01 Apr 2023 13:18:45,935 INFO : Copying experiment "Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral Factor" from folder /Princeton University - Cristea Lab/KSHV TPCA_NUCKS1 IP-PRM to /Panorama Public/2023/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM

01 Apr 2023 13:18:45,935 INFO : =======================================

01 Apr 2023 13:18:45,957 DEBUG: Resetting Job ID: 46343d1a-b2f8-103b-a13f-fea6ddf5751c

01 Apr 2023 13:18:45,987 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

01 Apr 2023 13:18:45,987 INFO : 

01 Apr 2023 13:18:45,987 INFO : Exporting experiment.

01 Apr 2023 13:20:01,028 INFO : Exporting files metadata.

01 Apr 2023 13:20:01,028 DEBUG: [/Princeton University - Cristea Lab/KSHV TPCA_NUCKS1 IP-PRM]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export

01 Apr 2023 13:20:01,034 INFO : 

01 Apr 2023 13:20:01,035 INFO : Experiment export completed successfully.

01 Apr 2023 13:20:01,035 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

01 Apr 2023 13:20:01,061 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

01 Apr 2023 13:20:01,061 INFO : 

01 Apr 2023 13:20:01,061 INFO : Importing experiment.

01 Apr 2023 13:20:01,063 DEBUG: [/Panorama Public/2023/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export

01 Apr 2023 13:20:01,064 INFO : Loading folder properties (folder type, settings and active modules)

01 Apr 2023 13:20:01,064 DEBUG: [/Panorama Public/2023/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM] Folder type: Targeted MS

01 Apr 2023 13:20:01,064 DEBUG: [/Panorama Public/2023/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM] Active modules: Core, Announcements, Query, MS2, Experiment, Issues, FileContent, PanoramaPublic, Search, TargetedMS, Pipeline, Wiki, API, Assay

01 Apr 2023 13:20:01,127 INFO : Done importing folder properties (folder type, settings and active modules)

01 Apr 2023 13:20:01,128 INFO : Loading container specific module properties

01 Apr 2023 13:20:01,138 INFO : Done importing container specific module properties

01 Apr 2023 13:20:01,139 INFO : Loading etl definitions

01 Apr 2023 13:20:01,141 INFO : Loading wikis

01 Apr 2023 13:20:01,142 INFO : 0 wikis imported

01 Apr 2023 13:20:01,142 INFO : Done importing wikis

01 Apr 2023 13:20:01,142 INFO : Starting to copy files

01 Apr 2023 13:21:08,927 INFO : Copied 19 files

01 Apr 2023 13:21:08,927 INFO : Ensuring exp.data rows exist for imported files

01 Apr 2023 13:21:10,098 INFO : Starting Sample Type and Data Class import

01 Apr 2023 13:21:10,098 INFO : No types XAR file to process.

01 Apr 2023 13:21:10,098 INFO : Finished importing Sample Types and Data Classes

01 Apr 2023 13:21:10,099 INFO : Loading xar

01 Apr 2023 13:21:11,148 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip'

01 Apr 2023 13:21:11,150 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip.Core'

01 Apr 2023 13:21:11,152 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip.Output'

01 Apr 2023 13:21:11,152 DEBUG: Protocol import complete

01 Apr 2023 13:21:11,153 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11352:NUCKS1+IP-PRM_KSHV+48hpr'

01 Apr 2023 13:21:11,153 DEBUG: Experiment/Run group import complete

01 Apr 2023 13:21:11,162 DEBUG: Protocol action set import complete

01 Apr 2023 13:21:11,172 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip'

01 Apr 2023 13:21:11,177 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11352:58424537-b093-103b-a3e9-fea6ddf59764'

01 Apr 2023 13:21:11,182 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11352:584244e1-b093-103b-a3e9-fea6ddf59764'

01 Apr 2023 13:21:11,182 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip.Core'

01 Apr 2023 13:21:11,184 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11352:TargetedMS.ImportSkyZip.Output'

01 Apr 2023 13:21:11,185 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11352:5842461f-b093-103b-a3e9-fea6ddf59764'

01 Apr 2023 13:21:11,186 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyd into the system

01 Apr 2023 13:21:11,186 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyd into the system

01 Apr 2023 13:21:11,186 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip into the system

01 Apr 2023 13:21:11,187 INFO : Starting import from 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip

01 Apr 2023 13:21:11,191 INFO : Starting to import Skyline document from 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip

01 Apr 2023 13:21:11,192 INFO : Expanding human_herpesvirus_background.protdb

01 Apr 2023 13:21:13,394 INFO : Expanding 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.blib

01 Apr 2023 13:21:13,432 INFO : Expanding 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyd

01 Apr 2023 13:21:13,460 INFO : Expanding 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.sky.view

01 Apr 2023 13:21:13,460 INFO : Expanding 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.sky

01 Apr 2023 13:21:13,461 INFO : Expanding 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyl

01 Apr 2023 13:21:13,477 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

01 Apr 2023 13:21:13,481 INFO : 7% Done

01 Apr 2023 13:21:13,484 DEBUG: Starting to load chromatogram headers

01 Apr 2023 13:21:13,484 DEBUG: Done loading chromatogram headers

01 Apr 2023 13:21:13,619 INFO : Inserting RIR1

01 Apr 2023 13:21:13,628 INFO : 20% Done

01 Apr 2023 13:21:13,648 INFO : 30% Done

01 Apr 2023 13:21:13,658 DEBUG: Total peptides inserted: 2

01 Apr 2023 13:21:13,658 INFO : Inserting sp|F5HAW0|RIR2_HHV8P

01 Apr 2023 13:21:13,671 INFO : 52% Done

01 Apr 2023 13:21:13,700 INFO : 70% Done

01 Apr 2023 13:21:13,716 DEBUG: Total peptides inserted: 2

01 Apr 2023 13:21:13,716 INFO : Inserting sp|Q9H1E3|NUCKS_HUMAN

01 Apr 2023 13:21:13,725 INFO : 80% Done

01 Apr 2023 13:21:13,741 INFO : 91% Done

01 Apr 2023 13:21:13,757 INFO : 98% Done

01 Apr 2023 13:21:13,769 DEBUG: Total peptides inserted: 3

01 Apr 2023 13:21:13,769 INFO : Done parsing Skyline document.

01 Apr 2023 13:21:21,423 INFO : Creating and populating temp tables for Proportion values

01 Apr 2023 13:21:21,479 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

01 Apr 2023 13:21:21,482 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

01 Apr 2023 13:21:21,484 INFO : Cleaning up temp tables

01 Apr 2023 13:21:21,721 INFO : Completed import of Skyline document from 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip

01 Apr 2023 13:21:21,724 INFO : 100% Done

01 Apr 2023 13:21:21,727 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip into the system

01 Apr 2023 13:21:21,734 INFO : Done importing xar

01 Apr 2023 13:21:21,735 INFO : Loading pages and webpart properties

01 Apr 2023 13:21:21,795 INFO : Done importing 3 page(s) with 5 webpart(s)

01 Apr 2023 13:21:21,795 INFO : Loading File Browser config

01 Apr 2023 13:21:21,795 INFO : Done importing File Browser config

01 Apr 2023 13:21:21,799 INFO : Starting Sample Status Data import

01 Apr 2023 13:21:21,799 INFO : No sample types XAR file to process.

01 Apr 2023 13:21:21,799 INFO : Finished importing Sample Status Data

01 Apr 2023 13:21:21,803 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

01 Apr 2023 13:21:21,804 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping

01 Apr 2023 13:21:21,805 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping

01 Apr 2023 13:21:21,805 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping

01 Apr 2023 13:21:21,805 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

01 Apr 2023 13:21:21,805 INFO : Importing files metadata.

01 Apr 2023 13:21:21,805 DEBUG: [/Panorama Public/2023/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export

01 Apr 2023 13:21:21,806 INFO : 

01 Apr 2023 13:21:21,806 INFO : Experiment import completed successfully.

01 Apr 2023 13:21:21,806 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

01 Apr 2023 13:21:21,842 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

01 Apr 2023 13:21:21,842 INFO : 

01 Apr 2023 13:21:21,842 INFO : Checking for library folders.

01 Apr 2023 13:21:21,843 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

01 Apr 2023 13:21:21,863 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

01 Apr 2023 13:21:21,863 INFO : 

01 Apr 2023 13:21:21,863 INFO : Finishing up experiment copy.

01 Apr 2023 13:21:21,865 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

01 Apr 2023 13:21:21,865 INFO : Setting version on new experiment to 1

01 Apr 2023 13:21:21,865 INFO : Assigning a ProteomeXchange ID.

01 Apr 2023 13:21:24,189 INFO : Assigning a DOI.

01 Apr 2023 13:21:24,944 INFO : Assigned DOI: 10.6069/j1h8-5785

01 Apr 2023 13:21:24,949 INFO : Updating permanent link to point to the new copy of the data.

01 Apr 2023 13:21:24,955 INFO : Removing copy permissions given to Panorama Public

01 Apr 2023 13:21:24,969 INFO : Adding read permissions to all users that are folder admins in the source folder.

01 Apr 2023 13:21:24,971 INFO : Assigning PanoramaPublicSubmitterRole to mtyl@princeton.edu

01 Apr 2023 13:21:24,971 INFO : Assigning PanoramaPublicSubmitterRole to icristea@princeton.edu

01 Apr 2023 13:21:24,971 INFO : Assigning PanoramaPublicSubmitterRole to mtyl@princeton.edu

01 Apr 2023 13:21:24,973 INFO : User mtyl@princeton.edu is already a member of group Panorama Public Submitters

01 Apr 2023 13:21:24,973 INFO : User icristea@princeton.edu is already a member of group Panorama Public Submitters

01 Apr 2023 13:21:24,974 INFO : User mtyl@princeton.edu is already a member of group Panorama Public Submitters

01 Apr 2023 13:21:24,982 INFO : Updating the 'Raw Data' tab configuration

01 Apr 2023 13:21:24,984 INFO : Updating dataFileUrls for run 202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip; targetedms run ID 156439

01 Apr 2023 13:21:24,984 INFO : Updating dataFileUrl...

01 Apr 2023 13:21:24,984 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip

01 Apr 2023 13:21:24,984 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM/@files/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49.sky.zip

01 Apr 2023 13:21:24,986 INFO : Updating dataFileUrl...

01 Apr 2023 13:21:24,986 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM_46343cf8-b2f8-103b-a13f-fea6ddf5751c/_temp__2023-04-01_13-18-45/export/xar/experiments_and_runs.xar.exploded/Run154262/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyd

01 Apr 2023 13:21:24,986 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Princeton%20University%20Cristea%20Lab%20-%20KSHV%20TPCA_NUCKS1%20IP-PRM/@files/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT_2023-03-29_15-10-49/202205_KSHV_NUCKS1_RIR1-2-NUCKS1_QUANT.skyd

01 Apr 2023 13:21:24,992 INFO : Creating a reviewer account.

01 Apr 2023 13:21:25,215 INFO : Created reviewer with email: User panorama+reviewer180@proteinms.net

01 Apr 2023 13:21:25,230 INFO : Adding user panorama+reviewer180@proteinms.net to group Reviewers

01 Apr 2023 13:21:25,235 INFO : Hiding the Data Pipeline tab.

01 Apr 2023 13:21:25,239 INFO : Updating Submission. Setting copiedExperimentId to 1600

01 Apr 2023 13:21:25,327 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'