15 Sep 2022 19:28:18,555 INFO : Copying experiment "The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector" from folder /Sainsbury Lab - TSL Proteomics/Yu et al.,2022 to /Panorama Public/2022/Sainsbury Lab TSL Proteomics - Yu et al.,2022
15 Sep 2022 19:28:18,555 INFO : =======================================
15 Sep 2022 19:28:18,622 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
15 Sep 2022 19:28:18,622 INFO :
15 Sep 2022 19:28:18,622 INFO : Exporting experiment.
15 Sep 2022 19:30:13,218 INFO : Exporting files metadata.
15 Sep 2022 19:30:13,218 DEBUG: [/Sainsbury Lab - TSL Proteomics/Yu et al.,2022] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury Lab TSL Proteomics - Yu et al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export
15 Sep 2022 19:30:13,221 INFO :
15 Sep 2022 19:30:13,221 INFO : Experiment export completed successfully.
15 Sep 2022 19:30:13,221 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
15 Sep 2022 19:30:13,251 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
15 Sep 2022 19:30:13,251 INFO :
15 Sep 2022 19:30:13,251 INFO : Importing experiment.
15 Sep 2022 19:30:13,253 DEBUG: [/Panorama Public/2022/Sainsbury Lab TSL Proteomics - Yu et al.,2022] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury Lab TSL Proteomics - Yu et al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export
15 Sep 2022 19:30:13,255 INFO : Loading folder properties (folder type, settings and active modules)
15 Sep 2022 19:30:13,255 DEBUG: [/Panorama Public/2022/Sainsbury Lab TSL Proteomics - Yu et al.,2022] Folder type: Targeted MS
15 Sep 2022 19:30:13,255 DEBUG: [/Panorama Public/2022/Sainsbury Lab TSL Proteomics - Yu et al.,2022] Active modules: API, TargetedMS, Wiki, Announcements, Issues, MS2, PanoramaPublic, Query, Internal, FileContent, Experiment, Pipeline, Core, Search, Assay
15 Sep 2022 19:30:13,341 INFO : Done importing folder properties (folder type, settings and active modules)
15 Sep 2022 19:30:13,342 INFO : Loading container specific module properties
15 Sep 2022 19:30:13,353 INFO : Done importing container specific module properties
15 Sep 2022 19:30:13,355 INFO : Loading etl definitions
15 Sep 2022 19:30:13,357 INFO : Loading wikis
15 Sep 2022 19:30:13,359 INFO : 0 wikis imported
15 Sep 2022 19:30:13,359 INFO : Done importing wikis
15 Sep 2022 19:30:13,359 INFO : Starting to copy files
15 Sep 2022 19:31:37,590 INFO : Copied 36 files
15 Sep 2022 19:31:37,590 INFO : Ensuring exp.data rows exist for imported files
15 Sep 2022 19:31:37,743 INFO : Starting Sample Type and Data Class import
15 Sep 2022 19:31:37,743 INFO : No types XAR file to process.
15 Sep 2022 19:31:37,743 INFO : Finished importing Sample Types and Data Classes
15 Sep 2022 19:31:37,744 INFO : Loading xar
15 Sep 2022 19:31:42,277 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip'
15 Sep 2022 19:31:42,280 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip.Core'
15 Sep 2022 19:31:42,282 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip.Output'
15 Sep 2022 19:31:42,282 DEBUG: Protocol import complete
15 Sep 2022 19:31:42,284 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-10719:The+Arabidopsis+E3+ubiquitin+ligase+PUB4+regulates+BIK1+and+is+targeted+by+a+bacterial+type-III+effector'
15 Sep 2022 19:31:42,284 DEBUG: Experiment/Run group import complete
15 Sep 2022 19:31:42,297 DEBUG: Protocol action set import complete
15 Sep 2022 19:31:42,308 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip'
15 Sep 2022 19:31:42,318 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-10719:9a08dbf2-15af-103b-adec-fea6ddf58494'
15 Sep 2022 19:31:42,323 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-10719:9a08dad6-15af-103b-adec-fea6ddf58494'
15 Sep 2022 19:31:42,323 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip.Core'
15 Sep 2022 19:31:42,326 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10719:TargetedMS.ImportSkyZip.Output'
15 Sep 2022 19:31:42,326 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-10719:9a08dc23-15af-103b-adec-fea6ddf58494'
15 Sep 2022 19:31:42,329 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15/PUB4_PRM_02_refined_for_EMBO.skyd into the system
15 Sep 2022 19:31:42,329 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15/PUB4_PRM_02_refined_for_EMBO.skyd into the system
15 Sep 2022 19:31:42,329 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip into the system
15 Sep 2022 19:31:42,330 INFO : Starting import from PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip
15 Sep 2022 19:31:42,334 INFO : Starting to import Skyline document from PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip
15 Sep 2022 19:31:42,343 INFO : Expanding TAIR10.protdb
15 Sep 2022 19:31:49,927 INFO : Expanding PUB4_PRM_02_refined_for_EMBO.blib
15 Sep 2022 19:31:50,354 INFO : Expanding PUB4_PRM_02_refined_for_EMBO.redundant.blib
15 Sep 2022 19:31:52,260 INFO : Expanding PUB4_all.blib
15 Sep 2022 19:31:52,274 INFO : Expanding PUB4_all.redundant.blib
15 Sep 2022 19:31:52,301 INFO : Expanding PUB4_PRM_02_refined_for_EMBO.skyd
15 Sep 2022 19:31:52,544 INFO : Expanding PUB4_PRM_02_refined_for_EMBO.sky.view
15 Sep 2022 19:31:52,544 INFO : Expanding PUB4_PRM_02_refined_for_EMBO.sky
15 Sep 2022 19:31:52,563 INFO : 4% Done
15 Sep 2022 19:31:52,997 DEBUG: Starting to load chromatogram headers
15 Sep 2022 19:31:53,002 DEBUG: Done loading chromatogram headers
15 Sep 2022 19:31:53,204 INFO : Inserting Library Peptides
15 Sep 2022 19:31:53,213 INFO : 8% Done
15 Sep 2022 19:31:53,275 INFO : 11% Done
15 Sep 2022 19:31:53,327 INFO : 14% Done
15 Sep 2022 19:31:53,375 INFO : 17% Done
15 Sep 2022 19:31:53,418 INFO : 20% Done
15 Sep 2022 19:31:53,475 INFO : 24% Done
15 Sep 2022 19:31:53,536 INFO : 27% Done
15 Sep 2022 19:31:53,598 INFO : 30% Done
15 Sep 2022 19:31:53,641 INFO : 33% Done
15 Sep 2022 19:31:53,691 INFO : 36% Done
15 Sep 2022 19:31:53,740 DEBUG: Total peptides inserted: 11
15 Sep 2022 19:31:53,741 INFO : Inserting AT2G23140.1
15 Sep 2022 19:31:53,759 INFO : 39% Done
15 Sep 2022 19:31:53,806 INFO : 42% Done
15 Sep 2022 19:31:53,849 INFO : 45% Done
15 Sep 2022 19:31:53,892 INFO : 48% Done
15 Sep 2022 19:31:53,933 INFO : 51% Done
15 Sep 2022 19:31:53,974 INFO : 54% Done
15 Sep 2022 19:31:54,019 INFO : 56% Done
15 Sep 2022 19:31:54,054 INFO : 59% Done
15 Sep 2022 19:31:54,094 INFO : 62% Done
15 Sep 2022 19:31:54,137 INFO : 65% Done
15 Sep 2022 19:31:54,175 INFO : 68% Done
15 Sep 2022 19:31:54,214 INFO : 71% Done
15 Sep 2022 19:31:54,254 INFO : 74% Done
15 Sep 2022 19:31:54,298 INFO : 76% Done
15 Sep 2022 19:31:54,341 INFO : 79% Done
15 Sep 2022 19:31:54,403 INFO : 82% Done
15 Sep 2022 19:31:54,442 INFO : 85% Done
15 Sep 2022 19:31:54,481 INFO : 88% Done
15 Sep 2022 19:31:54,522 INFO : 92% Done
15 Sep 2022 19:31:54,558 INFO : 93% Done
15 Sep 2022 19:31:54,581 INFO : 95% Done
15 Sep 2022 19:31:54,616 INFO : 98% Done
15 Sep 2022 19:31:54,648 DEBUG: Total peptides inserted: 22
15 Sep 2022 19:31:54,648 INFO : Done parsing Skyline document.
15 Sep 2022 19:31:54,649 INFO : Creating and populating temp tables for Proportion values
15 Sep 2022 19:31:54,689 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
15 Sep 2022 19:31:54,719 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
15 Sep 2022 19:31:54,740 INFO : Cleaning up temp tables
15 Sep 2022 19:31:55,006 INFO : Completed import of Skyline document from PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip
15 Sep 2022 19:31:55,008 INFO : 100% Done
15 Sep 2022 19:31:55,012 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip into the system
15 Sep 2022 19:31:55,018 INFO : Done importing xar
15 Sep 2022 19:31:55,020 INFO : Loading pages and webpart properties
15 Sep 2022 19:31:55,103 INFO : Done importing 4 page(s) with 6 webpart(s)
15 Sep 2022 19:31:55,104 INFO : Starting Sample Status Data import
15 Sep 2022 19:31:55,104 INFO : No sample types XAR file to process.
15 Sep 2022 19:31:55,104 INFO : Finished importing Sample Status Data
15 Sep 2022 19:31:55,109 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
15 Sep 2022 19:31:55,111 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping
15 Sep 2022 19:31:55,112 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping
15 Sep 2022 19:31:55,112 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping
15 Sep 2022 19:31:55,112 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
15 Sep 2022 19:31:55,112 INFO : Importing files metadata.
15 Sep 2022 19:31:55,112 DEBUG: [/Panorama Public/2022/Sainsbury Lab TSL Proteomics - Yu et al.,2022] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury Lab TSL Proteomics - Yu et al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export
15 Sep 2022 19:31:55,114 INFO :
15 Sep 2022 19:31:55,114 INFO : Experiment import completed successfully.
15 Sep 2022 19:31:55,114 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
15 Sep 2022 19:31:55,138 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
15 Sep 2022 19:31:55,138 INFO :
15 Sep 2022 19:31:55,138 INFO : Checking for library folders.
15 Sep 2022 19:31:55,140 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
15 Sep 2022 19:31:55,165 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
15 Sep 2022 19:31:55,165 INFO :
15 Sep 2022 19:31:55,165 INFO : Finishing up experiment copy.
15 Sep 2022 19:31:55,167 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
15 Sep 2022 19:31:55,167 INFO : Setting version on new experiment to 1
15 Sep 2022 19:31:55,167 INFO : Assigning a ProteomeXchange ID.
15 Sep 2022 19:31:55,584 INFO : Assigning a DOI.
15 Sep 2022 19:31:56,462 INFO : Assigned DOI: 10.6069/m997-a291
15 Sep 2022 19:31:56,466 INFO : Updating access URL to point to the new copy of the data.
15 Sep 2022 19:31:56,471 INFO : Removing copy permissions given to Panorama Public
15 Sep 2022 19:31:56,482 INFO : Adding read permissions to all users that are folder admins in the source folder.
15 Sep 2022 19:31:56,490 INFO : Updating the 'Raw Data' tab configuration
15 Sep 2022 19:31:56,492 INFO : Updating dataFileUrls for run PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip; targetedms run ID 144814
15 Sep 2022 19:31:56,493 INFO : Updating dataFileUrl...
15 Sep 2022 19:31:56,493 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15/PUB4_PRM_02_refined_for_EMBO.skyd
15 Sep 2022 19:31:56,493 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022/@files/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15/PUB4_PRM_02_refined_for_EMBO.skyd
15 Sep 2022 19:31:56,495 INFO : Updating dataFileUrl...
15 Sep 2022 19:31:56,495 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022_e2ae50a4-1794-103b-adec-fea6ddf58494/_temp__2022-09-15_19-28-17/export/xar/experiments_and_runs.xar.exploded/Run142649/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip
15 Sep 2022 19:31:56,495 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Yu%20et%20al.,2022/@files/PUB4_PRM_02_refined_for_EMBO_2022-09-13_17-31-15.sky.zip
15 Sep 2022 19:31:56,502 INFO : Creating a reviewer account.
15 Sep 2022 19:31:56,738 INFO : Created reviewer with email: User panorama+reviewer145@proteinms.net
15 Sep 2022 19:31:56,747 INFO : Hiding the Data Pipeline tab.
15 Sep 2022 19:31:56,751 INFO : Updating Submission. Setting copiedExperimentId to 1506
15 Sep 2022 19:31:56,827 INFO : Emailing submitter.
15 Sep 2022 19:31:56,919 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'