13 Jun 2022 09:48:29,616 INFO : Copying experiment "Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipids" from folder /MPI-CBG - Shevchenko Lab/CD1d to /Panorama Public/2022/MPI-CBG Shevchenko Lab - CD1d

13 Jun 2022 09:48:29,616 INFO : =======================================

13 Jun 2022 09:48:29,781 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

13 Jun 2022 09:48:29,781 INFO : 

13 Jun 2022 09:48:29,781 INFO : Exporting experiment.

13 Jun 2022 09:49:21,660 INFO : Exporting files metadata.

13 Jun 2022 09:49:21,660 DEBUG: [/MPI-CBG - Shevchenko Lab/CD1d]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG Shevchenko Lab - CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export

13 Jun 2022 09:49:21,669 INFO : 

13 Jun 2022 09:49:21,669 INFO : Experiment export completed successfully.

13 Jun 2022 09:49:21,669 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

13 Jun 2022 09:49:21,822 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

13 Jun 2022 09:49:21,822 INFO : 

13 Jun 2022 09:49:21,822 INFO : Importing experiment.

13 Jun 2022 09:49:21,825 DEBUG: [/Panorama Public/2022/MPI-CBG Shevchenko Lab - CD1d] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG Shevchenko Lab - CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export

13 Jun 2022 09:49:21,867 INFO : Loading folder properties (folder type, settings and active modules)

13 Jun 2022 09:49:21,867 DEBUG: [/Panorama Public/2022/MPI-CBG Shevchenko Lab - CD1d] Folder type: Targeted MS

13 Jun 2022 09:49:21,867 DEBUG: [/Panorama Public/2022/MPI-CBG Shevchenko Lab - CD1d] Active modules: Core, FileContent, Query, Pipeline, Wiki, Issues, TargetedMS, MS2, Assay, API, PanoramaPublic, Search, Experiment, Announcements, Internal

13 Jun 2022 09:49:21,932 INFO : Done importing folder properties (folder type, settings and active modules)

13 Jun 2022 09:49:21,974 INFO : Loading container specific module properties

13 Jun 2022 09:49:21,985 INFO : Done importing container specific module properties

13 Jun 2022 09:49:22,028 INFO : Loading etl definitions

13 Jun 2022 09:49:22,070 INFO : Loading wikis

13 Jun 2022 09:49:22,072 INFO : 0 wikis imported

13 Jun 2022 09:49:22,072 INFO : Done importing wikis

13 Jun 2022 09:49:22,072 INFO : Starting to copy files

13 Jun 2022 09:50:12,710 INFO : Copied 11 files

13 Jun 2022 09:50:12,710 INFO : Ensuring exp.data rows exist for imported files

13 Jun 2022 09:50:12,821 INFO : Starting Sample Type and Data Class import

13 Jun 2022 09:50:12,821 INFO : No types XAR file to process.

13 Jun 2022 09:50:12,821 INFO : Finished importing Sample Types and Data Classes

13 Jun 2022 09:50:12,865 INFO : Loading xar

13 Jun 2022 09:50:12,908 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip'

13 Jun 2022 09:50:12,911 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip.Core'

13 Jun 2022 09:50:12,912 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip.Output'

13 Jun 2022 09:50:12,912 DEBUG: Protocol import complete

13 Jun 2022 09:50:12,913 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-10409:Sortase+A-cleavable+CD1d+identifies+sphingomyelins+as+major+class+of+CD1d-associated+lipids'

13 Jun 2022 09:50:12,913 DEBUG: Experiment/Run group import complete

13 Jun 2022 09:50:12,922 DEBUG: Protocol action set import complete

13 Jun 2022 09:50:12,938 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip'

13 Jun 2022 09:50:12,949 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-10409:f3dd983b-cd41-103a-b0c0-fea6ddf5cd3a'

13 Jun 2022 09:50:12,953 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-10409:f3dd9824-cd41-103a-b0c0-fea6ddf5cd3a'

13 Jun 2022 09:50:12,953 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip.Core'

13 Jun 2022 09:50:12,955 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-10409:TargetedMS.ImportSkyZip.Output'

13 Jun 2022 09:50:12,956 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-10409:f3dd9886-cd41-103a-b0c0-fea6ddf5cd3a'

13 Jun 2022 09:50:12,959 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16/20220609_cd1d.skyd into the system

13 Jun 2022 09:50:12,960 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16/20220609_cd1d.skyd into the system

13 Jun 2022 09:50:12,960 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16.sky.zip into the system

13 Jun 2022 09:50:12,961 INFO : Starting import from 20220609_cd1d_2022-06-13_14-26-16.sky.zip

13 Jun 2022 09:50:12,963 INFO : Starting to import Skyline document from 20220609_cd1d_2022-06-13_14-26-16.sky.zip

13 Jun 2022 09:50:12,964 INFO : Expanding 20220609_cd1d.skyd

13 Jun 2022 09:50:12,973 INFO : Expanding 20220609_cd1d.sky.view

13 Jun 2022 09:50:12,973 INFO : Expanding 20220609_cd1d.sky

13 Jun 2022 09:50:12,974 INFO : Expanding 20220609_cd1d.skyl

13 Jun 2022 09:50:13,004 WARN : The version of this Skyline document is 21.2. This is newer than the highest supported version 20.22

13 Jun 2022 09:50:13,051 INFO : 6% Done

13 Jun 2022 09:50:13,055 DEBUG: Starting to load chromatogram headers

13 Jun 2022 09:50:13,056 DEBUG: Done loading chromatogram headers

13 Jun 2022 09:50:13,194 INFO : Inserting CD1D

13 Jun 2022 09:50:13,268 INFO : 64% Done

13 Jun 2022 09:50:13,407 INFO : 98% Done

13 Jun 2022 09:50:13,576 DEBUG: Total peptides inserted: 2

13 Jun 2022 09:50:13,577 INFO : Done parsing Skyline document.

13 Jun 2022 09:50:14,640 INFO : Creating and populating temp tables for Proportion values

13 Jun 2022 09:50:14,668 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

13 Jun 2022 09:50:14,669 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

13 Jun 2022 09:50:14,670 INFO : Cleaning up temp tables

13 Jun 2022 09:50:14,995 INFO : Completed import of Skyline document from 20220609_cd1d_2022-06-13_14-26-16.sky.zip

13 Jun 2022 09:50:15,037 INFO : 100% Done

13 Jun 2022 09:50:15,043 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16.sky.zip into the system

13 Jun 2022 09:50:15,050 INFO : Done importing xar

13 Jun 2022 09:50:15,092 INFO : Loading pages and webpart properties

13 Jun 2022 09:50:15,170 INFO : Done importing 4 page(s) with 7 webpart(s)

13 Jun 2022 09:50:15,212 INFO : Starting Sample Status Data import

13 Jun 2022 09:50:15,212 INFO : No sample types XAR file to process.

13 Jun 2022 09:50:15,212 INFO : Finished importing Sample Status Data

13 Jun 2022 09:50:15,258 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

13 Jun 2022 09:50:15,263 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping

13 Jun 2022 09:50:15,264 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping

13 Jun 2022 09:50:15,264 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping

13 Jun 2022 09:50:15,265 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

13 Jun 2022 09:50:15,265 INFO : Starting QC Plot settings import

13 Jun 2022 09:50:15,266 INFO : Finished importing 0 QC Plot settings from PlotSettings.properties as properties.

13 Jun 2022 09:50:15,268 INFO : Importing files metadata.

13 Jun 2022 09:50:15,268 DEBUG: [/Panorama Public/2022/MPI-CBG Shevchenko Lab - CD1d]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG Shevchenko Lab - CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export

13 Jun 2022 09:50:15,269 INFO : 

13 Jun 2022 09:50:15,269 INFO : Experiment import completed successfully.

13 Jun 2022 09:50:15,269 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

13 Jun 2022 09:50:15,415 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

13 Jun 2022 09:50:15,415 INFO : 

13 Jun 2022 09:50:15,415 INFO : Checking for library folders.

13 Jun 2022 09:50:15,417 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

13 Jun 2022 09:50:15,559 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

13 Jun 2022 09:50:15,560 INFO : 

13 Jun 2022 09:50:15,560 INFO : Finishing up experiment copy.

13 Jun 2022 09:50:15,562 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

13 Jun 2022 09:50:15,562 INFO : Setting version on new experiment to 1

13 Jun 2022 09:50:15,562 INFO : Assigning a ProteomeXchange ID.

13 Jun 2022 09:50:16,450 INFO : Assigning a DOI.

13 Jun 2022 09:50:17,397 INFO : Assigned DOI: 10.6069/e53r-0052

13 Jun 2022 09:50:17,400 INFO : Updating access URL to point to the new copy of the data.

13 Jun 2022 09:50:17,404 INFO : Removing copy permissions given to Panorama Public

13 Jun 2022 09:50:17,419 INFO : Adding read permissions to all users that are folder admins in the source folder.

13 Jun 2022 09:50:17,425 INFO : Updating the 'Raw Data' tab configuration

13 Jun 2022 09:50:17,428 INFO : Updating dataFileUrls for run 20220609_cd1d_2022-06-13_14-26-16.sky.zip; targetedms run ID 139545

13 Jun 2022 09:50:17,428 INFO : Updating dataFileUrl...

13 Jun 2022 09:50:17,428 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16.sky.zip

13 Jun 2022 09:50:17,429 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d/@files/20220609_cd1d_2022-06-13_14-26-16.sky.zip

13 Jun 2022 09:50:17,430 INFO : Updating dataFileUrl...

13 Jun 2022 09:50:17,430 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d_8e2a9954-cd65-103a-b0c0-fea6ddf5cd3a/_temp__2022-06-13_09-48-29/export/xar/experiments_and_runs.xar.exploded/Run137268/20220609_cd1d_2022-06-13_14-26-16/20220609_cd1d.skyd

13 Jun 2022 09:50:17,430 INFO : to: file:///data/labkey/files/Panorama%20Public/2022/MPI-CBG%20Shevchenko%20Lab%20-%20CD1d/@files/20220609_cd1d_2022-06-13_14-26-16/20220609_cd1d.skyd

13 Jun 2022 09:50:17,435 INFO : Making folder public.

13 Jun 2022 09:50:17,440 INFO : Hiding the Data Pipeline tab.

13 Jun 2022 09:50:17,444 INFO : Updating Submission. Setting copiedExperimentId to 1458

13 Jun 2022 09:50:17,500 INFO : Emailing submitter.

13 Jun 2022 09:50:17,571 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'