20 Aug 2021 07:37:31,622 INFO : Copying experiment "A hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzae" from folder /Sainsbury Lab - TSL Proteomics/Osés-Ruiz et al to /Panorama Public/2021/Sainsbury Lab TSL Proteomics - Osés-Ruiz et al
20 Aug 2021 07:37:31,622 INFO : =======================================
20 Aug 2021 07:37:31,680 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
20 Aug 2021 07:37:31,680 INFO :
20 Aug 2021 07:37:31,680 INFO : Exporting experiment.
20 Aug 2021 07:43:18,877 INFO :
20 Aug 2021 07:43:18,878 INFO : Experiment export completed successfully.
20 Aug 2021 07:43:18,878 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
20 Aug 2021 07:49:50,882 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
20 Aug 2021 07:49:50,882 INFO :
20 Aug 2021 07:49:50,882 INFO : Importing experiment.
20 Aug 2021 07:49:50,889 INFO : Loading folder properties (folder type, settings and active modules)
20 Aug 2021 07:49:50,969 INFO : Done importing folder properties (folder type, settings and active modules)
20 Aug 2021 07:49:50,977 INFO : Loading etl definitions
20 Aug 2021 07:49:50,980 INFO : Loading wikis
20 Aug 2021 07:49:50,983 INFO : 0 wikis imported
20 Aug 2021 07:49:50,983 INFO : Done importing wikis
20 Aug 2021 07:49:50,983 INFO : Starting to copy files
20 Aug 2021 07:51:51,514 INFO : 49 files copied, now copying ncr190608_ncr190516_03.raw
20 Aug 2021 07:54:15,526 INFO : 99 files copied, now copying ncr200619_03.raw
20 Aug 2021 07:55:08,242 INFO : Copied 121 files
20 Aug 2021 07:55:08,242 INFO : Ensuring exp.data rows exist for imported files
20 Aug 2021 07:55:08,837 INFO : Starting Sample Type and Data Class import
20 Aug 2021 07:55:08,838 INFO : No types XAR file to process.
20 Aug 2021 07:55:08,838 INFO : Finished importing Sample Types and Data Classes
20 Aug 2021 07:55:08,840 INFO : Loading xar
20 Aug 2021 07:55:11,269 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip'
20 Aug 2021 07:55:11,272 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip.Core'
20 Aug 2021 07:55:11,274 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip.Output'
20 Aug 2021 07:55:11,274 DEBUG: Protocol import complete
20 Aug 2021 07:55:11,276 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9027:A+hierarchical+transcriptional+network+controls+appressorium-mediated+plant+infection+by+the+rice+blast+fungus+Magnaporthe+oryzae'
20 Aug 2021 07:55:11,276 DEBUG: Experiment/Run group import complete
20 Aug 2021 07:55:11,285 DEBUG: Protocol action set import complete
20 Aug 2021 07:55:11,300 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip'
20 Aug 2021 07:55:11,308 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:Data.Folder-9027-Xar-d424a54e-e3f3-1039-a2b1-fea6ddf522ee:Run115945%2FM_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip'
20 Aug 2021 07:55:11,312 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9027:63621394-e3f0-1039-a2b1-fea6ddf522ee'
20 Aug 2021 07:55:11,312 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip.Core'
20 Aug 2021 07:55:11,316 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9027:TargetedMS.ImportSkyZip.Output'
20 Aug 2021 07:55:11,316 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9027:6362148d-e3f0-1039-a2b1-fea6ddf522ee'
20 Aug 2021 07:55:11,317 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip into the system
20 Aug 2021 07:55:11,319 INFO : Starting import from M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip
20 Aug 2021 07:55:11,323 INFO : Starting to import Skyline document from M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip
20 Aug 2021 07:55:11,372 INFO : Expanding M_oryzae_20140513.protdb
20 Aug 2021 07:55:12,794 INFO : Expanding M_oryzae_PRM_TEMP_07_with_spectra_panorama.skyd
20 Aug 2021 07:55:14,021 INFO : Expanding M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.view
20 Aug 2021 07:55:14,022 INFO : Expanding M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky
20 Aug 2021 07:55:14,100 INFO : 1% Done
20 Aug 2021 07:55:17,928 DEBUG: Starting to load chromatogram headers
20 Aug 2021 07:55:17,969 DEBUG: Done loading chromatogram headers
20 Aug 2021 07:55:18,103 INFO : Inserting Library Peptides
20 Aug 2021 07:55:18,125 INFO : 3% Done
20 Aug 2021 07:55:18,286 INFO : 5% Done
20 Aug 2021 07:55:18,530 INFO : 8% Done
20 Aug 2021 07:55:18,728 INFO : 10% Done
20 Aug 2021 07:55:18,885 INFO : 12% Done
20 Aug 2021 07:55:19,122 INFO : 15% Done
20 Aug 2021 07:55:19,307 INFO : 17% Done
20 Aug 2021 07:55:19,512 INFO : 20% Done
20 Aug 2021 07:55:19,710 INFO : 22% Done
20 Aug 2021 07:55:19,907 INFO : 25% Done
20 Aug 2021 07:55:20,133 INFO : 26% Done
20 Aug 2021 07:55:20,340 DEBUG: Total peptides inserted: 11
20 Aug 2021 07:55:20,342 INFO : Inserting MGG_12865T0
20 Aug 2021 07:55:20,362 INFO : 27% Done
20 Aug 2021 07:55:20,521 INFO : 29% Done
20 Aug 2021 07:55:20,689 INFO : 30% Done
20 Aug 2021 07:55:20,759 DEBUG: Total peptides inserted: 3
20 Aug 2021 07:55:20,759 INFO : Inserting MGG_14118T0
20 Aug 2021 07:55:20,823 INFO : 34% Done
20 Aug 2021 07:55:21,052 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:21,052 INFO : Inserting gi|39941692|ref|XP_360383.1|
20 Aug 2021 07:55:21,109 INFO : 37% Done
20 Aug 2021 07:55:21,332 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:21,332 INFO : Inserting MGG_00432T0
20 Aug 2021 07:55:21,378 INFO : 40% Done
20 Aug 2021 07:55:21,594 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:21,594 INFO : Inserting MGG_04462T0
20 Aug 2021 07:55:21,652 INFO : 43% Done
20 Aug 2021 07:55:21,878 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:21,879 INFO : Inserting gi|39977471|ref|XP_370123.1|
20 Aug 2021 07:55:21,947 INFO : 47% Done
20 Aug 2021 07:55:22,195 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:22,195 INFO : Inserting gi|149209241|ref|XP_001521995.1|
20 Aug 2021 07:55:22,261 INFO : 50% Done
20 Aug 2021 07:55:22,503 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:22,504 INFO : Inserting gi|145608756|ref|XP_369881.2|
20 Aug 2021 07:55:22,554 INFO : 53% Done
20 Aug 2021 07:55:22,781 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:22,782 INFO : Inserting MGG_04651T0
20 Aug 2021 07:55:22,846 INFO : 56% Done
20 Aug 2021 07:55:23,111 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:23,111 INFO : Inserting gi|145611142|ref|XP_001410978.1|
20 Aug 2021 07:55:23,169 INFO : 60% Done
20 Aug 2021 07:55:23,374 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:23,374 INFO : Inserting gi|39949100|ref|XP_363161.1|
20 Aug 2021 07:55:23,444 INFO : 64% Done
20 Aug 2021 07:55:23,708 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:23,708 INFO : Inserting MGG_08084T0
20 Aug 2021 07:55:23,773 INFO : 68% Done
20 Aug 2021 07:55:23,996 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:23,996 INFO : Inserting MGG_03725T0
20 Aug 2021 07:55:24,051 INFO : 71% Done
20 Aug 2021 07:55:24,292 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:24,292 INFO : Inserting MGG_11236T0
20 Aug 2021 07:55:24,343 INFO : 74% Done
20 Aug 2021 07:55:24,547 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:24,547 INFO : Inserting gi|145605439|ref|XP_001406149.1|
20 Aug 2021 07:55:24,587 INFO : 76% Done
20 Aug 2021 07:55:24,746 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:24,746 INFO : Inserting gi|39963526|ref|XP_364916.1|
20 Aug 2021 07:55:24,783 INFO : 78% Done
20 Aug 2021 07:55:24,941 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:24,941 INFO : Inserting MGG_00455T0
20 Aug 2021 07:55:25,009 INFO : 82% Done
20 Aug 2021 07:55:25,320 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:25,320 INFO : Inserting MGG_01378T0
20 Aug 2021 07:55:25,376 INFO : 86% Done
20 Aug 2021 07:55:25,610 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:25,610 INFO : Inserting gi|39939816|ref|XP_359445.1|
20 Aug 2021 07:55:25,645 INFO : 88% Done
20 Aug 2021 07:55:25,800 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:25,800 INFO : Inserting MGG_05287T0
20 Aug 2021 07:55:25,847 INFO : 91% Done
20 Aug 2021 07:55:26,038 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:26,038 INFO : Inserting gi|39971711|ref|XP_367246.1|
20 Aug 2021 07:55:26,088 INFO : 94% Done
20 Aug 2021 07:55:26,301 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:26,301 INFO : Inserting MGG_05208T0
20 Aug 2021 07:55:26,364 INFO : 98% Done
20 Aug 2021 07:55:26,636 DEBUG: Total peptides inserted: 1
20 Aug 2021 07:55:26,637 INFO : Done parsing Skyline document.
20 Aug 2021 07:55:26,638 INFO : Creating and populating temp tables for Proportion values
20 Aug 2021 07:55:26,670 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
20 Aug 2021 07:55:26,819 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
20 Aug 2021 07:55:26,925 INFO : Cleaning up temp tables
20 Aug 2021 07:55:27,150 INFO : Completed import of Skyline document from M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip
20 Aug 2021 07:55:27,152 INFO : 100% Done
20 Aug 2021 07:55:27,157 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip into the system
20 Aug 2021 07:55:27,157 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama/M_oryzae_PRM_TEMP_07_with_spectra_panorama.skyd into the system
20 Aug 2021 07:55:27,158 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama/M_oryzae_PRM_TEMP_07_with_spectra_panorama.skyd into the system
20 Aug 2021 07:55:27,165 INFO : Done importing xar
20 Aug 2021 07:55:27,167 INFO : Loading pages and webpart properties
20 Aug 2021 07:55:27,241 INFO : Done importing pages and webpart properties
20 Aug 2021 07:55:27,242 INFO :
20 Aug 2021 07:55:27,242 INFO : Experiment import completed successfully.
20 Aug 2021 07:55:27,242 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
20 Aug 2021 07:55:27,288 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
20 Aug 2021 07:55:27,289 INFO :
20 Aug 2021 07:55:27,289 INFO : Finishing up experiment copy.
20 Aug 2021 07:55:27,291 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
20 Aug 2021 07:55:27,293 INFO : Assigning a ProteomeXchange ID.
20 Aug 2021 07:55:27,977 INFO : Assigning a DOI.
20 Aug 2021 07:55:29,207 INFO : Assigned DOI: 10.6069/gdq7-2b37
20 Aug 2021 07:55:29,210 INFO : Updating access URL to point to the new copy of the data.
20 Aug 2021 07:55:29,216 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
20 Aug 2021 07:55:29,217 INFO : Removing copy permissions given to journal.
20 Aug 2021 07:55:29,224 INFO : Adding read permissions to all users that are folder admins in the source container.
20 Aug 2021 07:55:29,230 INFO : Setting the TargetedMS folder type to 'Experimental Data'
20 Aug 2021 07:55:29,239 INFO : Updating the 'Raw Data' tab configuration
20 Aug 2021 07:55:29,242 INFO : Updating dataFileUrls for run M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip; targetedms run ID 118467
20 Aug 2021 07:55:29,242 INFO : Updating dataFileUrl...
20 Aug 2021 07:55:29,242 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama/M_oryzae_PRM_TEMP_07_with_spectra_panorama.skyd
20 Aug 2021 07:55:29,242 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al/@files/M_oryzae_PRM_TEMP_07_with_spectra_panorama/M_oryzae_PRM_TEMP_07_with_spectra_panorama.skyd
20 Aug 2021 07:55:29,245 INFO : Updating dataFileUrl...
20 Aug 2021 07:55:29,245 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al_a04c6a5b-e3f1-1039-a2b1-fea6ddf522ee/_temp__2021-08-20_07-37-31/export/xar/experiments_and_runs.xar.exploded/Run115945/M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip
20 Aug 2021 07:55:29,245 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Sainsbury%20Lab%20TSL%20Proteomics%20-%20Os%C3%A9s-Ruiz%20et%20al/@files/M_oryzae_PRM_TEMP_07_with_spectra_panorama.sky.zip
20 Aug 2021 07:55:29,249 INFO : Creating a reviewer account.
20 Aug 2021 07:55:29,464 INFO : Created reviewer with email: User panorama+reviewer59@proteinms.net
20 Aug 2021 07:55:29,470 INFO : Hiding the Data Pipeline tab.
20 Aug 2021 07:55:29,571 INFO : Emailing submitter.
20 Aug 2021 07:55:29,700 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'