15 Dec 2021 17:07:37,392 INFO : Copying experiment "Proteomic Blueprint of the Pituitary anterior and posterior lobes for better understanding of the physiology of pituitary gland." from folder /IIT Bombay - Proteomics/Anteriror vs Posterior Pituitary PRM to /Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM
15 Dec 2021 17:07:37,392 INFO : =======================================
15 Dec 2021 17:07:37,459 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
15 Dec 2021 17:07:37,459 INFO :
15 Dec 2021 17:07:37,459 INFO : Exporting experiment.
15 Dec 2021 17:08:04,762 INFO : Exporting files metadata.
15 Dec 2021 17:08:04,762 DEBUG: [/IIT Bombay - Proteomics/Anteriror vs Posterior Pituitary PRM] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export
15 Dec 2021 17:08:04,765 INFO :
15 Dec 2021 17:08:04,765 INFO : Experiment export completed successfully.
15 Dec 2021 17:08:04,765 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
15 Dec 2021 17:08:04,796 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
15 Dec 2021 17:08:04,796 INFO :
15 Dec 2021 17:08:04,796 INFO : Importing experiment.
15 Dec 2021 17:08:04,799 DEBUG: [/Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export
15 Dec 2021 17:08:04,801 INFO : Loading folder properties (folder type, settings and active modules)
15 Dec 2021 17:08:04,801 DEBUG: [/Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM] Folder type: Targeted MS
15 Dec 2021 17:08:04,801 DEBUG: [/Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM] Active modules: Wiki, Pipeline, Experiment, Announcements, Internal, PanoramaPublic, TargetedMS, MS2, FileContent, Assay, Core, Search, Query, API, Issues
15 Dec 2021 17:08:04,862 INFO : Done importing folder properties (folder type, settings and active modules)
15 Dec 2021 17:08:04,864 INFO : Loading etl definitions
15 Dec 2021 17:08:04,866 INFO : Loading wikis
15 Dec 2021 17:08:04,872 INFO : 1 wiki imported
15 Dec 2021 17:08:04,872 INFO : Done importing wikis
15 Dec 2021 17:08:04,872 INFO : Starting to copy files
15 Dec 2021 17:08:17,075 INFO : Copied 14 files
15 Dec 2021 17:08:17,075 INFO : Ensuring exp.data rows exist for imported files
15 Dec 2021 17:08:17,434 INFO : Starting Sample Type and Data Class import
15 Dec 2021 17:08:17,434 INFO : No types XAR file to process.
15 Dec 2021 17:08:17,435 INFO : Finished importing Sample Types and Data Classes
15 Dec 2021 17:08:17,436 INFO : Loading xar
15 Dec 2021 17:08:18,883 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip.Core'
15 Dec 2021 17:08:18,885 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip.Output'
15 Dec 2021 17:08:18,887 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip'
15 Dec 2021 17:08:18,887 DEBUG: Protocol import complete
15 Dec 2021 17:08:18,889 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9430:Proteomic+Blueprint+of+the+Pituitary+anterior+and+posterior+lobes+for+better+understanding+of+the+physiology+of+pituitary+gland.'
15 Dec 2021 17:08:18,889 DEBUG: Experiment/Run group import complete
15 Dec 2021 17:08:18,910 DEBUG: Protocol action set import complete
15 Dec 2021 17:08:18,926 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip'
15 Dec 2021 17:08:18,937 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9430:052eef79-3006-103a-bfdd-fea6ddf55ce4'
15 Dec 2021 17:08:18,941 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9430:052eef52-3006-103a-bfdd-fea6ddf55ce4'
15 Dec 2021 17:08:18,941 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip.Core'
15 Dec 2021 17:08:18,944 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9430:TargetedMS.ImportSkyZip.Output'
15 Dec 2021 17:08:18,944 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9430:052eefc9-3006-103a-bfdd-fea6ddf55ce4'
15 Dec 2021 17:08:18,946 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30/101021_AB_AntvsPos_PRM%20for%20pprV1.skyd into the system
15 Dec 2021 17:08:18,947 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30/101021_AB_AntvsPos_PRM%20for%20pprV1.skyd into the system
15 Dec 2021 17:08:18,947 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30.sky.zip into the system
15 Dec 2021 17:08:18,948 INFO : Starting import from 101021_AB_AntvsPos_PRM for pprV1_2021-11-25_15-32-30.sky.zip
15 Dec 2021 17:08:18,951 INFO : Starting to import Skyline document from 101021_AB_AntvsPos_PRM for pprV1_2021-11-25_15-32-30.sky.zip
15 Dec 2021 17:08:18,952 INFO : Expanding Human_Cov_2.protdb
15 Dec 2021 17:08:21,104 INFO : Expanding Anterior_vs_Poseterior.blib
15 Dec 2021 17:08:22,568 INFO : Expanding 101021_AB_AntvsPos_PRM for pprV1.skyd
15 Dec 2021 17:08:22,589 INFO : Expanding 101021_AB_AntvsPos_PRM for pprV1.sky.view
15 Dec 2021 17:08:22,590 INFO : Expanding 101021_AB_AntvsPos_PRM for pprV1.sky
15 Dec 2021 17:08:22,592 INFO : Expanding 101021_AB_AntvsPos_PRM for pprV1.skyl
15 Dec 2021 17:08:22,595 WARN : The version of this Skyline document is 21.12. This is newer than the highest supported version 20.22
15 Dec 2021 17:08:22,602 INFO : 2% Done
15 Dec 2021 17:08:22,620 DEBUG: Starting to load chromatogram headers
15 Dec 2021 17:08:22,621 DEBUG: Done loading chromatogram headers
15 Dec 2021 17:08:22,762 INFO : Inserting sp|P62805|H4_HUMAN
15 Dec 2021 17:08:22,768 INFO : 6% Done
15 Dec 2021 17:08:22,786 INFO : 8% Done
15 Dec 2021 17:08:22,794 DEBUG: Total peptides inserted: 2
15 Dec 2021 17:08:22,797 INFO : Inserting sp|P01241|SOMA_HUMAN
15 Dec 2021 17:08:22,801 INFO : 12% Done
15 Dec 2021 17:08:22,814 INFO : 15% Done
15 Dec 2021 17:08:22,828 INFO : 19% Done
15 Dec 2021 17:08:22,838 DEBUG: Total peptides inserted: 3
15 Dec 2021 17:08:22,842 INFO : Inserting sp|Q9Y2W1|TR150_HUMAN
15 Dec 2021 17:08:22,845 INFO : 22% Done
15 Dec 2021 17:08:22,855 INFO : 23% Done
15 Dec 2021 17:08:22,862 DEBUG: Total peptides inserted: 2
15 Dec 2021 17:08:22,863 INFO : 24% Done
15 Dec 2021 17:08:22,866 INFO : Inserting sp|P01222|TSHB_HUMAN
15 Dec 2021 17:08:22,869 INFO : 26% Done
15 Dec 2021 17:08:22,882 INFO : 29% Done
15 Dec 2021 17:08:22,893 DEBUG: Total peptides inserted: 2
15 Dec 2021 17:08:22,895 INFO : 30% Done
15 Dec 2021 17:08:22,898 INFO : Inserting sp|P01185|NEU2_HUMAN
15 Dec 2021 17:08:22,902 INFO : 32% Done
15 Dec 2021 17:08:22,913 INFO : 35% Done
15 Dec 2021 17:08:22,925 INFO : 39% Done
15 Dec 2021 17:08:22,937 DEBUG: Total peptides inserted: 3
15 Dec 2021 17:08:22,941 INFO : Inserting sp|P01178|NEU1_HUMAN
15 Dec 2021 17:08:22,944 INFO : 42% Done
15 Dec 2021 17:08:22,958 INFO : 47% Done
15 Dec 2021 17:08:22,970 DEBUG: Total peptides inserted: 2
15 Dec 2021 17:08:22,973 INFO : Inserting sp|P01189|COLI_HUMAN
15 Dec 2021 17:08:22,977 INFO : 51% Done
15 Dec 2021 17:08:22,992 INFO : 55% Done
15 Dec 2021 17:08:23,005 INFO : 58% Done
15 Dec 2021 17:08:23,018 INFO : 61% Done
15 Dec 2021 17:08:23,029 DEBUG: Total peptides inserted: 4
15 Dec 2021 17:08:23,031 INFO : 62% Done
15 Dec 2021 17:08:23,035 INFO : Inserting sp|Q14393|GAS6_HUMAN
15 Dec 2021 17:08:23,038 INFO : 64% Done
15 Dec 2021 17:08:23,048 INFO : 66% Done
15 Dec 2021 17:08:23,059 DEBUG: Total peptides inserted: 2
15 Dec 2021 17:08:23,061 INFO : 67% Done
15 Dec 2021 17:08:23,065 INFO : Inserting sp|P28069|PIT1_HUMAN
15 Dec 2021 17:08:23,068 INFO : 70% Done
15 Dec 2021 17:08:23,080 DEBUG: Total peptides inserted: 1
15 Dec 2021 17:08:23,083 INFO : Inserting sp|P47972|NPTX2_HUMAN
15 Dec 2021 17:08:23,087 INFO : 73% Done
15 Dec 2021 17:08:23,096 INFO : 74% Done
15 Dec 2021 17:08:23,106 INFO : 78% Done
15 Dec 2021 17:08:23,119 INFO : 80% Done
15 Dec 2021 17:08:23,126 DEBUG: Total peptides inserted: 4
15 Dec 2021 17:08:23,130 INFO : Inserting sp|Q9UKZ9|PCOC2_HUMAN
15 Dec 2021 17:08:23,133 INFO : 83% Done
15 Dec 2021 17:08:23,142 INFO : 85% Done
15 Dec 2021 17:08:23,151 INFO : 87% Done
15 Dec 2021 17:08:23,159 DEBUG: Total peptides inserted: 3
15 Dec 2021 17:08:23,162 INFO : Inserting sp|O43719|HTSF1_HUMAN
15 Dec 2021 17:08:23,165 INFO : 90% Done
15 Dec 2021 17:08:23,175 INFO : 93% Done
15 Dec 2021 17:08:23,186 INFO : 95% Done
15 Dec 2021 17:08:23,192 DEBUG: Total peptides inserted: 3
15 Dec 2021 17:08:23,194 INFO : 96% Done
15 Dec 2021 17:08:23,198 INFO : Inserting sp|P56937|DHB7_HUMAN
15 Dec 2021 17:08:23,201 INFO : 98% Done
15 Dec 2021 17:08:23,211 DEBUG: Total peptides inserted: 1
15 Dec 2021 17:08:23,212 INFO : Done parsing Skyline document.
15 Dec 2021 17:08:23,288 INFO : Creating and populating temp tables for Proportion values
15 Dec 2021 17:08:23,302 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
15 Dec 2021 17:08:23,310 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
15 Dec 2021 17:08:23,316 INFO : Cleaning up temp tables
15 Dec 2021 17:08:23,591 INFO : Completed import of Skyline document from 101021_AB_AntvsPos_PRM for pprV1_2021-11-25_15-32-30.sky.zip
15 Dec 2021 17:08:23,594 INFO : 100% Done
15 Dec 2021 17:08:23,599 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30.sky.zip into the system
15 Dec 2021 17:08:23,607 INFO : Done importing xar
15 Dec 2021 17:08:23,609 INFO : Loading pages and webpart properties
15 Dec 2021 17:08:23,701 INFO : Done importing 4 page(s) with 8 webpart(s)
15 Dec 2021 17:08:23,702 INFO : Importing files metadata.
15 Dec 2021 17:08:23,702 DEBUG: [/Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export
15 Dec 2021 17:08:23,703 INFO :
15 Dec 2021 17:08:23,703 INFO : Experiment import completed successfully.
15 Dec 2021 17:08:23,703 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
15 Dec 2021 17:08:23,735 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.UpdateFolderTypeTask' at location 'webserver-high-priority'
15 Dec 2021 17:08:23,735 INFO :
15 Dec 2021 17:08:23,735 INFO : Updating the folder type.
15 Dec 2021 17:08:23,738 INFO : Setting the TargetedMS folder type to 'Experimental Data' for folder '/Panorama Public/2021/IIT Bombay Proteomics - Anteriror vs Posterior Pituitary PRM'.
15 Dec 2021 17:08:23,740 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.UpdateFolderTypeTask'
15 Dec 2021 17:08:23,768 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
15 Dec 2021 17:08:23,768 INFO :
15 Dec 2021 17:08:23,768 INFO : Finishing up experiment copy.
15 Dec 2021 17:08:23,775 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
15 Dec 2021 17:08:23,776 INFO : Setting version on new experiment to 2
15 Dec 2021 17:08:23,776 INFO : Copying ProteomeXchange ID from the previous copy of the data.
15 Dec 2021 17:08:23,776 INFO : Copying DOI from the previous copy of the data.
15 Dec 2021 17:08:23,781 INFO : Updating access URL to point to the new copy of the data.
15 Dec 2021 17:08:23,784 INFO : Removing copy permissions given to Panorama Public
15 Dec 2021 17:08:23,793 INFO : Adding read permissions to all users that are folder admins in the source folder.
15 Dec 2021 17:08:23,795 INFO : Adding read permissions to all users that had read access to previous copy.
15 Dec 2021 17:08:23,801 INFO : Updating the 'Raw Data' tab configuration
15 Dec 2021 17:08:23,803 INFO : Updating dataFileUrls for run 101021_AB_AntvsPos_PRM for pprV1_2021-11-25_15-32-30.sky.zip; targetedms run ID 127144
15 Dec 2021 17:08:23,804 INFO : Updating dataFileUrl...
15 Dec 2021 17:08:23,804 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30/101021_AB_AntvsPos_PRM%20for%20pprV1.skyd
15 Dec 2021 17:08:23,804 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM/@files/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30/101021_AB_AntvsPos_PRM%20for%20pprV1.skyd
15 Dec 2021 17:08:23,806 INFO : Updating dataFileUrl...
15 Dec 2021 17:08:23,806 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM_fa6e09a5-4038-103a-9c44-fea6ddf5fb78/_temp__2021-12-15_17-07-36/export/xar/experiments_and_runs.xar.exploded/Run122562/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30.sky.zip
15 Dec 2021 17:08:23,806 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20Anteriror%20vs%20Posterior%20Pituitary%20PRM/@files/101021_AB_AntvsPos_PRM%20for%20pprV1_2021-11-25_15-32-30.sky.zip
15 Dec 2021 17:08:23,808 INFO : Hiding the Data Pipeline tab.
15 Dec 2021 17:08:23,811 INFO : Creating a new versioned URL for the previous copy of the data: antpstpituitary_v1
15 Dec 2021 17:08:23,816 INFO : Setting the short access URL on the previous copy to antpstpituitary_v1
15 Dec 2021 17:08:23,816 INFO : Removing DOI from the previous copy
15 Dec 2021 17:08:23,819 INFO : Updating Submission. Setting copiedExperimentId to 1351
15 Dec 2021 17:08:23,936 INFO : Emailing submitter.
15 Dec 2021 17:08:24,061 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'