05 Oct 2021 21:18:58,081 INFO : Copying experiment "Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment Analysis" from folder /KTH - Uhlen Lab/SARS-CoV-2 SISCAPA to /Panorama Public/2021/KTH Uhlen Lab - SARS-CoV-2 SISCAPA
05 Oct 2021 21:18:58,081 INFO : =======================================
05 Oct 2021 21:18:58,304 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
05 Oct 2021 21:18:58,304 INFO :
05 Oct 2021 21:18:58,305 INFO : Exporting experiment.
05 Oct 2021 21:19:05,196 INFO :
05 Oct 2021 21:19:05,196 INFO : Experiment export completed successfully.
05 Oct 2021 21:19:05,196 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
05 Oct 2021 21:19:05,259 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
05 Oct 2021 21:19:05,259 INFO :
05 Oct 2021 21:19:05,260 INFO : Importing experiment.
05 Oct 2021 21:19:05,265 INFO : Loading folder properties (folder type, settings and active modules)
05 Oct 2021 21:19:05,376 INFO : Done importing folder properties (folder type, settings and active modules)
05 Oct 2021 21:19:05,380 INFO : Loading etl definitions
05 Oct 2021 21:19:05,382 INFO : Loading wikis
05 Oct 2021 21:19:05,384 INFO : 0 wikis imported
05 Oct 2021 21:19:05,384 INFO : Done importing wikis
05 Oct 2021 21:19:05,384 INFO : Starting to copy files
05 Oct 2021 21:19:06,088 INFO : Copied 376 files
05 Oct 2021 21:19:06,088 INFO : Ensuring exp.data rows exist for imported files
05 Oct 2021 21:19:07,790 INFO : Starting Sample Type and Data Class import
05 Oct 2021 21:19:07,791 INFO : No types XAR file to process.
05 Oct 2021 21:19:07,791 INFO : Finished importing Sample Types and Data Classes
05 Oct 2021 21:19:07,793 INFO : Loading xar
05 Oct 2021 21:19:07,899 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip'
05 Oct 2021 21:19:07,902 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip.Core'
05 Oct 2021 21:19:07,904 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip.Output'
05 Oct 2021 21:19:07,904 DEBUG: Protocol import complete
05 Oct 2021 21:19:07,906 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9172:Rapid+and+Sensitive+Detection+of+SARS-CoV-2+Infection+Using+Quantitative+Peptide+Enrichment+Analysis'
05 Oct 2021 21:19:07,906 DEBUG: Experiment/Run group import complete
05 Oct 2021 21:19:07,916 DEBUG: Protocol action set import complete
05 Oct 2021 21:19:07,929 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip'
05 Oct 2021 21:19:07,937 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9172:7f33cd98-042c-103a-b54f-fea6ddf5779e'
05 Oct 2021 21:19:07,942 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9172:7f33ca20-042c-103a-b54f-fea6ddf5779e'
05 Oct 2021 21:19:07,942 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip.Core'
05 Oct 2021 21:19:07,945 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9172:TargetedMS.ImportSkyZip.Output'
05 Oct 2021 21:19:07,945 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9172:7f33cda8-042c-103a-b54f-fea6ddf5779e'
05 Oct 2021 21:19:07,947 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52/sars-cov-2_siscapa.skyd into the system
05 Oct 2021 21:19:07,947 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52/sars-cov-2_siscapa.skyd into the system
05 Oct 2021 21:19:07,948 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip into the system
05 Oct 2021 21:19:07,949 INFO : Starting import from sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip
05 Oct 2021 21:19:07,954 INFO : Starting to import Skyline document from sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip
05 Oct 2021 21:19:07,957 INFO : Expanding sars-cov-2_siscapa.skyd
05 Oct 2021 21:19:08,015 INFO : Expanding sars-cov-2_siscapa.sky.view
05 Oct 2021 21:19:08,016 INFO : Expanding sars-cov-2_siscapa.sky
05 Oct 2021 21:19:08,018 INFO : Expanding sars-cov-2_siscapa.skyl
05 Oct 2021 21:19:08,021 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
05 Oct 2021 21:19:08,045 INFO : 18% Done
05 Oct 2021 21:19:08,106 DEBUG: Starting to load chromatogram headers
05 Oct 2021 21:19:08,113 DEBUG: Done loading chromatogram headers
05 Oct 2021 21:19:08,516 INFO : Inserting NCAP peptide
05 Oct 2021 21:19:08,579 INFO : 98% Done
05 Oct 2021 21:19:09,087 DEBUG: Total peptides inserted: 1
05 Oct 2021 21:19:09,089 INFO : Done parsing Skyline document.
05 Oct 2021 21:19:10,746 INFO : Creating and populating temp tables for Proportion values
05 Oct 2021 21:19:10,766 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
05 Oct 2021 21:19:10,797 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
05 Oct 2021 21:19:10,809 INFO : Cleaning up temp tables
05 Oct 2021 21:19:11,081 INFO : Completed import of Skyline document from sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip
05 Oct 2021 21:19:11,086 INFO : 100% Done
05 Oct 2021 21:19:11,092 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip into the system
05 Oct 2021 21:19:11,100 INFO : Done importing xar
05 Oct 2021 21:19:11,103 INFO : Loading pages and webpart properties
05 Oct 2021 21:19:11,197 INFO : Done importing pages and webpart properties
05 Oct 2021 21:19:11,198 INFO :
05 Oct 2021 21:19:11,198 INFO : Experiment import completed successfully.
05 Oct 2021 21:19:11,198 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
05 Oct 2021 21:19:11,248 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
05 Oct 2021 21:19:11,248 INFO :
05 Oct 2021 21:19:11,249 INFO : Finishing up experiment copy.
05 Oct 2021 21:19:11,251 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
05 Oct 2021 21:19:11,256 INFO : Copying ProteomeXchange ID from the previous copy of the data.
05 Oct 2021 21:19:11,256 INFO : Copying DOI from the previous copy of the data.
05 Oct 2021 21:19:11,261 INFO : Updating access URL to point to the new copy of the data.
05 Oct 2021 21:19:11,269 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
05 Oct 2021 21:19:11,271 INFO : Removing copy permissions given to journal.
05 Oct 2021 21:19:11,289 INFO : Adding read permissions to all users that are folder admins in the source container.
05 Oct 2021 21:19:11,291 INFO : Adding read permissions to all users that had read access to previous copy.
05 Oct 2021 21:19:11,303 INFO : Setting the TargetedMS folder type to 'Experimental Data'
05 Oct 2021 21:19:11,310 INFO : Updating the 'Raw Data' tab configuration
05 Oct 2021 21:19:11,313 INFO : Updating dataFileUrls for run sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip; targetedms run ID 121567
05 Oct 2021 21:19:11,313 INFO : Updating dataFileUrl...
05 Oct 2021 21:19:11,314 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip
05 Oct 2021 21:19:11,314 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA/@files/sars-cov-2_siscapa_2021-09-30_16-56-52.sky.zip
05 Oct 2021 21:19:11,316 INFO : Updating dataFileUrl...
05 Oct 2021 21:19:11,317 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA_46a990a4-088a-103a-b54f-fea6ddf5779e/_temp__2021-10-05_21-18-57/export/xar/experiments_and_runs.xar.exploded/Run118336/sars-cov-2_siscapa_2021-09-30_16-56-52/sars-cov-2_siscapa.skyd
05 Oct 2021 21:19:11,317 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA/@files/sars-cov-2_siscapa_2021-09-30_16-56-52/sars-cov-2_siscapa.skyd
05 Oct 2021 21:19:11,320 INFO : Hiding the Data Pipeline tab.
05 Oct 2021 21:19:11,536 INFO : Emailing submitter.
05 Oct 2021 21:19:11,754 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'