05 Sep 2022 14:45:53,972 INFO : Copying experiment "Reduction of MRM protein target list using correlation analysis" from folder /Nestle NDC - Askeaton/Ebhardt_CorrAnalysis/MRM_data to /Panorama Public/2022/Nestle NDC Askeaton - MRM_data
05 Sep 2022 14:45:53,972 INFO : =======================================
05 Sep 2022 14:46:18,845 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
05 Sep 2022 14:46:18,845 INFO :
05 Sep 2022 14:46:18,845 INFO : Exporting experiment.
05 Sep 2022 14:48:31,581 INFO : Exporting files metadata.
05 Sep 2022 14:48:31,581 DEBUG: [/Nestle NDC - Askeaton/Ebhardt_CorrAnalysis/MRM_data] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle NDC Askeaton - MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export
05 Sep 2022 14:48:31,672 INFO :
05 Sep 2022 14:48:31,672 INFO : Experiment export completed successfully.
05 Sep 2022 14:48:31,672 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
05 Sep 2022 14:48:31,700 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
05 Sep 2022 14:48:31,700 INFO :
05 Sep 2022 14:48:31,700 INFO : Importing experiment.
05 Sep 2022 14:48:31,701 DEBUG: [/Panorama Public/2022/Nestle NDC Askeaton - MRM_data] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle NDC Askeaton - MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export
05 Sep 2022 14:48:31,703 INFO : Loading folder properties (folder type, settings and active modules)
05 Sep 2022 14:48:31,703 DEBUG: [/Panorama Public/2022/Nestle NDC Askeaton - MRM_data] Folder type: Targeted MS
05 Sep 2022 14:48:31,703 DEBUG: [/Panorama Public/2022/Nestle NDC Askeaton - MRM_data] Active modules: API, TargetedMS, Wiki, Announcements, Issues, MS2, PanoramaPublic, Query, Internal, FileContent, Experiment, Pipeline, Core, Search, Assay
05 Sep 2022 14:48:31,797 INFO : Done importing folder properties (folder type, settings and active modules)
05 Sep 2022 14:48:31,799 INFO : Loading container specific module properties
05 Sep 2022 14:48:31,810 INFO : Done importing container specific module properties
05 Sep 2022 14:48:31,811 INFO : Loading etl definitions
05 Sep 2022 14:48:31,813 INFO : Loading wikis
05 Sep 2022 14:48:31,814 INFO : 0 wikis imported
05 Sep 2022 14:48:31,814 INFO : Done importing wikis
05 Sep 2022 14:48:31,815 INFO : Starting to copy files
05 Sep 2022 14:50:31,833 INFO : 192 files copied, now copying P9H-00038.mzXML
05 Sep 2022 14:50:34,828 INFO : 211 files copied, now copying Ebhardt_CorrAnalysis_MRM_data.skyl
05 Sep 2022 14:50:35,273 INFO : 215 files copied, now copying MFGM_24_prot_DB.blib
05 Sep 2022 14:50:35,375 INFO : 221 files copied, now copying Ebhardt_CorrAnalysis_MRM_data.skyl
05 Sep 2022 14:50:35,429 INFO : Copied 227 files
05 Sep 2022 14:50:35,430 INFO : Ensuring exp.data rows exist for imported files
05 Sep 2022 14:50:36,560 INFO : Starting Sample Type and Data Class import
05 Sep 2022 14:50:36,560 INFO : No types XAR file to process.
05 Sep 2022 14:50:36,560 INFO : Finished importing Sample Types and Data Classes
05 Sep 2022 14:50:36,561 INFO : Loading xar
05 Sep 2022 14:50:36,650 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip.Core'
05 Sep 2022 14:50:36,652 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip.Output'
05 Sep 2022 14:50:36,654 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip'
05 Sep 2022 14:50:36,654 DEBUG: Protocol import complete
05 Sep 2022 14:50:36,655 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-10707:Reduction+of+MRM+protein+target+list+using+correlation+analysis'
05 Sep 2022 14:50:36,655 DEBUG: Experiment/Run group import complete
05 Sep 2022 14:50:36,665 DEBUG: Protocol action set import complete
05 Sep 2022 14:50:36,675 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip'
05 Sep 2022 14:50:36,685 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-10707:c3f085f3-0b61-103b-adec-fea6ddf58494'
05 Sep 2022 14:50:36,690 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-10707:c3f085da-0b61-103b-adec-fea6ddf58494'
05 Sep 2022 14:50:36,690 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip.Core'
05 Sep 2022 14:50:36,693 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10707:TargetedMS.ImportSkyZip.Output'
05 Sep 2022 14:50:36,694 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-10707:c3f085ff-0b61-103b-adec-fea6ddf58494'
05 Sep 2022 14:50:36,699 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01/Ebhardt_CorrAnalysis_MRM_data.skyd into the system
05 Sep 2022 14:50:36,699 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01/Ebhardt_CorrAnalysis_MRM_data.skyd into the system
05 Sep 2022 14:50:36,700 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip into the system
05 Sep 2022 14:50:36,701 INFO : Starting import from Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip
05 Sep 2022 14:50:36,707 INFO : Starting to import Skyline document from Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip
05 Sep 2022 14:50:36,708 INFO : Expanding 2022_03_timsToF.blib
05 Sep 2022 14:50:36,722 INFO : Expanding MFGM_24_prot_DB.blib
05 Sep 2022 14:50:36,740 INFO : Expanding Ebhardt_CorrAnalysis_MRM_data.skyd
05 Sep 2022 14:50:36,785 INFO : Expanding Ebhardt_CorrAnalysis_MRM_data.sky.view
05 Sep 2022 14:50:36,785 INFO : Expanding Ebhardt_CorrAnalysis_MRM_data.sky
05 Sep 2022 14:50:36,788 INFO : Expanding Ebhardt_CorrAnalysis_MRM_data.skyl
05 Sep 2022 14:50:36,797 INFO : 2% Done
05 Sep 2022 14:50:36,813 DEBUG: Starting to load chromatogram headers
05 Sep 2022 14:50:36,814 DEBUG: Done loading chromatogram headers
05 Sep 2022 14:50:37,027 INFO : Inserting 1|P02754|LACB_BOVIN
05 Sep 2022 14:50:37,047 INFO : 14% Done
05 Sep 2022 14:50:37,130 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,130 INFO : Inserting 2|P31096|OSTP_BOVIN
05 Sep 2022 14:50:37,144 INFO : 25% Done
05 Sep 2022 14:50:37,199 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,200 INFO : Inserting 3|P80457|XDH_BOVIN
05 Sep 2022 14:50:37,214 INFO : 35% Done
05 Sep 2022 14:50:37,292 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,293 INFO : Inserting 4|Q8WML4|MUC1_BOVIN
05 Sep 2022 14:50:37,399 INFO : 45% Done
05 Sep 2022 14:50:37,455 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,457 INFO : 46% Done
05 Sep 2022 14:50:37,457 INFO : Inserting 5|P24627|TRFL_BOVIN
05 Sep 2022 14:50:37,470 INFO : 58% Done
05 Sep 2022 14:50:37,533 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,533 INFO : Inserting 6|P00711|LALBA_BOVIN
05 Sep 2022 14:50:37,547 INFO : 69% Done
05 Sep 2022 14:50:37,604 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,604 INFO : Inserting 7|Q9TUM6|PLIN2_BOVIN
05 Sep 2022 14:50:37,618 INFO : 79% Done
05 Sep 2022 14:50:37,671 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,672 INFO : Inserting 8|P18892|BT1A1_BOVIN
05 Sep 2022 14:50:37,685 INFO : 90% Done
05 Sep 2022 14:50:37,739 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,739 INFO : Inserting 9|P02666|CASB_BOVIN
05 Sep 2022 14:50:37,753 INFO : 98% Done
05 Sep 2022 14:50:37,801 DEBUG: Total peptides inserted: 1
05 Sep 2022 14:50:37,802 INFO : Done parsing Skyline document.
05 Sep 2022 14:50:37,863 INFO : Creating and populating temp tables for Proportion values
05 Sep 2022 14:50:37,932 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
05 Sep 2022 14:50:37,951 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
05 Sep 2022 14:50:37,958 INFO : Cleaning up temp tables
05 Sep 2022 14:50:40,463 INFO : Completed import of Skyline document from Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip
05 Sep 2022 14:50:40,465 INFO : 100% Done
05 Sep 2022 14:50:40,470 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip into the system
05 Sep 2022 14:50:40,477 INFO : Done importing xar
05 Sep 2022 14:50:40,481 INFO : Loading pages and webpart properties
05 Sep 2022 14:50:40,566 INFO : Done importing 4 page(s) with 7 webpart(s)
05 Sep 2022 14:50:40,567 INFO : Starting Sample Status Data import
05 Sep 2022 14:50:40,567 INFO : No sample types XAR file to process.
05 Sep 2022 14:50:40,567 INFO : Finished importing Sample Status Data
05 Sep 2022 14:50:40,572 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
05 Sep 2022 14:50:40,574 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping
05 Sep 2022 14:50:40,575 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping
05 Sep 2022 14:50:40,575 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping
05 Sep 2022 14:50:40,576 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
05 Sep 2022 14:50:40,576 INFO : Importing files metadata.
05 Sep 2022 14:50:40,576 DEBUG: [/Panorama Public/2022/Nestle NDC Askeaton - MRM_data] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle NDC Askeaton - MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export
05 Sep 2022 14:50:40,577 INFO :
05 Sep 2022 14:50:40,577 INFO : Experiment import completed successfully.
05 Sep 2022 14:50:40,577 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
05 Sep 2022 14:50:40,603 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
05 Sep 2022 14:50:40,603 INFO :
05 Sep 2022 14:50:40,603 INFO : Checking for library folders.
05 Sep 2022 14:50:40,605 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
05 Sep 2022 14:50:40,627 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
05 Sep 2022 14:50:40,627 INFO :
05 Sep 2022 14:50:40,627 INFO : Finishing up experiment copy.
05 Sep 2022 14:50:40,629 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
05 Sep 2022 14:50:40,630 INFO : Setting version on new experiment to 1
05 Sep 2022 14:50:40,630 INFO : Assigning a ProteomeXchange ID.
05 Sep 2022 14:50:40,736 INFO : Assigning a DOI.
05 Sep 2022 14:50:41,452 INFO : Assigned DOI: 10.6069/2r4h-rm14
05 Sep 2022 14:50:41,455 INFO : Updating access URL to point to the new copy of the data.
05 Sep 2022 14:50:41,459 INFO : Removing copy permissions given to Panorama Public
05 Sep 2022 14:50:41,473 INFO : Adding read permissions to all users that are folder admins in the source folder.
05 Sep 2022 14:50:41,483 INFO : Updating the 'Raw Data' tab configuration
05 Sep 2022 14:50:41,486 INFO : Updating dataFileUrls for run Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip; targetedms run ID 144169
05 Sep 2022 14:50:41,486 INFO : Updating dataFileUrl...
05 Sep 2022 14:50:41,486 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip
05 Sep 2022 14:50:41,486 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/Nestle%20NDC%20Askeaton%20-%20MRM_data/@files/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01.sky.zip
05 Sep 2022 14:50:41,488 INFO : Updating dataFileUrl...
05 Sep 2022 14:50:41,488 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Nestle%20NDC%20Askeaton%20-%20MRM_data_a7789da2-0f91-103b-adec-fea6ddf58494/_temp__2022-09-05_14-45-53/export/xar/experiments_and_runs.xar.exploded/Run141797/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01/Ebhardt_CorrAnalysis_MRM_data.skyd
05 Sep 2022 14:50:41,488 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/Nestle%20NDC%20Askeaton%20-%20MRM_data/@files/Ebhardt_CorrAnalysis_MRM_data_2022-08-31_14-52-01/Ebhardt_CorrAnalysis_MRM_data.skyd
05 Sep 2022 14:50:41,496 INFO : Creating a reviewer account.
05 Sep 2022 14:50:41,723 INFO : Created reviewer with email: User panorama+reviewer143@proteinms.net
05 Sep 2022 14:50:41,734 INFO : Hiding the Data Pipeline tab.
05 Sep 2022 14:50:41,739 INFO : Updating Submission. Setting copiedExperimentId to 1503
05 Sep 2022 14:50:41,816 INFO : Emailing submitter.
05 Sep 2022 14:50:41,919 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'