Copying experiment: HAMSAB modified gut microbiota signature in human type 1 diabetes delays disease after transfer into gnotobiotic mice

QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study

Job Status

Created: 2023-10-02 18:51:21
Modified: 2023-10-02 18:51:33
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: HAMSAB modified gut microbiota signature in human type 1 diabetes delays disease after transfer into gnotobiotic mice
File Path: /data/labkey/files/Panorama Public/2023/QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study/@files/Experiment_1781.log
Files: Experiment_1781.log
Completed Runs: 210928_SCFA_dMRM_2022-02-23_16-35-51.sky.zip
210928_2-methylbutyric acid_dMRM_2022-02-23_16-36-21.sky.zip

Log File


02 Oct 2023 18:51:21,889 INFO : Copying experiment "HAMSAB modified gut microbiota signature in human type 1 diabetes delays disease after transfer into gnotobiotic mice" from folder /QIMRBerghofer Medical Research Institute/Precision & Systems Biomedicine (Hill Group)/SCFA in mouse feces - HAMSAB diet study to /Panorama Public/2023/QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study
02 Oct 2023 18:51:21,889 INFO : =======================================
02 Oct 2023 18:51:21,928 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
02 Oct 2023 18:51:21,928 INFO :
02 Oct 2023 18:51:21,928 INFO : Exporting experiment.
02 Oct 2023 18:51:24,632 INFO : Exporting files metadata.
02 Oct 2023 18:51:24,738 INFO :
02 Oct 2023 18:51:24,738 INFO : Experiment export completed successfully.
02 Oct 2023 18:51:24,738 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
02 Oct 2023 18:51:24,762 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
02 Oct 2023 18:51:24,762 INFO :
02 Oct 2023 18:51:24,762 INFO : Importing experiment.
02 Oct 2023 18:51:24,764 INFO : Loading folder properties (folder type, settings and active modules)
02 Oct 2023 18:51:24,832 INFO : Done importing folder properties (folder type, settings and active modules)
02 Oct 2023 18:51:24,833 INFO : Loading container specific module properties
02 Oct 2023 18:51:24,837 INFO : Done importing container specific module properties
02 Oct 2023 18:51:24,838 INFO : Loading etl definitions
02 Oct 2023 18:51:24,839 INFO : Loading wikis
02 Oct 2023 18:51:24,840 INFO : 0 wikis imported
02 Oct 2023 18:51:24,840 INFO : Done importing wikis
02 Oct 2023 18:51:24,842 INFO : Starting Data Class Importer
02 Oct 2023 18:51:24,842 INFO : No types XAR file to process.
02 Oct 2023 18:51:24,842 INFO : Finished Data Class Importer
02 Oct 2023 18:51:24,842 INFO : Starting to copy files
02 Oct 2023 18:51:24,842 INFO : Copied 0 files
02 Oct 2023 18:51:24,842 INFO : Ensuring exp.data rows exist for imported files
02 Oct 2023 18:51:24,896 INFO : Starting Sample Type Importer
02 Oct 2023 18:51:24,896 INFO : No types XAR file to process.
02 Oct 2023 18:51:24,896 INFO : Finished Sample Type Importer
02 Oct 2023 18:51:24,897 INFO : Loading xar
02 Oct 2023 18:51:25,319 INFO : Starting import from 210928_SCFA_dMRM_2022-02-23_16-35-51.sky.zip
02 Oct 2023 18:51:25,322 INFO : Starting to import Skyline document from 210928_SCFA_dMRM_2022-02-23_16-35-51.sky.zip
02 Oct 2023 18:51:25,324 INFO : Expanding 210928_SCFA_dMRM.skyd
02 Oct 2023 18:51:25,410 INFO : Expanding 210928_SCFA_dMRM.sky.view
02 Oct 2023 18:51:25,410 INFO : Expanding 210928_SCFA_dMRM.sky
02 Oct 2023 18:51:25,424 INFO : Expanding 210928_SCFA_dMRM.skyl
02 Oct 2023 18:51:25,510 INFO : 3% Done
02 Oct 2023 18:51:25,956 INFO : Inserting SCFA
02 Oct 2023 18:51:25,989 INFO : 14% Done
02 Oct 2023 18:51:26,213 INFO : 22% Done
02 Oct 2023 18:51:26,387 INFO : 31% Done
02 Oct 2023 18:51:26,589 INFO : 41% Done
02 Oct 2023 18:51:26,781 INFO : 48% Done
02 Oct 2023 18:51:26,945 INFO : 56% Done
02 Oct 2023 18:51:27,108 INFO : 63% Done
02 Oct 2023 18:51:27,271 INFO : 70% Done
02 Oct 2023 18:51:27,448 INFO : 80% Done
02 Oct 2023 18:51:27,624 INFO : Done parsing Skyline document.
02 Oct 2023 18:51:27,684 INFO : Calculating fold changes
02 Oct 2023 18:51:27,964 INFO : 89% Done
02 Oct 2023 18:51:27,964 INFO : Done calculating fold changes.
02 Oct 2023 18:51:27,964 INFO : Calculating calibration curves
02 Oct 2023 18:51:28,261 INFO : 98% Done
02 Oct 2023 18:51:28,468 INFO : Done calculating calibration curves.
02 Oct 2023 18:51:28,600 INFO : Creating and populating temp tables for Proportion values
02 Oct 2023 18:51:28,702 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Oct 2023 18:51:28,817 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Oct 2023 18:51:28,858 INFO : Cleaning up temp tables
02 Oct 2023 18:51:29,113 INFO : Completed import of Skyline document from 210928_SCFA_dMRM_2022-02-23_16-35-51.sky.zip
02 Oct 2023 18:51:29,114 INFO : 100% Done
02 Oct 2023 18:51:29,119 INFO : Starting import from 210928_2-methylbutyric acid_dMRM_2022-02-23_16-36-21.sky.zip
02 Oct 2023 18:51:29,121 INFO : Starting to import Skyline document from 210928_2-methylbutyric acid_dMRM_2022-02-23_16-36-21.sky.zip
02 Oct 2023 18:51:29,122 INFO : Expanding 210928_2-methylbutyric acid_dMRM.skyd
02 Oct 2023 18:51:29,207 INFO : Expanding 210928_2-methylbutyric acid_dMRM.sky.view
02 Oct 2023 18:51:29,210 INFO : Expanding 210928_2-methylbutyric acid_dMRM.sky
02 Oct 2023 18:51:29,212 INFO : Expanding 210928_2-methylbutyric acid_dMRM.skyl
02 Oct 2023 18:51:29,244 INFO : 23% Done
02 Oct 2023 18:51:29,742 INFO : Inserting SCFA
02 Oct 2023 18:51:29,754 INFO : 48% Done
02 Oct 2023 18:51:29,850 INFO : 80% Done
02 Oct 2023 18:51:29,937 INFO : Done parsing Skyline document.
02 Oct 2023 18:51:29,998 INFO : Calculating fold changes
02 Oct 2023 18:51:30,024 INFO : 89% Done
02 Oct 2023 18:51:30,024 INFO : Done calculating fold changes.
02 Oct 2023 18:51:30,024 INFO : Calculating calibration curves
02 Oct 2023 18:51:30,054 INFO : 98% Done
02 Oct 2023 18:51:30,054 INFO : Done calculating calibration curves.
02 Oct 2023 18:51:30,181 INFO : Creating and populating temp tables for Proportion values
02 Oct 2023 18:51:30,257 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Oct 2023 18:51:30,269 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Oct 2023 18:51:30,278 INFO : Cleaning up temp tables
02 Oct 2023 18:51:30,543 INFO : Completed import of Skyline document from 210928_2-methylbutyric acid_dMRM_2022-02-23_16-36-21.sky.zip
02 Oct 2023 18:51:30,545 INFO : 100% Done
02 Oct 2023 18:51:30,556 INFO : Done importing xar
02 Oct 2023 18:51:30,557 INFO : Loading pages and webpart properties
02 Oct 2023 18:51:30,614 INFO : Done importing 3 page(s) with 5 webpart(s)
02 Oct 2023 18:51:30,614 INFO : Loading File Browser config
02 Oct 2023 18:51:30,614 INFO : Done importing File Browser config
02 Oct 2023 18:51:30,615 INFO : Starting Sample Status Data import
02 Oct 2023 18:51:30,615 INFO : No sample types XAR file to process.
02 Oct 2023 18:51:30,615 INFO : Finished importing Sample Status Data
02 Oct 2023 18:51:30,620 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
02 Oct 2023 18:51:30,623 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
02 Oct 2023 18:51:30,623 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
02 Oct 2023 18:51:30,624 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
02 Oct 2023 18:51:30,624 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
02 Oct 2023 18:51:30,624 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
02 Oct 2023 18:51:30,626 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
02 Oct 2023 18:51:30,631 INFO : Moving files to folder /Panorama Public/2023/QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study and creating symlinks
02 Oct 2023 18:51:31,006 INFO : Aligning data files urls in folder: /Panorama Public/2023/QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study
02 Oct 2023 18:51:31,021 INFO : Importing files metadata.
02 Oct 2023 18:51:31,022 INFO :
02 Oct 2023 18:51:31,022 INFO : Experiment import completed successfully.
02 Oct 2023 18:51:31,022 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
02 Oct 2023 18:51:31,046 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
02 Oct 2023 18:51:31,046 INFO :
02 Oct 2023 18:51:31,046 INFO : Checking for library folders.
02 Oct 2023 18:51:31,048 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
02 Oct 2023 18:51:31,069 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
02 Oct 2023 18:51:31,069 INFO :
02 Oct 2023 18:51:31,069 INFO : Finishing up experiment copy.
02 Oct 2023 18:51:31,070 INFO : Updating TargetedMS experiment entry in target folder /Panorama Public/2023/QIMRBerghofer Medical Research Institute - SCFA in mouse feces - HAMSAB diet study
02 Oct 2023 18:51:31,071 INFO : Setting version on new experiment to 1
02 Oct 2023 18:51:31,074 INFO : Updating permanent link to point to the new copy of the data.
02 Oct 2023 18:51:31,080 INFO : Removing copy permissions given to Panorama Public
02 Oct 2023 18:51:31,093 INFO : Adding read permissions to all users that are folder admins in the source folder.
02 Oct 2023 18:51:31,093 INFO : Assigning ReaderRole to alok.shah@qimrberghofer.edu.au
02 Oct 2023 18:51:31,093 INFO : Assigning ReaderRole to michelle.hill@qimrberghofer.edu.au
02 Oct 2023 18:51:31,093 INFO : Assigning ReaderRole to thomas.stoll@qimrberghofer.edu.au
02 Oct 2023 18:51:31,094 INFO : Assigning ReaderRole to ahmed.mohamed@qimrberghofer.edu.au
02 Oct 2023 18:51:31,094 INFO : Assigning ReaderRole to dutt.mriga@gmail.com
02 Oct 2023 18:51:31,094 INFO : Assigning PanoramaPublicSubmitterRole to michelle.hill@qimrberghofer.edu.au
02 Oct 2023 18:51:31,094 INFO : Assigning PanoramaPublicSubmitterRole to thomas.stoll@qimrberghofer.edu.au
02 Oct 2023 18:51:31,107 INFO : User michelle.hill@qimrberghofer.edu.au is already a member of group Panorama Public Submitters
02 Oct 2023 18:51:31,107 INFO : User thomas.stoll@qimrberghofer.edu.au is already a member of group Panorama Public Submitters
02 Oct 2023 18:51:31,107 INFO : Updating the 'Raw Data' tab configuration
02 Oct 2023 18:51:31,108 INFO : Creating a reviewer account.
02 Oct 2023 18:51:31,315 INFO : Created reviewer with email: User panorama+reviewer213@proteinms.net
02 Oct 2023 18:51:31,332 INFO : Adding user panorama+reviewer213@proteinms.net to group Reviewers
02 Oct 2023 18:51:31,334 INFO : Hiding the Data Pipeline tab.
02 Oct 2023 18:51:31,339 INFO : Updating Submission. Setting copiedExperimentId to 1698
02 Oct 2023 18:51:32,922 INFO : Assigning a DOI.
02 Oct 2023 18:51:33,582 INFO : Assigned DOI: 10.6069/fj63-1p25
02 Oct 2023 18:51:33,645 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'