Copying experiment: Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk

Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics

Job Status

Created: 2023-11-25 10:27:34
Modified: 2023-11-25 10:28:09
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk
File Path: /data/labkey/files/Panorama Public/2023/Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics/@files/Experiment_1812.log
Files: Experiment_1812.log
Completed Runs: EDIA_SRM_to_panorama_2023-10-11_17-36-18.sky.zip

Log File


25 Nov 2023 10:27:34,157 INFO : Copying experiment "Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk" from folder /Turku Bioscience - Lahesmaa Group/Mother-infant serum proteomics to /Panorama Public/2023/Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics
25 Nov 2023 10:27:34,158 INFO : =======================================
25 Nov 2023 10:27:34,190 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
25 Nov 2023 10:27:34,190 INFO :
25 Nov 2023 10:27:34,190 INFO : Exporting experiment.
25 Nov 2023 10:27:47,213 INFO : Exporting files metadata.
25 Nov 2023 10:27:47,217 INFO :
25 Nov 2023 10:27:47,217 INFO : Experiment export completed successfully.
25 Nov 2023 10:27:47,217 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
25 Nov 2023 10:27:47,239 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
25 Nov 2023 10:27:47,239 INFO :
25 Nov 2023 10:27:47,239 INFO : Importing experiment.
25 Nov 2023 10:27:47,242 INFO : Loading folder properties (folder type, settings and active modules)
25 Nov 2023 10:27:47,318 INFO : Done importing folder properties (folder type, settings and active modules)
25 Nov 2023 10:27:47,319 INFO : Loading container specific module properties
25 Nov 2023 10:27:47,323 INFO : Done importing container specific module properties
25 Nov 2023 10:27:47,324 INFO : Loading etl definitions
25 Nov 2023 10:27:47,325 INFO : Loading wikis
25 Nov 2023 10:27:47,326 INFO : 0 wikis imported
25 Nov 2023 10:27:47,326 INFO : Done importing wikis
25 Nov 2023 10:27:47,328 INFO : Starting Data Class Importer
25 Nov 2023 10:27:47,329 INFO : No types XAR file to process.
25 Nov 2023 10:27:47,329 INFO : Finished Data Class Importer
25 Nov 2023 10:27:47,329 INFO : Starting to copy files
25 Nov 2023 10:27:47,329 INFO : Copied 0 files
25 Nov 2023 10:27:47,329 INFO : Ensuring exp.data rows exist for imported files
25 Nov 2023 10:27:47,393 INFO : Starting Sample Type Importer
25 Nov 2023 10:27:47,393 INFO : No types XAR file to process.
25 Nov 2023 10:27:47,393 INFO : Finished Sample Type Importer
25 Nov 2023 10:27:47,394 INFO : Loading xar
25 Nov 2023 10:27:50,125 INFO : Starting import from EDIA_SRM_to_panorama_2023-10-11_17-36-18.sky.zip
25 Nov 2023 10:27:50,127 INFO : Starting to import Skyline document from EDIA_SRM_to_panorama_2023-10-11_17-36-18.sky.zip
25 Nov 2023 10:27:50,129 INFO : Expanding Human_add.protdb
25 Nov 2023 10:27:54,690 INFO : Expanding INNODIA.irtdb
25 Nov 2023 10:27:54,693 INFO : Expanding PANC_Dec2018x.blib
25 Nov 2023 10:27:54,706 INFO : Expanding TH17newer.blib
25 Nov 2023 10:27:54,710 INFO : Expanding BC1713.blib
25 Nov 2023 10:27:54,712 INFO : Expanding BC1713.redundant.blib
25 Nov 2023 10:27:54,718 INFO : Expanding BC101613.blib
25 Nov 2023 10:27:54,720 INFO : Expanding PQ500.blib
25 Nov 2023 10:27:54,743 INFO : Expanding T1D_All_Syn_Pep.blib
25 Nov 2023 10:27:54,863 INFO : Expanding T1D_master.blib
25 Nov 2023 10:27:54,901 INFO : Expanding T1D_master.redundant.blib
25 Nov 2023 10:27:54,995 INFO : Expanding PQ5002.blib
25 Nov 2023 10:27:55,009 INFO : Expanding STEM2.blib
25 Nov 2023 10:27:55,015 INFO : Expanding STEM2.redundant.blib
25 Nov 2023 10:27:55,069 INFO : Expanding THIS.blib
25 Nov 2023 10:27:55,079 INFO : Expanding THIS.redundant.blib
25 Nov 2023 10:27:55,380 INFO : Expanding BetaCatenin.blib
25 Nov 2023 10:27:55,381 INFO : Expanding BetaCatenin.redundant.blib
25 Nov 2023 10:27:55,382 INFO : Expanding Sep20Extra.blib
25 Nov 2023 10:27:55,496 INFO : Expanding Sep20Extra.redundant.blib
25 Nov 2023 10:27:55,526 INFO : Expanding EDIA_SRM_to_panorama.skyd
25 Nov 2023 10:27:55,737 INFO : Expanding EDIA_SRM_to_panorama.sky.view
25 Nov 2023 10:27:55,738 INFO : Expanding EDIA_SRM_to_panorama.sky
25 Nov 2023 10:27:55,890 INFO : 1% Done
25 Nov 2023 10:27:56,655 INFO : Inserting sp|P60709|ACTB_HUMAN
25 Nov 2023 10:27:56,669 INFO : 3% Done
25 Nov 2023 10:27:56,733 INFO : Inserting sp|Q92820|GGH_HUMAN
25 Nov 2023 10:27:56,746 INFO : 5% Done
25 Nov 2023 10:27:56,817 INFO : 7% Done
25 Nov 2023 10:27:56,899 INFO : 10% Done
25 Nov 2023 10:27:56,960 INFO : Inserting sp|Q15166|PON3_HUMAN
25 Nov 2023 10:27:56,975 INFO : 12% Done
25 Nov 2023 10:27:57,045 INFO : 14% Done
25 Nov 2023 10:27:57,114 INFO : 15% Done
25 Nov 2023 10:27:57,163 INFO : Inserting sp|O75636|FCN3_HUMAN
25 Nov 2023 10:27:57,188 INFO : 20% Done
25 Nov 2023 10:27:57,327 INFO : 24% Done
25 Nov 2023 10:27:57,445 INFO : 26% Done
25 Nov 2023 10:27:57,494 INFO : Inserting sp|MSRT1|MSRT1_HUMAN
25 Nov 2023 10:27:57,542 INFO : 28% Done
25 Nov 2023 10:27:57,589 INFO : 29% Done
25 Nov 2023 10:27:57,633 INFO : 30% Done
25 Nov 2023 10:27:57,677 INFO : 31% Done
25 Nov 2023 10:27:57,723 INFO : 32% Done
25 Nov 2023 10:27:57,766 INFO : 34% Done
25 Nov 2023 10:27:57,865 INFO : 36% Done
25 Nov 2023 10:27:57,914 INFO : 37% Done
25 Nov 2023 10:27:57,967 INFO : 38% Done
25 Nov 2023 10:27:58,012 INFO : Inserting tr|C9JTX5|C9JTX5_HUMAN
25 Nov 2023 10:27:58,024 INFO : 40% Done
25 Nov 2023 10:27:58,088 INFO : Inserting sp|P01042|KNG1_HUMAN
25 Nov 2023 10:27:58,100 INFO : 42% Done
25 Nov 2023 10:27:58,182 INFO : 45% Done
25 Nov 2023 10:27:58,260 INFO : Inserting sp|P02768|ALBU_HUMAN
25 Nov 2023 10:27:58,275 INFO : 48% Done
25 Nov 2023 10:27:58,350 INFO : Inserting sp|P02671|FIBA_HUMAN
25 Nov 2023 10:27:58,366 INFO : 50% Done
25 Nov 2023 10:27:58,458 INFO : 53% Done
25 Nov 2023 10:27:58,544 INFO : Inserting sp|P68871|HBB_HUMAN
25 Nov 2023 10:27:58,559 INFO : 55% Done
25 Nov 2023 10:27:58,638 INFO : 58% Done
25 Nov 2023 10:27:58,713 INFO : Inserting sp|P00450|CERU_HUMAN
25 Nov 2023 10:27:58,731 INFO : 60% Done
25 Nov 2023 10:27:58,816 INFO : Inserting sp|P04217|A1BG_HUMAN
25 Nov 2023 10:27:58,827 INFO : 61% Done
25 Nov 2023 10:27:58,881 INFO : 62% Done
25 Nov 2023 10:27:58,928 INFO : 63% Done
25 Nov 2023 10:27:58,966 INFO : Inserting sp|P48740|MASP1_HUMAN
25 Nov 2023 10:27:58,987 INFO : 66% Done
25 Nov 2023 10:27:59,078 INFO : 69% Done
25 Nov 2023 10:27:59,173 INFO : 72% Done
25 Nov 2023 10:27:59,285 INFO : 77% Done
25 Nov 2023 10:27:59,444 INFO : 80% Done
25 Nov 2023 10:27:59,537 INFO : Done parsing Skyline document.
25 Nov 2023 10:27:59,537 INFO : Calculating iRT correlations for 66 sample(s)
25 Nov 2023 10:27:59,545 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,549 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,552 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,556 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,560 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,564 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,568 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,571 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,575 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,579 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,583 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,587 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,590 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,594 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,598 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,602 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,605 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,609 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,613 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,617 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,620 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,624 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,628 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,632 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,636 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,639 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,643 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,647 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,651 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,654 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,658 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,662 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,666 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,669 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,673 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,677 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,681 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,685 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,689 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,692 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,696 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,700 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,704 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,707 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,711 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,715 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,719 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,722 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,726 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,730 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,733 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,738 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,742 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,746 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,750 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,753 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,757 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,761 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,764 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,768 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,772 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,776 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,779 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,783 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,787 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,791 INFO : Calculated iRT regression line from full standard list.
25 Nov 2023 10:27:59,791 INFO : Finished calculating iRT correlations for all samples. 66 had a regression line calculated.
25 Nov 2023 10:27:59,847 INFO : Calculating fold changes
25 Nov 2023 10:28:00,491 INFO : 98% Done
25 Nov 2023 10:28:00,491 INFO : Done calculating fold changes.
25 Nov 2023 10:28:00,492 INFO : Creating and populating temp tables for Proportion values
25 Nov 2023 10:28:00,632 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
25 Nov 2023 10:28:00,809 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
25 Nov 2023 10:28:00,880 INFO : Cleaning up temp tables
25 Nov 2023 10:28:01,199 INFO : Completed import of Skyline document from EDIA_SRM_to_panorama_2023-10-11_17-36-18.sky.zip
25 Nov 2023 10:28:01,201 INFO : 100% Done
25 Nov 2023 10:28:01,211 INFO : Done importing xar
25 Nov 2023 10:28:01,212 INFO : Loading pages and webpart properties
25 Nov 2023 10:28:01,272 INFO : Done importing 3 page(s) with 5 webpart(s)
25 Nov 2023 10:28:01,272 INFO : Loading File Browser config
25 Nov 2023 10:28:01,272 INFO : Done importing File Browser config
25 Nov 2023 10:28:01,273 INFO : Starting Sample Status Data import
25 Nov 2023 10:28:01,273 INFO : No sample types XAR file to process.
25 Nov 2023 10:28:01,273 INFO : Finished importing Sample Status Data
25 Nov 2023 10:28:01,278 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
25 Nov 2023 10:28:01,280 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
25 Nov 2023 10:28:01,280 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
25 Nov 2023 10:28:01,281 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
25 Nov 2023 10:28:01,281 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
25 Nov 2023 10:28:01,281 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
25 Nov 2023 10:28:01,283 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
25 Nov 2023 10:28:01,290 INFO : Moving files to folder /Panorama Public/2023/Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics and creating symlinks
25 Nov 2023 10:28:06,180 INFO : Aligning data files urls in folder: /Panorama Public/2023/Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics
25 Nov 2023 10:28:06,187 INFO : Importing files metadata.
25 Nov 2023 10:28:06,188 INFO :
25 Nov 2023 10:28:06,188 INFO : Experiment import completed successfully.
25 Nov 2023 10:28:06,188 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
25 Nov 2023 10:28:06,207 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
25 Nov 2023 10:28:06,207 INFO :
25 Nov 2023 10:28:06,207 INFO : Checking for library folders.
25 Nov 2023 10:28:06,209 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
25 Nov 2023 10:28:06,225 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
25 Nov 2023 10:28:06,226 INFO :
25 Nov 2023 10:28:06,226 INFO : Finishing up experiment copy.
25 Nov 2023 10:28:06,227 INFO : Updating TargetedMS experiment entry in target folder /Panorama Public/2023/Turku Bioscience Lahesmaa Group - Mother-infant serum proteomics
25 Nov 2023 10:28:06,228 INFO : Setting version on new experiment to 1
25 Nov 2023 10:28:06,230 INFO : Updating permanent link to point to the new copy of the data.
25 Nov 2023 10:28:06,235 INFO : Removing copy permissions given to Panorama Public
25 Nov 2023 10:28:06,251 INFO : Adding read permissions to all users that are folder admins in the source folder.
25 Nov 2023 10:28:06,252 INFO : Assigning ReaderRole to rilahes@utu.fi
25 Nov 2023 10:28:06,252 INFO : Assigning ReaderRole to robmou@utu.fi
25 Nov 2023 10:28:06,252 INFO : Assigning PanoramaPublicSubmitterRole to rilahes@utu.fi
25 Nov 2023 10:28:06,252 INFO : Assigning PanoramaPublicSubmitterRole to robmou@utu.fi
25 Nov 2023 10:28:06,262 INFO : User rilahes@utu.fi is already a member of group Panorama Public Submitters
25 Nov 2023 10:28:06,262 INFO : User robmou@utu.fi is already a member of group Panorama Public Submitters
25 Nov 2023 10:28:06,262 INFO : Updating the 'Raw Data' tab configuration
25 Nov 2023 10:28:06,263 INFO : Creating a reviewer account.
25 Nov 2023 10:28:06,468 INFO : Created reviewer with email: User panorama+reviewer225@proteinms.net
25 Nov 2023 10:28:06,484 INFO : Adding user panorama+reviewer225@proteinms.net to group Reviewers
25 Nov 2023 10:28:06,488 INFO : Hiding the Data Pipeline tab.
25 Nov 2023 10:28:06,492 INFO : Updating Submission. Setting copiedExperimentId to 1726
25 Nov 2023 10:28:08,104 INFO : Assigning a ProteomeXchange ID.
25 Nov 2023 10:28:08,490 INFO : Assigned ProteomeXchange ID: PXD047235
25 Nov 2023 10:28:08,491 INFO : Assigning a DOI.
25 Nov 2023 10:28:09,277 INFO : Assigned DOI: 10.6069/aqx4-e482
25 Nov 2023 10:28:09,348 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'