17 Nov 2022 15:58:56,513 INFO : Copying experiment "Effects of alpha-crystallin gene knockout on zebrafish lens development" from folder /OHSU - Proteomics Shared Resource/PSR Projects/Larry David Projects/Posner-Effect of alpha-crystallin KO to /Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO
17 Nov 2022 15:58:56,513 INFO : =======================================
17 Nov 2022 15:58:56,562 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
17 Nov 2022 15:58:56,562 INFO :
17 Nov 2022 15:58:56,563 INFO : Exporting experiment.
17 Nov 2022 15:59:42,048 INFO : Exporting files metadata.
17 Nov 2022 15:59:42,048 DEBUG: [/OHSU - Proteomics Shared Resource/PSR Projects/Larry David Projects/Posner-Effect of alpha-crystallin KO] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export
17 Nov 2022 15:59:42,052 INFO :
17 Nov 2022 15:59:42,052 INFO : Experiment export completed successfully.
17 Nov 2022 15:59:42,052 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
17 Nov 2022 15:59:42,080 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
17 Nov 2022 15:59:42,080 INFO :
17 Nov 2022 15:59:42,080 INFO : Importing experiment.
17 Nov 2022 15:59:42,081 DEBUG: [/Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export
17 Nov 2022 15:59:42,083 INFO : Loading folder properties (folder type, settings and active modules)
17 Nov 2022 15:59:42,083 DEBUG: [/Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO] Folder type: Targeted MS
17 Nov 2022 15:59:42,083 DEBUG: [/Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO] Active modules: Assay, Core, Issues, Search, API, Query, Wiki, TargetedMS, Announcements, MS2, PanoramaPublic, Internal, FileContent, Experiment, Pipeline
17 Nov 2022 15:59:42,158 INFO : Done importing folder properties (folder type, settings and active modules)
17 Nov 2022 15:59:42,160 INFO : Loading container specific module properties
17 Nov 2022 15:59:42,170 INFO : Done importing container specific module properties
17 Nov 2022 15:59:42,173 INFO : Loading grid views
17 Nov 2022 15:59:42,178 INFO : 1 custom view imported
17 Nov 2022 15:59:42,178 INFO : Done importing grid views
17 Nov 2022 15:59:42,180 INFO : Loading etl definitions
17 Nov 2022 15:59:42,181 INFO : Loading wikis
17 Nov 2022 15:59:42,182 INFO : 0 wikis imported
17 Nov 2022 15:59:42,182 INFO : Done importing wikis
17 Nov 2022 15:59:42,182 INFO : Starting to copy files
17 Nov 2022 16:00:17,552 INFO : Copied 24 files
17 Nov 2022 16:00:17,552 INFO : Ensuring exp.data rows exist for imported files
17 Nov 2022 16:00:17,670 INFO : Starting Sample Type and Data Class import
17 Nov 2022 16:00:17,670 INFO : No types XAR file to process.
17 Nov 2022 16:00:17,670 INFO : Finished importing Sample Types and Data Classes
17 Nov 2022 16:00:17,672 INFO : Loading xar
17 Nov 2022 16:00:19,006 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip.Core'
17 Nov 2022 16:00:19,008 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip.Output'
17 Nov 2022 16:00:19,010 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip'
17 Nov 2022 16:00:19,010 DEBUG: Protocol import complete
17 Nov 2022 16:00:19,012 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-10874:Effects+of+alpha-crystallin+gene+knockout+on+zebrafish+lens+development'
17 Nov 2022 16:00:19,012 DEBUG: Experiment/Run group import complete
17 Nov 2022 16:00:19,021 DEBUG: Protocol action set import complete
17 Nov 2022 16:00:19,031 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip'
17 Nov 2022 16:00:19,038 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-10874:52981f8d-4788-103b-9131-fea6ddf592cc'
17 Nov 2022 16:00:19,042 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-10874:52981e5a-4788-103b-9131-fea6ddf592cc'
17 Nov 2022 16:00:19,042 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip.Core'
17 Nov 2022 16:00:19,044 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10874:TargetedMS.ImportSkyZip.Output'
17 Nov 2022 16:00:19,045 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-10874:52981fbb-4788-103b-9131-fea6ddf592cc'
17 Nov 2022 16:00:19,047 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39/alpha_Aa_Ba_Bb_KO_lenses.skyd into the system
17 Nov 2022 16:00:19,048 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39/alpha_Aa_Ba_Bb_KO_lenses.skyd into the system
17 Nov 2022 16:00:19,048 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip into the system
17 Nov 2022 16:00:19,049 INFO : Starting import from alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip
17 Nov 2022 16:00:19,053 INFO : Starting to import Skyline document from alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip
17 Nov 2022 16:00:19,054 INFO : Expanding Uniprot_zebrafish_20220518.protdb
17 Nov 2022 16:00:21,932 INFO : Expanding zebrafish.blib
17 Nov 2022 16:00:21,941 INFO : Expanding zebrafish.redundant.blib
17 Nov 2022 16:00:21,954 INFO : Expanding alpha_Aa_Ba_Bb_KO_lenses.skyd
17 Nov 2022 16:00:21,965 INFO : Expanding alpha_Aa_Ba_Bb_KO_lenses.sky.view
17 Nov 2022 16:00:21,965 INFO : Expanding alpha_Aa_Ba_Bb_KO_lenses.sky
17 Nov 2022 16:00:21,966 INFO : Expanding alpha_Aa_Ba_Bb_KO_lenses.skyl
17 Nov 2022 16:00:21,970 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
17 Nov 2022 16:00:21,979 INFO : 4% Done
17 Nov 2022 16:00:21,984 DEBUG: Starting to load chromatogram headers
17 Nov 2022 16:00:21,984 DEBUG: Done loading chromatogram headers
17 Nov 2022 16:00:22,136 INFO : Inserting tr|A0A0R4IG31|A0A0R4IG31_DANRE
17 Nov 2022 16:00:22,146 INFO : 16% Done
17 Nov 2022 16:00:22,167 INFO : 26% Done
17 Nov 2022 16:00:22,184 INFO : 36% Done
17 Nov 2022 16:00:22,196 DEBUG: Total peptides inserted: 3
17 Nov 2022 16:00:22,198 INFO : 37% Done
17 Nov 2022 16:00:22,198 INFO : Inserting tr|Q8UUZ6|Q8UUZ6_DANRE
17 Nov 2022 16:00:22,208 INFO : 47% Done
17 Nov 2022 16:00:22,225 INFO : 58% Done
17 Nov 2022 16:00:22,243 INFO : 68% Done
17 Nov 2022 16:00:22,254 DEBUG: Total peptides inserted: 3
17 Nov 2022 16:00:22,254 INFO : Inserting tr|Q9PUR2|Q9PUR2_DANRE
17 Nov 2022 16:00:22,265 INFO : 78% Done
17 Nov 2022 16:00:22,283 INFO : 88% Done
17 Nov 2022 16:00:22,301 INFO : 98% Done
17 Nov 2022 16:00:22,314 DEBUG: Total peptides inserted: 3
17 Nov 2022 16:00:22,315 INFO : Done parsing Skyline document.
17 Nov 2022 16:00:22,469 INFO : Creating and populating temp tables for Proportion values
17 Nov 2022 16:00:22,515 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
17 Nov 2022 16:00:22,519 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
17 Nov 2022 16:00:22,523 INFO : Cleaning up temp tables
17 Nov 2022 16:00:22,732 INFO : Completed import of Skyline document from alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip
17 Nov 2022 16:00:22,735 INFO : 100% Done
17 Nov 2022 16:00:22,739 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip into the system
17 Nov 2022 16:00:22,746 INFO : Done importing xar
17 Nov 2022 16:00:22,748 INFO : Loading pages and webpart properties
17 Nov 2022 16:00:22,866 INFO : Done importing 4 page(s) with 9 webpart(s)
17 Nov 2022 16:00:22,867 INFO : Starting Sample Status Data import
17 Nov 2022 16:00:22,868 INFO : No sample types XAR file to process.
17 Nov 2022 16:00:22,868 INFO : Finished importing Sample Status Data
17 Nov 2022 16:00:22,885 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
17 Nov 2022 16:00:22,888 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping
17 Nov 2022 16:00:22,889 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping
17 Nov 2022 16:00:22,889 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping
17 Nov 2022 16:00:22,889 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
17 Nov 2022 16:00:22,889 INFO : Importing files metadata.
17 Nov 2022 16:00:22,889 DEBUG: [/Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export
17 Nov 2022 16:00:22,910 INFO :
17 Nov 2022 16:00:22,910 INFO : Experiment import completed successfully.
17 Nov 2022 16:00:22,910 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
17 Nov 2022 16:00:22,946 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
17 Nov 2022 16:00:22,946 INFO :
17 Nov 2022 16:00:22,946 INFO : Checking for library folders.
17 Nov 2022 16:00:22,948 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
17 Nov 2022 16:00:22,968 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
17 Nov 2022 16:00:22,968 INFO :
17 Nov 2022 16:00:22,968 INFO : Finishing up experiment copy.
17 Nov 2022 16:00:22,976 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
17 Nov 2022 16:00:22,976 INFO : Setting version on new experiment to 2
17 Nov 2022 16:00:22,976 INFO : Copying ProteomeXchange ID from the previous copy of the data.
17 Nov 2022 16:00:22,977 INFO : Copying DOI from the previous copy of the data.
17 Nov 2022 16:00:22,979 INFO : Updating access URL to point to the new copy of the data.
17 Nov 2022 16:00:22,983 INFO : Removing copy permissions given to Panorama Public
17 Nov 2022 16:00:22,992 INFO : Adding read permissions to all users that are folder admins in the source folder.
17 Nov 2022 16:00:22,993 INFO : Adding read permissions to all users that had read access to previous copy.
17 Nov 2022 16:00:23,001 INFO : Updating the 'Raw Data' tab configuration
17 Nov 2022 16:00:23,003 INFO : Updating dataFileUrls for run alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip; targetedms run ID 147877
17 Nov 2022 16:00:23,003 INFO : Updating dataFileUrl...
17 Nov 2022 16:00:23,003 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip
17 Nov 2022 16:00:23,003 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO/@files/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39.sky.zip
17 Nov 2022 16:00:23,005 INFO : Updating dataFileUrl...
17 Nov 2022 16:00:23,005 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO_476524e4-4901-103b-9131-fea6ddf592cc/_temp__2022-11-17_15-58-55/export/xar/experiments_and_runs.xar.exploded/Run145910/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39/alpha_Aa_Ba_Bb_KO_lenses.skyd
17 Nov 2022 16:00:23,005 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/OHSU%20Proteomics%20Shared%20Resource%20-%20Posner-Effect%20of%20alpha-crystallin%20KO/@files/alpha_Aa_Ba_Bb_KO_lenses_2022-11-15_18-58-39/alpha_Aa_Ba_Bb_KO_lenses.skyd
17 Nov 2022 16:00:23,011 INFO : Making folder public.
17 Nov 2022 16:00:23,018 INFO : Hiding the Data Pipeline tab.
17 Nov 2022 16:00:23,023 INFO : Updating Submission. Setting copiedExperimentId to 1529
17 Nov 2022 16:00:23,024 INFO : Deleting old folder /Panorama Public/2022/OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO V.1
17 Nov 2022 16:00:25,938 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'