13 Oct 2021 12:23:30,124 INFO : Copying experiment "RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunity" from folder /BayBioMS/Stegmann_GLV2_phytocytokine_peptide_Arabidopsis to /Panorama Public/2021/BayBioMS - Stegmann_GLV2_phytocytokine_peptide_Arabidopsis
13 Oct 2021 12:23:30,124 INFO : =======================================
13 Oct 2021 12:23:30,379 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
13 Oct 2021 12:23:30,379 INFO :
13 Oct 2021 12:23:30,379 INFO : Exporting experiment.
13 Oct 2021 12:27:24,419 INFO :
13 Oct 2021 12:27:24,419 INFO : Experiment export completed successfully.
13 Oct 2021 12:27:24,419 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
13 Oct 2021 12:27:24,510 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
13 Oct 2021 12:27:24,511 INFO :
13 Oct 2021 12:27:24,511 INFO : Importing experiment.
13 Oct 2021 12:27:24,517 INFO : Loading folder properties (folder type, settings and active modules)
13 Oct 2021 12:27:24,619 INFO : Done importing folder properties (folder type, settings and active modules)
13 Oct 2021 12:27:24,625 INFO : Loading etl definitions
13 Oct 2021 12:27:24,630 INFO : Loading wikis
13 Oct 2021 12:27:24,633 INFO : 0 wikis imported
13 Oct 2021 12:27:24,633 INFO : Done importing wikis
13 Oct 2021 12:27:24,633 INFO : Starting to copy files
13 Oct 2021 12:29:39,067 INFO : 40 files copied, now copying BBM_362_P155_04_HEK_014.raw
13 Oct 2021 12:31:07,643 INFO : 54 files copied, now copying P155_04_Panorama.sky
13 Oct 2021 12:31:08,693 INFO : 58 files copied, now copying P155_06_WT_Pto_treatment_Panorama.skyd
13 Oct 2021 12:31:09,872 INFO : 62 files copied, now copying P155_06_refined_Wildtype.sky
13 Oct 2021 12:31:11,334 INFO : 66 files copied, now copying P155_06_refined_Wildtype.sky
13 Oct 2021 12:31:11,620 INFO : 70 files copied, now copying P155_06_WT_Pto_treatment_Panorama.skyd
13 Oct 2021 12:31:11,701 INFO : 74 files copied, now copying P155_04_WT_GLV2_flg22_treatment_Panorama.skyd
13 Oct 2021 12:31:11,776 INFO : Copied 78 files
13 Oct 2021 12:31:11,776 INFO : Ensuring exp.data rows exist for imported files
13 Oct 2021 12:31:12,290 INFO : Starting Sample Type and Data Class import
13 Oct 2021 12:31:12,291 INFO : No types XAR file to process.
13 Oct 2021 12:31:12,291 INFO : Finished importing Sample Types and Data Classes
13 Oct 2021 12:31:12,294 INFO : Loading xar
13 Oct 2021 12:31:12,444 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip'
13 Oct 2021 12:31:12,448 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Core'
13 Oct 2021 12:31:12,450 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Output'
13 Oct 2021 12:31:12,451 DEBUG: Protocol import complete
13 Oct 2021 12:31:12,452 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9198:RGI-GOLVEN+signalling+promotes+FLS2+abundance+to+regulate+plant+immunity'
13 Oct 2021 12:31:12,453 DEBUG: Experiment/Run group import complete
13 Oct 2021 12:31:12,466 DEBUG: Protocol action set import complete
13 Oct 2021 12:31:12,483 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip'
13 Oct 2021 12:31:12,494 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9198:98da45a6-0a67-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,499 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9198:98da4594-0a67-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,500 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Core'
13 Oct 2021 12:31:12,504 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Output'
13 Oct 2021 12:31:12,505 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9198:98da45c6-0a67-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,517 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip'
13 Oct 2021 12:31:12,524 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9198:df1c60de-0a69-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,531 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9198:df1c60cd-0a69-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,531 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Core'
13 Oct 2021 12:31:12,534 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9198:TargetedMS.ImportSkyZip.Output'
13 Oct 2021 12:31:12,535 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9198:df1c610d-0a69-103a-b54f-fea6ddf5779e'
13 Oct 2021 12:31:12,538 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyd into the system
13 Oct 2021 12:31:12,539 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyd into the system
13 Oct 2021 12:31:12,539 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip into the system
13 Oct 2021 12:31:12,541 INFO : Starting import from P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip
13 Oct 2021 12:31:12,547 INFO : Starting to import Skyline document from P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip
13 Oct 2021 12:31:12,549 INFO : Expanding P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyd
13 Oct 2021 12:31:12,600 INFO : Expanding P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.sky.view
13 Oct 2021 12:31:12,600 INFO : Expanding P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.sky
13 Oct 2021 12:31:12,602 INFO : Expanding P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyl
13 Oct 2021 12:31:12,605 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
13 Oct 2021 12:31:12,617 INFO : 3% Done
13 Oct 2021 12:31:12,639 DEBUG: Starting to load chromatogram headers
13 Oct 2021 12:31:12,640 DEBUG: Done loading chromatogram headers
13 Oct 2021 12:31:12,703 INFO : Inserting GLV2-peptide
13 Oct 2021 12:31:12,733 INFO : 17% Done
13 Oct 2021 12:31:12,800 DEBUG: Total peptides inserted: 1
13 Oct 2021 12:31:12,801 INFO : Inserting PROCAL Retention Time Standard Peptides
13 Oct 2021 12:31:12,810 INFO : 25% Done
13 Oct 2021 12:31:12,844 INFO : 33% Done
13 Oct 2021 12:31:12,872 INFO : 42% Done
13 Oct 2021 12:31:12,899 INFO : 50% Done
13 Oct 2021 12:31:12,926 INFO : 57% Done
13 Oct 2021 12:31:12,951 INFO : 65% Done
13 Oct 2021 12:31:12,978 INFO : 73% Done
13 Oct 2021 12:31:13,006 INFO : 82% Done
13 Oct 2021 12:31:13,038 INFO : 90% Done
13 Oct 2021 12:31:13,065 INFO : 98% Done
13 Oct 2021 12:31:13,087 DEBUG: Total peptides inserted: 10
13 Oct 2021 12:31:13,088 INFO : Done parsing Skyline document.
13 Oct 2021 12:31:13,279 INFO : Creating and populating temp tables for Proportion values
13 Oct 2021 12:31:13,296 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
13 Oct 2021 12:31:13,307 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
13 Oct 2021 12:31:13,316 INFO : Cleaning up temp tables
13 Oct 2021 12:31:13,584 INFO : Completed import of Skyline document from P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip
13 Oct 2021 12:31:13,588 INFO : 100% Done
13 Oct 2021 12:31:13,593 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip into the system
13 Oct 2021 12:31:13,594 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38/P155_06_WT_Pto_treatment_Panorama.skyd into the system
13 Oct 2021 12:31:13,594 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38/P155_06_WT_Pto_treatment_Panorama.skyd into the system
13 Oct 2021 12:31:13,594 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip into the system
13 Oct 2021 12:31:13,597 INFO : Starting import from P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip
13 Oct 2021 12:31:13,600 INFO : Starting to import Skyline document from P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip
13 Oct 2021 12:31:13,601 INFO : Expanding P155_06_WT_Pto_treatment_Panorama.skyd
13 Oct 2021 12:31:13,634 INFO : Expanding P155_06_WT_Pto_treatment_Panorama.sky.view
13 Oct 2021 12:31:13,635 INFO : Expanding P155_06_WT_Pto_treatment_Panorama.sky
13 Oct 2021 12:31:13,636 INFO : Expanding P155_06_WT_Pto_treatment_Panorama.skyl
13 Oct 2021 12:31:13,639 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
13 Oct 2021 12:31:13,648 INFO : 4% Done
13 Oct 2021 12:31:13,664 DEBUG: Starting to load chromatogram headers
13 Oct 2021 12:31:13,665 DEBUG: Done loading chromatogram headers
13 Oct 2021 12:31:13,717 INFO : Inserting peptides1
13 Oct 2021 12:31:13,727 INFO : 15% Done
13 Oct 2021 12:31:13,763 DEBUG: Total peptides inserted: 1
13 Oct 2021 12:31:13,763 INFO : Inserting PROCAL Retention Time Standard Peptides
13 Oct 2021 12:31:13,770 INFO : 22% Done
13 Oct 2021 12:31:13,789 INFO : 28% Done
13 Oct 2021 12:31:13,809 INFO : 35% Done
13 Oct 2021 12:31:13,828 INFO : 41% Done
13 Oct 2021 12:31:13,847 INFO : 46% Done
13 Oct 2021 12:31:13,863 INFO : 54% Done
13 Oct 2021 12:31:13,882 INFO : 59% Done
13 Oct 2021 12:31:13,901 INFO : 67% Done
13 Oct 2021 12:31:13,922 INFO : 74% Done
13 Oct 2021 12:31:13,942 INFO : 80% Done
13 Oct 2021 12:31:13,956 DEBUG: Total peptides inserted: 10
13 Oct 2021 12:31:13,957 INFO : Done parsing Skyline document.
13 Oct 2021 12:31:13,960 INFO : Calculating fold changes
13 Oct 2021 12:31:13,960 DEBUG: Calculating fold change for group comparison Col, 1 of 2
13 Oct 2021 12:31:14,110 INFO : 89% Done
13 Oct 2021 12:31:14,110 DEBUG: Calculating fold change for group comparison GLV2OX, 2 of 2
13 Oct 2021 12:31:14,238 INFO : 98% Done
13 Oct 2021 12:31:14,238 INFO : Done calculating fold changes.
13 Oct 2021 12:31:14,981 INFO : Creating and populating temp tables for Proportion values
13 Oct 2021 12:31:14,995 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
13 Oct 2021 12:31:15,002 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
13 Oct 2021 12:31:15,008 INFO : Cleaning up temp tables
13 Oct 2021 12:31:15,238 INFO : Completed import of Skyline document from P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip
13 Oct 2021 12:31:15,241 INFO : 100% Done
13 Oct 2021 12:31:15,246 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip into the system
13 Oct 2021 12:31:15,268 INFO : Done importing xar
13 Oct 2021 12:31:15,270 INFO : Loading pages and webpart properties
13 Oct 2021 12:31:15,369 INFO : Done importing pages and webpart properties
13 Oct 2021 12:31:15,369 INFO :
13 Oct 2021 12:31:15,369 INFO : Experiment import completed successfully.
13 Oct 2021 12:31:15,369 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
13 Oct 2021 12:31:15,420 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
13 Oct 2021 12:31:15,420 INFO :
13 Oct 2021 12:31:15,421 INFO : Finishing up experiment copy.
13 Oct 2021 12:31:15,422 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
13 Oct 2021 12:31:15,425 INFO : Copying ProteomeXchange ID from the previous copy of the data.
13 Oct 2021 12:31:15,425 INFO : Assigning a DOI.
13 Oct 2021 12:31:19,381 INFO : Assigned DOI: 10.6069/qqqz-ad87
13 Oct 2021 12:31:19,388 INFO : Updating access URL to point to the new copy of the data.
13 Oct 2021 12:31:19,401 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
13 Oct 2021 12:31:19,404 INFO : Removing copy permissions given to journal.
13 Oct 2021 12:31:19,422 INFO : Adding read permissions to all users that are folder admins in the source container.
13 Oct 2021 12:31:19,425 INFO : Adding read permissions to all users that had read access to previous copy.
13 Oct 2021 12:31:19,438 INFO : Setting the TargetedMS folder type to 'Experimental Data'
13 Oct 2021 12:31:19,444 INFO : Updating the 'Raw Data' tab configuration
13 Oct 2021 12:31:19,447 INFO : Updating dataFileUrls for run P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip; targetedms run ID 122337
13 Oct 2021 12:31:19,447 INFO : Updating dataFileUrl...
13 Oct 2021 12:31:19,448 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip
13 Oct 2021 12:31:19,448 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis/@files/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12.sky.zip
13 Oct 2021 12:31:19,451 INFO : Updating dataFileUrl...
13 Oct 2021 12:31:19,451 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119169/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyd
13 Oct 2021 12:31:19,451 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis/@files/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test_2021-10-08_15-29-12/P155_04_WT_GLV2_flg22_treatment_Panorama_new_test.skyd
13 Oct 2021 12:31:19,456 INFO : Updating dataFileUrls for run P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip; targetedms run ID 122338
13 Oct 2021 12:31:19,456 INFO : Updating dataFileUrl...
13 Oct 2021 12:31:19,456 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38/P155_06_WT_Pto_treatment_Panorama.skyd
13 Oct 2021 12:31:19,456 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis/@files/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38/P155_06_WT_Pto_treatment_Panorama.skyd
13 Oct 2021 12:31:19,459 INFO : Updating dataFileUrl...
13 Oct 2021 12:31:19,459 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis_d161ba06-0e87-103a-b54f-fea6ddf5779e/_temp__2021-10-13_12-23-29/export/xar/experiments_and_runs.xar.exploded/Run119171/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip
13 Oct 2021 12:31:19,459 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/BayBioMS%20-%20Stegmann_GLV2_phytocytokine_peptide_Arabidopsis/@files/P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip
13 Oct 2021 12:31:19,462 INFO : Making folder public.
13 Oct 2021 12:31:19,472 INFO : Hiding the Data Pipeline tab.
13 Oct 2021 12:31:19,658 INFO : Emailing submitter.
13 Oct 2021 12:31:19,870 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'