Copying experiment: Factor H and related proteins in AMD: /Panorama Public/2021/U of Manchester Unwin Lab

Copying experiment: Factor H and related proteins in AMD

U of Manchester Unwin Lab - FH Skyline

Job Status

Created:

2021-01-07 17:40:06

Modified:

2021-01-07 17:41:52

Email:

vsharma@uw.edu

Status:

COMPLETE

Info:

Description:

Copying experiment: Factor H and related proteins in AMD

File Path:

/data/labkey/files/Panorama Public/2021/U of Manchester Unwin Lab - FH Skyline/@files/Experiment_1134.log

Files:

Experiment_1134.log

Join job:

Status	Description

Split jobs:

Status	Description

Completed Runs:

FH AMD_template_2020-12-03_14-09-56.sky.zip
FH AMD_populated_2020-12-03_14-04-13.sky.zip

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Log File

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07 Jan 2021 17:40:06,139 INFO : Copying experiment "Factor H and related proteins in AMD" from folder /U of Manchester - Unwin Lab/FH Skyline to /Panorama Public/2021/U of Manchester Unwin Lab - FH Skyline

07 Jan 2021 17:40:06,139 INFO : =======================================

07 Jan 2021 17:40:06,396 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

07 Jan 2021 17:40:06,396 INFO :

07 Jan 2021 17:40:06,396 INFO : Exporting experiment.

07 Jan 2021 17:40:51,890 INFO :

07 Jan 2021 17:40:51,890 INFO : Experiment export completed successfully.

07 Jan 2021 17:40:51,890 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

07 Jan 2021 17:40:52,031 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

07 Jan 2021 17:40:52,031 INFO :

07 Jan 2021 17:40:52,032 INFO : Importing experiment.

07 Jan 2021 17:40:52,056 INFO : Loading folder properties (folder type, settings and active modules)

07 Jan 2021 17:40:52,245 INFO : Done importing folder properties (folder type, settings and active modules)

07 Jan 2021 17:40:52,254 INFO : Loading etl definitions

07 Jan 2021 17:40:52,260 INFO : Loading wikis

07 Jan 2021 17:40:52,590 INFO : 2 wikis imported

07 Jan 2021 17:40:52,590 INFO : Done importing wikis

07 Jan 2021 17:40:52,590 INFO : Starting to copy files

07 Jan 2021 17:41:43,035 INFO : Copied 102 files

07 Jan 2021 17:41:43,036 INFO : Ensuring exp.data rows exist for imported files

07 Jan 2021 17:41:44,964 INFO : Loading xar

07 Jan 2021 17:41:45,200 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip'

07 Jan 2021 17:41:45,210 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Core'

07 Jan 2021 17:41:45,216 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Output'

07 Jan 2021 17:41:45,216 DEBUG: Protocol import complete

07 Jan 2021 17:41:45,289 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8018:Factor+H+and+related+proteins+in+AMD'

07 Jan 2021 17:41:45,289 DEBUG: Experiment/Run group import complete

07 Jan 2021 17:41:45,312 DEBUG: Protocol action set import complete

07 Jan 2021 17:41:45,373 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip'

07 Jan 2021 17:41:45,486 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8018:41feb004-179e-1039-927b-3013bb9ba7ed'

07 Jan 2021 17:41:45,486 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Core'

07 Jan 2021 17:41:45,492 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Output'

07 Jan 2021 17:41:45,493 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8018:41feb036-179e-1039-927b-3013bb9ba7ed'

07 Jan 2021 17:41:45,511 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip'

07 Jan 2021 17:41:45,521 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8018:41fe9021-179e-1039-927b-3013bb9ba7ed'

07 Jan 2021 17:41:45,529 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8018:41fe900e-179e-1039-927b-3013bb9ba7ed'

07 Jan 2021 17:41:45,529 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Core'

07 Jan 2021 17:41:45,533 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8018:TargetedMS.ImportSkyZip.Output'

07 Jan 2021 17:41:45,534 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8018:41fe9042-179e-1039-927b-3013bb9ba7ed'

07 Jan 2021 17:41:45,537 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95822/FH%20AMD_template_2020-12-03_14-09-56.sky.zip into the system

07 Jan 2021 17:41:45,540 INFO : Starting import from FH AMD_template_2020-12-03_14-09-56.sky.zip

07 Jan 2021 17:41:45,546 INFO : Starting to import Skyline document from FH AMD_template_2020-12-03_14-09-56.sky.zip

07 Jan 2021 17:41:45,547 INFO : Expanding FH AMD_template.sky.view

07 Jan 2021 17:41:45,547 INFO : Expanding FH AMD_template.sky

07 Jan 2021 17:41:45,548 INFO : Expanding FH AMD_template.skyl

07 Jan 2021 17:41:45,577 INFO : 13% Done

07 Jan 2021 17:41:45,577 WARN : Unable to find file /data/apache-tomcat/temp/Pipeline_temp/U of Manchester Unwin Lab - FH Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95822/FH AMD_template_2020-12-03_14-09-56/FH AMD_template.skyd, unable to import chromatograms

07 Jan 2021 17:41:45,666 INFO : Inserting CFH

07 Jan 2021 17:41:45,697 INFO : 30% Done

07 Jan 2021 17:41:45,808 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,808 INFO : Inserting FHL-1

07 Jan 2021 17:41:45,828 INFO : 46% Done

07 Jan 2021 17:41:45,853 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,853 INFO : Inserting FHR3

07 Jan 2021 17:41:45,861 INFO : 61% Done

07 Jan 2021 17:41:45,878 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,878 INFO : Inserting FHR4

07 Jan 2021 17:41:45,890 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,895 INFO : 76% Done

07 Jan 2021 17:41:45,895 INFO : Inserting FHR1

07 Jan 2021 17:41:45,962 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,962 INFO : Inserting FHR5

07 Jan 2021 17:41:45,970 INFO : 91% Done

07 Jan 2021 17:41:45,995 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:45,995 INFO : Inserting FHR2b

07 Jan 2021 17:41:46,001 INFO : 98% Done

07 Jan 2021 17:41:46,028 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:46,031 INFO : Done parsing Skyline document.

07 Jan 2021 17:41:46,103 INFO : Creating and populating temp tables for Proportion values

07 Jan 2021 17:41:46,170 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

07 Jan 2021 17:41:46,172 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

07 Jan 2021 17:41:46,174 INFO : Cleaning up temp tables

07 Jan 2021 17:41:46,177 INFO : Completed import of Skyline document from FH AMD_template_2020-12-03_14-09-56.sky.zip

07 Jan 2021 17:41:46,184 INFO : 100% Done

07 Jan 2021 17:41:46,196 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95822/FH%20AMD_template_2020-12-03_14-09-56.sky.zip into the system

07 Jan 2021 17:41:46,196 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13/FH%20AMD_populated.skyd into the system

07 Jan 2021 17:41:46,198 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13/FH%20AMD_populated.skyd into the system

07 Jan 2021 17:41:46,198 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13.sky.zip into the system

07 Jan 2021 17:41:46,203 INFO : Starting import from FH AMD_populated_2020-12-03_14-04-13.sky.zip

07 Jan 2021 17:41:46,209 INFO : Starting to import Skyline document from FH AMD_populated_2020-12-03_14-04-13.sky.zip

07 Jan 2021 17:41:46,213 INFO : Expanding FH AMD_populated.skyd

07 Jan 2021 17:41:46,354 INFO : Expanding FH AMD_populated.sky.view

07 Jan 2021 17:41:46,355 INFO : Expanding FH AMD_populated.sky

07 Jan 2021 17:41:46,360 INFO : Expanding FH AMD_populated.skyl

07 Jan 2021 17:41:46,380 INFO : 4% Done

07 Jan 2021 17:41:46,393 DEBUG: Starting to load chromatogram headers

07 Jan 2021 17:41:46,395 DEBUG: Done loading chromatogram headers

07 Jan 2021 17:41:46,526 INFO : Inserting CFH

07 Jan 2021 17:41:46,541 INFO : 19% Done

07 Jan 2021 17:41:46,864 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:46,864 INFO : Inserting FHL-1

07 Jan 2021 17:41:46,875 INFO : 32% Done

07 Jan 2021 17:41:47,186 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:47,186 INFO : Inserting FHR3

07 Jan 2021 17:41:47,196 INFO : 43% Done

07 Jan 2021 17:41:47,329 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:47,329 INFO : Inserting FHR4

07 Jan 2021 17:41:47,339 INFO : 56% Done

07 Jan 2021 17:41:47,515 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:47,521 INFO : 57% Done

07 Jan 2021 17:41:47,521 INFO : Inserting FHR1

07 Jan 2021 17:41:47,530 INFO : 71% Done

07 Jan 2021 17:41:47,812 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:47,812 INFO : Inserting FHR5

07 Jan 2021 17:41:47,822 INFO : 84% Done

07 Jan 2021 17:41:48,057 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:48,057 INFO : Inserting FHR2b

07 Jan 2021 17:41:48,066 INFO : 98% Done

07 Jan 2021 17:41:48,341 DEBUG: Total peptides inserted: 1

07 Jan 2021 17:41:48,344 INFO : Done parsing Skyline document.

07 Jan 2021 17:41:48,434 INFO : Creating and populating temp tables for Proportion values

07 Jan 2021 17:41:48,468 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

07 Jan 2021 17:41:48,606 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

07 Jan 2021 17:41:48,632 INFO : Cleaning up temp tables

07 Jan 2021 17:41:49,231 INFO : Completed import of Skyline document from FH AMD_populated_2020-12-03_14-04-13.sky.zip

07 Jan 2021 17:41:49,241 INFO : 100% Done

07 Jan 2021 17:41:49,253 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13.sky.zip into the system

07 Jan 2021 17:41:49,287 INFO : Done importing xar

07 Jan 2021 17:41:49,293 INFO : Loading pages and webpart properties

07 Jan 2021 17:41:49,530 INFO : Done importing pages and webpart properties

07 Jan 2021 17:41:49,530 INFO :

07 Jan 2021 17:41:49,530 INFO : Experiment import completed successfully.

07 Jan 2021 17:41:49,531 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

07 Jan 2021 17:41:49,612 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

07 Jan 2021 17:41:49,613 INFO :

07 Jan 2021 17:41:49,613 INFO : Finishing up experiment copy.

07 Jan 2021 17:41:49,616 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

07 Jan 2021 17:41:49,620 INFO : Assigning a ProteomeXchange ID.

07 Jan 2021 17:41:49,980 INFO : Updating access URL to point to the new copy of the data.

07 Jan 2021 17:41:50,163 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.

07 Jan 2021 17:41:50,283 INFO : Removing copy permissions given to journal.

07 Jan 2021 17:41:50,300 INFO : Adding read permissions to all users that are folder admins in the source container.

07 Jan 2021 17:41:50,318 INFO : Setting the TargetedMS folder type to 'Experimental Data'

07 Jan 2021 17:41:50,327 INFO : Updating the 'Raw Data' tab configuration

07 Jan 2021 17:41:50,333 INFO : Updating dataFileUrls for run FH AMD_populated_2020-12-03_14-04-13.sky.zip; targetedms run ID 99328

07 Jan 2021 17:41:50,333 INFO : Updating dataFileUrl...

07 Jan 2021 17:41:50,333 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13.sky.zip

07 Jan 2021 17:41:50,334 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline/@files/FH%20AMD_populated_2020-12-03_14-04-13.sky.zip

07 Jan 2021 17:41:50,338 INFO : Updating dataFileUrl...

07 Jan 2021 17:41:50,338 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95820/FH%20AMD_populated_2020-12-03_14-04-13/FH%20AMD_populated.skyd

07 Jan 2021 17:41:50,338 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline/@files/FH%20AMD_populated_2020-12-03_14-04-13/FH%20AMD_populated.skyd

07 Jan 2021 17:41:50,351 INFO : Updating dataFileUrls for run FH AMD_template_2020-12-03_14-09-56.sky.zip; targetedms run ID 99327

07 Jan 2021 17:41:50,351 INFO : Targetedms run 99327 in container org.labkey.api.data.Container@534841631 /Panorama Public/2021/U of Manchester Unwin Lab - FH Skyline/ 99f92694-337f-1039-b990-3013bb9b12b3 does not have a skydDataId.

07 Jan 2021 17:41:50,352 INFO : Updating dataFileUrl...

07 Jan 2021 17:41:50,352 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline_99f92694-337f-1039-b990-3013bb9b12b3/_temp__2021-01-07_17-40-05/export/xar/experiments_and_runs.xar.exploded/Run95822/FH%20AMD_template_2020-12-03_14-09-56.sky.zip

07 Jan 2021 17:41:50,352 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Manchester%20Unwin%20Lab%20-%20FH%20Skyline/@files/FH%20AMD_template_2020-12-03_14-09-56.sky.zip

07 Jan 2021 17:41:50,369 INFO : Making folder public.

07 Jan 2021 17:41:50,382 INFO : Hiding the Data Pipeline tab.

07 Jan 2021 17:41:50,594 INFO : Emailing submitter.

07 Jan 2021 17:41:51,380 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'