Copying experiment: Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel

JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel

Job Status

Created: 2025-08-07 17:30:52
Modified: 2025-08-07 17:30:59
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Copying experiment: Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
File Path: /data/labkey/files/Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel/@files/Experiment_2203.log
Files: Experiment_2203.log
Completed Runs: Kang_et_al_Proteomics_FigS3_2025-08-06_12-31-18.sky.zip

Log File


07 Aug 2025 17:30:52,852 INFO : Copying experiment "Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel" from folder /JBEI/On-going work/Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel to /Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
07 Aug 2025 17:30:52,852 INFO : =======================================
07 Aug 2025 17:30:52,880 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
07 Aug 2025 17:30:52,880 INFO :
07 Aug 2025 17:30:52,880 INFO : Exporting experiment.
07 Aug 2025 17:30:53,314 INFO : Exporting files metadata.
07 Aug 2025 17:30:53,327 INFO :
07 Aug 2025 17:30:53,327 INFO : Experiment export completed successfully.
07 Aug 2025 17:30:53,327 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
07 Aug 2025 17:30:53,344 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
07 Aug 2025 17:30:53,344 INFO :
07 Aug 2025 17:30:53,344 INFO : Importing experiment.
07 Aug 2025 17:30:53,346 INFO : Loading folder properties (folder type, settings and active modules)
07 Aug 2025 17:30:53,376 INFO : Done importing folder properties (folder type, settings and active modules)
07 Aug 2025 17:30:53,377 INFO : Loading container specific module properties
07 Aug 2025 17:30:53,381 INFO : Done importing container specific module properties
07 Aug 2025 17:30:53,382 INFO : Loading queries
07 Aug 2025 17:30:53,383 INFO : 1 query imported
07 Aug 2025 17:30:53,383 INFO : Done importing queries
07 Aug 2025 17:30:53,384 INFO : Loading etl definitions
07 Aug 2025 17:30:53,385 INFO : Loading wikis
07 Aug 2025 17:30:53,386 INFO : 0 wikis imported
07 Aug 2025 17:30:53,386 INFO : Done importing wikis
07 Aug 2025 17:30:53,387 INFO : Starting Data Class Importer
07 Aug 2025 17:30:53,387 INFO : No types XAR file to process.
07 Aug 2025 17:30:53,387 INFO : Finished Data Class Importer
07 Aug 2025 17:30:53,387 INFO : Starting to copy files to @files
07 Aug 2025 17:30:53,387 INFO : Copied 0 files to @files
07 Aug 2025 17:30:53,388 INFO : Starting to copy files to @assayfiles
07 Aug 2025 17:30:53,388 INFO : Copied 0 files to @assayfiles
07 Aug 2025 17:30:53,388 INFO : Ensuring exp.data rows exist for imported files
07 Aug 2025 17:30:53,438 INFO : Starting Sample Type Importer
07 Aug 2025 17:30:53,438 INFO : No types XAR file to process.
07 Aug 2025 17:30:53,438 INFO : Finished Sample Type Importer
07 Aug 2025 17:30:53,439 INFO : Loading xar
07 Aug 2025 17:30:53,523 INFO : Starting import from Kang_et_al_Proteomics_FigS3_2025-08-06_12-31-18.sky.zip
07 Aug 2025 17:30:53,525 INFO : Starting to import Skyline document from Kang_et_al_Proteomics_FigS3_2025-08-06_12-31-18.sky.zip
07 Aug 2025 17:30:53,526 INFO : Expanding Kang_et_al_Proteomics_FigS3.skyd
07 Aug 2025 17:30:53,560 INFO : Expanding Kang_et_al_Proteomics_FigS3.sky.view
07 Aug 2025 17:30:53,560 INFO : Expanding Kang_et_al_Proteomics_FigS3.sky
07 Aug 2025 17:30:53,563 INFO : Expanding Kang_et_al_Proteomics_FigS3.skyl
07 Aug 2025 17:30:53,564 INFO : Reading Skyline file, Kang_et_al_Proteomics_FigS3.sky, to determine if the TransitionChromInfos in the document should be stored...
07 Aug 2025 17:30:53,568 INFO : TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored
07 Aug 2025 17:30:53,568 WARN : The version of this Skyline document is 25.1. This is newer than the highest supported version 23.1
07 Aug 2025 17:30:53,570 INFO : 2% Done
07 Aug 2025 17:30:53,570 INFO : Copying SKYD to temp directory for import purposes
07 Aug 2025 17:30:53,588 INFO : Copying complete
07 Aug 2025 17:30:53,721 INFO : Inserting sp|Q9FD71|HMGCS_ENTFL
07 Aug 2025 17:30:53,726 INFO : 8% Done
07 Aug 2025 17:30:53,742 INFO : 14% Done
07 Aug 2025 17:30:53,757 INFO : 20% Done
07 Aug 2025 17:30:53,771 INFO : Inserting sp|P32377|MVD1_YEAST
07 Aug 2025 17:30:53,775 INFO : 25% Done
07 Aug 2025 17:30:53,790 INFO : 30% Done
07 Aug 2025 17:30:53,804 INFO : 35% Done
07 Aug 2025 17:30:53,818 INFO : Inserting tr|Q8PW39|Q8PW39_METMA
07 Aug 2025 17:30:53,822 INFO : 41% Done
07 Aug 2025 17:30:53,837 INFO : 47% Done
07 Aug 2025 17:30:53,852 INFO : 52% Done
07 Aug 2025 17:30:53,865 INFO : Inserting sp|P0AE22|APHA_ECOLI
07 Aug 2025 17:30:53,868 INFO : 58% Done
07 Aug 2025 17:30:53,883 INFO : 62% Done
07 Aug 2025 17:30:53,897 INFO : 68% Done
07 Aug 2025 17:30:53,911 INFO : Inserting sp|P07277|ERG12_YEAST
07 Aug 2025 17:30:53,914 INFO : 74% Done
07 Aug 2025 17:30:53,929 INFO : 76% Done
07 Aug 2025 17:30:53,945 INFO : Inserting sp|P40353|ATF1_YEAST
07 Aug 2025 17:30:53,948 INFO : 82% Done
07 Aug 2025 17:30:53,963 INFO : 87% Done
07 Aug 2025 17:30:53,978 INFO : 93% Done
07 Aug 2025 17:30:53,993 INFO : 98% Done
07 Aug 2025 17:30:54,007 INFO : Done parsing Skyline document.
07 Aug 2025 17:30:54,034 INFO : Creating and populating temp tables for Proportion values
07 Aug 2025 17:30:54,039 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
07 Aug 2025 17:30:54,054 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
07 Aug 2025 17:30:54,064 INFO : Cleaning up temp tables
07 Aug 2025 17:30:54,310 INFO : Deleted temp copy of SKYD file
07 Aug 2025 17:30:54,310 INFO : Completed import of Skyline document from Kang_et_al_Proteomics_FigS3_2025-08-06_12-31-18.sky.zip
07 Aug 2025 17:30:54,312 INFO : 100% Done
07 Aug 2025 17:30:54,519 INFO : Done importing xar
07 Aug 2025 17:30:54,520 INFO : Loading pages and webpart properties
07 Aug 2025 17:30:54,566 INFO : Done importing 3 page(s) with 5 webpart(s)
07 Aug 2025 17:30:54,566 INFO : Loading File Browser config
07 Aug 2025 17:30:54,566 INFO : Done importing File Browser config
07 Aug 2025 17:30:54,567 INFO : Starting Sample Status Data import
07 Aug 2025 17:30:54,567 INFO : No sample types XAR file to process.
07 Aug 2025 17:30:54,567 INFO : Finished importing Sample Status Data
07 Aug 2025 17:30:54,570 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
07 Aug 2025 17:30:54,572 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping
07 Aug 2025 17:30:54,572 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping
07 Aug 2025 17:30:54,572 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping
07 Aug 2025 17:30:54,573 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping
07 Aug 2025 17:30:54,573 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
07 Aug 2025 17:30:54,574 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
07 Aug 2025 17:30:54,577 INFO : Moving files to folder /Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel and creating symlinks
07 Aug 2025 17:30:54,660 INFO : Aligning data files urls in folder: /Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
07 Aug 2025 17:30:54,666 INFO : Updating skydDataIds in folder: /Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
07 Aug 2025 17:30:54,667 INFO : Importing files metadata.
07 Aug 2025 17:30:54,668 INFO :
07 Aug 2025 17:30:54,668 INFO : Experiment import completed successfully.
07 Aug 2025 17:30:54,668 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
07 Aug 2025 17:30:54,686 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
07 Aug 2025 17:30:54,686 INFO :
07 Aug 2025 17:30:54,686 INFO : Checking for library folders.
07 Aug 2025 17:30:54,687 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
07 Aug 2025 17:30:54,701 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
07 Aug 2025 17:30:54,701 INFO :
07 Aug 2025 17:30:54,701 INFO : Finishing up experiment copy.
07 Aug 2025 17:30:54,703 INFO : Updating TargetedMS experiment entry in target folder /Panorama Public/2025/JBEI - Kang_et_al Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
07 Aug 2025 17:30:54,703 INFO : Setting version on new experiment to 1
07 Aug 2025 17:30:54,705 INFO : Updating permanent link to point to the new copy of the data.
07 Aug 2025 17:30:54,721 INFO : Removing copy permissions given to Panorama Public
07 Aug 2025 17:30:54,723 INFO : Adding read permissions to all users that are folder admins in the source folder.
07 Aug 2025 17:30:54,723 INFO : Assigning ReaderRole to cjpetzold@lbl.gov
07 Aug 2025 17:30:54,723 INFO : Assigning PanoramaPublicSubmitterRole to cjpetzold@lbl.gov
07 Aug 2025 17:30:54,725 INFO : User cjpetzold@lbl.gov is already a member of group Panorama Public Submitters
07 Aug 2025 17:30:54,725 INFO : Updating the 'Raw Data' tab configuration
07 Aug 2025 17:30:54,726 INFO : Making folder public.
07 Aug 2025 17:30:54,727 INFO : Hiding the Data Pipeline tab.
07 Aug 2025 17:30:54,730 INFO : Updating Submission. Setting copiedExperimentId to 2114
07 Aug 2025 17:30:56,678 INFO : Assigning a ProteomeXchange ID.
07 Aug 2025 17:30:56,880 INFO : Assigned ProteomeXchange ID: PXD067104
07 Aug 2025 17:30:56,881 INFO : Assigning a DOI.
07 Aug 2025 17:30:59,107 INFO : Assigned DOI: 10.6069/wzph-vj55
07 Aug 2025 17:30:59,142 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'