20 Jul 2023 17:07:10,401 INFO : Copying experiment "Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells." from folder /DKFZ - Krijgsveld Lab/QuaNPA to /Panorama Public/2023/DKFZ Krijgsveld Lab - QuaNPA
20 Jul 2023 17:07:10,402 INFO : =======================================
20 Jul 2023 17:07:10,414 DEBUG: Resetting Job ID: 4561c58c-0987-103c-afc6-fea6ddf51ba4
20 Jul 2023 17:07:10,434 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
20 Jul 2023 17:07:10,434 INFO :
20 Jul 2023 17:07:10,434 INFO : Exporting experiment.
20 Jul 2023 17:10:35,963 INFO : Exporting files metadata.
20 Jul 2023 17:10:35,963 DEBUG: [/DKFZ - Krijgsveld Lab/QuaNPA] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ Krijgsveld Lab - QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export
20 Jul 2023 17:10:35,966 INFO :
20 Jul 2023 17:10:35,966 INFO : Experiment export completed successfully.
20 Jul 2023 17:10:35,966 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
20 Jul 2023 17:10:35,990 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
20 Jul 2023 17:10:35,990 INFO :
20 Jul 2023 17:10:35,990 INFO : Importing experiment.
20 Jul 2023 17:10:35,991 DEBUG: [/Panorama Public/2023/DKFZ Krijgsveld Lab - QuaNPA] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ Krijgsveld Lab - QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export
20 Jul 2023 17:10:35,992 INFO : Loading folder properties (folder type, settings and active modules)
20 Jul 2023 17:10:35,992 DEBUG: [/Panorama Public/2023/DKFZ Krijgsveld Lab - QuaNPA] Folder type: Targeted MS
20 Jul 2023 17:10:35,993 DEBUG: [/Panorama Public/2023/DKFZ Krijgsveld Lab - QuaNPA] Active modules: PanoramaPublic, Wiki, Experiment, API, Query, Announcements, Pipeline, Assay, MS2, Core, Search, FileContent, Issues, TargetedMS
20 Jul 2023 17:10:36,065 INFO : Done importing folder properties (folder type, settings and active modules)
20 Jul 2023 17:10:36,066 INFO : Loading container specific module properties
20 Jul 2023 17:10:36,069 INFO : Done importing container specific module properties
20 Jul 2023 17:10:36,071 INFO : Loading grid views
20 Jul 2023 17:10:36,075 INFO : 1 custom view imported
20 Jul 2023 17:10:36,075 INFO : Done importing grid views
20 Jul 2023 17:10:36,076 INFO : Loading etl definitions
20 Jul 2023 17:10:36,077 INFO : Loading wikis
20 Jul 2023 17:10:36,092 INFO : 2 wikis imported
20 Jul 2023 17:10:36,092 INFO : Done importing wikis
20 Jul 2023 17:10:36,092 INFO : Starting to copy files
20 Jul 2023 17:12:46,143 INFO : 21 files copied, now copying 20230530_QE1_TB_4h_BSA_R1.raw
20 Jul 2023 17:13:52,422 INFO : 25 files copied, now copying myPrositLib_version2.msp
20 Jul 2023 17:13:53,813 INFO : Copied 30 files
20 Jul 2023 17:13:53,813 INFO : Ensuring exp.data rows exist for imported files
20 Jul 2023 17:13:54,382 INFO : Starting Sample Type and Data Class import
20 Jul 2023 17:13:54,383 INFO : No types XAR file to process.
20 Jul 2023 17:13:54,383 INFO : Finished importing Sample Types and Data Classes
20 Jul 2023 17:13:54,384 INFO : Loading xar
20 Jul 2023 17:13:55,223 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip'
20 Jul 2023 17:13:55,225 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip.Core'
20 Jul 2023 17:13:55,227 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip.Output'
20 Jul 2023 17:13:55,227 DEBUG: Protocol import complete
20 Jul 2023 17:13:55,228 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11897:Label-free+Parallel+Reaction+Monitoring+%28PRM%29+analysis+of+selected+novel+potential+targets+of+IFNg+stimulation+in+Hela+cells.'
20 Jul 2023 17:13:55,228 DEBUG: Experiment/Run group import complete
20 Jul 2023 17:13:55,236 DEBUG: Protocol action set import complete
20 Jul 2023 17:13:55,258 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip'
20 Jul 2023 17:13:55,264 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11897:21846185-08a6-103c-afc6-fea6ddf51ba4'
20 Jul 2023 17:13:55,267 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11897:218460f8-08a6-103c-afc6-fea6ddf51ba4'
20 Jul 2023 17:13:55,267 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip.Core'
20 Jul 2023 17:13:55,269 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11897:TargetedMS.ImportSkyZip.Output'
20 Jul 2023 17:13:55,270 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11897:2184631f-08a6-103c-afc6-fea6ddf51ba4'
20 Jul 2023 17:13:55,270 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08/01_refined_TB_IFNg_target_PRM.skyd into the system
20 Jul 2023 17:13:55,271 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08/01_refined_TB_IFNg_target_PRM.skyd into the system
20 Jul 2023 17:13:55,271 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip into the system
20 Jul 2023 17:13:55,272 INFO : Starting import from 01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
20 Jul 2023 17:13:55,274 INFO : Starting to import Skyline document from 01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
20 Jul 2023 17:13:55,290 INFO : Expanding myPrositLib_version2.msp
20 Jul 2023 17:13:55,290 INFO : Expanding 01_refined_TB_IFNg_target_PRM.skyd
20 Jul 2023 17:13:55,807 INFO : Expanding 01_refined_TB_IFNg_target_PRM.sky.view
20 Jul 2023 17:13:55,808 INFO : Expanding 01_refined_TB_IFNg_target_PRM.sky
20 Jul 2023 17:13:55,816 INFO : Expanding 01_refined_TB_IFNg_target_PRM.skyl
20 Jul 2023 17:13:55,818 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
20 Jul 2023 17:13:55,822 INFO : 1% Done
20 Jul 2023 17:13:55,876 DEBUG: Starting to load chromatogram headers
20 Jul 2023 17:13:55,877 DEBUG: Done loading chromatogram headers
20 Jul 2023 17:13:56,016 INFO : Inserting Library Peptides
20 Jul 2023 17:13:56,017 INFO : Inserting sp|P42224|STAT1_HUMAN
20 Jul 2023 17:13:56,027 INFO : 4% Done
20 Jul 2023 17:13:56,059 INFO : 5% Done
20 Jul 2023 17:13:56,078 INFO : 8% Done
20 Jul 2023 17:13:56,106 INFO : 11% Done
20 Jul 2023 17:13:56,128 DEBUG: Total peptides inserted: 4
20 Jul 2023 17:13:56,128 INFO : Inserting sp|P06703|S10A6_HUMAN
20 Jul 2023 17:13:56,135 INFO : 13% Done
20 Jul 2023 17:13:56,158 INFO : 16% Done
20 Jul 2023 17:13:56,184 INFO : 18% Done
20 Jul 2023 17:13:56,205 DEBUG: Total peptides inserted: 3
20 Jul 2023 17:13:56,205 INFO : Inserting sp|Q03518|TAP1_HUMAN
20 Jul 2023 17:13:56,210 INFO : 19% Done
20 Jul 2023 17:13:56,231 INFO : 23% Done
20 Jul 2023 17:13:56,267 INFO : 25% Done
20 Jul 2023 17:13:56,293 DEBUG: Total peptides inserted: 3
20 Jul 2023 17:13:56,294 INFO : Inserting sp|P57682|KLF3_HUMAN
20 Jul 2023 17:13:56,302 INFO : 29% Done
20 Jul 2023 17:13:56,344 INFO : 33% Done
20 Jul 2023 17:13:56,379 DEBUG: Total peptides inserted: 2
20 Jul 2023 17:13:56,379 INFO : Inserting sp|P05362|ICAM1_HUMAN
20 Jul 2023 17:13:56,387 INFO : 36% Done
20 Jul 2023 17:13:56,415 INFO : 38% Done
20 Jul 2023 17:13:56,445 INFO : 42% Done
20 Jul 2023 17:13:56,478 INFO : 45% Done
20 Jul 2023 17:13:56,500 DEBUG: Total peptides inserted: 4
20 Jul 2023 17:13:56,500 INFO : Inserting sp|P63165|SUMO1_HUMAN
20 Jul 2023 17:13:56,509 INFO : 48% Done
20 Jul 2023 17:13:56,541 INFO : 51% Done
20 Jul 2023 17:13:56,564 DEBUG: Total peptides inserted: 2
20 Jul 2023 17:13:56,564 INFO : Inserting sp|O75182|SIN3B_HUMAN
20 Jul 2023 17:13:56,570 INFO : 53% Done
20 Jul 2023 17:13:56,590 INFO : 55% Done
20 Jul 2023 17:13:56,608 INFO : 57% Done
20 Jul 2023 17:13:56,624 DEBUG: Total peptides inserted: 3
20 Jul 2023 17:13:56,624 INFO : Inserting sp|Q8TD16|BICD2_HUMAN
20 Jul 2023 17:13:56,631 INFO : 59% Done
20 Jul 2023 17:13:56,656 INFO : 62% Done
20 Jul 2023 17:13:56,678 DEBUG: Total peptides inserted: 2
20 Jul 2023 17:13:56,678 INFO : Inserting sp|P46108|CRK_HUMAN
20 Jul 2023 17:13:56,686 INFO : 65% Done
20 Jul 2023 17:13:56,719 INFO : 69% Done
20 Jul 2023 17:13:56,750 INFO : 72% Done
20 Jul 2023 17:13:56,773 DEBUG: Total peptides inserted: 3
20 Jul 2023 17:13:56,773 INFO : Inserting Decoys
20 Jul 2023 17:13:56,775 INFO : 73% Done
20 Jul 2023 17:13:56,786 INFO : 74% Done
20 Jul 2023 17:13:56,806 INFO : 75% Done
20 Jul 2023 17:13:56,817 INFO : 76% Done
20 Jul 2023 17:13:56,828 INFO : 77% Done
20 Jul 2023 17:13:56,839 INFO : 78% Done
20 Jul 2023 17:13:56,849 INFO : 79% Done
20 Jul 2023 17:13:56,858 INFO : 80% Done
20 Jul 2023 17:13:56,869 INFO : 82% Done
20 Jul 2023 17:13:56,886 INFO : 83% Done
20 Jul 2023 17:13:56,896 INFO : 85% Done
20 Jul 2023 17:13:56,907 INFO : 86% Done
20 Jul 2023 17:13:56,917 INFO : 87% Done
20 Jul 2023 17:13:56,928 INFO : 88% Done
20 Jul 2023 17:13:56,938 INFO : 89% Done
20 Jul 2023 17:13:56,948 INFO : 90% Done
20 Jul 2023 17:13:56,958 INFO : 91% Done
20 Jul 2023 17:13:56,969 INFO : 92% Done
20 Jul 2023 17:13:56,979 INFO : 93% Done
20 Jul 2023 17:13:56,988 INFO : 94% Done
20 Jul 2023 17:13:56,999 INFO : 95% Done
20 Jul 2023 17:13:57,009 INFO : 96% Done
20 Jul 2023 17:13:57,018 INFO : 98% Done
20 Jul 2023 17:13:57,036 DEBUG: Total peptides inserted: 26
20 Jul 2023 17:13:57,038 INFO : Done parsing Skyline document.
20 Jul 2023 17:13:57,134 INFO : Creating and populating temp tables for Proportion values
20 Jul 2023 17:13:57,219 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
20 Jul 2023 17:13:57,245 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
20 Jul 2023 17:13:57,264 INFO : Cleaning up temp tables
20 Jul 2023 17:13:57,593 INFO : Completed import of Skyline document from 01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
20 Jul 2023 17:13:57,595 INFO : 100% Done
20 Jul 2023 17:13:57,599 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip into the system
20 Jul 2023 17:13:57,609 INFO : Done importing xar
20 Jul 2023 17:13:57,610 INFO : Loading pages and webpart properties
20 Jul 2023 17:13:57,672 INFO : Done importing 3 page(s) with 7 webpart(s)
20 Jul 2023 17:13:57,672 INFO : Loading File Browser config
20 Jul 2023 17:13:57,672 INFO : Done importing File Browser config
20 Jul 2023 17:13:57,673 INFO : Starting Sample Status Data import
20 Jul 2023 17:13:57,674 INFO : No sample types XAR file to process.
20 Jul 2023 17:13:57,674 INFO : Finished importing Sample Status Data
20 Jul 2023 17:13:57,679 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
20 Jul 2023 17:13:57,681 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
20 Jul 2023 17:13:57,681 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
20 Jul 2023 17:13:57,682 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
20 Jul 2023 17:13:57,683 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
20 Jul 2023 17:13:57,683 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
20 Jul 2023 17:13:57,683 INFO : Importing files metadata.
20 Jul 2023 17:13:57,683 DEBUG: [/Panorama Public/2023/DKFZ Krijgsveld Lab - QuaNPA] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ Krijgsveld Lab - QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export
20 Jul 2023 17:13:57,740 INFO :
20 Jul 2023 17:13:57,740 INFO : Experiment import completed successfully.
20 Jul 2023 17:13:57,740 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
20 Jul 2023 17:13:57,761 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
20 Jul 2023 17:13:57,761 INFO :
20 Jul 2023 17:13:57,761 INFO : Checking for library folders.
20 Jul 2023 17:13:57,762 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
20 Jul 2023 17:13:57,779 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
20 Jul 2023 17:13:57,779 INFO :
20 Jul 2023 17:13:57,779 INFO : Finishing up experiment copy.
20 Jul 2023 17:13:57,781 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
20 Jul 2023 17:13:57,781 INFO : Setting version on new experiment to 1
20 Jul 2023 17:13:57,782 INFO : Assigning a ProteomeXchange ID.
20 Jul 2023 17:13:58,016 INFO : Assigning a DOI.
20 Jul 2023 17:13:59,600 INFO : Assigned DOI: 10.6069/xmzz-y959
20 Jul 2023 17:13:59,603 INFO : Updating permanent link to point to the new copy of the data.
20 Jul 2023 17:13:59,607 INFO : Removing copy permissions given to Panorama Public
20 Jul 2023 17:13:59,619 INFO : Adding read permissions to all users that are folder admins in the source folder.
20 Jul 2023 17:13:59,619 INFO : Assigning PanoramaPublicSubmitterRole to t.bortecen@dkfz-heidelberg.de
20 Jul 2023 17:13:59,619 INFO : Assigning PanoramaPublicSubmitterRole to t.bortecen@dkfz-heidelberg.de
20 Jul 2023 17:13:59,622 INFO : Adding user t.bortecen@dkfz-heidelberg.de to group Panorama Public Submitters
20 Jul 2023 17:13:59,626 INFO : User t.bortecen@dkfz-heidelberg.de is already a member of group Panorama Public Submitters
20 Jul 2023 17:13:59,635 INFO : Updating the 'Raw Data' tab configuration
20 Jul 2023 17:13:59,637 INFO : Updating dataFileUrls for run 01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip; targetedms run ID 167533
20 Jul 2023 17:13:59,637 INFO : Updating dataFileUrl...
20 Jul 2023 17:13:59,637 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
20 Jul 2023 17:13:59,637 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA/@files/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
20 Jul 2023 17:13:59,640 INFO : Updating dataFileUrl...
20 Jul 2023 17:13:59,640 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA_4561c56b-0987-103c-afc6-fea6ddf51ba4/_temp__2023-07-20_17-07-09/export/xar/experiments_and_runs.xar.exploded/Run164960/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08/01_refined_TB_IFNg_target_PRM.skyd
20 Jul 2023 17:13:59,640 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/DKFZ%20Krijgsveld%20Lab%20-%20QuaNPA/@files/01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08/01_refined_TB_IFNg_target_PRM.skyd
20 Jul 2023 17:13:59,645 INFO : Creating a reviewer account.
20 Jul 2023 17:13:59,840 INFO : Created reviewer with email: User panorama+reviewer199@proteinms.net
20 Jul 2023 17:13:59,854 INFO : Adding user panorama+reviewer199@proteinms.net to group Reviewers
20 Jul 2023 17:13:59,855 INFO : Hiding the Data Pipeline tab.
20 Jul 2023 17:13:59,859 INFO : Updating Submission. Setting copiedExperimentId to 1655
20 Jul 2023 17:13:59,907 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'