28 Apr 2022 16:20:29,127 INFO : Copying experiment "Evaluation of anti-oxidant and anti-inflammatory treatments in Chronic Obstructive Pulmonary Disease" from folder /IIT Bombay - Proteomics/Lab users/Gautam Sharma/MRM_COPD to /Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD
28 Apr 2022 16:20:29,127 INFO : =======================================
28 Apr 2022 16:21:11,229 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
28 Apr 2022 16:21:11,230 INFO :
28 Apr 2022 16:21:11,230 INFO : Exporting experiment.
28 Apr 2022 16:21:38,043 INFO : Exporting files metadata.
28 Apr 2022 16:21:38,043 DEBUG: [/IIT Bombay - Proteomics/Lab users/Gautam Sharma/MRM_COPD] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export
28 Apr 2022 16:21:38,095 INFO :
28 Apr 2022 16:21:38,095 INFO : Experiment export completed successfully.
28 Apr 2022 16:21:38,095 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
28 Apr 2022 16:21:38,233 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
28 Apr 2022 16:21:38,233 INFO :
28 Apr 2022 16:21:38,233 INFO : Importing experiment.
28 Apr 2022 16:21:38,235 DEBUG: [/Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export
28 Apr 2022 16:21:38,276 INFO : Loading folder properties (folder type, settings and active modules)
28 Apr 2022 16:21:38,276 DEBUG: [/Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD] Folder type: Targeted MS
28 Apr 2022 16:21:38,276 DEBUG: [/Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD] Active modules: Experiment, FileContent, Pipeline, PanoramaPublic, Query, Internal, API, Core, Search, MS2, Announcements, Wiki, TargetedMS, Issues, Assay
28 Apr 2022 16:21:38,327 INFO : Done importing folder properties (folder type, settings and active modules)
28 Apr 2022 16:21:38,369 INFO : Loading etl definitions
28 Apr 2022 16:21:38,411 INFO : Loading wikis
28 Apr 2022 16:21:38,548 INFO : 2 wikis imported
28 Apr 2022 16:21:38,548 INFO : Done importing wikis
28 Apr 2022 16:21:38,548 INFO : Starting to copy files
28 Apr 2022 16:21:49,172 INFO : Copied 92 files
28 Apr 2022 16:21:49,172 INFO : Ensuring exp.data rows exist for imported files
28 Apr 2022 16:21:49,542 INFO : Starting Sample Type and Data Class import
28 Apr 2022 16:21:49,542 INFO : No types XAR file to process.
28 Apr 2022 16:21:49,542 INFO : Finished importing Sample Types and Data Classes
28 Apr 2022 16:21:49,583 INFO : Loading xar
28 Apr 2022 16:21:50,066 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip'
28 Apr 2022 16:21:50,068 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip.Core'
28 Apr 2022 16:21:50,070 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip.Output'
28 Apr 2022 16:21:50,070 DEBUG: Protocol import complete
28 Apr 2022 16:21:50,070 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-10312:Evaluation+of+anti-oxidant+and+anti-inflammatory+treatments+in+Chronic+Obstructive+Pulmonary+Disease'
28 Apr 2022 16:21:50,070 DEBUG: Experiment/Run group import complete
28 Apr 2022 16:21:50,078 DEBUG: Protocol action set import complete
28 Apr 2022 16:21:50,085 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip'
28 Apr 2022 16:21:50,091 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-10312:a9a1e7c1-a8db-103a-afa7-fea6ddf55ba2'
28 Apr 2022 16:21:50,094 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-10312:a9a1e798-a8db-103a-afa7-fea6ddf55ba2'
28 Apr 2022 16:21:50,094 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip.Core'
28 Apr 2022 16:21:50,096 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10312:TargetedMS.ImportSkyZip.Output'
28 Apr 2022 16:21:50,096 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-10312:a9a1e817-a8db-103a-afa7-fea6ddf55ba2'
28 Apr 2022 16:21:50,099 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04/Rat%20COPD_30022022_AllGroupsAnalysed.skyd into the system
28 Apr 2022 16:21:50,099 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04/Rat%20COPD_30022022_AllGroupsAnalysed.skyd into the system
28 Apr 2022 16:21:50,099 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip into the system
28 Apr 2022 16:21:50,100 INFO : Starting import from Rat COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip
28 Apr 2022 16:21:50,102 INFO : Starting to import Skyline document from Rat COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip
28 Apr 2022 16:21:50,104 INFO : Expanding RatCOPD.protdb
28 Apr 2022 16:21:50,953 INFO : Expanding RAT_COPD_MSMS.blib
28 Apr 2022 16:21:51,076 INFO : Expanding Rat COPD_30022022_AllGroupsAnalysed.skyd
28 Apr 2022 16:21:51,116 INFO : Expanding Rat COPD_30022022_AllGroupsAnalysed.sky.view
28 Apr 2022 16:21:51,116 INFO : Expanding Rat COPD_30022022_AllGroupsAnalysed.sky
28 Apr 2022 16:21:51,121 INFO : Expanding Rat COPD_30022022_AllGroupsAnalysed.skyl
28 Apr 2022 16:21:51,125 WARN : The version of this Skyline document is 21.2. This is newer than the highest supported version 20.22
28 Apr 2022 16:21:51,171 INFO : 5% Done
28 Apr 2022 16:21:51,324 DEBUG: Starting to load chromatogram headers
28 Apr 2022 16:21:51,326 DEBUG: Done loading chromatogram headers
28 Apr 2022 16:21:51,538 INFO : Inserting sp|P45479|PPT1_RAT
28 Apr 2022 16:21:51,581 INFO : 6% Done
28 Apr 2022 16:21:51,598 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:51,601 INFO : Inserting sp|O55012|PICAL_RAT
28 Apr 2022 16:21:51,646 INFO : 9% Done
28 Apr 2022 16:21:51,710 INFO : 12% Done
28 Apr 2022 16:21:51,782 INFO : 14% Done
28 Apr 2022 16:21:51,799 DEBUG: Total peptides inserted: 3
28 Apr 2022 16:21:51,801 INFO : Inserting sp|P11730|KCC2G_RAT
28 Apr 2022 16:21:51,847 INFO : 18% Done
28 Apr 2022 16:21:51,870 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:51,873 INFO : Inserting sp|B0BNN3|CAH1_RAT
28 Apr 2022 16:21:51,919 INFO : 21% Done
28 Apr 2022 16:21:51,985 INFO : 22% Done
28 Apr 2022 16:21:52,047 INFO : 26% Done
28 Apr 2022 16:21:52,072 DEBUG: Total peptides inserted: 3
28 Apr 2022 16:21:52,075 INFO : Inserting sp|P00406|COX2_RAT
28 Apr 2022 16:21:52,120 INFO : 29% Done
28 Apr 2022 16:21:52,142 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:52,145 INFO : Inserting sp|P05544|SPA3L_RAT
28 Apr 2022 16:21:52,189 INFO : 32% Done
28 Apr 2022 16:21:52,209 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:52,210 INFO : Inserting sp|P11730|KCC2G_RAT
28 Apr 2022 16:21:52,255 INFO : 34% Done
28 Apr 2022 16:21:52,275 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:52,277 INFO : Inserting sp|B0BNN3|CAH1_RAT
28 Apr 2022 16:21:52,323 INFO : 38% Done
28 Apr 2022 16:21:52,392 INFO : 41% Done
28 Apr 2022 16:21:52,417 DEBUG: Total peptides inserted: 2
28 Apr 2022 16:21:52,459 INFO : 42% Done
28 Apr 2022 16:21:52,461 INFO : Inserting sp|P00406|COX2_RAT
28 Apr 2022 16:21:52,505 INFO : 44% Done
28 Apr 2022 16:21:52,575 INFO : 47% Done
28 Apr 2022 16:21:52,603 DEBUG: Total peptides inserted: 2
28 Apr 2022 16:21:52,605 INFO : Inserting sp|P11730|KCC2G_RAT
28 Apr 2022 16:21:52,651 INFO : 50% Done
28 Apr 2022 16:21:52,674 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:52,676 INFO : Inserting sp|B0BNN3|CAH1_RAT
28 Apr 2022 16:21:52,722 INFO : 54% Done
28 Apr 2022 16:21:52,787 INFO : 57% Done
28 Apr 2022 16:21:52,853 INFO : 58% Done
28 Apr 2022 16:21:52,914 INFO : 62% Done
28 Apr 2022 16:21:52,939 DEBUG: Total peptides inserted: 4
28 Apr 2022 16:21:52,941 INFO : Inserting sp|P00406|COX2_RAT
28 Apr 2022 16:21:52,985 INFO : 65% Done
28 Apr 2022 16:21:53,055 INFO : 69% Done
28 Apr 2022 16:21:53,086 DEBUG: Total peptides inserted: 2
28 Apr 2022 16:21:53,088 INFO : Inserting sp|P05544|SPA3L_RAT
28 Apr 2022 16:21:53,132 INFO : 72% Done
28 Apr 2022 16:21:53,196 INFO : 74% Done
28 Apr 2022 16:21:53,215 DEBUG: Total peptides inserted: 2
28 Apr 2022 16:21:53,218 INFO : Inserting sp|P05545|SPA3K_RAT
28 Apr 2022 16:21:53,262 INFO : 77% Done
28 Apr 2022 16:21:53,286 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:53,287 INFO : Inserting sp|O55012|PICAL_RAT
28 Apr 2022 16:21:53,335 INFO : 80% Done
28 Apr 2022 16:21:53,359 DEBUG: Total peptides inserted: 1
28 Apr 2022 16:21:53,360 INFO : Done parsing Skyline document.
28 Apr 2022 16:21:53,410 INFO : Calculating fold changes
28 Apr 2022 16:21:53,410 DEBUG: Calculating fold change for group comparison DC vs NC, 1 of 5
28 Apr 2022 16:21:53,715 INFO : 84% Done
28 Apr 2022 16:21:53,715 DEBUG: Calculating fold change for group comparison CFO vs DC, 2 of 5
28 Apr 2022 16:21:54,017 INFO : 87% Done
28 Apr 2022 16:21:54,017 DEBUG: Calculating fold change for group comparison CPO vs DC, 3 of 5
28 Apr 2022 16:21:54,316 INFO : 91% Done
28 Apr 2022 16:21:54,316 DEBUG: Calculating fold change for group comparison EFI vs DC, 4 of 5
28 Apr 2022 16:21:54,610 INFO : 94% Done
28 Apr 2022 16:21:54,610 DEBUG: Calculating fold change for group comparison CFI vs DC, 5 of 5
28 Apr 2022 16:21:54,907 INFO : 98% Done
28 Apr 2022 16:21:54,907 INFO : Done calculating fold changes.
28 Apr 2022 16:21:55,079 INFO : Creating and populating temp tables for Proportion values
28 Apr 2022 16:21:55,105 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
28 Apr 2022 16:21:55,132 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
28 Apr 2022 16:21:55,151 INFO : Cleaning up temp tables
28 Apr 2022 16:21:55,347 INFO : Completed import of Skyline document from Rat COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip
28 Apr 2022 16:21:55,390 INFO : 100% Done
28 Apr 2022 16:21:55,393 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip into the system
28 Apr 2022 16:21:55,399 INFO : Done importing xar
28 Apr 2022 16:21:55,440 INFO : Loading pages and webpart properties
28 Apr 2022 16:21:55,510 INFO : Done importing 4 page(s) with 10 webpart(s)
28 Apr 2022 16:21:55,552 INFO : Starting Sample Status Data import
28 Apr 2022 16:21:55,552 INFO : No sample types XAR file to process.
28 Apr 2022 16:21:55,552 INFO : Finished importing Sample Status Data
28 Apr 2022 16:21:55,552 INFO : Importing files metadata.
28 Apr 2022 16:21:55,552 DEBUG: [/Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export
28 Apr 2022 16:21:55,553 INFO :
28 Apr 2022 16:21:55,553 INFO : Experiment import completed successfully.
28 Apr 2022 16:21:55,553 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
28 Apr 2022 16:21:55,692 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.UpdateFolderTypeTask' at location 'webserver-high-priority'
28 Apr 2022 16:21:55,692 INFO :
28 Apr 2022 16:21:55,692 INFO : Updating the folder type.
28 Apr 2022 16:21:55,693 INFO : Setting the TargetedMS folder type to 'Experimental Data' for folder '/Panorama Public/2022/IIT Bombay Proteomics - MRM_COPD'.
28 Apr 2022 16:21:55,695 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.UpdateFolderTypeTask'
28 Apr 2022 16:21:55,831 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
28 Apr 2022 16:21:55,831 INFO :
28 Apr 2022 16:21:55,831 INFO : Finishing up experiment copy.
28 Apr 2022 16:21:55,832 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
28 Apr 2022 16:21:55,833 INFO : Setting version on new experiment to 1
28 Apr 2022 16:21:55,833 INFO : Assigning a ProteomeXchange ID.
28 Apr 2022 16:21:55,941 INFO : Assigning a DOI.
28 Apr 2022 16:21:56,976 INFO : Assigned DOI: 10.6069/8q8d-9h53
28 Apr 2022 16:21:56,982 INFO : Updating access URL to point to the new copy of the data.
28 Apr 2022 16:21:56,986 INFO : Removing copy permissions given to Panorama Public
28 Apr 2022 16:21:56,993 INFO : Adding read permissions to all users that are folder admins in the source folder.
28 Apr 2022 16:21:56,999 INFO : Updating the 'Raw Data' tab configuration
28 Apr 2022 16:21:57,000 INFO : Updating dataFileUrls for run Rat COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip; targetedms run ID 136610
28 Apr 2022 16:21:57,001 INFO : Updating dataFileUrl...
28 Apr 2022 16:21:57,001 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04/Rat%20COPD_30022022_AllGroupsAnalysed.skyd
28 Apr 2022 16:21:57,001 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/IIT%20Bombay%20Proteomics%20-%20MRM_COPD/@files/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04/Rat%20COPD_30022022_AllGroupsAnalysed.skyd
28 Apr 2022 16:21:57,002 INFO : Updating dataFileUrl...
28 Apr 2022 16:21:57,002 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20MRM_COPD_45877a5c-a976-103a-afa7-fea6ddf55ba2/_temp__2022-04-28_16-20-28/export/xar/experiments_and_runs.xar.exploded/Run134640/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip
28 Apr 2022 16:21:57,002 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/IIT%20Bombay%20Proteomics%20-%20MRM_COPD/@files/Rat%20COPD_30022022_AllGroupsAnalysed_2022-04-28_10-15-04.sky.zip
28 Apr 2022 16:21:57,005 INFO : Creating a reviewer account.
28 Apr 2022 16:21:57,198 INFO : Created reviewer with email: User panorama+reviewer119@proteinms.net
28 Apr 2022 16:21:57,206 INFO : Hiding the Data Pipeline tab.
28 Apr 2022 16:21:57,210 INFO : Updating Submission. Setting copiedExperimentId to 1438
28 Apr 2022 16:21:57,273 INFO : Emailing submitter.
28 Apr 2022 16:21:57,356 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'