Copying experiment: Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infection: /Panorama Public/2023/IIT Bombay Proteomics

Copying experiment: Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infection

IIT Bombay Proteomics - SRM_Rohu_KidneyET

Job Status

Created:

2023-01-31 11:24:14

Modified:

2023-01-31 11:24:23

Email:

vsharma@uw.edu

Status:

COMPLETE

Info:

Description:

Copying experiment: Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infection

File Path:

/data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/Experiment_1646.log

Files:

Experiment_1646.log

Join job:

Status	Description

Split jobs:

Status	Description

Completed Runs:

29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

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Log File

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31 Jan 2023 11:24:13,991 INFO : Copying experiment "Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infection" from folder /IIT Bombay - Proteomics/Lab users/Mehar Un Nissa/SRM_Rohu_KidneyET to /Panorama Public/2023/IIT Bombay Proteomics - SRM_Rohu_KidneyET

31 Jan 2023 11:24:13,991 INFO : =======================================

31 Jan 2023 11:24:14,023 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

31 Jan 2023 11:24:14,023 INFO :

31 Jan 2023 11:24:14,023 INFO : Exporting experiment.

31 Jan 2023 11:24:17,035 INFO : Exporting files metadata.

31 Jan 2023 11:24:17,035 DEBUG: [/IIT Bombay - Proteomics/Lab users/Mehar Un Nissa/SRM_Rohu_KidneyET]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export

31 Jan 2023 11:24:17,046 INFO :

31 Jan 2023 11:24:17,046 INFO : Experiment export completed successfully.

31 Jan 2023 11:24:17,046 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

31 Jan 2023 11:24:17,061 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

31 Jan 2023 11:24:17,061 INFO :

31 Jan 2023 11:24:17,061 INFO : Importing experiment.

31 Jan 2023 11:24:17,062 DEBUG: [/Panorama Public/2023/IIT Bombay Proteomics - SRM_Rohu_KidneyET] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export

31 Jan 2023 11:24:17,063 INFO : Loading folder properties (folder type, settings and active modules)

31 Jan 2023 11:24:17,063 DEBUG: [/Panorama Public/2023/IIT Bombay Proteomics - SRM_Rohu_KidneyET] Folder type: Targeted MS

31 Jan 2023 11:24:17,063 DEBUG: [/Panorama Public/2023/IIT Bombay Proteomics - SRM_Rohu_KidneyET] Active modules: Issues, Core, Internal, Assay, Pipeline, Experiment, Wiki, MS2, Search, Query, Announcements, TargetedMS, PanoramaPublic, FileContent, API

31 Jan 2023 11:24:17,125 INFO : Done importing folder properties (folder type, settings and active modules)

31 Jan 2023 11:24:17,126 INFO : Loading container specific module properties

31 Jan 2023 11:24:17,134 INFO : Done importing container specific module properties

31 Jan 2023 11:24:17,135 INFO : Loading etl definitions

31 Jan 2023 11:24:17,136 INFO : Loading wikis

31 Jan 2023 11:24:17,148 INFO : 1 wiki imported

31 Jan 2023 11:24:17,148 INFO : Done importing wikis

31 Jan 2023 11:24:17,148 INFO : Starting to copy files

31 Jan 2023 11:24:18,379 INFO : Copied 25 files

31 Jan 2023 11:24:18,379 INFO : Ensuring exp.data rows exist for imported files

31 Jan 2023 11:24:18,470 INFO : Starting Sample Type and Data Class import

31 Jan 2023 11:24:18,470 INFO : No types XAR file to process.

31 Jan 2023 11:24:18,470 INFO : Finished importing Sample Types and Data Classes

31 Jan 2023 11:24:18,471 INFO : Loading xar

31 Jan 2023 11:24:18,533 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip'

31 Jan 2023 11:24:18,535 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip.Core'

31 Jan 2023 11:24:18,536 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip.Output'

31 Jan 2023 11:24:18,536 DEBUG: Protocol import complete

31 Jan 2023 11:24:18,538 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11061:Validation+of+protein+expression+in+kidney+tissue+of+Labeo+rohita+during+Edwardsiella+tarda+infection'

31 Jan 2023 11:24:18,538 DEBUG: Experiment/Run group import complete

31 Jan 2023 11:24:18,545 DEBUG: Protocol action set import complete

31 Jan 2023 11:24:18,551 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip'

31 Jan 2023 11:24:18,556 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11061:7e3a4965-82b8-103b-8435-fea6ddf5de34'

31 Jan 2023 11:24:18,559 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11061:7e3a493e-82b8-103b-8435-fea6ddf5de34'

31 Jan 2023 11:24:18,559 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip.Core'

31 Jan 2023 11:24:18,560 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11061:TargetedMS.ImportSkyZip.Output'

31 Jan 2023 11:24:18,561 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11061:7e3a49f7-82b8-103b-8435-fea6ddf5de34'

31 Jan 2023 11:24:18,561 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02/29112022_Kidney_ET.skyd into the system

31 Jan 2023 11:24:18,562 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02/29112022_Kidney_ET.skyd into the system

31 Jan 2023 11:24:18,562 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip into the system

31 Jan 2023 11:24:18,562 INFO : Starting import from 29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

31 Jan 2023 11:24:18,565 INFO : Starting to import Skyline document from 29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

31 Jan 2023 11:24:18,566 INFO : Expanding Kidney_ET_DR_Prosit.blib

31 Jan 2023 11:24:18,566 INFO : Expanding Kidney_ET_UR_Prosit.blib

31 Jan 2023 11:24:18,567 INFO : Expanding 29112022_Kidney_ET.skyd

31 Jan 2023 11:24:18,599 INFO : Expanding 29112022_Kidney_ET.sky.view

31 Jan 2023 11:24:18,599 INFO : Expanding 29112022_Kidney_ET.sky

31 Jan 2023 11:24:18,606 INFO : Expanding 29112022_Kidney_ET.skyl

31 Jan 2023 11:24:18,613 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

31 Jan 2023 11:24:18,618 INFO : 1% Done

31 Jan 2023 11:24:18,644 DEBUG: Starting to load chromatogram headers

31 Jan 2023 11:24:18,645 DEBUG: Done loading chromatogram headers

31 Jan 2023 11:24:18,780 INFO : Inserting tr|A0A498MT06|A0A498MT06_LABRO

31 Jan 2023 11:24:18,786 INFO : 2% Done

31 Jan 2023 11:24:18,811 INFO : 5% Done

31 Jan 2023 11:24:18,840 INFO : 7% Done

31 Jan 2023 11:24:18,868 INFO : 9% Done

31 Jan 2023 11:24:18,890 INFO : 10% Done

31 Jan 2023 11:24:18,917 INFO : 13% Done

31 Jan 2023 11:24:18,943 INFO : 14% Done

31 Jan 2023 11:24:18,967 DEBUG: Total peptides inserted: 7

31 Jan 2023 11:24:18,968 INFO : 15% Done

31 Jan 2023 11:24:18,969 INFO : Inserting tr|A0A498ME18|A0A498ME18_LABRO

31 Jan 2023 11:24:18,974 INFO : 17% Done

31 Jan 2023 11:24:18,995 INFO : 18% Done

31 Jan 2023 11:24:19,015 INFO : 19% Done

31 Jan 2023 11:24:19,033 INFO : 21% Done

31 Jan 2023 11:24:19,054 INFO : 22% Done

31 Jan 2023 11:24:19,073 DEBUG: Total peptides inserted: 5

31 Jan 2023 11:24:19,074 INFO : Inserting tr|A0A498M0I3|A0A498M0I3_LABRO

31 Jan 2023 11:24:19,078 INFO : 25% Done

31 Jan 2023 11:24:19,100 INFO : 26% Done

31 Jan 2023 11:24:19,119 INFO : 27% Done

31 Jan 2023 11:24:19,141 INFO : 29% Done

31 Jan 2023 11:24:19,156 DEBUG: Total peptides inserted: 4

31 Jan 2023 11:24:19,156 INFO : Inserting tr|A0A498MNZ5|A0A498MNZ5_LABRO

31 Jan 2023 11:24:19,160 INFO : 30% Done

31 Jan 2023 11:24:19,178 INFO : 32% Done

31 Jan 2023 11:24:19,198 INFO : 33% Done

31 Jan 2023 11:24:19,214 INFO : 34% Done

31 Jan 2023 11:24:19,233 INFO : 35% Done

31 Jan 2023 11:24:19,250 INFO : 37% Done

31 Jan 2023 11:24:19,266 DEBUG: Total peptides inserted: 6

31 Jan 2023 11:24:19,266 INFO : Inserting tr|A0A498N022|A0A498N022_LABRO

31 Jan 2023 11:24:19,270 INFO : 38% Done

31 Jan 2023 11:24:19,288 INFO : 39% Done

31 Jan 2023 11:24:19,309 INFO : 41% Done

31 Jan 2023 11:24:19,324 DEBUG: Total peptides inserted: 3

31 Jan 2023 11:24:19,324 INFO : Inserting tr|A0A498NFT9|A0A498NFT9_LABRO

31 Jan 2023 11:24:19,330 INFO : 43% Done

31 Jan 2023 11:24:19,358 INFO : 45% Done

31 Jan 2023 11:24:19,383 INFO : 46% Done

31 Jan 2023 11:24:19,400 INFO : 48% Done

31 Jan 2023 11:24:19,422 INFO : 50% Done

31 Jan 2023 11:24:19,439 DEBUG: Total peptides inserted: 5

31 Jan 2023 11:24:19,439 INFO : Inserting tr|A0A498NIQ5|A0A498NIQ5_LABRO

31 Jan 2023 11:24:19,443 INFO : 51% Done

31 Jan 2023 11:24:19,466 INFO : 52% Done

31 Jan 2023 11:24:19,485 INFO : 54% Done

31 Jan 2023 11:24:19,502 INFO : 55% Done

31 Jan 2023 11:24:19,521 DEBUG: Total peptides inserted: 4

31 Jan 2023 11:24:19,521 INFO : Inserting tr|A0A498MV63|A0A498MV63_LABRO

31 Jan 2023 11:24:19,526 INFO : 57% Done

31 Jan 2023 11:24:19,548 INFO : 58% Done

31 Jan 2023 11:24:19,565 INFO : 60% Done

31 Jan 2023 11:24:19,584 INFO : 62% Done

31 Jan 2023 11:24:19,606 INFO : 63% Done

31 Jan 2023 11:24:19,625 DEBUG: Total peptides inserted: 5

31 Jan 2023 11:24:19,625 INFO : Inserting tr|A0A498LXF0|A0A498LXF0_LABRO

31 Jan 2023 11:24:19,630 INFO : 64% Done

31 Jan 2023 11:24:19,648 INFO : 66% Done

31 Jan 2023 11:24:19,668 INFO : 67% Done

31 Jan 2023 11:24:19,684 INFO : 69% Done

31 Jan 2023 11:24:19,708 INFO : 70% Done

31 Jan 2023 11:24:19,723 DEBUG: Total peptides inserted: 5

31 Jan 2023 11:24:19,723 INFO : Inserting tr|A0A498MC15|A0A498MC15_LABRO

31 Jan 2023 11:24:19,727 INFO : 71% Done

31 Jan 2023 11:24:19,744 INFO : 73% Done

31 Jan 2023 11:24:19,759 INFO : 74% Done

31 Jan 2023 11:24:19,774 DEBUG: Total peptides inserted: 3

31 Jan 2023 11:24:19,774 INFO : Inserting tr|A0A498LR99|A0A498LR99_LABRO

31 Jan 2023 11:24:19,779 INFO : 76% Done

31 Jan 2023 11:24:19,807 INFO : 78% Done

31 Jan 2023 11:24:19,832 INFO : 80% Done

31 Jan 2023 11:24:19,853 DEBUG: Total peptides inserted: 3

31 Jan 2023 11:24:19,855 INFO : Done parsing Skyline document.

31 Jan 2023 11:24:19,906 INFO : Calculating fold changes

31 Jan 2023 11:24:19,906 DEBUG: Calculating fold change for group comparison ET vs Control, 1 of 1

31 Jan 2023 11:24:20,380 INFO : 98% Done

31 Jan 2023 11:24:20,380 INFO : Done calculating fold changes.

31 Jan 2023 11:24:21,267 INFO : Creating and populating temp tables for Proportion values

31 Jan 2023 11:24:21,327 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

31 Jan 2023 11:24:21,361 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

31 Jan 2023 11:24:21,384 INFO : Cleaning up temp tables

31 Jan 2023 11:24:21,655 INFO : Completed import of Skyline document from 29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

31 Jan 2023 11:24:21,657 INFO : 100% Done

31 Jan 2023 11:24:21,660 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip into the system

31 Jan 2023 11:24:21,666 INFO : Done importing xar

31 Jan 2023 11:24:21,667 INFO : Loading pages and webpart properties

31 Jan 2023 11:24:21,739 INFO : Done importing 4 page(s) with 8 webpart(s)

31 Jan 2023 11:24:21,739 INFO : Loading File Browser config

31 Jan 2023 11:24:21,739 INFO : Done importing File Browser config

31 Jan 2023 11:24:21,740 INFO : Starting Sample Status Data import

31 Jan 2023 11:24:21,740 INFO : No sample types XAR file to process.

31 Jan 2023 11:24:21,740 INFO : Finished importing Sample Status Data

31 Jan 2023 11:24:21,744 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

31 Jan 2023 11:24:21,747 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping

31 Jan 2023 11:24:21,747 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping

31 Jan 2023 11:24:21,748 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping

31 Jan 2023 11:24:21,748 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

31 Jan 2023 11:24:21,748 INFO : Importing files metadata.

31 Jan 2023 11:24:21,748 DEBUG: [/Panorama Public/2023/IIT Bombay Proteomics - SRM_Rohu_KidneyET]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT Bombay Proteomics - SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export

31 Jan 2023 11:24:21,748 INFO :

31 Jan 2023 11:24:21,748 INFO : Experiment import completed successfully.

31 Jan 2023 11:24:21,748 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

31 Jan 2023 11:24:21,764 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

31 Jan 2023 11:24:21,764 INFO :

31 Jan 2023 11:24:21,764 INFO : Checking for library folders.

31 Jan 2023 11:24:21,765 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

31 Jan 2023 11:24:21,779 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

31 Jan 2023 11:24:21,779 INFO :

31 Jan 2023 11:24:21,779 INFO : Finishing up experiment copy.

31 Jan 2023 11:24:21,781 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

31 Jan 2023 11:24:21,781 INFO : Setting version on new experiment to 1

31 Jan 2023 11:24:21,781 INFO : Assigning a ProteomeXchange ID.

31 Jan 2023 11:24:22,085 INFO : Assigning a DOI.

31 Jan 2023 11:24:23,646 INFO : Assigned DOI: 10.6069/17zs-0j70

31 Jan 2023 11:24:23,649 INFO : Updating access URL to point to the new copy of the data.

31 Jan 2023 11:24:23,667 INFO : Removing copy permissions given to Panorama Public

31 Jan 2023 11:24:23,677 INFO : Adding read permissions to all users that are folder admins in the source folder.

31 Jan 2023 11:24:23,685 INFO : Updating the 'Raw Data' tab configuration

31 Jan 2023 11:24:23,686 INFO : Updating dataFileUrls for run 29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip; targetedms run ID 151847

31 Jan 2023 11:24:23,686 INFO : Updating dataFileUrl...

31 Jan 2023 11:24:23,686 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02/29112022_Kidney_ET.skyd

31 Jan 2023 11:24:23,686 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET/@files/29112022_Kidney_ET_2023-01-30_16-12-02/29112022_Kidney_ET.skyd

31 Jan 2023 11:24:23,688 INFO : Updating dataFileUrl...

31 Jan 2023 11:24:23,688 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET_ca4ec698-83c8-103b-8435-fea6ddf5de34/_temp__2023-01-31_11-24-13/export/xar/experiments_and_runs.xar.exploded/Run149812/29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

31 Jan 2023 11:24:23,688 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/IIT%20Bombay%20Proteomics%20-%20SRM_Rohu_KidneyET/@files/29112022_Kidney_ET_2023-01-30_16-12-02.sky.zip

31 Jan 2023 11:24:23,692 INFO : Creating a reviewer account.

31 Jan 2023 11:24:23,888 INFO : Created reviewer with email: User panorama+reviewer168@proteinms.net

31 Jan 2023 11:24:23,898 INFO : Hiding the Data Pipeline tab.

31 Jan 2023 11:24:23,902 INFO : Updating Submission. Setting copiedExperimentId to 1567

31 Jan 2023 11:24:23,985 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'