Copying experiment: Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach

Radboud University Medical Center - Neurodegenerative Disorders

Job Status

Created: 2021-10-01 10:10:29
Modified: 2021-10-01 10:10:45
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach
File Path: /data/labkey/files/Panorama Public/2021/Radboud University Medical Center - Neurodegenerative Disorders/@files/Experiment_1366.log
Files: Experiment_1366.log
Completed Runs: 20210928_Clinical samples_panorama_v2_2021-09-30_19-48-04.sky.zip

Log File


01 Oct 2021 10:10:29,169 INFO : Copying experiment "Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach" from folder /Radboud University Medical Center - Translational Metabolic Lab/Neurodegenerative Disorders to /Panorama Public/2021/Radboud University Medical Center - Neurodegenerative Disorders
01 Oct 2021 10:10:29,169 INFO : =======================================
01 Oct 2021 10:10:29,235 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
01 Oct 2021 10:10:29,235 INFO :
01 Oct 2021 10:10:29,235 INFO : Exporting experiment.
01 Oct 2021 10:10:32,832 INFO :
01 Oct 2021 10:10:32,832 INFO : Experiment export completed successfully.
01 Oct 2021 10:10:32,832 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
01 Oct 2021 10:10:32,863 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
01 Oct 2021 10:10:32,864 INFO :
01 Oct 2021 10:10:32,864 INFO : Importing experiment.
01 Oct 2021 10:10:32,869 INFO : Loading folder properties (folder type, settings and active modules)
01 Oct 2021 10:10:32,936 INFO : Done importing folder properties (folder type, settings and active modules)
01 Oct 2021 10:10:32,940 INFO : Loading grid views
01 Oct 2021 10:10:32,945 INFO : 1 custom view imported
01 Oct 2021 10:10:32,945 INFO : Done importing grid views
01 Oct 2021 10:10:32,948 INFO : Loading etl definitions
01 Oct 2021 10:10:32,951 INFO : Loading wikis
01 Oct 2021 10:10:32,953 INFO : 0 wikis imported
01 Oct 2021 10:10:32,953 INFO : Done importing wikis
01 Oct 2021 10:10:32,953 INFO : Starting to copy files
01 Oct 2021 10:10:33,163 INFO : Copied 115 files
01 Oct 2021 10:10:33,163 INFO : Ensuring exp.data rows exist for imported files
01 Oct 2021 10:10:33,694 INFO : Starting Sample Type and Data Class import
01 Oct 2021 10:10:33,694 INFO : No types XAR file to process.
01 Oct 2021 10:10:33,695 INFO : Finished importing Sample Types and Data Classes
01 Oct 2021 10:10:33,697 INFO : Loading xar
01 Oct 2021 10:10:33,829 INFO : Starting import from 20210928_Clinical samples_panorama_v2_2021-09-30_19-48-04.sky.zip
01 Oct 2021 10:10:33,833 INFO : Starting to import Skyline document from 20210928_Clinical samples_panorama_v2_2021-09-30_19-48-04.sky.zip
01 Oct 2021 10:10:33,835 INFO : Expanding 20210928_Clinical samples_panorama_v2.skyd
01 Oct 2021 10:10:33,876 INFO : Expanding 20210928_Clinical samples_panorama_v2.sky.view
01 Oct 2021 10:10:33,877 INFO : Expanding 20210928_Clinical samples_panorama_v2.sky
01 Oct 2021 10:10:33,905 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
01 Oct 2021 10:10:33,914 INFO : 1% Done
01 Oct 2021 10:10:34,126 INFO : Inserting peptides_1
01 Oct 2021 10:10:34,143 INFO : 3% Done
01 Oct 2021 10:10:34,313 INFO : Inserting peptides_2
01 Oct 2021 10:10:34,328 INFO : 6% Done
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01 Oct 2021 10:10:34,829 INFO : Inserting peptides_5
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01 Oct 2021 10:10:34,996 INFO : Inserting peptides_6
01 Oct 2021 10:10:35,009 INFO : 16% Done
01 Oct 2021 10:10:35,161 INFO : Inserting peptides_7
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01 Oct 2021 10:10:35,303 INFO : Inserting peptides_8
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01 Oct 2021 10:10:35,470 INFO : Inserting peptides_9
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01 Oct 2021 10:10:35,653 INFO : Inserting peptides_10
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01 Oct 2021 10:10:35,868 INFO : Inserting peptides_11
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01 Oct 2021 10:10:36,034 INFO : Inserting peptides_12
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01 Oct 2021 10:10:36,200 INFO : Inserting peptides_13
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01 Oct 2021 10:10:36,699 INFO : Inserting peptides_16
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01 Oct 2021 10:10:36,864 INFO : Inserting peptides_17
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01 Oct 2021 10:10:37,038 INFO : Inserting peptides_18
01 Oct 2021 10:10:37,053 INFO : 46% Done
01 Oct 2021 10:10:37,205 INFO : Inserting peptides_19
01 Oct 2021 10:10:37,219 INFO : 48% Done
01 Oct 2021 10:10:37,372 INFO : Inserting peptides_20
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01 Oct 2021 10:10:37,515 INFO : Inserting peptides_21
01 Oct 2021 10:10:37,529 INFO : 53% Done
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01 Oct 2021 10:10:37,846 INFO : Inserting peptides_23
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01 Oct 2021 10:10:38,010 INFO : Inserting peptides_24
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01 Oct 2021 10:10:38,175 INFO : Inserting peptides_25
01 Oct 2021 10:10:38,190 INFO : 63% Done
01 Oct 2021 10:10:38,339 INFO : Inserting peptides_26
01 Oct 2021 10:10:38,350 INFO : 65% Done
01 Oct 2021 10:10:38,486 INFO : Inserting peptides_27
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01 Oct 2021 10:10:38,656 INFO : Inserting peptides_28
01 Oct 2021 10:10:38,670 INFO : 70% Done
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01 Oct 2021 10:10:39,005 INFO : 75% Done
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01 Oct 2021 10:10:39,169 INFO : 78% Done
01 Oct 2021 10:10:39,318 INFO : Inserting peptides_32
01 Oct 2021 10:10:39,333 INFO : 80% Done
01 Oct 2021 10:10:39,483 INFO : Done parsing Skyline document.
01 Oct 2021 10:10:39,492 INFO : Calculating fold changes
01 Oct 2021 10:10:40,695 INFO : 89% Done
01 Oct 2021 10:10:40,696 INFO : Done calculating fold changes.
01 Oct 2021 10:10:40,696 INFO : Calculating calibration curves
01 Oct 2021 10:10:40,795 INFO : 90% Done
01 Oct 2021 10:10:40,965 INFO : 91% Done
01 Oct 2021 10:10:41,081 INFO : 92% Done
01 Oct 2021 10:10:41,360 INFO : 93% Done
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01 Oct 2021 10:10:41,688 INFO : 95% Done
01 Oct 2021 10:10:41,855 INFO : 96% Done
01 Oct 2021 10:10:41,973 INFO : 97% Done
01 Oct 2021 10:10:42,152 INFO : 98% Done
01 Oct 2021 10:10:42,198 INFO : Done calculating calibration curves.
01 Oct 2021 10:10:42,199 INFO : Creating and populating temp tables for Proportion values
01 Oct 2021 10:10:42,261 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
01 Oct 2021 10:10:42,552 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
01 Oct 2021 10:10:42,657 INFO : Cleaning up temp tables
01 Oct 2021 10:10:42,872 INFO : Completed import of Skyline document from 20210928_Clinical samples_panorama_v2_2021-09-30_19-48-04.sky.zip
01 Oct 2021 10:10:42,876 INFO : 100% Done
01 Oct 2021 10:10:42,887 INFO : Done importing xar
01 Oct 2021 10:10:42,889 INFO : Loading pages and webpart properties
01 Oct 2021 10:10:42,956 INFO : Done importing pages and webpart properties
01 Oct 2021 10:10:42,961 INFO :
01 Oct 2021 10:10:42,962 INFO : Experiment import completed successfully.
01 Oct 2021 10:10:42,962 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
01 Oct 2021 10:10:43,013 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
01 Oct 2021 10:10:43,013 INFO :
01 Oct 2021 10:10:43,014 INFO : Finishing up experiment copy.
01 Oct 2021 10:10:43,015 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
01 Oct 2021 10:10:43,017 INFO : Assigning a ProteomeXchange ID.
01 Oct 2021 10:10:43,226 INFO : Assigning a DOI.
01 Oct 2021 10:10:44,436 INFO : Assigned DOI: 10.6069/2tvs-jz79
01 Oct 2021 10:10:44,441 INFO : Updating access URL to point to the new copy of the data.
01 Oct 2021 10:10:44,447 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
01 Oct 2021 10:10:44,448 INFO : Removing copy permissions given to journal.
01 Oct 2021 10:10:44,460 INFO : Adding read permissions to all users that are folder admins in the source container.
01 Oct 2021 10:10:44,468 INFO : Setting the TargetedMS folder type to 'Experimental Data'
01 Oct 2021 10:10:44,475 INFO : Updating the 'Raw Data' tab configuration
01 Oct 2021 10:10:44,478 INFO : Updating dataFileUrls for run 20210928_Clinical samples_panorama_v2_2021-09-30_19-48-04.sky.zip; targetedms run ID 121262
01 Oct 2021 10:10:44,478 INFO : Updating dataFileUrl...
01 Oct 2021 10:10:44,478 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Radboud%20University%20Medical%20Center%20-%20Neurodegenerative%20Disorders_dfc6cfd4-0506-103a-b54f-fea6ddf5779e/_temp__2021-10-01_10-10-29/export/xar/experiments_and_runs.xar.exploded/Run118348/20210928_Clinical%20samples_panorama_v2_2021-09-30_19-48-04/20210928_Clinical%20samples_panorama_v2.skyd
01 Oct 2021 10:10:44,478 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Radboud%20University%20Medical%20Center%20-%20Neurodegenerative%20Disorders/@files/20210928_Clinical%20samples_panorama_v2_2021-09-30_19-48-04/20210928_Clinical%20samples_panorama_v2.skyd
01 Oct 2021 10:10:44,481 INFO : Updating dataFileUrl...
01 Oct 2021 10:10:44,481 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Radboud%20University%20Medical%20Center%20-%20Neurodegenerative%20Disorders_dfc6cfd4-0506-103a-b54f-fea6ddf5779e/_temp__2021-10-01_10-10-29/export/xar/experiments_and_runs.xar.exploded/Run118348/20210928_Clinical%20samples_panorama_v2_2021-09-30_19-48-04.sky.zip
01 Oct 2021 10:10:44,481 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Radboud%20University%20Medical%20Center%20-%20Neurodegenerative%20Disorders/@files/20210928_Clinical%20samples_panorama_v2_2021-09-30_19-48-04.sky.zip
01 Oct 2021 10:10:44,485 INFO : Creating a reviewer account.
01 Oct 2021 10:10:44,724 INFO : Created reviewer with email: User panorama+reviewer71@proteinms.net
01 Oct 2021 10:10:44,733 INFO : Hiding the Data Pipeline tab.
01 Oct 2021 10:10:44,884 INFO : Emailing submitter.
01 Oct 2021 10:10:45,069 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'