Copying experiment: A division of labor controls the degradation of fucoidans in the ocean

ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan

Job Status

Created: 2025-07-02 21:47:54
Modified: 2025-07-02 21:48:07
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: A division of labor controls the degradation of fucoidans in the ocean
File Path: /data/labkey/files/Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan/@files/Experiment_2179.log
Files: Experiment_2179.log
Completed Runs: 7memberCommunity_PlateB.sky.zip
7memberCommunity_PlateC.sky.zip
7memberCommunity_PlateD.sky.zip
7memberCommunity_PlateA.sky.zip
7memberCommunity_PlateB.sky.zip

Log File


02 Jul 2025 21:47:54,922 INFO : Copying experiment "A division of labor controls the degradation of fucoidans in the ocean" from folder /ETH Zurich - IMSB - SauerLab - Sichert/Sichert2025_fucoidan to /Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan
02 Jul 2025 21:47:54,922 INFO : =======================================
02 Jul 2025 21:47:54,954 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
02 Jul 2025 21:47:54,954 INFO :
02 Jul 2025 21:47:54,954 INFO : Exporting experiment.
02 Jul 2025 21:47:56,086 INFO : Exporting files metadata.
02 Jul 2025 21:47:56,089 INFO :
02 Jul 2025 21:47:56,089 INFO : Experiment export completed successfully.
02 Jul 2025 21:47:56,089 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
02 Jul 2025 21:47:56,105 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
02 Jul 2025 21:47:56,105 INFO :
02 Jul 2025 21:47:56,105 INFO : Importing experiment.
02 Jul 2025 21:47:56,107 INFO : Loading folder properties (folder type, settings and active modules)
02 Jul 2025 21:47:56,139 INFO : Done importing folder properties (folder type, settings and active modules)
02 Jul 2025 21:47:56,139 INFO : Loading container specific module properties
02 Jul 2025 21:47:56,143 INFO : Done importing container specific module properties
02 Jul 2025 21:47:56,144 INFO : Loading queries
02 Jul 2025 21:47:56,146 INFO : 1 query imported
02 Jul 2025 21:47:56,146 INFO : Done importing queries
02 Jul 2025 21:47:56,147 INFO : Loading etl definitions
02 Jul 2025 21:47:56,147 INFO : Loading wikis
02 Jul 2025 21:47:56,148 INFO : 0 wikis imported
02 Jul 2025 21:47:56,148 INFO : Done importing wikis
02 Jul 2025 21:47:56,149 INFO : Starting Data Class Importer
02 Jul 2025 21:47:56,149 INFO : No types XAR file to process.
02 Jul 2025 21:47:56,149 INFO : Finished Data Class Importer
02 Jul 2025 21:47:56,149 INFO : Starting to copy files to @files
02 Jul 2025 21:47:56,150 INFO : Copied 0 files to @files
02 Jul 2025 21:47:56,150 INFO : Starting to copy files to @assayfiles
02 Jul 2025 21:47:56,150 INFO : Copied 0 files to @assayfiles
02 Jul 2025 21:47:56,150 INFO : Ensuring exp.data rows exist for imported files
02 Jul 2025 21:47:56,198 INFO : Starting Sample Type Importer
02 Jul 2025 21:47:56,198 INFO : No types XAR file to process.
02 Jul 2025 21:47:56,198 INFO : Finished Sample Type Importer
02 Jul 2025 21:47:56,198 INFO : Loading xar
02 Jul 2025 21:47:56,475 INFO : Starting import from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:47:56,477 INFO : Starting to import Skyline document from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:47:56,478 INFO : Expanding BU_B.skyd
02 Jul 2025 21:47:56,498 INFO : Expanding BU_B.sky.view
02 Jul 2025 21:47:56,499 INFO : Expanding BU_B.sky
02 Jul 2025 21:47:56,506 INFO : Expanding BU_B.skyl
02 Jul 2025 21:47:56,507 INFO : Reading Skyline file, BU_B.sky, to determine if the TransitionChromInfos in the document should be stored...
02 Jul 2025 21:47:56,516 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
02 Jul 2025 21:47:56,516 WARN : The version of this Skyline document is 24.1. This is newer than the highest supported version 23.1
02 Jul 2025 21:47:56,519 INFO : 6% Done
02 Jul 2025 21:47:56,519 INFO : Copying SKYD to temp directory for import purposes
02 Jul 2025 21:47:56,525 INFO : Copying complete
02 Jul 2025 21:47:56,783 INFO : Inserting 186da
02 Jul 2025 21:47:56,788 INFO : 16% Done
02 Jul 2025 21:47:56,852 INFO : 24% Done
02 Jul 2025 21:47:56,910 INFO : Inserting 164da
02 Jul 2025 21:47:56,914 INFO : 30% Done
02 Jul 2025 21:47:56,968 INFO : 38% Done
02 Jul 2025 21:47:57,019 INFO : Inserting 180da
02 Jul 2025 21:47:57,023 INFO : 46% Done
02 Jul 2025 21:47:57,079 INFO : 53% Done
02 Jul 2025 21:47:57,135 INFO : 61% Done
02 Jul 2025 21:47:57,192 INFO : 69% Done
02 Jul 2025 21:47:57,246 INFO : Inserting 192da
02 Jul 2025 21:47:57,249 INFO : 75% Done
02 Jul 2025 21:47:57,309 INFO : 83% Done
02 Jul 2025 21:47:57,362 INFO : Inserting 150da
02 Jul 2025 21:47:57,366 INFO : 90% Done
02 Jul 2025 21:47:57,424 INFO : 98% Done
02 Jul 2025 21:47:57,478 INFO : Done parsing Skyline document.
02 Jul 2025 21:47:57,496 INFO : Creating and populating temp tables for Proportion values
02 Jul 2025 21:47:57,504 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Jul 2025 21:47:57,579 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Jul 2025 21:47:57,632 INFO : Cleaning up temp tables
02 Jul 2025 21:47:57,866 INFO : Deleted temp copy of SKYD file
02 Jul 2025 21:47:57,866 INFO : Completed import of Skyline document from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:47:57,868 INFO : 100% Done
02 Jul 2025 21:47:57,873 INFO : Starting import from 7memberCommunity_PlateC.sky.zip
02 Jul 2025 21:47:57,875 INFO : Starting to import Skyline document from 7memberCommunity_PlateC.sky.zip
02 Jul 2025 21:47:57,876 INFO : Expanding BU_C.skyd
02 Jul 2025 21:47:57,900 INFO : Expanding BU_C.sky.view
02 Jul 2025 21:47:57,901 INFO : Expanding BU_C.sky
02 Jul 2025 21:47:57,910 INFO : Expanding BU_C.skyl
02 Jul 2025 21:47:57,911 INFO : Reading Skyline file, BU_C.sky, to determine if the TransitionChromInfos in the document should be stored...
02 Jul 2025 21:47:57,925 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
02 Jul 2025 21:47:57,926 WARN : The version of this Skyline document is 24.1. This is newer than the highest supported version 23.1
02 Jul 2025 21:47:57,929 INFO : 6% Done
02 Jul 2025 21:47:57,929 INFO : Copying SKYD to temp directory for import purposes
02 Jul 2025 21:47:57,935 INFO : Copying complete
02 Jul 2025 21:47:58,231 INFO : Inserting 186da
02 Jul 2025 21:47:58,236 INFO : 16% Done
02 Jul 2025 21:47:58,294 INFO : 23% Done
02 Jul 2025 21:47:58,349 INFO : 24% Done
02 Jul 2025 21:47:58,349 INFO : Inserting 164da
02 Jul 2025 21:47:58,353 INFO : 30% Done
02 Jul 2025 21:47:58,409 INFO : 38% Done
02 Jul 2025 21:47:58,463 INFO : Inserting 180da
02 Jul 2025 21:47:58,467 INFO : 45% Done
02 Jul 2025 21:47:58,524 INFO : 53% Done
02 Jul 2025 21:47:58,582 INFO : 61% Done
02 Jul 2025 21:47:58,638 INFO : 69% Done
02 Jul 2025 21:47:58,692 INFO : Inserting 192da
02 Jul 2025 21:47:58,695 INFO : 75% Done
02 Jul 2025 21:47:58,752 INFO : 83% Done
02 Jul 2025 21:47:58,812 INFO : Inserting 150da
02 Jul 2025 21:47:58,816 INFO : 90% Done
02 Jul 2025 21:47:58,873 INFO : 98% Done
02 Jul 2025 21:47:58,927 INFO : Done parsing Skyline document.
02 Jul 2025 21:47:58,945 INFO : Creating and populating temp tables for Proportion values
02 Jul 2025 21:47:58,953 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Jul 2025 21:47:59,028 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Jul 2025 21:47:59,081 INFO : Cleaning up temp tables
02 Jul 2025 21:47:59,291 INFO : Deleted temp copy of SKYD file
02 Jul 2025 21:47:59,291 INFO : Completed import of Skyline document from 7memberCommunity_PlateC.sky.zip
02 Jul 2025 21:47:59,293 INFO : 100% Done
02 Jul 2025 21:47:59,298 INFO : Starting import from 7memberCommunity_PlateD.sky.zip
02 Jul 2025 21:47:59,299 INFO : Starting to import Skyline document from 7memberCommunity_PlateD.sky.zip
02 Jul 2025 21:47:59,300 INFO : Expanding BU_D.skyd
02 Jul 2025 21:47:59,319 INFO : Expanding BU_D.sky.view
02 Jul 2025 21:47:59,320 INFO : Expanding BU_D.sky
02 Jul 2025 21:47:59,327 INFO : Expanding BU_D.skyl
02 Jul 2025 21:47:59,328 INFO : Reading Skyline file, BU_D.sky, to determine if the TransitionChromInfos in the document should be stored...
02 Jul 2025 21:47:59,337 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
02 Jul 2025 21:47:59,337 WARN : The version of this Skyline document is 24.1. This is newer than the highest supported version 23.1
02 Jul 2025 21:47:59,340 INFO : 6% Done
02 Jul 2025 21:47:59,340 INFO : Copying SKYD to temp directory for import purposes
02 Jul 2025 21:47:59,346 INFO : Copying complete
02 Jul 2025 21:47:59,674 INFO : Inserting 186da
02 Jul 2025 21:47:59,679 INFO : 16% Done
02 Jul 2025 21:47:59,738 INFO : 23% Done
02 Jul 2025 21:47:59,792 INFO : Inserting 164da
02 Jul 2025 21:47:59,796 INFO : 30% Done
02 Jul 2025 21:47:59,853 INFO : 38% Done
02 Jul 2025 21:47:59,907 INFO : Inserting 180da
02 Jul 2025 21:47:59,911 INFO : 45% Done
02 Jul 2025 21:47:59,968 INFO : 53% Done
02 Jul 2025 21:48:00,025 INFO : 61% Done
02 Jul 2025 21:48:00,081 INFO : 68% Done
02 Jul 2025 21:48:00,135 INFO : 69% Done
02 Jul 2025 21:48:00,135 INFO : Inserting 192da
02 Jul 2025 21:48:00,139 INFO : 75% Done
02 Jul 2025 21:48:00,197 INFO : 83% Done
02 Jul 2025 21:48:00,252 INFO : Inserting 150da
02 Jul 2025 21:48:00,256 INFO : 90% Done
02 Jul 2025 21:48:00,315 INFO : 98% Done
02 Jul 2025 21:48:00,370 INFO : Done parsing Skyline document.
02 Jul 2025 21:48:00,389 INFO : Creating and populating temp tables for Proportion values
02 Jul 2025 21:48:00,397 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Jul 2025 21:48:00,473 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Jul 2025 21:48:00,527 INFO : Cleaning up temp tables
02 Jul 2025 21:48:00,736 INFO : Deleted temp copy of SKYD file
02 Jul 2025 21:48:00,736 INFO : Completed import of Skyline document from 7memberCommunity_PlateD.sky.zip
02 Jul 2025 21:48:00,738 INFO : 100% Done
02 Jul 2025 21:48:00,742 INFO : Starting import from BU_A_2025-07-02_14-21-05.sky.zip
02 Jul 2025 21:48:00,743 INFO : Starting to import Skyline document from BU_A_2025-07-02_14-21-05.sky.zip
02 Jul 2025 21:48:00,744 INFO : Expanding BU_A.skyd
02 Jul 2025 21:48:00,765 INFO : Expanding BU_A.sky.view
02 Jul 2025 21:48:00,765 INFO : Expanding BU_A.sky
02 Jul 2025 21:48:00,773 INFO : Expanding BU_A.skyl
02 Jul 2025 21:48:00,774 INFO : Reading Skyline file, BU_A.sky, to determine if the TransitionChromInfos in the document should be stored...
02 Jul 2025 21:48:00,782 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
02 Jul 2025 21:48:00,783 WARN : The version of this Skyline document is 24.1. This is newer than the highest supported version 23.1
02 Jul 2025 21:48:00,786 INFO : 6% Done
02 Jul 2025 21:48:00,786 INFO : Copying SKYD to temp directory for import purposes
02 Jul 2025 21:48:00,791 INFO : Copying complete
02 Jul 2025 21:48:01,076 INFO : Inserting 186da
02 Jul 2025 21:48:01,081 INFO : 16% Done
02 Jul 2025 21:48:01,139 INFO : 23% Done
02 Jul 2025 21:48:01,193 INFO : 24% Done
02 Jul 2025 21:48:01,193 INFO : Inserting 164da
02 Jul 2025 21:48:01,197 INFO : 30% Done
02 Jul 2025 21:48:01,253 INFO : 38% Done
02 Jul 2025 21:48:01,306 INFO : Inserting 180da
02 Jul 2025 21:48:01,310 INFO : 46% Done
02 Jul 2025 21:48:01,371 INFO : 53% Done
02 Jul 2025 21:48:01,433 INFO : 61% Done
02 Jul 2025 21:48:01,495 INFO : 69% Done
02 Jul 2025 21:48:01,549 INFO : Inserting 192da
02 Jul 2025 21:48:01,553 INFO : 75% Done
02 Jul 2025 21:48:01,610 INFO : 83% Done
02 Jul 2025 21:48:01,663 INFO : Inserting 150da
02 Jul 2025 21:48:01,667 INFO : 91% Done
02 Jul 2025 21:48:01,723 INFO : 98% Done
02 Jul 2025 21:48:01,776 INFO : Done parsing Skyline document.
02 Jul 2025 21:48:01,795 INFO : Creating and populating temp tables for Proportion values
02 Jul 2025 21:48:01,803 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Jul 2025 21:48:01,876 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Jul 2025 21:48:01,929 INFO : Cleaning up temp tables
02 Jul 2025 21:48:02,137 INFO : Deleted temp copy of SKYD file
02 Jul 2025 21:48:02,137 INFO : Completed import of Skyline document from BU_A_2025-07-02_14-21-05.sky.zip
02 Jul 2025 21:48:02,139 INFO : 100% Done
02 Jul 2025 21:48:02,142 INFO : Starting import from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:48:02,143 INFO : Starting to import Skyline document from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:48:02,144 INFO : Expanding BU_B.skyd
02 Jul 2025 21:48:02,164 INFO : Expanding BU_B.sky.view
02 Jul 2025 21:48:02,165 INFO : Expanding BU_B.sky
02 Jul 2025 21:48:02,172 INFO : Expanding BU_B.skyl
02 Jul 2025 21:48:02,173 INFO : Reading Skyline file, BU_B.sky, to determine if the TransitionChromInfos in the document should be stored...
02 Jul 2025 21:48:02,182 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
02 Jul 2025 21:48:02,182 WARN : The version of this Skyline document is 24.1. This is newer than the highest supported version 23.1
02 Jul 2025 21:48:02,185 INFO : 6% Done
02 Jul 2025 21:48:02,185 INFO : Copying SKYD to temp directory for import purposes
02 Jul 2025 21:48:02,190 INFO : Copying complete
02 Jul 2025 21:48:02,489 INFO : Inserting 186da
02 Jul 2025 21:48:02,494 INFO : 16% Done
02 Jul 2025 21:48:02,553 INFO : 24% Done
02 Jul 2025 21:48:02,606 INFO : Inserting 164da
02 Jul 2025 21:48:02,610 INFO : 30% Done
02 Jul 2025 21:48:02,666 INFO : 38% Done
02 Jul 2025 21:48:02,719 INFO : Inserting 180da
02 Jul 2025 21:48:02,723 INFO : 46% Done
02 Jul 2025 21:48:02,779 INFO : 53% Done
02 Jul 2025 21:48:02,835 INFO : 61% Done
02 Jul 2025 21:48:02,891 INFO : 69% Done
02 Jul 2025 21:48:02,943 INFO : Inserting 192da
02 Jul 2025 21:48:02,947 INFO : 75% Done
02 Jul 2025 21:48:03,004 INFO : 83% Done
02 Jul 2025 21:48:03,057 INFO : Inserting 150da
02 Jul 2025 21:48:03,061 INFO : 90% Done
02 Jul 2025 21:48:03,117 INFO : 98% Done
02 Jul 2025 21:48:03,170 INFO : Done parsing Skyline document.
02 Jul 2025 21:48:03,188 INFO : Creating and populating temp tables for Proportion values
02 Jul 2025 21:48:03,198 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
02 Jul 2025 21:48:03,272 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
02 Jul 2025 21:48:03,325 INFO : Cleaning up temp tables
02 Jul 2025 21:48:03,538 INFO : Deleted temp copy of SKYD file
02 Jul 2025 21:48:03,538 INFO : Completed import of Skyline document from 7memberCommunity_PlateB.sky.zip
02 Jul 2025 21:48:03,540 INFO : 100% Done
02 Jul 2025 21:48:04,681 INFO : Done importing xar
02 Jul 2025 21:48:04,682 INFO : Loading pages and webpart properties
02 Jul 2025 21:48:04,727 INFO : Done importing 3 page(s) with 5 webpart(s)
02 Jul 2025 21:48:04,727 INFO : Loading File Browser config
02 Jul 2025 21:48:04,727 INFO : Done importing File Browser config
02 Jul 2025 21:48:04,728 INFO : Starting Sample Status Data import
02 Jul 2025 21:48:04,728 INFO : No sample types XAR file to process.
02 Jul 2025 21:48:04,728 INFO : Finished importing Sample Status Data
02 Jul 2025 21:48:04,731 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
02 Jul 2025 21:48:04,733 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
02 Jul 2025 21:48:04,733 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
02 Jul 2025 21:48:04,734 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
02 Jul 2025 21:48:04,734 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
02 Jul 2025 21:48:04,734 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
02 Jul 2025 21:48:04,735 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
02 Jul 2025 21:48:04,740 INFO : Moving files to folder /Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan and creating symlinks
02 Jul 2025 21:48:04,797 INFO : Aligning data files urls in folder: /Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan
02 Jul 2025 21:48:04,813 INFO : Updating skydDataIds in folder: /Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan
02 Jul 2025 21:48:04,817 INFO : Importing files metadata.
02 Jul 2025 21:48:04,821 INFO :
02 Jul 2025 21:48:04,821 INFO : Experiment import completed successfully.
02 Jul 2025 21:48:04,821 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
02 Jul 2025 21:48:04,838 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
02 Jul 2025 21:48:04,838 INFO :
02 Jul 2025 21:48:04,838 INFO : Checking for library folders.
02 Jul 2025 21:48:04,839 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
02 Jul 2025 21:48:04,852 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
02 Jul 2025 21:48:04,852 INFO :
02 Jul 2025 21:48:04,852 INFO : Finishing up experiment copy.
02 Jul 2025 21:48:04,853 INFO : Updating TargetedMS experiment entry in target folder /Panorama Public/2025/ETH Zurich IMSB SauerLab Sichert - Sichert2025_fucoidan
02 Jul 2025 21:48:04,853 INFO : Setting version on new experiment to 1
02 Jul 2025 21:48:04,855 INFO : Updating permanent link to point to the new copy of the data.
02 Jul 2025 21:48:04,870 INFO : Removing copy permissions given to Panorama Public
02 Jul 2025 21:48:04,872 INFO : Adding read permissions to all users that are folder admins in the source folder.
02 Jul 2025 21:48:04,872 INFO : Assigning ReaderRole to asichert@ethz.ch
02 Jul 2025 21:48:04,872 INFO : Assigning PanoramaPublicSubmitterRole to asichert@ethz.ch
02 Jul 2025 21:48:04,875 INFO : Adding user asichert@ethz.ch to group Panorama Public Submitters
02 Jul 2025 21:48:04,876 INFO : Updating the 'Raw Data' tab configuration
02 Jul 2025 21:48:04,876 INFO : Making folder public.
02 Jul 2025 21:48:04,878 INFO : Hiding the Data Pipeline tab.
02 Jul 2025 21:48:04,881 INFO : Updating Submission. Setting copiedExperimentId to 2090
02 Jul 2025 21:48:06,379 INFO : Assigning a DOI.
02 Jul 2025 21:48:07,059 INFO : Assigned DOI: 10.6069/r2z3-7b10
02 Jul 2025 21:48:07,092 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'