10 Jun 2021 10:07:06,078 INFO : Copying experiment "The global Proteome and Ubiquitinome of bacterial and viral co-infected Bronchial Epithelial Cells" from folder /U Greifswald - Inst. Microbiology - MS Lab/Co-infection_16HBE to /Panorama Public/2021/U Greifswald Inst. Microbiology MS Lab - Co-infection_16HBE
10 Jun 2021 10:07:06,078 INFO : =======================================
10 Jun 2021 10:07:06,205 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
10 Jun 2021 10:07:06,205 INFO :
10 Jun 2021 10:07:06,205 INFO : Exporting experiment.
10 Jun 2021 10:12:28,258 INFO :
10 Jun 2021 10:12:28,258 INFO : Experiment export completed successfully.
10 Jun 2021 10:12:28,258 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
10 Jun 2021 10:12:28,298 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
10 Jun 2021 10:12:28,298 INFO :
10 Jun 2021 10:12:28,298 INFO : Importing experiment.
10 Jun 2021 10:12:28,303 INFO : Loading folder properties (folder type, settings and active modules)
10 Jun 2021 10:12:28,377 INFO : Done importing folder properties (folder type, settings and active modules)
10 Jun 2021 10:12:28,380 INFO : Loading etl definitions
10 Jun 2021 10:12:28,382 INFO : Loading wikis
10 Jun 2021 10:12:28,383 INFO : 0 wikis imported
10 Jun 2021 10:12:28,384 INFO : Done importing wikis
10 Jun 2021 10:12:28,384 INFO : Starting to copy files
10 Jun 2021 10:14:40,105 INFO : 10 files copied, now copying 210603_QE1_PM1_ThS_16HBE_TP_PRM_H1N1_01.raw
10 Jun 2021 10:16:47,794 INFO : 19 files copied, now copying 210602_QE1_PM1_ThS_16HBE_TP_PRM_LUG2012_01.raw
10 Jun 2021 10:17:50,027 INFO : 23 files copied, now copying 16HBE_TP_PRM_validation.sky.view
10 Jun 2021 10:17:51,170 INFO : Copied 27 files
10 Jun 2021 10:17:51,170 INFO : Ensuring exp.data rows exist for imported files
10 Jun 2021 10:17:51,314 INFO : Starting Sample Type and Data Class import
10 Jun 2021 10:17:51,314 INFO : No types XAR file to process.
10 Jun 2021 10:17:51,314 INFO : Finished importing Sample Types and Data Classes
10 Jun 2021 10:17:51,316 INFO : Loading xar
10 Jun 2021 10:17:51,419 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip'
10 Jun 2021 10:17:51,423 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip.Core'
10 Jun 2021 10:17:51,425 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip.Output'
10 Jun 2021 10:17:51,426 DEBUG: Protocol import complete
10 Jun 2021 10:17:51,427 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8679:The+global+Proteome+and+Ubiquitinome+of+bacterial+and+viral+co-infected+Bronchial+Epithelial+Cells'
10 Jun 2021 10:17:51,427 DEBUG: Experiment/Run group import complete
10 Jun 2021 10:17:51,437 DEBUG: Protocol action set import complete
10 Jun 2021 10:17:51,467 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip'
10 Jun 2021 10:17:51,477 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8679:a4ebfc58-ab54-1039-be5b-fea6ddf5138a'
10 Jun 2021 10:17:51,482 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8679:a4ebfc49-ab54-1039-be5b-fea6ddf5138a'
10 Jun 2021 10:17:51,482 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip.Core'
10 Jun 2021 10:17:51,486 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8679:TargetedMS.ImportSkyZip.Output'
10 Jun 2021 10:17:51,487 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8679:a4ebfcba-ab54-1039-be5b-fea6ddf5138a'
10 Jun 2021 10:17:51,489 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52/16HBE_TP_PRM_validation.skyd into the system
10 Jun 2021 10:17:51,490 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52/16HBE_TP_PRM_validation.skyd into the system
10 Jun 2021 10:17:51,490 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip into the system
10 Jun 2021 10:17:51,492 INFO : Starting import from 16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip
10 Jun 2021 10:17:51,497 INFO : Starting to import Skyline document from 16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip
10 Jun 2021 10:17:51,499 INFO : Expanding 16HBE_TP_PRM_validation.skyd
10 Jun 2021 10:17:51,549 INFO : Expanding 16HBE_TP_PRM_validation.sky.view
10 Jun 2021 10:17:51,550 INFO : Expanding 16HBE_TP_PRM_validation.sky
10 Jun 2021 10:17:51,556 INFO : Expanding 16HBE_TP_PRM_validation.skyl
10 Jun 2021 10:17:51,569 INFO : 2% Done
10 Jun 2021 10:17:51,617 DEBUG: Starting to load chromatogram headers
10 Jun 2021 10:17:51,619 DEBUG: Done loading chromatogram headers
10 Jun 2021 10:17:51,661 INFO : Inserting Q9Y281
10 Jun 2021 10:17:51,673 INFO : 3% Done
10 Jun 2021 10:17:51,706 INFO : 5% Done
10 Jun 2021 10:17:51,726 DEBUG: Total peptides inserted: 2
10 Jun 2021 10:17:51,726 INFO : Inserting P07305
10 Jun 2021 10:17:51,732 INFO : 8% Done
10 Jun 2021 10:17:51,758 INFO : 9% Done
10 Jun 2021 10:17:51,784 INFO : 12% Done
10 Jun 2021 10:17:51,804 DEBUG: Total peptides inserted: 3
10 Jun 2021 10:17:51,805 INFO : Inserting Q6ZUT6
10 Jun 2021 10:17:51,812 INFO : 15% Done
10 Jun 2021 10:17:51,840 INFO : 17% Done
10 Jun 2021 10:17:51,859 DEBUG: Total peptides inserted: 2
10 Jun 2021 10:17:51,860 INFO : Inserting P16401
10 Jun 2021 10:17:51,867 INFO : 20% Done
10 Jun 2021 10:17:51,891 INFO : 22% Done
10 Jun 2021 10:17:51,911 INFO : 24% Done
10 Jun 2021 10:17:51,926 DEBUG: Total peptides inserted: 3
10 Jun 2021 10:17:51,927 INFO : Inserting Q9P0M6
10 Jun 2021 10:17:51,936 INFO : 25% Done
10 Jun 2021 10:17:51,955 INFO : 26% Done
10 Jun 2021 10:17:51,975 INFO : 29% Done
10 Jun 2021 10:17:51,998 DEBUG: Total peptides inserted: 3
10 Jun 2021 10:17:51,998 INFO : Inserting P62805
10 Jun 2021 10:17:52,003 INFO : 32% Done
10 Jun 2021 10:17:52,026 INFO : 34% Done
10 Jun 2021 10:17:52,049 INFO : 37% Done
10 Jun 2021 10:17:52,077 INFO : 40% Done
10 Jun 2021 10:17:52,098 DEBUG: Total peptides inserted: 4
10 Jun 2021 10:17:52,098 INFO : Inserting Q6DKK2
10 Jun 2021 10:17:52,103 INFO : 42% Done
10 Jun 2021 10:17:52,121 INFO : 44% Done
10 Jun 2021 10:17:52,139 INFO : 46% Done
10 Jun 2021 10:17:52,158 INFO : 48% Done
10 Jun 2021 10:17:52,173 DEBUG: Total peptides inserted: 4
10 Jun 2021 10:17:52,173 INFO : Inserting P11387
10 Jun 2021 10:17:52,179 INFO : 50% Done
10 Jun 2021 10:17:52,204 INFO : 52% Done
10 Jun 2021 10:17:52,224 INFO : 55% Done
10 Jun 2021 10:17:52,245 INFO : 57% Done
10 Jun 2021 10:17:52,267 INFO : 59% Done
10 Jun 2021 10:17:52,286 INFO : 61% Done
10 Jun 2021 10:17:52,303 INFO : 63% Done
10 Jun 2021 10:17:52,317 DEBUG: Total peptides inserted: 7
10 Jun 2021 10:17:52,317 INFO : Inserting Q00059
10 Jun 2021 10:17:52,322 INFO : 65% Done
10 Jun 2021 10:17:52,344 INFO : 67% Done
10 Jun 2021 10:17:52,364 INFO : 69% Done
10 Jun 2021 10:17:52,378 DEBUG: Total peptides inserted: 3
10 Jun 2021 10:17:52,379 INFO : Inserting P55072
10 Jun 2021 10:17:52,384 INFO : 72% Done
10 Jun 2021 10:17:52,409 INFO : 74% Done
10 Jun 2021 10:17:52,428 INFO : 75% Done
10 Jun 2021 10:17:52,450 INFO : 78% Done
10 Jun 2021 10:17:52,477 INFO : 80% Done
10 Jun 2021 10:17:52,496 INFO : 83% Done
10 Jun 2021 10:17:52,522 INFO : 85% Done
10 Jun 2021 10:17:52,544 INFO : 88% Done
10 Jun 2021 10:17:52,563 DEBUG: Total peptides inserted: 8
10 Jun 2021 10:17:52,563 INFO : Inserting O95983
10 Jun 2021 10:17:52,567 INFO : 90% Done
10 Jun 2021 10:17:52,585 INFO : 92% Done
10 Jun 2021 10:17:52,605 INFO : 94% Done
10 Jun 2021 10:17:52,619 DEBUG: Total peptides inserted: 3
10 Jun 2021 10:17:52,620 INFO : Inserting Q9NZZ3
10 Jun 2021 10:17:52,625 INFO : 96% Done
10 Jun 2021 10:17:52,644 INFO : 98% Done
10 Jun 2021 10:17:52,659 DEBUG: Total peptides inserted: 2
10 Jun 2021 10:17:52,660 INFO : Done parsing Skyline document.
10 Jun 2021 10:17:54,496 INFO : Creating and populating temp tables for Proportion values
10 Jun 2021 10:17:54,512 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
10 Jun 2021 10:17:54,554 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
10 Jun 2021 10:17:54,584 INFO : Cleaning up temp tables
10 Jun 2021 10:17:54,593 INFO : Completed import of Skyline document from 16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip
10 Jun 2021 10:17:54,597 INFO : 100% Done
10 Jun 2021 10:17:54,601 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip into the system
10 Jun 2021 10:17:54,609 INFO : Done importing xar
10 Jun 2021 10:17:54,612 INFO : Loading pages and webpart properties
10 Jun 2021 10:17:54,703 INFO : Done importing pages and webpart properties
10 Jun 2021 10:17:54,703 INFO :
10 Jun 2021 10:17:54,703 INFO : Experiment import completed successfully.
10 Jun 2021 10:17:54,703 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
10 Jun 2021 10:18:42,761 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
10 Jun 2021 10:18:42,762 INFO :
10 Jun 2021 10:18:42,762 INFO : Finishing up experiment copy.
10 Jun 2021 10:18:42,763 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
10 Jun 2021 10:18:42,766 INFO : Assigning a ProteomeXchange ID.
10 Jun 2021 10:18:42,887 INFO : Assigning a DOI.
10 Jun 2021 10:18:43,647 INFO : Assigned DOI: 10.6069/gxkd-es83
10 Jun 2021 10:18:43,650 INFO : Updating access URL to point to the new copy of the data.
10 Jun 2021 10:18:43,654 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
10 Jun 2021 10:18:43,655 INFO : Removing copy permissions given to journal.
10 Jun 2021 10:18:43,664 INFO : Adding read permissions to all users that are folder admins in the source container.
10 Jun 2021 10:18:43,671 INFO : Setting the TargetedMS folder type to 'Experimental Data'
10 Jun 2021 10:18:43,675 INFO : Updating the 'Raw Data' tab configuration
10 Jun 2021 10:18:43,678 INFO : Updating dataFileUrls for run 16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip; targetedms run ID 113495
10 Jun 2021 10:18:43,678 INFO : Updating dataFileUrl...
10 Jun 2021 10:18:43,678 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip
10 Jun 2021 10:18:43,679 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE/@files/16HBE_TP_PRM_validation_2021-06-09_15-32-52.sky.zip
10 Jun 2021 10:18:43,683 INFO : Updating dataFileUrl...
10 Jun 2021 10:18:43,684 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE_cf4a6e78-ac3a-1039-be5b-fea6ddf5138a/_temp__2021-06-10_10-07-05/export/xar/experiments_and_runs.xar.exploded/Run111217/16HBE_TP_PRM_validation_2021-06-09_15-32-52/16HBE_TP_PRM_validation.skyd
10 Jun 2021 10:18:43,684 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20Greifswald%20Inst.%20Microbiology%20MS%20Lab%20-%20Co-infection_16HBE/@files/16HBE_TP_PRM_validation_2021-06-09_15-32-52/16HBE_TP_PRM_validation.skyd
10 Jun 2021 10:18:43,687 INFO : Creating a reviewer account.
10 Jun 2021 10:18:43,896 INFO : Created reviewer with email: User panorama+reviewer37@proteinms.net
10 Jun 2021 10:18:43,904 INFO : Hiding the Data Pipeline tab.
10 Jun 2021 10:18:44,027 INFO : Emailing submitter.
10 Jun 2021 10:18:44,159 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'