06 Jul 2023 09:32:08,581 INFO : Copying experiment "Gut Microbiome IMS-MS Experiments" from folder /UNC - Baker Lab/James Dodds- Gut Microbiome IMS Publication to /Panorama Public/2023/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication
06 Jul 2023 09:32:08,581 INFO : =======================================
06 Jul 2023 09:32:08,600 DEBUG: Resetting Job ID: 30c96540-fe48-103b-afc6-fea6ddf51ba4
06 Jul 2023 09:32:08,622 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
06 Jul 2023 09:32:08,622 INFO :
06 Jul 2023 09:32:08,622 INFO : Exporting experiment.
06 Jul 2023 09:32:26,682 INFO : Exporting files metadata.
06 Jul 2023 09:32:26,682 DEBUG: [/UNC - Baker Lab/James Dodds- Gut Microbiome IMS Publication] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export
06 Jul 2023 09:32:26,685 INFO :
06 Jul 2023 09:32:26,685 INFO : Experiment export completed successfully.
06 Jul 2023 09:32:26,685 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
06 Jul 2023 09:32:26,709 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
06 Jul 2023 09:32:26,709 INFO :
06 Jul 2023 09:32:26,709 INFO : Importing experiment.
06 Jul 2023 09:32:26,710 DEBUG: [/Panorama Public/2023/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export
06 Jul 2023 09:32:26,711 INFO : Loading folder properties (folder type, settings and active modules)
06 Jul 2023 09:32:26,711 DEBUG: [/Panorama Public/2023/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication] Folder type: Targeted MS
06 Jul 2023 09:32:26,711 DEBUG: [/Panorama Public/2023/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication] Active modules: PanoramaPublic, Wiki, Experiment, API, Query, Announcements, Pipeline, Assay, MS2, Core, Search, FileContent, Issues, TargetedMS
06 Jul 2023 09:32:26,772 INFO : Done importing folder properties (folder type, settings and active modules)
06 Jul 2023 09:32:26,773 INFO : Loading container specific module properties
06 Jul 2023 09:32:26,776 INFO : Done importing container specific module properties
06 Jul 2023 09:32:26,777 INFO : Loading etl definitions
06 Jul 2023 09:32:26,778 INFO : Loading wikis
06 Jul 2023 09:32:26,779 INFO : 0 wikis imported
06 Jul 2023 09:32:26,779 INFO : Done importing wikis
06 Jul 2023 09:32:26,779 INFO : Starting to copy files
06 Jul 2023 09:32:31,148 INFO : Copied 12 files
06 Jul 2023 09:32:31,148 INFO : Ensuring exp.data rows exist for imported files
06 Jul 2023 09:32:31,207 INFO : Starting Sample Type and Data Class import
06 Jul 2023 09:32:31,207 INFO : No types XAR file to process.
06 Jul 2023 09:32:31,207 INFO : Finished importing Sample Types and Data Classes
06 Jul 2023 09:32:31,208 INFO : Loading xar
06 Jul 2023 09:32:33,226 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip'
06 Jul 2023 09:32:33,228 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Core'
06 Jul 2023 09:32:33,229 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Output'
06 Jul 2023 09:32:33,229 DEBUG: Protocol import complete
06 Jul 2023 09:32:33,230 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11736:Gut+Microbiome+IMS-MS+Experiments'
06 Jul 2023 09:32:33,230 DEBUG: Experiment/Run group import complete
06 Jul 2023 09:32:33,238 DEBUG: Protocol action set import complete
06 Jul 2023 09:32:33,245 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip'
06 Jul 2023 09:32:33,251 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11736:ddb64d37-e152-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,253 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11736:ddb64c9f-e152-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,254 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Core'
06 Jul 2023 09:32:33,255 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Output'
06 Jul 2023 09:32:33,256 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11736:ddb64e60-e152-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,260 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip'
06 Jul 2023 09:32:33,264 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11736:f7fc09aa-e153-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,266 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11736:f7fc0912-e153-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,266 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Core'
06 Jul 2023 09:32:33,268 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11736:TargetedMS.ImportSkyZip.Output'
06 Jul 2023 09:32:33,268 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11736:f7fc0ae3-e153-103b-965b-fea6ddf56188'
06 Jul 2023 09:32:33,269 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023.skyd into the system
06 Jul 2023 09:32:33,269 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023.skyd into the system
06 Jul 2023 09:32:33,269 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37.sky.zip into the system
06 Jul 2023 09:32:33,270 INFO : Starting import from FMT Study MCBA Conjugates May 30 2023_2023-05-30_16-08-37.sky.zip
06 Jul 2023 09:32:33,274 INFO : Starting to import Skyline document from FMT Study MCBA Conjugates May 30 2023_2023-05-30_16-08-37.sky.zip
06 Jul 2023 09:32:33,290 INFO : Expanding FMT Study MCBA Conjugates May 30 2023.skyd
06 Jul 2023 09:32:33,796 INFO : Expanding FMT Study MCBA Conjugates May 30 2023.sky.view
06 Jul 2023 09:32:33,796 INFO : Expanding FMT Study MCBA Conjugates May 30 2023.sky
06 Jul 2023 09:32:33,799 INFO : Expanding FMT Study MCBA Conjugates May 30 2023.skyl
06 Jul 2023 09:32:33,800 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
06 Jul 2023 09:32:33,809 INFO : 2% Done
06 Jul 2023 09:32:34,090 DEBUG: Starting to load chromatogram headers
06 Jul 2023 09:32:34,103 DEBUG: Done loading chromatogram headers
06 Jul 2023 09:32:34,321 INFO : Inserting Bile Acid Standards
06 Jul 2023 09:32:34,324 INFO : 5% Done
06 Jul 2023 09:32:34,342 INFO : 7% Done
06 Jul 2023 09:32:34,354 INFO : 10% Done
06 Jul 2023 09:32:34,366 INFO : 12% Done
06 Jul 2023 09:32:34,378 INFO : 15% Done
06 Jul 2023 09:32:34,390 INFO : 18% Done
06 Jul 2023 09:32:34,404 INFO : 20% Done
06 Jul 2023 09:32:34,415 INFO : 23% Done
06 Jul 2023 09:32:34,426 INFO : 25% Done
06 Jul 2023 09:32:34,437 INFO : 26% Done
06 Jul 2023 09:32:34,449 INFO : 29% Done
06 Jul 2023 09:32:34,461 INFO : 31% Done
06 Jul 2023 09:32:34,472 INFO : 34% Done
06 Jul 2023 09:32:34,483 INFO : 36% Done
06 Jul 2023 09:32:34,494 INFO : 39% Done
06 Jul 2023 09:32:34,505 INFO : 41% Done
06 Jul 2023 09:32:34,518 INFO : 44% Done
06 Jul 2023 09:32:34,527 DEBUG: Total molecules inserted: 17
06 Jul 2023 09:32:34,527 INFO : Inserting BA-AA Synthetic Conjugates
06 Jul 2023 09:32:34,530 INFO : 46% Done
06 Jul 2023 09:32:34,542 INFO : 49% Done
06 Jul 2023 09:32:34,554 INFO : 52% Done
06 Jul 2023 09:32:34,565 INFO : 54% Done
06 Jul 2023 09:32:34,576 INFO : 57% Done
06 Jul 2023 09:32:34,587 INFO : 59% Done
06 Jul 2023 09:32:34,597 INFO : 62% Done
06 Jul 2023 09:32:34,609 INFO : 64% Done
06 Jul 2023 09:32:34,621 INFO : 67% Done
06 Jul 2023 09:32:34,634 INFO : 69% Done
06 Jul 2023 09:32:34,646 INFO : 71% Done
06 Jul 2023 09:32:34,658 INFO : 74% Done
06 Jul 2023 09:32:34,668 INFO : 75% Done
06 Jul 2023 09:32:34,680 INFO : 78% Done
06 Jul 2023 09:32:34,692 INFO : 81% Done
06 Jul 2023 09:32:34,703 INFO : 83% Done
06 Jul 2023 09:32:34,714 INFO : 86% Done
06 Jul 2023 09:32:34,726 INFO : 88% Done
06 Jul 2023 09:32:34,739 INFO : 91% Done
06 Jul 2023 09:32:34,750 INFO : 93% Done
06 Jul 2023 09:32:34,763 INFO : 96% Done
06 Jul 2023 09:32:34,775 INFO : 98% Done
06 Jul 2023 09:32:34,785 DEBUG: Total molecules inserted: 22
06 Jul 2023 09:32:34,785 INFO : Done parsing Skyline document.
06 Jul 2023 09:32:34,842 INFO : Creating and populating temp tables for Proportion values
06 Jul 2023 09:32:34,918 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
06 Jul 2023 09:32:34,956 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
06 Jul 2023 09:32:34,983 INFO : Cleaning up temp tables
06 Jul 2023 09:32:35,249 INFO : Completed import of Skyline document from FMT Study MCBA Conjugates May 30 2023_2023-05-30_16-08-37.sky.zip
06 Jul 2023 09:32:35,251 INFO : 100% Done
06 Jul 2023 09:32:35,254 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37.sky.zip into the system
06 Jul 2023 09:32:35,255 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40/Mouse%20Cecal%20IDs%20May%2030%202023.skyd into the system
06 Jul 2023 09:32:35,255 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40/Mouse%20Cecal%20IDs%20May%2030%202023.skyd into the system
06 Jul 2023 09:32:35,255 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40.sky.zip into the system
06 Jul 2023 09:32:35,256 INFO : Starting import from Mouse Cecal IDs May 30 2023_2023-05-30_16-10-40.sky.zip
06 Jul 2023 09:32:35,259 INFO : Starting to import Skyline document from Mouse Cecal IDs May 30 2023_2023-05-30_16-10-40.sky.zip
06 Jul 2023 09:32:35,289 INFO : Expanding Mouse Cecal IDs May 30 2023.skyd
06 Jul 2023 09:32:35,893 INFO : Expanding Mouse Cecal IDs May 30 2023.sky.view
06 Jul 2023 09:32:35,894 INFO : Expanding Mouse Cecal IDs May 30 2023.sky
06 Jul 2023 09:32:35,897 INFO : Expanding Mouse Cecal IDs May 30 2023.skyl
06 Jul 2023 09:32:35,899 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
06 Jul 2023 09:32:35,902 INFO : 2% Done
06 Jul 2023 09:32:36,170 DEBUG: Starting to load chromatogram headers
06 Jul 2023 09:32:36,183 DEBUG: Done loading chromatogram headers
06 Jul 2023 09:32:36,377 INFO : Inserting Bile Acid Standards
06 Jul 2023 09:32:36,380 INFO : 4% Done
06 Jul 2023 09:32:36,394 INFO : 6% Done
06 Jul 2023 09:32:36,406 INFO : 8% Done
06 Jul 2023 09:32:36,416 INFO : 10% Done
06 Jul 2023 09:32:36,428 INFO : 12% Done
06 Jul 2023 09:32:36,438 INFO : 14% Done
06 Jul 2023 09:32:36,450 INFO : 16% Done
06 Jul 2023 09:32:36,462 INFO : 18% Done
06 Jul 2023 09:32:36,473 INFO : 20% Done
06 Jul 2023 09:32:36,484 INFO : 22% Done
06 Jul 2023 09:32:36,495 INFO : 24% Done
06 Jul 2023 09:32:36,507 INFO : 25% Done
06 Jul 2023 09:32:36,519 INFO : 27% Done
06 Jul 2023 09:32:36,530 INFO : 29% Done
06 Jul 2023 09:32:36,541 INFO : 31% Done
06 Jul 2023 09:32:36,556 INFO : 33% Done
06 Jul 2023 09:32:36,567 INFO : 35% Done
06 Jul 2023 09:32:36,579 INFO : 38% Done
06 Jul 2023 09:32:36,590 INFO : 40% Done
06 Jul 2023 09:32:36,602 INFO : 42% Done
06 Jul 2023 09:32:36,611 DEBUG: Total molecules inserted: 20
06 Jul 2023 09:32:36,611 INFO : Inserting BA-AA Synthetic Conjugates
06 Jul 2023 09:32:36,614 INFO : 44% Done
06 Jul 2023 09:32:36,625 INFO : 46% Done
06 Jul 2023 09:32:36,636 INFO : 48% Done
06 Jul 2023 09:32:36,648 INFO : 50% Done
06 Jul 2023 09:32:36,659 INFO : 52% Done
06 Jul 2023 09:32:36,671 INFO : 54% Done
06 Jul 2023 09:32:36,682 INFO : 56% Done
06 Jul 2023 09:32:36,693 INFO : 58% Done
06 Jul 2023 09:32:36,705 INFO : 60% Done
06 Jul 2023 09:32:36,717 INFO : 62% Done
06 Jul 2023 09:32:36,730 INFO : 64% Done
06 Jul 2023 09:32:36,741 INFO : 66% Done
06 Jul 2023 09:32:36,754 INFO : 68% Done
06 Jul 2023 09:32:36,766 INFO : 70% Done
06 Jul 2023 09:32:36,778 INFO : 72% Done
06 Jul 2023 09:32:36,788 INFO : 74% Done
06 Jul 2023 09:32:36,800 INFO : 75% Done
06 Jul 2023 09:32:36,811 INFO : 77% Done
06 Jul 2023 09:32:36,822 INFO : 80% Done
06 Jul 2023 09:32:36,833 INFO : 82% Done
06 Jul 2023 09:32:36,845 INFO : 84% Done
06 Jul 2023 09:32:36,856 INFO : 86% Done
06 Jul 2023 09:32:36,868 INFO : 88% Done
06 Jul 2023 09:32:36,880 INFO : 90% Done
06 Jul 2023 09:32:36,893 INFO : 92% Done
06 Jul 2023 09:32:36,905 INFO : 94% Done
06 Jul 2023 09:32:36,916 INFO : 96% Done
06 Jul 2023 09:32:36,927 INFO : 98% Done
06 Jul 2023 09:32:36,938 DEBUG: Total molecules inserted: 28
06 Jul 2023 09:32:36,939 INFO : Done parsing Skyline document.
06 Jul 2023 09:32:37,011 INFO : Creating and populating temp tables for Proportion values
06 Jul 2023 09:32:37,082 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
06 Jul 2023 09:32:37,129 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
06 Jul 2023 09:32:37,164 INFO : Cleaning up temp tables
06 Jul 2023 09:32:37,406 INFO : Completed import of Skyline document from Mouse Cecal IDs May 30 2023_2023-05-30_16-10-40.sky.zip
06 Jul 2023 09:32:37,408 INFO : 100% Done
06 Jul 2023 09:32:37,412 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40.sky.zip into the system
06 Jul 2023 09:32:37,421 INFO : Done importing xar
06 Jul 2023 09:32:37,422 INFO : Loading pages and webpart properties
06 Jul 2023 09:32:37,474 INFO : Done importing 3 page(s) with 5 webpart(s)
06 Jul 2023 09:32:37,474 INFO : Loading File Browser config
06 Jul 2023 09:32:37,474 INFO : Done importing File Browser config
06 Jul 2023 09:32:37,475 INFO : Starting Sample Status Data import
06 Jul 2023 09:32:37,475 INFO : No sample types XAR file to process.
06 Jul 2023 09:32:37,475 INFO : Finished importing Sample Status Data
06 Jul 2023 09:32:37,479 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
06 Jul 2023 09:32:37,480 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
06 Jul 2023 09:32:37,480 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
06 Jul 2023 09:32:37,481 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
06 Jul 2023 09:32:37,481 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
06 Jul 2023 09:32:37,481 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
06 Jul 2023 09:32:37,481 INFO : Importing files metadata.
06 Jul 2023 09:32:37,481 DEBUG: [/Panorama Public/2023/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC Baker Lab - James Dodds Gut Microbiome IMS Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export
06 Jul 2023 09:32:37,482 INFO :
06 Jul 2023 09:32:37,482 INFO : Experiment import completed successfully.
06 Jul 2023 09:32:37,482 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
06 Jul 2023 09:32:37,500 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
06 Jul 2023 09:32:37,500 INFO :
06 Jul 2023 09:32:37,500 INFO : Checking for library folders.
06 Jul 2023 09:32:37,501 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
06 Jul 2023 09:32:37,515 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
06 Jul 2023 09:32:37,515 INFO :
06 Jul 2023 09:32:37,515 INFO : Finishing up experiment copy.
06 Jul 2023 09:32:37,517 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
06 Jul 2023 09:32:37,517 INFO : Setting version on new experiment to 1
06 Jul 2023 09:32:37,517 INFO : Assigning a DOI.
06 Jul 2023 09:32:38,334 INFO : Assigned DOI: 10.6069/wnvs-pg83
06 Jul 2023 09:32:38,336 INFO : Updating permanent link to point to the new copy of the data.
06 Jul 2023 09:32:38,340 INFO : Removing copy permissions given to Panorama Public
06 Jul 2023 09:32:38,340 INFO : Adding read permissions to all users that are folder admins in the source folder.
06 Jul 2023 09:32:38,340 INFO : Assigning PanoramaPublicSubmitterRole to jndodds@unc.edu
06 Jul 2023 09:32:38,340 INFO : Assigning PanoramaPublicSubmitterRole to erinmsb@unc.edu
06 Jul 2023 09:32:38,340 INFO : Assigning PanoramaPublicSubmitterRole to jndodds@unc.edu
06 Jul 2023 09:32:38,340 INFO : Adding user jndodds@unc.edu to group Panorama Public Submitters
06 Jul 2023 09:32:38,344 INFO : Adding user erinmsb@unc.edu to group Panorama Public Submitters
06 Jul 2023 09:32:38,346 INFO : User jndodds@unc.edu is already a member of group Panorama Public Submitters
06 Jul 2023 09:32:38,359 INFO : Updating the 'Raw Data' tab configuration
06 Jul 2023 09:32:38,360 INFO : Updating dataFileUrls for run FMT Study MCBA Conjugates May 30 2023_2023-05-30_16-08-37.sky.zip; targetedms run ID 165938
06 Jul 2023 09:32:38,361 INFO : Updating dataFileUrl...
06 Jul 2023 09:32:38,361 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37.sky.zip
06 Jul 2023 09:32:38,361 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication/@files/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37.sky.zip
06 Jul 2023 09:32:38,362 INFO : Updating dataFileUrl...
06 Jul 2023 09:32:38,362 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159936/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023.skyd
06 Jul 2023 09:32:38,362 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication/@files/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023_2023-05-30_16-08-37/FMT%20Study%20MCBA%20Conjugates%20May%2030%202023.skyd
06 Jul 2023 09:32:38,365 INFO : Updating dataFileUrls for run Mouse Cecal IDs May 30 2023_2023-05-30_16-10-40.sky.zip; targetedms run ID 165939
06 Jul 2023 09:32:38,365 INFO : Updating dataFileUrl...
06 Jul 2023 09:32:38,365 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40/Mouse%20Cecal%20IDs%20May%2030%202023.skyd
06 Jul 2023 09:32:38,365 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication/@files/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40/Mouse%20Cecal%20IDs%20May%2030%202023.skyd
06 Jul 2023 09:32:38,366 INFO : Updating dataFileUrl...
06 Jul 2023 09:32:38,366 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication_30c96520-fe48-103b-afc6-fea6ddf51ba4/_temp__2023-07-06_09-32-07/export/xar/experiments_and_runs.xar.exploded/Run159937/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40.sky.zip
06 Jul 2023 09:32:38,366 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/UNC%20Baker%20Lab%20-%20James%20Dodds%20Gut%20Microbiome%20IMS%20Publication/@files/Mouse%20Cecal%20IDs%20May%2030%202023_2023-05-30_16-10-40.sky.zip
06 Jul 2023 09:32:38,370 INFO : Creating a reviewer account.
06 Jul 2023 09:32:38,556 INFO : Created reviewer with email: User panorama+reviewer195@proteinms.net
06 Jul 2023 09:32:38,572 INFO : Adding user panorama+reviewer195@proteinms.net to group Reviewers
06 Jul 2023 09:32:38,573 INFO : Hiding the Data Pipeline tab.
06 Jul 2023 09:32:38,577 INFO : Updating Submission. Setting copiedExperimentId to 1645
06 Jul 2023 09:32:38,640 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'