07 Jun 2023 22:06:07,962 INFO : Copying experiment "In-vitro differential redox-labeling of NTRC" from folder /IBBP Münster - Hippler Lab/NTRC_ox_red_labelling to /Panorama Public/2023/IBBP Münster Hippler Lab - NTRC_ox_red_labelling

07 Jun 2023 22:06:07,962 INFO : =======================================

07 Jun 2023 22:06:07,977 DEBUG: Resetting Job ID: 792607d7-e7e7-103b-82c0-fea6ddf5f252

07 Jun 2023 22:06:07,999 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

07 Jun 2023 22:06:07,999 INFO : 

07 Jun 2023 22:06:07,999 INFO : Exporting experiment.

07 Jun 2023 22:08:49,441 INFO : Exporting files metadata.

07 Jun 2023 22:08:49,441 DEBUG: [/IBBP Münster - Hippler Lab/NTRC_ox_red_labelling]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP Münster Hippler Lab - NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export

07 Jun 2023 22:08:49,468 INFO : 

07 Jun 2023 22:08:49,468 INFO : Experiment export completed successfully.

07 Jun 2023 22:08:49,468 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

07 Jun 2023 22:08:49,491 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

07 Jun 2023 22:08:49,491 INFO : 

07 Jun 2023 22:08:49,491 INFO : Importing experiment.

07 Jun 2023 22:08:49,493 DEBUG: [/Panorama Public/2023/IBBP Münster Hippler Lab - NTRC_ox_red_labelling] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP Münster Hippler Lab - NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export

07 Jun 2023 22:08:49,494 INFO : Loading folder properties (folder type, settings and active modules)

07 Jun 2023 22:08:49,494 DEBUG: [/Panorama Public/2023/IBBP Münster Hippler Lab - NTRC_ox_red_labelling] Folder type: Targeted MS

07 Jun 2023 22:08:49,494 DEBUG: [/Panorama Public/2023/IBBP Münster Hippler Lab - NTRC_ox_red_labelling] Active modules: FileContent, Wiki, Issues, Core, Pipeline, Announcements, MS2, PanoramaPublic, TargetedMS, Query, API, Assay, Search, Experiment

07 Jun 2023 22:08:49,549 INFO : Done importing folder properties (folder type, settings and active modules)

07 Jun 2023 22:08:49,550 INFO : Loading container specific module properties

07 Jun 2023 22:08:49,559 INFO : Done importing container specific module properties

07 Jun 2023 22:08:49,560 INFO : Loading etl definitions

07 Jun 2023 22:08:49,561 INFO : Loading wikis

07 Jun 2023 22:08:49,562 INFO : 0 wikis imported

07 Jun 2023 22:08:49,562 INFO : Done importing wikis

07 Jun 2023 22:08:49,562 INFO : Starting to copy files

07 Jun 2023 22:10:50,776 INFO : 37 files copied, now copying ZZ_MS_20230415_1-2_B.raw

07 Jun 2023 22:11:26,762 INFO : 46 files copied, now copying 20230417_NTRC__ox_label_PRM100.skyl

07 Jun 2023 22:11:26,771 INFO : Copied 52 files

07 Jun 2023 22:11:26,772 INFO : Ensuring exp.data rows exist for imported files

07 Jun 2023 22:11:26,960 INFO : Starting Sample Type and Data Class import

07 Jun 2023 22:11:26,960 INFO : No types XAR file to process.

07 Jun 2023 22:11:26,960 INFO : Finished importing Sample Types and Data Classes

07 Jun 2023 22:11:26,961 INFO : Loading xar

07 Jun 2023 22:11:26,988 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip'

07 Jun 2023 22:11:26,990 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip.Core'

07 Jun 2023 22:11:26,992 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip.Output'

07 Jun 2023 22:11:26,992 DEBUG: Protocol import complete

07 Jun 2023 22:11:26,993 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11659:In-vitro+differential+redox-labeling+of+NTRC'

07 Jun 2023 22:11:26,993 DEBUG: Experiment/Run group import complete

07 Jun 2023 22:11:27,003 DEBUG: Protocol action set import complete

07 Jun 2023 22:11:27,012 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip'

07 Jun 2023 22:11:27,018 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11659:935f95f1-cca3-103b-965b-fea6ddf56188'

07 Jun 2023 22:11:27,021 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11659:935f94de-cca3-103b-965b-fea6ddf56188'

07 Jun 2023 22:11:27,021 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip.Core'

07 Jun 2023 22:11:27,023 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11659:TargetedMS.ImportSkyZip.Output'

07 Jun 2023 22:11:27,024 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11659:bb4dec39-cca3-103b-965b-fea6ddf56188'

07 Jun 2023 22:11:27,025 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19/20230417_NTRC__ox_label_PRM100.skyd into the system

07 Jun 2023 22:11:27,026 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19/20230417_NTRC__ox_label_PRM100.skyd into the system

07 Jun 2023 22:11:27,026 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip into the system

07 Jun 2023 22:11:27,027 INFO : Starting import from 20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip

07 Jun 2023 22:11:27,030 INFO : Starting to import Skyline document from 20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip

07 Jun 2023 22:11:27,030 INFO : Expanding NTRC_CRX_TRXf1.protdb

07 Jun 2023 22:11:27,031 INFO : Expanding NTRC_CRX_TRXf1.blib

07 Jun 2023 22:11:27,042 INFO : Expanding 20230417_NTRC__ox_label_PRM100.skyd

07 Jun 2023 22:11:27,048 INFO : Expanding 20230417_NTRC__ox_label_PRM100.sky.view

07 Jun 2023 22:11:27,048 INFO : Expanding 20230417_NTRC__ox_label_PRM100.sky

07 Jun 2023 22:11:27,050 INFO : Expanding 20230417_NTRC__ox_label_PRM100.skyl

07 Jun 2023 22:11:27,053 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

07 Jun 2023 22:11:27,058 INFO : 2% Done

07 Jun 2023 22:11:27,062 DEBUG: Starting to load chromatogram headers

07 Jun 2023 22:11:27,063 DEBUG: Done loading chromatogram headers

07 Jun 2023 22:11:27,215 INFO : Inserting NTRC_His|NTRC_His

07 Jun 2023 22:11:27,220 INFO : 6% Done

07 Jun 2023 22:11:27,234 INFO : 10% Done

07 Jun 2023 22:11:27,247 INFO : 14% Done

07 Jun 2023 22:11:27,259 INFO : 17% Done

07 Jun 2023 22:11:27,270 INFO : 20% Done

07 Jun 2023 22:11:27,283 INFO : 23% Done

07 Jun 2023 22:11:27,320 INFO : 26% Done

07 Jun 2023 22:11:27,334 INFO : 30% Done

07 Jun 2023 22:11:27,349 INFO : 34% Done

07 Jun 2023 22:11:27,363 INFO : 37% Done

07 Jun 2023 22:11:27,380 INFO : 40% Done

07 Jun 2023 22:11:27,393 INFO : 46% Done

07 Jun 2023 22:11:27,411 INFO : 50% Done

07 Jun 2023 22:11:27,427 INFO : 55% Done

07 Jun 2023 22:11:27,443 INFO : 59% Done

07 Jun 2023 22:11:27,457 INFO : 62% Done

07 Jun 2023 22:11:27,470 INFO : 66% Done

07 Jun 2023 22:11:27,484 INFO : 70% Done

07 Jun 2023 22:11:27,499 INFO : 71% Done

07 Jun 2023 22:11:27,514 INFO : 74% Done

07 Jun 2023 22:11:27,528 INFO : 78% Done

07 Jun 2023 22:11:27,539 DEBUG: Total peptides inserted: 21

07 Jun 2023 22:11:27,539 INFO : Inserting NTRC_His|NTRC_His

07 Jun 2023 22:11:27,543 INFO : 80% Done

07 Jun 2023 22:11:27,560 DEBUG: Total peptides inserted: 1

07 Jun 2023 22:11:27,561 INFO : Done parsing Skyline document.

07 Jun 2023 22:11:27,616 INFO : Calculating fold changes

07 Jun 2023 22:11:27,616 DEBUG: Calculating fold change for group comparison Comparison CRX, 1 of 2

07 Jun 2023 22:11:27,827 INFO : 89% Done

07 Jun 2023 22:11:27,828 DEBUG: Calculating fold change for group comparison Comparison TRXf, 2 of 2

07 Jun 2023 22:11:27,994 INFO : 98% Done

07 Jun 2023 22:11:27,994 INFO : Done calculating fold changes.

07 Jun 2023 22:11:28,048 INFO : Creating and populating temp tables for Proportion values

07 Jun 2023 22:11:28,122 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

07 Jun 2023 22:11:28,134 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

07 Jun 2023 22:11:28,144 INFO : Cleaning up temp tables

07 Jun 2023 22:11:28,392 INFO : Completed import of Skyline document from 20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip

07 Jun 2023 22:11:28,394 INFO : 100% Done

07 Jun 2023 22:11:28,398 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip into the system

07 Jun 2023 22:11:28,405 INFO : Done importing xar

07 Jun 2023 22:11:28,406 INFO : Loading pages and webpart properties

07 Jun 2023 22:11:28,458 INFO : Done importing 3 page(s) with 5 webpart(s)

07 Jun 2023 22:11:28,458 INFO : Loading File Browser config

07 Jun 2023 22:11:28,458 INFO : Done importing File Browser config

07 Jun 2023 22:11:28,459 INFO : Starting Sample Status Data import

07 Jun 2023 22:11:28,459 INFO : No sample types XAR file to process.

07 Jun 2023 22:11:28,459 INFO : Finished importing Sample Status Data

07 Jun 2023 22:11:28,463 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

07 Jun 2023 22:11:28,464 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping

07 Jun 2023 22:11:28,464 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping

07 Jun 2023 22:11:28,465 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping

07 Jun 2023 22:11:28,465 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

07 Jun 2023 22:11:28,465 INFO : Importing files metadata.

07 Jun 2023 22:11:28,465 DEBUG: [/Panorama Public/2023/IBBP Münster Hippler Lab - NTRC_ox_red_labelling]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP Münster Hippler Lab - NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export

07 Jun 2023 22:11:28,465 INFO : 

07 Jun 2023 22:11:28,466 INFO : Experiment import completed successfully.

07 Jun 2023 22:11:28,466 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

07 Jun 2023 22:11:28,484 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

07 Jun 2023 22:11:28,484 INFO : 

07 Jun 2023 22:11:28,484 INFO : Checking for library folders.

07 Jun 2023 22:11:28,485 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

07 Jun 2023 22:11:28,500 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

07 Jun 2023 22:11:28,500 INFO : 

07 Jun 2023 22:11:28,500 INFO : Finishing up experiment copy.

07 Jun 2023 22:11:28,502 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

07 Jun 2023 22:11:28,502 INFO : Setting version on new experiment to 1

07 Jun 2023 22:11:28,502 INFO : Assigning a ProteomeXchange ID.

07 Jun 2023 22:11:29,029 INFO : Assigning a DOI.

07 Jun 2023 22:11:30,613 INFO : Assigned DOI: 10.6069/s18n-c667

07 Jun 2023 22:11:30,616 INFO : Updating permanent link to point to the new copy of the data.

07 Jun 2023 22:11:30,620 INFO : Removing copy permissions given to Panorama Public

07 Jun 2023 22:11:30,630 INFO : Adding read permissions to all users that are folder admins in the source folder.

07 Jun 2023 22:11:30,630 INFO : Assigning PanoramaPublicSubmitterRole to mscholz@uni-muenster.de

07 Jun 2023 22:11:30,630 INFO : Assigning PanoramaPublicSubmitterRole to mscholz@uni-muenster.de

07 Jun 2023 22:11:30,630 INFO : User mscholz@uni-muenster.de is already a member of group Panorama Public Submitters

07 Jun 2023 22:11:30,631 INFO : User mscholz@uni-muenster.de is already a member of group Panorama Public Submitters

07 Jun 2023 22:11:30,636 INFO : Updating the 'Raw Data' tab configuration

07 Jun 2023 22:11:30,638 INFO : Updating dataFileUrls for run 20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip; targetedms run ID 163215

07 Jun 2023 22:11:30,638 INFO : Updating dataFileUrl...

07 Jun 2023 22:11:30,638 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19/20230417_NTRC__ox_label_PRM100.skyd

07 Jun 2023 22:11:30,638 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling/@files/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19/20230417_NTRC__ox_label_PRM100.skyd

07 Jun 2023 22:11:30,640 INFO : Updating dataFileUrl...

07 Jun 2023 22:11:30,640 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling_792607b5-e7e7-103b-82c0-fea6ddf5f252/_temp__2023-06-07_22-06-07/export/xar/experiments_and_runs.xar.exploded/Run156820/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip

07 Jun 2023 22:11:30,640 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/IBBP%20M%C3%BCnster%20Hippler%20Lab%20-%20NTRC_ox_red_labelling/@files/20230417_NTRC__ox_label_PRM100_2023-05-04_14-18-19.sky.zip

07 Jun 2023 22:11:30,644 INFO : Making folder public.

07 Jun 2023 22:11:30,649 INFO : Hiding the Data Pipeline tab.

07 Jun 2023 22:11:30,653 INFO : Updating Submission. Setting copiedExperimentId to 1628

07 Jun 2023 22:11:30,712 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'