01 Nov 2021 09:22:02,551 INFO : Copying experiment "Targeted proteomic validation of dysregulated proteins in liver tissue of Labeo rohita after Aeromonas hydrophila infection" from folder /IIT Bombay - Proteomics/SRM_Rohu_LiverAH to /Panorama Public/2021/IIT Bombay Proteomics - SRM_Rohu_LiverAH

01 Nov 2021 09:22:02,552 INFO : =======================================

01 Nov 2021 09:22:02,636 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

01 Nov 2021 09:22:02,636 INFO : 

01 Nov 2021 09:22:02,636 INFO : Exporting experiment.

01 Nov 2021 09:22:07,541 INFO : 

01 Nov 2021 09:22:07,541 INFO : Experiment export completed successfully.

01 Nov 2021 09:22:07,541 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

01 Nov 2021 09:22:07,578 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

01 Nov 2021 09:22:07,578 INFO : 

01 Nov 2021 09:22:07,578 INFO : Importing experiment.

01 Nov 2021 09:22:07,583 INFO : Loading folder properties (folder type, settings and active modules)

01 Nov 2021 09:22:07,682 INFO : Done importing folder properties (folder type, settings and active modules)

01 Nov 2021 09:22:07,685 INFO : Loading etl definitions

01 Nov 2021 09:22:07,688 INFO : Loading wikis

01 Nov 2021 09:22:07,712 INFO : 2 wikis imported

01 Nov 2021 09:22:07,712 INFO : Done importing wikis

01 Nov 2021 09:22:07,712 INFO : Starting to copy files

01 Nov 2021 09:22:10,405 INFO : Copied 29 files

01 Nov 2021 09:22:10,406 INFO : Ensuring exp.data rows exist for imported files

01 Nov 2021 09:22:10,605 INFO : Starting Sample Type and Data Class import

01 Nov 2021 09:22:10,606 INFO : No types XAR file to process.

01 Nov 2021 09:22:10,606 INFO : Finished importing Sample Types and Data Classes

01 Nov 2021 09:22:10,609 INFO : Loading xar

01 Nov 2021 09:22:10,679 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip'

01 Nov 2021 09:22:10,682 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip.Core'

01 Nov 2021 09:22:10,685 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip.Output'

01 Nov 2021 09:22:10,685 DEBUG: Protocol import complete

01 Nov 2021 09:22:10,687 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9245:Targeted+proteomic+validation+of+dysregulated+proteins+in+liver+tissue+of+Labeo+rohita+after+of+Aeromonas+hydrophila+infection'

01 Nov 2021 09:22:10,687 DEBUG: Experiment/Run group import complete

01 Nov 2021 09:22:10,697 DEBUG: Protocol action set import complete

01 Nov 2021 09:22:10,723 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip'

01 Nov 2021 09:22:10,733 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9245:dd1b5574-1b97-103a-b54f-fea6ddf5779e'

01 Nov 2021 09:22:10,737 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9245:dd1b541f-1b97-103a-b54f-fea6ddf5779e'

01 Nov 2021 09:22:10,737 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip.Core'

01 Nov 2021 09:22:10,740 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9245:TargetedMS.ImportSkyZip.Output'

01 Nov 2021 09:22:10,741 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9245:dd1b55e3-1b97-103a-b54f-fea6ddf5779e'

01 Nov 2021 09:22:10,742 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53/30102021_SRM_Rohu_LiverAH_vs_Control.skyd into the system

01 Nov 2021 09:22:10,743 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53/30102021_SRM_Rohu_LiverAH_vs_Control.skyd into the system

01 Nov 2021 09:22:10,743 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip into the system

01 Nov 2021 09:22:10,745 INFO : Starting import from 30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip

01 Nov 2021 09:22:10,749 INFO : Starting to import Skyline document from 30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip

01 Nov 2021 09:22:10,750 INFO : Expanding Liver_AH_LFQ_DDA.blib

01 Nov 2021 09:22:10,830 INFO : Expanding 30102021_SRM_Rohu_LiverAH_vs_Control.skyd

01 Nov 2021 09:22:10,845 INFO : Expanding 30102021_SRM_Rohu_LiverAH_vs_Control.sky.view

01 Nov 2021 09:22:10,845 INFO : Expanding 30102021_SRM_Rohu_LiverAH_vs_Control.sky

01 Nov 2021 09:22:10,850 INFO : Expanding 30102021_SRM_Rohu_LiverAH_vs_Control.skyl

01 Nov 2021 09:22:10,860 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22

01 Nov 2021 09:22:10,866 INFO : 2% Done

01 Nov 2021 09:22:10,906 DEBUG: Starting to load chromatogram headers

01 Nov 2021 09:22:10,907 DEBUG: Done loading chromatogram headers

01 Nov 2021 09:22:10,969 INFO : Inserting peptides1

01 Nov 2021 09:22:10,981 INFO : 6% Done

01 Nov 2021 09:22:11,014 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,017 INFO : Inserting tr|A0A498LPT3|A0A498LPT3_LABRO

01 Nov 2021 09:22:11,023 INFO : 8% Done

01 Nov 2021 09:22:11,045 INFO : 10% Done

01 Nov 2021 09:22:11,065 INFO : 11% Done

01 Nov 2021 09:22:11,086 INFO : 14% Done

01 Nov 2021 09:22:11,110 INFO : 15% Done

01 Nov 2021 09:22:11,136 INFO : 18% Done

01 Nov 2021 09:22:11,165 INFO : 21% Done

01 Nov 2021 09:22:11,187 INFO : 22% Done

01 Nov 2021 09:22:11,210 DEBUG: Total peptides inserted: 8

01 Nov 2021 09:22:11,213 INFO : Inserting tr|A0A498MGE6|A0A498MGE6_LABRO

01 Nov 2021 09:22:11,217 INFO : 25% Done

01 Nov 2021 09:22:11,234 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,237 INFO : Inserting tr|A0A498N951|A0A498N951_LABRO

01 Nov 2021 09:22:11,242 INFO : 26% Done

01 Nov 2021 09:22:11,260 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,266 INFO : Inserting tr|A0A498NDH5|A0A498NDH5_LABRO

01 Nov 2021 09:22:11,271 INFO : 28% Done

01 Nov 2021 09:22:11,286 INFO : 30% Done

01 Nov 2021 09:22:11,303 INFO : 31% Done

01 Nov 2021 09:22:11,321 INFO : 33% Done

01 Nov 2021 09:22:11,334 DEBUG: Total peptides inserted: 4

01 Nov 2021 09:22:11,336 INFO : Inserting tr|A0A498LTZ8|A0A498LTZ8_LABRO

01 Nov 2021 09:22:11,340 INFO : 34% Done

01 Nov 2021 09:22:11,358 INFO : 36% Done

01 Nov 2021 09:22:11,376 INFO : 37% Done

01 Nov 2021 09:22:11,391 INFO : 38% Done

01 Nov 2021 09:22:11,409 INFO : 40% Done

01 Nov 2021 09:22:11,428 INFO : 42% Done

01 Nov 2021 09:22:11,450 INFO : 44% Done

01 Nov 2021 09:22:11,467 DEBUG: Total peptides inserted: 7

01 Nov 2021 09:22:11,470 INFO : Inserting tr|A0A498NIH3|A0A498NIH3_LABRO

01 Nov 2021 09:22:11,474 INFO : 46% Done

01 Nov 2021 09:22:11,494 INFO : 47% Done

01 Nov 2021 09:22:11,519 INFO : 49% Done

01 Nov 2021 09:22:11,536 INFO : 50% Done

01 Nov 2021 09:22:11,548 DEBUG: Total peptides inserted: 4

01 Nov 2021 09:22:11,550 INFO : Inserting tr|A0A498M886|A0A498M886_LABRO

01 Nov 2021 09:22:11,554 INFO : 51% Done

01 Nov 2021 09:22:11,568 INFO : 54% Done

01 Nov 2021 09:22:11,582 DEBUG: Total peptides inserted: 2

01 Nov 2021 09:22:11,584 INFO : Inserting tr|A0A498N1B9|A0A498N1B9_LABRO

01 Nov 2021 09:22:11,597 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,600 INFO : Inserting tr|A0A498NCT8|A0A498NCT8_LABRO

01 Nov 2021 09:22:11,604 INFO : 56% Done

01 Nov 2021 09:22:11,617 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,621 INFO : Inserting tr|A0A498L4W1|A0A498L4W1_LABRO

01 Nov 2021 09:22:11,625 INFO : 58% Done

01 Nov 2021 09:22:11,660 INFO : 61% Done

01 Nov 2021 09:22:11,677 DEBUG: Total peptides inserted: 3

01 Nov 2021 09:22:11,679 INFO : Inserting tr|A0A498P0B5|A0A498P0B5_LABRO

01 Nov 2021 09:22:11,684 INFO : 63% Done

01 Nov 2021 09:22:11,707 INFO : 65% Done

01 Nov 2021 09:22:11,722 DEBUG: Total peptides inserted: 2

01 Nov 2021 09:22:11,725 INFO : Inserting tr|A0A498M8P4|A0A498M8P4_LABRO

01 Nov 2021 09:22:11,730 INFO : 66% Done

01 Nov 2021 09:22:11,746 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,750 INFO : Inserting tr|A0A498N7B5|A0A498N7B5_LABRO

01 Nov 2021 09:22:11,756 INFO : 67% Done

01 Nov 2021 09:22:11,772 INFO : 70% Done

01 Nov 2021 09:22:11,801 DEBUG: Total peptides inserted: 3

01 Nov 2021 09:22:11,805 INFO : Inserting tr|A0A498LPH1|A0A498LPH1_LABRO

01 Nov 2021 09:22:11,809 INFO : 72% Done

01 Nov 2021 09:22:11,823 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,826 INFO : Inserting tr|A0A498NZF5|A0A498NZF5_LABRO

01 Nov 2021 09:22:11,830 INFO : 74% Done

01 Nov 2021 09:22:11,846 INFO : 76% Done

01 Nov 2021 09:22:11,868 INFO : 78% Done

01 Nov 2021 09:22:11,896 DEBUG: Total peptides inserted: 4

01 Nov 2021 09:22:11,898 INFO : Inserting tr|A0A498MZR8|A0A498MZR8_LABRO

01 Nov 2021 09:22:11,901 INFO : 80% Done

01 Nov 2021 09:22:11,913 DEBUG: Total peptides inserted: 1

01 Nov 2021 09:22:11,915 INFO : Done parsing Skyline document.

01 Nov 2021 09:22:11,918 INFO : Calculating fold changes

01 Nov 2021 09:22:11,918 DEBUG: Calculating fold change for group comparison AH vs Control, 1 of 1

01 Nov 2021 09:22:12,571 INFO : 98% Done

01 Nov 2021 09:22:12,572 INFO : Done calculating fold changes.

01 Nov 2021 09:22:17,946 INFO : Creating and populating temp tables for Proportion values

01 Nov 2021 09:22:17,962 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

01 Nov 2021 09:22:17,983 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

01 Nov 2021 09:22:17,997 INFO : Cleaning up temp tables

01 Nov 2021 09:22:18,297 INFO : Completed import of Skyline document from 30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip

01 Nov 2021 09:22:18,301 INFO : 100% Done

01 Nov 2021 09:22:18,305 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip into the system

01 Nov 2021 09:22:18,311 INFO : Done importing xar

01 Nov 2021 09:22:18,313 INFO : Loading pages and webpart properties

01 Nov 2021 09:22:18,388 INFO : Done importing pages and webpart properties

01 Nov 2021 09:22:18,388 INFO : 

01 Nov 2021 09:22:18,389 INFO : Experiment import completed successfully.

01 Nov 2021 09:22:18,389 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

01 Nov 2021 09:22:18,423 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

01 Nov 2021 09:22:18,423 INFO : 

01 Nov 2021 09:22:18,423 INFO : Finishing up experiment copy.

01 Nov 2021 09:22:18,424 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

01 Nov 2021 09:22:18,427 INFO : Assigning a ProteomeXchange ID.

01 Nov 2021 09:22:18,952 INFO : Assigning a DOI.

01 Nov 2021 09:22:20,606 INFO : Assigned DOI: 10.6069/xxae-4w76

01 Nov 2021 09:22:20,611 INFO : Updating access URL to point to the new copy of the data.

01 Nov 2021 09:22:20,620 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.

01 Nov 2021 09:22:20,621 INFO : Removing copy permissions given to journal.

01 Nov 2021 09:22:20,656 INFO : Adding read permissions to all users that are folder admins in the source container.

01 Nov 2021 09:22:20,667 INFO : Setting the TargetedMS folder type to 'Experimental Data'

01 Nov 2021 09:22:20,680 INFO : Updating the 'Raw Data' tab configuration

01 Nov 2021 09:22:20,682 INFO : Updating dataFileUrls for run 30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip; targetedms run ID 123639

01 Nov 2021 09:22:20,683 INFO : Updating dataFileUrl...

01 Nov 2021 09:22:20,683 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53/30102021_SRM_Rohu_LiverAH_vs_Control.skyd

01 Nov 2021 09:22:20,683 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH/@files/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53/30102021_SRM_Rohu_LiverAH_vs_Control.skyd

01 Nov 2021 09:22:20,686 INFO : Updating dataFileUrl...

01 Nov 2021 09:22:20,686 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH_50d7ab5a-1d5c-103a-b54f-fea6ddf5779e/_temp__2021-11-01_09-22-01/export/xar/experiments_and_runs.xar.exploded/Run120658/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip

01 Nov 2021 09:22:20,686 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_LiverAH/@files/30102021_SRM_Rohu_LiverAH_vs_Control_2021-10-30_15-50-53.sky.zip

01 Nov 2021 09:22:20,689 INFO : Creating a reviewer account.

01 Nov 2021 09:22:20,965 INFO : Created reviewer with email: User panorama+reviewer75@proteinms.net

01 Nov 2021 09:22:20,978 INFO : Hiding the Data Pipeline tab.

01 Nov 2021 09:22:21,075 INFO : Emailing submitter.

01 Nov 2021 09:22:21,201 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'