27 Sep 2021 07:18:48,851 INFO : Copying experiment "Diagnosing pleural effusions using mass spectrometry-based multiplexed targeted proteomics quantitating mid- to high-abundance markers of cancer, infection/inflammation and tuberculosis" from folder /Polish Acad Sciences - IBB MS Lab/34 marker panel/34 marker panel to /Panorama Public/2021/Polish Acad Sciences IBB MS Lab - 34 marker panel
27 Sep 2021 07:18:48,852 INFO : =======================================
27 Sep 2021 07:18:49,238 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
27 Sep 2021 07:18:49,238 INFO : 
27 Sep 2021 07:18:49,238 INFO : Exporting experiment.
27 Sep 2021 07:21:51,354 INFO : 
27 Sep 2021 07:21:51,354 INFO : Experiment export completed successfully.
27 Sep 2021 07:21:51,354 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
27 Sep 2021 07:21:51,429 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
27 Sep 2021 07:21:51,430 INFO : 
27 Sep 2021 07:21:51,430 INFO : Importing experiment.
27 Sep 2021 07:21:51,436 INFO : Loading folder properties (folder type, settings and active modules)
27 Sep 2021 07:21:51,535 INFO : Done importing folder properties (folder type, settings and active modules)
27 Sep 2021 07:21:51,539 INFO : Loading etl definitions
27 Sep 2021 07:21:51,542 INFO : Loading wikis
27 Sep 2021 07:21:51,544 INFO : 0 wikis imported
27 Sep 2021 07:21:51,545 INFO : Done importing wikis
27 Sep 2021 07:21:51,545 INFO : Starting to copy files
27 Sep 2021 07:23:07,416 INFO : Copied 6 files
27 Sep 2021 07:23:07,416 INFO : Ensuring exp.data rows exist for imported files
27 Sep 2021 07:23:09,100 INFO : Starting Sample Type and Data Class import
27 Sep 2021 07:23:09,101 INFO : No types XAR file to process.
27 Sep 2021 07:23:09,101 INFO : Finished importing Sample Types and Data Classes
27 Sep 2021 07:23:09,104 INFO : Loading xar
27 Sep 2021 07:23:18,287 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip'
27 Sep 2021 07:23:18,289 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip.Core'
27 Sep 2021 07:23:18,292 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip.Output'
27 Sep 2021 07:23:18,292 DEBUG: Protocol import complete
27 Sep 2021 07:23:18,306 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9143:Diagnosing+pleural+effusions+using+mass+spectrometry-based+multiplexed+targeted+proteomics+quantitating+mid-+to+high-abundance+markers+of+cancer%2C+infection%2Finflammation+and+tuberculosis'
27 Sep 2021 07:23:18,306 DEBUG: Experiment/Run group import complete
27 Sep 2021 07:23:18,317 DEBUG: Protocol action set import complete
27 Sep 2021 07:23:18,335 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip'
27 Sep 2021 07:23:18,343 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9143:5172a8e7-fe93-1039-b54f-fea6ddf5779e'
27 Sep 2021 07:23:18,347 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9143:5172a580-fe93-1039-b54f-fea6ddf5779e'
27 Sep 2021 07:23:18,348 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip.Core'
27 Sep 2021 07:23:18,351 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9143:TargetedMS.ImportSkyZip.Output'
27 Sep 2021 07:23:18,352 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9143:5172aa07-fe93-1039-b54f-fea6ddf5779e'
27 Sep 2021 07:23:18,354 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26/Robak%20et%20al.%202021_MRM%20panel.skyd into the system
27 Sep 2021 07:23:18,355 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26/Robak%20et%20al.%202021_MRM%20panel.skyd into the system
27 Sep 2021 07:23:18,355 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26.sky.zip into the system
27 Sep 2021 07:23:18,358 INFO : Starting import from Robak et al. 2021_MRM panel_2021-09-23_13-50-26.sky.zip
27 Sep 2021 07:23:18,363 INFO : Starting to import Skyline document from Robak et al. 2021_MRM panel_2021-09-23_13-50-26.sky.zip
27 Sep 2021 07:23:18,396 INFO : Expanding human_hcd_selected.msp
27 Sep 2021 07:23:59,922 INFO : Expanding Robak et al. 2021_MRM panel.skyd
27 Sep 2021 07:24:00,952 INFO : Expanding Robak et al. 2021_MRM panel.sky.view
27 Sep 2021 07:24:00,952 INFO : Expanding Robak et al. 2021_MRM panel.sky
27 Sep 2021 07:24:02,419 DEBUG: Starting to load chromatogram headers
27 Sep 2021 07:24:02,488 DEBUG: Done loading chromatogram headers
27 Sep 2021 07:24:02,745 INFO : Inserting ADA2
27 Sep 2021 07:24:02,819 INFO : 2% Done
27 Sep 2021 07:24:03,507 INFO : 3% Done
27 Sep 2021 07:24:03,863 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:03,863 INFO : Inserting CXCL10
27 Sep 2021 07:24:03,889 INFO : 4% Done
27 Sep 2021 07:24:04,295 INFO : 5% Done
27 Sep 2021 07:24:04,651 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:04,651 INFO : Inserting C9
27 Sep 2021 07:24:04,675 INFO : 6% Done
27 Sep 2021 07:24:05,045 INFO : 8% Done
27 Sep 2021 07:24:05,405 INFO : 9% Done
27 Sep 2021 07:24:05,800 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:05,800 INFO : Inserting CK6A,B,C
27 Sep 2021 07:24:05,829 INFO : 10% Done
27 Sep 2021 07:24:06,231 DEBUG: Total peptides inserted: 1
27 Sep 2021 07:24:06,231 INFO : Inserting CK7
27 Sep 2021 07:24:06,258 INFO : 12% Done
27 Sep 2021 07:24:06,682 INFO : 13% Done
27 Sep 2021 07:24:07,130 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:07,131 INFO : Inserting CK8
27 Sep 2021 07:24:07,159 INFO : 15% Done
27 Sep 2021 07:24:07,617 INFO : 16% Done
27 Sep 2021 07:24:08,043 INFO : 17% Done
27 Sep 2021 07:24:08,460 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:08,460 INFO : Inserting CK18
27 Sep 2021 07:24:08,484 INFO : 19% Done
27 Sep 2021 07:24:08,872 INFO : 20% Done
27 Sep 2021 07:24:09,223 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:09,223 INFO : Inserting CK19
27 Sep 2021 07:24:09,252 INFO : 21% Done
27 Sep 2021 07:24:09,687 INFO : 22% Done
27 Sep 2021 07:24:10,112 INFO : 23% Done
27 Sep 2021 07:24:10,461 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:10,461 INFO : Inserting Vimentin
27 Sep 2021 07:24:10,485 INFO : 25% Done
27 Sep 2021 07:24:11,288 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:11,288 INFO : Inserting Complement C3
27 Sep 2021 07:24:11,315 INFO : 26% Done
27 Sep 2021 07:24:11,769 INFO : 28% Done
27 Sep 2021 07:24:12,138 INFO : 29% Done
27 Sep 2021 07:24:12,474 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:12,474 INFO : Inserting Hemopexin
27 Sep 2021 07:24:12,497 INFO : 30% Done
27 Sep 2021 07:24:12,871 INFO : 31% Done
27 Sep 2021 07:24:13,286 INFO : 32% Done
27 Sep 2021 07:24:13,631 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:13,631 INFO : Inserting S100A9
27 Sep 2021 07:24:13,654 INFO : 33% Done
27 Sep 2021 07:24:14,046 INFO : 35% Done
27 Sep 2021 07:24:14,524 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:14,524 INFO : Inserting SERPINF1
27 Sep 2021 07:24:14,547 INFO : 36% Done
27 Sep 2021 07:24:14,920 INFO : 37% Done
27 Sep 2021 07:24:15,395 INFO : 39% Done
27 Sep 2021 07:24:15,808 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:15,808 INFO : Inserting Serum amyloid P
27 Sep 2021 07:24:15,832 INFO : 40% Done
27 Sep 2021 07:24:16,251 INFO : 41% Done
27 Sep 2021 07:24:16,654 INFO : 42% Done
27 Sep 2021 07:24:17,001 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:17,002 INFO : Inserting SVEP1
27 Sep 2021 07:24:17,031 INFO : 44% Done
27 Sep 2021 07:24:17,471 INFO : 45% Done
27 Sep 2021 07:24:17,808 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:17,809 INFO : Inserting Thrombospondin 4
27 Sep 2021 07:24:17,831 INFO : 46% Done
27 Sep 2021 07:24:18,206 INFO : 47% Done
27 Sep 2021 07:24:18,552 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:18,552 INFO : Inserting CD166 antigen
27 Sep 2021 07:24:18,576 INFO : 48% Done
27 Sep 2021 07:24:18,956 INFO : 50% Done
27 Sep 2021 07:24:19,404 INFO : 51% Done
27 Sep 2021 07:24:19,809 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:19,809 INFO : Inserting Galectin 1
27 Sep 2021 07:24:19,830 INFO : 52% Done
27 Sep 2021 07:24:20,185 INFO : 53% Done
27 Sep 2021 07:24:20,557 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:20,557 INFO : Inserting Kunitz type protease inhibitor 1
27 Sep 2021 07:24:20,580 INFO : 54% Done
27 Sep 2021 07:24:20,934 DEBUG: Total peptides inserted: 1
27 Sep 2021 07:24:20,934 INFO : Inserting Mucin 1
27 Sep 2021 07:24:20,954 INFO : 55% Done
27 Sep 2021 07:24:21,261 INFO : 56% Done
27 Sep 2021 07:24:21,673 INFO : 58% Done
27 Sep 2021 07:24:22,079 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:22,079 INFO : Inserting Cadherin 1
27 Sep 2021 07:24:22,109 INFO : 59% Done
27 Sep 2021 07:24:22,557 INFO : 60% Done
27 Sep 2021 07:24:22,912 DEBUG: Total peptides inserted: 2
27 Sep 2021 07:24:22,912 INFO : Inserting MMP 9
27 Sep 2021 07:24:22,945 INFO : 62% Done
27 Sep 2021 07:24:23,389 INFO : 63% Done
27 Sep 2021 07:24:23,764 INFO : 64% Done
27 Sep 2021 07:24:24,142 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:24,142 INFO : Inserting C reactive protein
27 Sep 2021 07:24:24,172 INFO : 66% Done
27 Sep 2021 07:24:24,688 INFO : 67% Done
27 Sep 2021 07:24:25,079 INFO : 68% Done
27 Sep 2021 07:24:25,429 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:25,430 INFO : Inserting GSN
27 Sep 2021 07:24:25,460 INFO : 69% Done
27 Sep 2021 07:24:25,900 INFO : 70% Done
27 Sep 2021 07:24:26,298 INFO : 72% Done
27 Sep 2021 07:24:26,727 INFO : 73% Done
27 Sep 2021 07:24:27,125 DEBUG: Total peptides inserted: 4
27 Sep 2021 07:24:27,125 INFO : Inserting SERPINA4
27 Sep 2021 07:24:27,154 INFO : 74% Done
27 Sep 2021 07:24:27,637 INFO : 75% Done
27 Sep 2021 07:24:28,007 INFO : 76% Done
27 Sep 2021 07:24:28,347 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:28,347 INFO : Inserting WARS
27 Sep 2021 07:24:28,372 INFO : 77% Done
27 Sep 2021 07:24:28,741 INFO : 78% Done
27 Sep 2021 07:24:29,168 INFO : 80% Done
27 Sep 2021 07:24:29,533 INFO : 81% Done
27 Sep 2021 07:24:29,876 DEBUG: Total peptides inserted: 4
27 Sep 2021 07:24:29,876 INFO : Inserting LDHA
27 Sep 2021 07:24:29,901 INFO : 82% Done
27 Sep 2021 07:24:30,264 INFO : 83% Done
27 Sep 2021 07:24:30,641 INFO : 84% Done
27 Sep 2021 07:24:31,077 INFO : 86% Done
27 Sep 2021 07:24:31,463 INFO : 87% Done
27 Sep 2021 07:24:31,932 DEBUG: Total peptides inserted: 5
27 Sep 2021 07:24:31,932 INFO : Inserting LDHB
27 Sep 2021 07:24:31,964 INFO : 89% Done
27 Sep 2021 07:24:32,415 INFO : 90% Done
27 Sep 2021 07:24:32,875 INFO : 91% Done
27 Sep 2021 07:24:33,438 INFO : 93% Done
27 Sep 2021 07:24:33,801 DEBUG: Total peptides inserted: 4
27 Sep 2021 07:24:33,801 INFO : Inserting LDH
27 Sep 2021 07:24:33,829 INFO : 94% Done
27 Sep 2021 07:24:34,260 DEBUG: Total peptides inserted: 1
27 Sep 2021 07:24:34,260 INFO : Inserting MSLN
27 Sep 2021 07:24:34,285 INFO : 95% Done
27 Sep 2021 07:24:34,665 INFO : 97% Done
27 Sep 2021 07:24:35,105 INFO : 98% Done
27 Sep 2021 07:24:35,525 DEBUG: Total peptides inserted: 3
27 Sep 2021 07:24:35,527 INFO : Done parsing Skyline document.
27 Sep 2021 07:24:35,529 INFO : Creating and populating temp tables for Proportion values
27 Sep 2021 07:24:35,775 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
27 Sep 2021 07:24:37,249 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
27 Sep 2021 07:24:37,823 INFO : Cleaning up temp tables
27 Sep 2021 07:24:38,249 INFO : Completed import of Skyline document from Robak et al. 2021_MRM panel_2021-09-23_13-50-26.sky.zip
27 Sep 2021 07:24:38,253 INFO : 100% Done
27 Sep 2021 07:24:38,259 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26.sky.zip into the system
27 Sep 2021 07:24:38,267 INFO : Done importing xar
27 Sep 2021 07:24:38,270 INFO : Loading pages and webpart properties
27 Sep 2021 07:24:38,381 INFO : Done importing pages and webpart properties
27 Sep 2021 07:24:38,381 INFO : 
27 Sep 2021 07:24:38,381 INFO : Experiment import completed successfully.
27 Sep 2021 07:24:38,382 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
27 Sep 2021 07:24:38,477 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
27 Sep 2021 07:24:38,478 INFO : 
27 Sep 2021 07:24:38,478 INFO : Finishing up experiment copy.
27 Sep 2021 07:24:38,481 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
27 Sep 2021 07:24:38,484 INFO : Assigning a DOI.
27 Sep 2021 07:24:39,787 INFO : Assigned DOI: 10.6069/rkkz-1z80
27 Sep 2021 07:24:39,792 INFO : Updating access URL to point to the new copy of the data.
27 Sep 2021 07:24:39,798 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
27 Sep 2021 07:24:39,799 INFO : Removing copy permissions given to journal.
27 Sep 2021 07:24:39,811 INFO : Adding read permissions to all users that are folder admins in the source container.
27 Sep 2021 07:24:39,821 INFO : Setting the TargetedMS folder type to 'Experimental Data'
27 Sep 2021 07:24:39,832 INFO : Updating the 'Raw Data' tab configuration
27 Sep 2021 07:24:39,835 INFO : Updating dataFileUrls for run Robak et al. 2021_MRM panel_2021-09-23_13-50-26.sky.zip; targetedms run ID 120986
27 Sep 2021 07:24:39,835 INFO : Updating dataFileUrl...
27 Sep 2021 07:24:39,835 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26.sky.zip
27 Sep 2021 07:24:39,836 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel/@files/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26.sky.zip
27 Sep 2021 07:24:39,839 INFO : Updating dataFileUrl...
27 Sep 2021 07:24:39,839 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel_0d1987c4-01cb-103a-b54f-fea6ddf5779e/_temp__2021-09-27_07-18-47/export/xar/experiments_and_runs.xar.exploded/Run117925/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26/Robak%20et%20al.%202021_MRM%20panel.skyd
27 Sep 2021 07:24:39,839 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Polish%20Acad%20Sciences%20IBB%20MS%20Lab%20-%2034%20marker%20panel/@files/Robak%20et%20al.%202021_MRM%20panel_2021-09-23_13-50-26/Robak%20et%20al.%202021_MRM%20panel.skyd
27 Sep 2021 07:24:39,842 INFO : Creating a reviewer account.
27 Sep 2021 07:24:40,054 INFO : Created reviewer with email: User panorama+reviewer70@proteinms.net
27 Sep 2021 07:24:40,062 INFO : Hiding the Data Pipeline tab.
27 Sep 2021 07:24:40,161 INFO : Emailing submitter.
27 Sep 2021 07:24:40,288 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'