20:43:30,851 INFO : Done importing pages and webpart properties
07 Feb 2021 20:43:30,852 INFO : 
07 Feb 2021 20:43:30,852 INFO : Experiment import completed successfully.
07 Feb 2021 20:43:30,852 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
07 Feb 2021 20:43:30,954 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
07 Feb 2021 20:43:30,954 INFO : 
07 Feb 2021 20:43:30,954 INFO : Finishing up experiment copy.
07 Feb 2021 20:43:30,968 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
07 Feb 2021 20:43:30,972 INFO : Assigning a ProteomeXchange ID.
07 Feb 2021 20:43:31,830 INFO : Updating access URL to point to the new copy of the data.
07 Feb 2021 20:43:32,012 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
07 Feb 2021 20:43:32,050 INFO : Removing copy permissions given to journal.
07 Feb 2021 20:43:32,265 INFO : Adding read permissions to all users that are folder admins in the source container.
07 Feb 2021 20:43:32,301 INFO : Setting the TargetedMS folder type to 'Experimental Data'
07 Feb 2021 20:43:32,322 INFO : Updating the 'Raw Data' tab configuration
07 Feb 2021 20:43:32,331 INFO : Updating dataFileUrls for run OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip; targetedms run ID 102861
07 Feb 2021 20:43:32,331 INFO : Updating dataFileUrl...
07 Feb 2021 20:43:32,331 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip
07 Feb 2021 20:43:32,332 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Kreitmeier_OLG_PSE/@files/OLG_PSE_PRM_2021-02-07_13-57-40.sky.zip
07 Feb 2021 20:43:32,339 INFO : Updating dataFileUrl...
07 Feb 2021 20:43:32,339 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Kreitmeier_OLG_PSE_589fd415-4bf3-1039-9674-3013bb9b91fd/_temp__2021-02-07_20-27-58/export/xar/experiments_and_runs.xar.exploded/Run100608/OLG_PSE_PRM_2021-02-07_13-57-40/OLG_PSE_PRM.skyd
07 Feb 2021 20:43:32,340 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Kreitmeier_OLG_PSE/@files/OLG_PSE_PRM_2021-02-07_13-57-40/OLG_PSE_PRM.skyd
07 Feb 2021 20:43:32,355 INFO : Making folder public.
07 Feb 2021 20:43:32,397 INFO : Hiding the Data Pipeline tab.
07 Feb 2021 20:43:32,840 INFO : Emailing submitter.
07 Feb 2021 20:43:33,582 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'