Copying experiment: Development of mass spectrometry-based targeted assay for the diagnosis of novel SARS-CoV-2 coronavirus from clinical specimens: /Panorama Public/2020/Mayo Clinic Pandey Lab

Copying experiment: Development of mass spectrometry-based targeted assay for the diagnosis of novel SARS-CoV-2 coronavirus from clinical specimens

Mayo Clinic Pandey Lab - PRM diagnosis of COVID-19

Job Status

Created:

2020-09-11 05:40:23

Modified:

2020-09-11 05:41:29

Email:

vsharma@uw.edu

Status:

COMPLETE

Info:

Description:

Copying experiment: Development of mass spectrometry-based targeted assay for the diagnosis of novel SARS-CoV-2 coronavirus from clinical specimens

File Path:

/data/labkey/files/Panorama Public/2020/Mayo Clinic Pandey Lab - PRM diagnosis of COVID-19/@files/Experiment_1069.log

Files:

Experiment_1069.log

Join job:

Status	Description

Split jobs:

Status	Description

Show Grid Data Browse Files

Log File

Show full log file Show raw log file Copy to clipboard

11 Sep 2020 05:40:23,662 INFO : Copying experiment "Development of mass spectrometry-based targeted assay for the diagnosis of novel SARS-CoV-2 coronavirus from clinical specimens" from folder /Mayo Clinic - Pandey Lab/PRM diagnosis of COVID-19 to /Panorama Public/2020/Mayo Clinic  Pandey Lab - PRM diagnosis of COVID-19

11 Sep 2020 05:40:23,662 INFO : =======================================

11 Sep 2020 05:40:23,858 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

11 Sep 2020 05:40:23,858 INFO :

11 Sep 2020 05:40:23,858 INFO : Exporting experiment.

11 Sep 2020 05:40:27,867 INFO :

11 Sep 2020 05:40:27,867 INFO : Experiment export completed successfully.

11 Sep 2020 05:40:27,867 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

11 Sep 2020 05:40:28,113 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

11 Sep 2020 05:40:28,113 INFO :

11 Sep 2020 05:40:28,113 INFO : Importing experiment.

11 Sep 2020 05:40:28,124 INFO : Loading folder properties (folder type, settings and active modules)

11 Sep 2020 05:40:28,425 INFO : Done importing folder properties (folder type, settings and active modules)

11 Sep 2020 05:40:28,432 INFO : Loading etl definitions

11 Sep 2020 05:40:28,439 INFO : Loading wikis

11 Sep 2020 05:40:28,443 INFO : 0 wikis imported

11 Sep 2020 05:40:28,443 INFO : Done importing wikis

11 Sep 2020 05:40:28,443 INFO : Starting to copy files

11 Sep 2020 05:40:29,602 INFO : Copied 13 files

11 Sep 2020 05:40:29,602 INFO : Ensuring exp.data rows exist for imported files

11 Sep 2020 05:40:30,307 INFO : Loading xar

11 Sep 2020 05:40:31,084 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip'

11 Sep 2020 05:40:31,087 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Core'

11 Sep 2020 05:40:31,091 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Output'

11 Sep 2020 05:40:31,091 DEBUG: Protocol import complete

11 Sep 2020 05:40:31,151 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-7591:Development+of+mass+spectrometry-based+targeted+assay+for+the+diagnosis+of+novel+SARS-CoV-2+coronavirus+from+clinical+specimens'

11 Sep 2020 05:40:31,151 DEBUG: Experiment/Run group import complete

11 Sep 2020 05:40:31,194 DEBUG: Protocol action set import complete

11 Sep 2020 05:40:31,281 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip'

11 Sep 2020 05:40:31,516 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7591:30fce29e-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,541 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7591:30fce43a-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,541 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Core'

11 Sep 2020 05:40:31,550 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Output'

11 Sep 2020 05:40:31,552 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7591:30fce502-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,573 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip'

11 Sep 2020 05:40:31,591 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7591:30fce14d-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,602 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7591:30fce35d-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,602 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Core'

11 Sep 2020 05:40:31,609 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7591:TargetedMS.ImportSkyZip.Output'

11 Sep 2020 05:40:31,610 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7591:30fce3fa-d593-1038-9455-3013bb9b8170'

11 Sep 2020 05:40:31,613 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation%20Data.sky.zip into the system

11 Sep 2020 05:40:31,619 INFO : Starting import from Validation Data.sky.zip

11 Sep 2020 05:40:31,629 INFO : Starting to import Skyline document from Validation Data.sky.zip

11 Sep 2020 05:40:31,630 INFO : Expanding Validation_Data.sky

11 Sep 2020 05:40:31,685 INFO : Expanding Validation_Data.sky.view

11 Sep 2020 05:40:31,686 INFO : Expanding Validation_Data.skyd

11 Sep 2020 05:40:31,848 INFO : Expanding Validation_Data.skyl

11 Sep 2020 05:40:31,864 WARN : The version of this Skyline document is 20.14. This is newer than the highest supported version 4.1

11 Sep 2020 05:40:31,953 INFO : 2% Done

11 Sep 2020 05:40:33,350 INFO : Inserting peptides1

11 Sep 2020 05:40:33,510 INFO : 29% Done

11 Sep 2020 05:40:39,577 INFO : 80% Done

11 Sep 2020 05:40:49,455 DEBUG: Total peptides inserted: 2

11 Sep 2020 05:40:49,457 INFO : Done parsing Skyline document.

11 Sep 2020 05:40:49,574 INFO : No group comparisons found.

11 Sep 2020 05:40:49,574 INFO : Calculating calibration curves

11 Sep 2020 05:40:49,576 DEBUG: Calculating calibration curve for peptides1, 1 of 1

11 Sep 2020 05:40:51,244 INFO : 98% Done

11 Sep 2020 05:40:51,360 INFO : Done calculating calibration curves.

11 Sep 2020 05:40:52,237 INFO : Creating and populating temp tables for Proportion values

11 Sep 2020 05:40:52,281 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

11 Sep 2020 05:40:52,564 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

11 Sep 2020 05:40:52,621 INFO : Cleaning up temp tables

11 Sep 2020 05:40:53,069 INFO : Completed import of Skyline document from Validation Data.sky.zip

11 Sep 2020 05:40:53,077 INFO : 100% Done

11 Sep 2020 05:40:53,090 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation%20Data.sky.zip into the system

11 Sep 2020 05:40:53,091 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation_Data.skyd into the system

11 Sep 2020 05:40:53,092 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation_Data.skyd into the system

11 Sep 2020 05:40:53,092 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training%20Data.sky.zip into the system

11 Sep 2020 05:40:53,096 INFO : Starting import from Training Data.sky.zip

11 Sep 2020 05:40:53,103 INFO : Starting to import Skyline document from Training Data.sky.zip

11 Sep 2020 05:40:53,104 INFO : Expanding Training_Data.sky

11 Sep 2020 05:40:53,166 INFO : Expanding Training_Data.sky.view

11 Sep 2020 05:40:53,167 INFO : Expanding Training_Data.skyd

11 Sep 2020 05:40:53,402 INFO : Expanding Training_Data.skyl

11 Sep 2020 05:40:53,413 WARN : The version of this Skyline document is 20.14. This is newer than the highest supported version 4.1

11 Sep 2020 05:40:53,430 INFO : 2% Done

11 Sep 2020 05:40:54,841 INFO : Inserting peptides1

11 Sep 2020 05:40:54,944 INFO : 35% Done

11 Sep 2020 05:41:00,786 INFO : 98% Done

11 Sep 2020 05:41:10,878 DEBUG: Total peptides inserted: 2

11 Sep 2020 05:41:10,878 INFO : Done parsing Skyline document.

11 Sep 2020 05:41:11,329 INFO : Creating and populating temp tables for Proportion values

11 Sep 2020 05:41:11,375 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

11 Sep 2020 05:41:11,637 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

11 Sep 2020 05:41:11,699 INFO : Cleaning up temp tables

11 Sep 2020 05:41:12,198 INFO : Completed import of Skyline document from Training Data.sky.zip

11 Sep 2020 05:41:12,207 INFO : 100% Done

11 Sep 2020 05:41:12,218 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training%20Data.sky.zip into the system

11 Sep 2020 05:41:12,218 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training_Data.skyd into the system

11 Sep 2020 05:41:12,220 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training_Data.skyd into the system

11 Sep 2020 05:41:12,249 INFO : Done importing xar

11 Sep 2020 05:41:12,271 INFO : Loading pages and webpart properties

11 Sep 2020 05:41:12,480 INFO : Done importing pages and webpart properties

11 Sep 2020 05:41:12,481 INFO :

11 Sep 2020 05:41:12,481 INFO : Experiment import completed successfully.

11 Sep 2020 05:41:12,481 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

11 Sep 2020 05:41:12,550 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

11 Sep 2020 05:41:12,550 INFO :

11 Sep 2020 05:41:12,550 INFO : Finishing up experiment copy.

11 Sep 2020 05:41:12,553 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

11 Sep 2020 05:41:12,774 INFO : Updating access URL to point to the new copy of the data.

11 Sep 2020 05:41:12,807 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.

11 Sep 2020 05:41:12,871 INFO : Removing copy permissions given to journal.

11 Sep 2020 05:41:12,923 INFO : Adding read permissions to all users that are folder admins in the source container.

11 Sep 2020 05:41:12,927 INFO : Adding read permissions to all users that had read access to previous copy.

11 Sep 2020 05:41:12,952 INFO : Setting the TargetedMS folder type to 'Experimental Data'

11 Sep 2020 05:41:12,969 INFO : Updating the 'Raw Data' tab configuration

11 Sep 2020 05:41:12,981 INFO : Updating dataFileUrls for run Training Data.sky.zip; targetedms run ID 93957

11 Sep 2020 05:41:12,983 INFO : Adding ExpData for .skyd file

11 Sep 2020 05:41:12,984 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:12,984 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training_Data.skyd

11 Sep 2020 05:41:12,984 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Training%20Data/Training_Data.skyd

11 Sep 2020 05:41:12,990 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:12,991 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training%20Data.sky.zip

11 Sep 2020 05:41:12,991 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Training%20Data.sky.zip

11 Sep 2020 05:41:12,996 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:12,996 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91784/Training%20Data/Training_Data.skyd

11 Sep 2020 05:41:12,996 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Training%20Data/Training_Data.skyd

11 Sep 2020 05:41:13,028 INFO : Updating dataFileUrls for run Validation Data.sky.zip; targetedms run ID 93956

11 Sep 2020 05:41:13,029 INFO : Adding ExpData for .skyd file

11 Sep 2020 05:41:13,030 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:13,030 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation_Data.skyd

11 Sep 2020 05:41:13,030 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Validation%20Data/Validation_Data.skyd

11 Sep 2020 05:41:13,035 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:13,035 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation%20Data.sky.zip

11 Sep 2020 05:41:13,036 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Validation%20Data.sky.zip

11 Sep 2020 05:41:13,040 INFO : Updating dataFileUrl...

11 Sep 2020 05:41:13,041 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19_efd407dd-d658-1038-9455-3013bb9b8170/_temp__2020-09-11_05-40-23/export/xar/experiments_and_runs.xar.exploded/Run91785/Validation%20Data/Validation_Data.skyd

11 Sep 2020 05:41:13,041 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Mayo%20Clinic%20%20Pandey%20Lab%20-%20PRM%20diagnosis%20of%20COVID-19/@files/Validation%20Data/Validation_Data.skyd

11 Sep 2020 05:41:13,046 INFO : Hiding the Data Pipeline tab.

11 Sep 2020 05:41:13,048 INFO : Deleting old container /Panorama Public/2020/Mayo Clinic Pandey Lab - PRM diagnosis of COVID-19 V.1

11 Sep 2020 05:41:28,806 INFO : Emailing submitter.

11 Sep 2020 05:41:29,153 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'