14 Jul 2023 16:57:12,336 INFO : Copying experiment "A novel overlapping gene azyx-1 affects the translation of zyxin in C. elegans" from folder /BayBioMS/Parmar_azyx1_zyx1 to /Panorama Public/2023/BayBioMS - Parmar_azyx1_zyx1

14 Jul 2023 16:57:12,336 INFO : =======================================

14 Jul 2023 16:57:12,356 DEBUG: Resetting Job ID: 051e0855-04d0-103c-afc6-fea6ddf51ba4

14 Jul 2023 17:19:09,082 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'

14 Jul 2023 17:19:09,083 INFO : 

14 Jul 2023 17:19:09,083 INFO : Exporting experiment.

14 Jul 2023 17:29:12,210 INFO : Exporting files metadata.

14 Jul 2023 17:29:12,210 DEBUG: [/BayBioMS/Parmar_azyx1_zyx1]  Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS - Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export

14 Jul 2023 17:29:12,241 INFO : 

14 Jul 2023 17:29:12,241 INFO : Experiment export completed successfully.

14 Jul 2023 17:29:12,241 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'

14 Jul 2023 17:30:42,008 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'

14 Jul 2023 17:30:42,008 INFO : 

14 Jul 2023 17:30:42,008 INFO : Importing experiment.

14 Jul 2023 17:30:42,009 DEBUG: [/Panorama Public/2023/BayBioMS - Parmar_azyx1_zyx1] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS - Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export

14 Jul 2023 17:30:42,011 INFO : Loading folder properties (folder type, settings and active modules)

14 Jul 2023 17:30:42,011 DEBUG: [/Panorama Public/2023/BayBioMS - Parmar_azyx1_zyx1] Folder type: Targeted MS

14 Jul 2023 17:30:42,011 DEBUG: [/Panorama Public/2023/BayBioMS - Parmar_azyx1_zyx1] Active modules: PanoramaPublic, Wiki, Experiment, API, Query, Announcements, Pipeline, Assay, MS2, Core, Search, FileContent, Issues, TargetedMS

14 Jul 2023 17:30:42,089 INFO : Done importing folder properties (folder type, settings and active modules)

14 Jul 2023 17:30:42,090 INFO : Loading container specific module properties

14 Jul 2023 17:30:42,094 INFO : Done importing container specific module properties

14 Jul 2023 17:30:42,095 INFO : Loading etl definitions

14 Jul 2023 17:30:42,096 INFO : Loading wikis

14 Jul 2023 17:30:42,098 INFO : 0 wikis imported

14 Jul 2023 17:30:42,098 INFO : Done importing wikis

14 Jul 2023 17:30:42,098 INFO : Starting to copy files

14 Jul 2023 17:32:53,032 INFO : 23 files copied, now copying BBM_393_P108_12_03_ISS_007.raw

14 Jul 2023 17:34:54,829 INFO : 32 files copied, now copying BBM_393_P108_12_03_ISS_013.raw

14 Jul 2023 17:37:00,495 INFO : 41 files copied, now copying BBM_654_P267_01_CHL_018.raw

14 Jul 2023 17:38:28,649 INFO : 49 files copied, now copying C_elegans_PlusOLG.protdb

14 Jul 2023 17:38:35,373 INFO : 57 files copied, now copying Final_P108_12_03_scheduledPRM_34prec_refined.sky

14 Jul 2023 17:38:42,256 INFO : 65 files copied, now copying Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd

14 Jul 2023 17:38:49,312 INFO : 73 files copied, now copying Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd

14 Jul 2023 17:38:56,173 INFO : Copied 81 files

14 Jul 2023 17:38:56,173 INFO : Ensuring exp.data rows exist for imported files

14 Jul 2023 17:38:56,573 INFO : Starting Sample Type and Data Class import

14 Jul 2023 17:38:56,574 INFO : No types XAR file to process.

14 Jul 2023 17:38:56,574 INFO : Finished importing Sample Types and Data Classes

14 Jul 2023 17:38:56,576 INFO : Loading xar

14 Jul 2023 17:39:01,639 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Core'

14 Jul 2023 17:39:01,641 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Output'

14 Jul 2023 17:39:01,643 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip'

14 Jul 2023 17:39:01,643 DEBUG: Protocol import complete

14 Jul 2023 17:39:01,645 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11870:A+novel+overlapping+gene+peu-1+affects+the+translation+of+zyxin+in+C.+elegans.'

14 Jul 2023 17:39:01,645 DEBUG: Experiment/Run group import complete

14 Jul 2023 17:39:01,655 DEBUG: Protocol action set import complete

14 Jul 2023 17:39:01,664 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip'

14 Jul 2023 17:39:01,671 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11870:11191b0f-02ff-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,675 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11870:11191849-02ff-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,675 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Core'

14 Jul 2023 17:39:01,677 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Output'

14 Jul 2023 17:39:01,678 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11870:11191ce2-02ff-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,684 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip'

14 Jul 2023 17:39:01,689 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11870:b83e75f0-037c-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,693 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11870:b83e730e-037c-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,693 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Core'

14 Jul 2023 17:39:01,695 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11870:TargetedMS.ImportSkyZip.Output'

14 Jul 2023 17:39:01,696 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11870:b83e77ee-037c-103c-afc6-fea6ddf51ba4'

14 Jul 2023 17:39:01,698 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyd into the system

14 Jul 2023 17:39:01,699 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyd into the system

14 Jul 2023 17:39:01,699 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip into the system

14 Jul 2023 17:39:01,700 INFO : Starting import from FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip

14 Jul 2023 17:39:01,705 INFO : Starting to import Skyline document from FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip

14 Jul 2023 17:39:01,707 INFO : Expanding C_elegans_PlusOLG.protdb

14 Jul 2023 17:39:03,950 INFO : Expanding P108_12_03_PRM.blib

14 Jul 2023 17:39:04,022 INFO : Expanding P108_12_03_PRM.redundant.blib

14 Jul 2023 17:39:07,332 INFO : Expanding Prosit_2023_01_25.blib

14 Jul 2023 17:39:07,332 INFO : Expanding FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyd

14 Jul 2023 17:39:07,395 INFO : Expanding FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.sky.view

14 Jul 2023 17:39:07,395 INFO : Expanding FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.sky

14 Jul 2023 17:39:07,400 INFO : Expanding FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyl

14 Jul 2023 17:39:07,410 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

14 Jul 2023 17:39:07,416 INFO : 2% Done

14 Jul 2023 17:39:07,464 DEBUG: Starting to load chromatogram headers

14 Jul 2023 17:39:07,465 DEBUG: Done loading chromatogram headers

14 Jul 2023 17:39:07,897 INFO : Inserting ce|ZYX-1a|F42G4.3a

14 Jul 2023 17:39:07,905 INFO : 5% Done

14 Jul 2023 17:39:07,928 INFO : 8% Done

14 Jul 2023 17:39:07,955 INFO : 11% Done

14 Jul 2023 17:39:07,974 INFO : 12% Done

14 Jul 2023 17:39:08,001 INFO : 16% Done

14 Jul 2023 17:39:08,035 INFO : 17% Done

14 Jul 2023 17:39:08,064 DEBUG: Total peptides inserted: 6

14 Jul 2023 17:39:08,064 INFO : Inserting ce|AZYX-1|IP_1559020_OLG

14 Jul 2023 17:39:08,070 INFO : 19% Done

14 Jul 2023 17:39:08,094 INFO : 22% Done

14 Jul 2023 17:39:08,121 INFO : 24% Done

14 Jul 2023 17:39:08,150 INFO : 25% Done

14 Jul 2023 17:39:08,185 INFO : 28% Done

14 Jul 2023 17:39:08,207 INFO : 32% Done

14 Jul 2023 17:39:08,227 DEBUG: Total peptides inserted: 6

14 Jul 2023 17:39:08,228 INFO : Inserting ce|GPD-3|K10B3.7

14 Jul 2023 17:39:08,233 INFO : 35% Done

14 Jul 2023 17:39:08,253 INFO : 39% Done

14 Jul 2023 17:39:08,274 INFO : 42% Done

14 Jul 2023 17:39:08,295 INFO : 46% Done

14 Jul 2023 17:39:08,312 DEBUG: Total peptides inserted: 4

14 Jul 2023 17:39:08,312 INFO : Inserting ce|HIS-24|M163.3

14 Jul 2023 17:39:08,317 INFO : 49% Done

14 Jul 2023 17:39:08,337 INFO : 53% Done

14 Jul 2023 17:39:08,361 INFO : 57% Done

14 Jul 2023 17:39:08,383 INFO : 60% Done

14 Jul 2023 17:39:08,400 DEBUG: Total peptides inserted: 4

14 Jul 2023 17:39:08,400 INFO : Inserting Biognoysis_IRT

14 Jul 2023 17:39:08,404 INFO : 64% Done

14 Jul 2023 17:39:08,424 INFO : 67% Done

14 Jul 2023 17:39:08,444 INFO : 71% Done

14 Jul 2023 17:39:08,465 INFO : 74% Done

14 Jul 2023 17:39:08,485 INFO : 77% Done

14 Jul 2023 17:39:08,505 INFO : 80% Done

14 Jul 2023 17:39:08,525 INFO : 84% Done

14 Jul 2023 17:39:08,554 INFO : 88% Done

14 Jul 2023 17:39:08,574 INFO : 91% Done

14 Jul 2023 17:39:08,594 INFO : 94% Done

14 Jul 2023 17:39:08,614 INFO : 98% Done

14 Jul 2023 17:39:08,631 DEBUG: Total peptides inserted: 11

14 Jul 2023 17:39:08,632 INFO : Done parsing Skyline document.

14 Jul 2023 17:39:08,632 INFO : Calculating iRT correlations for 15 sample(s)

14 Jul 2023 17:39:08,646 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,649 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,653 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,656 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,659 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,663 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,666 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,670 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,673 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,677 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,680 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,684 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,687 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,691 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,694 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:08,694 INFO : Finished calculating iRT correlations for all samples. 15 had a regression line calculated.

14 Jul 2023 17:39:09,467 INFO : Creating and populating temp tables for Proportion values

14 Jul 2023 17:39:09,542 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

14 Jul 2023 17:39:09,560 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

14 Jul 2023 17:39:09,573 INFO : Cleaning up temp tables

14 Jul 2023 17:39:09,837 INFO : Completed import of Skyline document from FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip

14 Jul 2023 17:39:09,839 INFO : 100% Done

14 Jul 2023 17:39:09,842 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip into the system

14 Jul 2023 17:39:09,842 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd into the system

14 Jul 2023 17:39:09,843 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd into the system

14 Jul 2023 17:39:09,843 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip into the system

14 Jul 2023 17:39:09,844 INFO : Starting import from Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip

14 Jul 2023 17:39:09,846 INFO : Starting to import Skyline document from Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip

14 Jul 2023 17:39:09,848 INFO : Expanding C_elegans_PlusOLG.protdb

14 Jul 2023 17:39:12,075 INFO : Expanding P108_12_03_PRM.blib

14 Jul 2023 17:39:12,143 INFO : Expanding P108_12_03_PRM.redundant.blib

14 Jul 2023 17:39:15,403 INFO : Expanding Prosit.blib

14 Jul 2023 17:39:15,405 INFO : Expanding Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd

14 Jul 2023 17:39:15,466 INFO : Expanding Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.sky.view

14 Jul 2023 17:39:15,467 INFO : Expanding Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.sky

14 Jul 2023 17:39:15,472 INFO : Expanding Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyl

14 Jul 2023 17:39:15,479 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13

14 Jul 2023 17:39:15,527 INFO : 3% Done

14 Jul 2023 17:39:15,589 DEBUG: Starting to load chromatogram headers

14 Jul 2023 17:39:15,590 DEBUG: Done loading chromatogram headers

14 Jul 2023 17:39:17,390 INFO : Inserting ce|ZYX-1a|F42G4.3a

14 Jul 2023 17:39:17,395 INFO : 7% Done

14 Jul 2023 17:39:17,416 INFO : 10% Done

14 Jul 2023 17:39:17,435 INFO : 12% Done

14 Jul 2023 17:39:17,453 INFO : 15% Done

14 Jul 2023 17:39:17,473 INFO : 18% Done

14 Jul 2023 17:39:17,495 INFO : 24% Done

14 Jul 2023 17:39:17,528 DEBUG: Total peptides inserted: 6

14 Jul 2023 17:39:17,528 INFO : Inserting ce|AZYX-1|IP_1559020_OLG

14 Jul 2023 17:39:17,533 INFO : 25% Done

14 Jul 2023 17:39:17,555 INFO : 27% Done

14 Jul 2023 17:39:17,576 INFO : 30% Done

14 Jul 2023 17:39:17,600 INFO : 32% Done

14 Jul 2023 17:39:17,617 INFO : 35% Done

14 Jul 2023 17:39:17,637 INFO : 38% Done

14 Jul 2023 17:39:17,655 INFO : 40% Done

14 Jul 2023 17:39:17,673 DEBUG: Total peptides inserted: 7

14 Jul 2023 17:39:17,673 INFO : Inserting ce|GPD-3|K10B3.7

14 Jul 2023 17:39:17,677 INFO : 43% Done

14 Jul 2023 17:39:17,697 INFO : 46% Done

14 Jul 2023 17:39:17,715 INFO : 49% Done

14 Jul 2023 17:39:17,732 INFO : 52% Done

14 Jul 2023 17:39:17,749 DEBUG: Total peptides inserted: 4

14 Jul 2023 17:39:17,749 INFO : Inserting ce|HIS-24|M163.3

14 Jul 2023 17:39:17,753 INFO : 55% Done

14 Jul 2023 17:39:17,771 INFO : 58% Done

14 Jul 2023 17:39:17,790 INFO : 61% Done

14 Jul 2023 17:39:17,809 INFO : 64% Done

14 Jul 2023 17:39:17,824 DEBUG: Total peptides inserted: 4

14 Jul 2023 17:39:17,824 INFO : Inserting ce|SPIKE|IP_1559020_OLGSpike

14 Jul 2023 17:39:17,828 INFO : 67% Done

14 Jul 2023 17:39:17,845 DEBUG: Total peptides inserted: 1

14 Jul 2023 17:39:17,845 INFO : Inserting Biognoysis_IRT

14 Jul 2023 17:39:17,849 INFO : 70% Done

14 Jul 2023 17:39:17,869 INFO : 73% Done

14 Jul 2023 17:39:17,889 INFO : 74% Done

14 Jul 2023 17:39:17,909 INFO : 77% Done

14 Jul 2023 17:39:17,928 INFO : 80% Done

14 Jul 2023 17:39:17,952 INFO : 83% Done

14 Jul 2023 17:39:17,975 INFO : 86% Done

14 Jul 2023 17:39:18,000 INFO : 89% Done

14 Jul 2023 17:39:18,026 INFO : 92% Done

14 Jul 2023 17:39:18,051 INFO : 95% Done

14 Jul 2023 17:39:18,074 INFO : 98% Done

14 Jul 2023 17:39:18,091 DEBUG: Total peptides inserted: 11

14 Jul 2023 17:39:18,093 INFO : Done parsing Skyline document.

14 Jul 2023 17:39:18,093 INFO : Calculating iRT correlations for 16 sample(s)

14 Jul 2023 17:39:18,105 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,109 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,114 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,118 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,122 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,127 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,131 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,135 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,138 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,142 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,146 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,150 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,153 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,157 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,162 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,165 INFO : Calculated iRT regression line from full standard list.

14 Jul 2023 17:39:18,166 INFO : Finished calculating iRT correlations for all samples. 16 had a regression line calculated.

14 Jul 2023 17:39:18,638 INFO : Creating and populating temp tables for Proportion values

14 Jul 2023 17:39:18,735 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo

14 Jul 2023 17:39:18,760 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo

14 Jul 2023 17:39:18,777 INFO : Cleaning up temp tables

14 Jul 2023 17:39:19,065 INFO : Completed import of Skyline document from Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip

14 Jul 2023 17:39:19,067 INFO : 100% Done

14 Jul 2023 17:39:19,071 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip into the system

14 Jul 2023 17:39:19,081 INFO : Done importing xar

14 Jul 2023 17:39:19,082 INFO : Loading pages and webpart properties

14 Jul 2023 17:39:19,146 INFO : Done importing 3 page(s) with 5 webpart(s)

14 Jul 2023 17:39:19,146 INFO : Loading File Browser config

14 Jul 2023 17:39:19,146 INFO : Done importing File Browser config

14 Jul 2023 17:39:19,147 INFO : Starting Sample Status Data import

14 Jul 2023 17:39:19,147 INFO : No sample types XAR file to process.

14 Jul 2023 17:39:19,147 INFO : Finished importing Sample Status Data

14 Jul 2023 17:39:19,152 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType

14 Jul 2023 17:39:19,155 INFO : A row containing [Name: 'Reagent Change', Description: 'null', Color: '800000'] values already exists. Skipping

14 Jul 2023 17:39:19,155 INFO : A row containing [Name: 'Instrumentation Change', Description: 'null', Color: 'FF0000'] values already exists. Skipping

14 Jul 2023 17:39:19,156 INFO : A row containing [Name: 'Technician Change', Description: 'null', Color: '0000FF'] values already exists. Skipping

14 Jul 2023 17:39:19,156 INFO : A row containing [Name: 'Instrument Downtime', Description: 'null', Color: 'CCCC00'] values already exists. Skipping

14 Jul 2023 17:39:19,156 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType

14 Jul 2023 17:39:19,156 INFO : Importing files metadata.

14 Jul 2023 17:39:19,156 DEBUG: [/Panorama Public/2023/BayBioMS - Parmar_azyx1_zyx1]  Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS - Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export

14 Jul 2023 17:39:19,157 INFO : 

14 Jul 2023 17:39:19,157 INFO : Experiment import completed successfully.

14 Jul 2023 17:39:19,157 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'

14 Jul 2023 17:40:43,933 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'

14 Jul 2023 17:40:43,933 INFO : 

14 Jul 2023 17:40:43,933 INFO : Checking for library folders.

14 Jul 2023 17:40:43,935 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'

14 Jul 2023 17:40:43,954 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'

14 Jul 2023 17:40:43,954 INFO : 

14 Jul 2023 17:40:43,954 INFO : Finishing up experiment copy.

14 Jul 2023 17:40:43,961 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.

14 Jul 2023 17:40:43,961 INFO : Setting version on new experiment to 2

14 Jul 2023 17:40:43,961 INFO : Copying ProteomeXchange ID from the previous copy of the data.

14 Jul 2023 17:40:43,961 INFO : Copying DOI from the previous copy of the data.

14 Jul 2023 17:40:43,964 INFO : Updating permanent link to point to the new copy of the data.

14 Jul 2023 17:40:43,968 INFO : Removing copy permissions given to Panorama Public

14 Jul 2023 17:40:43,981 INFO : Adding read permissions to all users that are folder admins in the source folder.

14 Jul 2023 17:40:43,982 INFO : Assigning PanoramaPublicSubmitterRole to tina.ludwig@tum.de

14 Jul 2023 17:40:43,982 INFO : Assigning PanoramaPublicSubmitterRole to tina.ludwig@tum.de

14 Jul 2023 17:40:43,982 INFO : Assigning PanoramaPublicSubmitterRole to tina.ludwig@tum.de

14 Jul 2023 17:40:43,984 INFO : User tina.ludwig@tum.de is already a member of group Panorama Public Submitters

14 Jul 2023 17:40:43,984 INFO : User tina.ludwig@tum.de is already a member of group Panorama Public Submitters

14 Jul 2023 17:40:43,984 INFO : User tina.ludwig@tum.de is already a member of group Panorama Public Submitters

14 Jul 2023 17:40:43,984 INFO : Adding read permissions to all users that had read access to previous copy.

14 Jul 2023 17:40:43,994 INFO : Updating the 'Raw Data' tab configuration

14 Jul 2023 17:40:43,998 INFO : Updating dataFileUrls for run FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip; targetedms run ID 166918

14 Jul 2023 17:40:43,998 INFO : Updating dataFileUrl...

14 Jul 2023 17:40:43,998 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip

14 Jul 2023 17:40:43,998 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/BayBioMS%20-%20Parmar_azyx1_zyx1/@files/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03.sky.zip

14 Jul 2023 17:40:44,000 INFO : Updating dataFileUrl...

14 Jul 2023 17:40:44,001 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164222/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyd

14 Jul 2023 17:40:44,001 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/BayBioMS%20-%20Parmar_azyx1_zyx1/@files/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM_2023-07-12_18-25-03/FigS4_azyx-1a_start_codon_deletion_mutants_P267_01_PRM.skyd

14 Jul 2023 17:40:44,004 INFO : Updating dataFileUrls for run Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip; targetedms run ID 166919

14 Jul 2023 17:40:44,004 INFO : Updating dataFileUrl...

14 Jul 2023 17:40:44,004 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip

14 Jul 2023 17:40:44,004 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/BayBioMS%20-%20Parmar_azyx1_zyx1/@files/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17.sky.zip

14 Jul 2023 17:40:44,006 INFO : Updating dataFileUrl...

14 Jul 2023 17:40:44,006 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/BayBioMS%20-%20Parmar_azyx1_zyx1_051e0835-04d0-103c-afc6-fea6ddf51ba4/_temp__2023-07-14_16-57-12/export/xar/experiments_and_runs.xar.exploded/Run164277/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd

14 Jul 2023 17:40:44,006 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/BayBioMS%20-%20Parmar_azyx1_zyx1/@files/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM_2023-07-13_09-29-17/Fig3_azyx-1a_deletion_mutant_age_dependent_P108_12_03_PRM.skyd

14 Jul 2023 17:40:44,011 INFO : Making folder public.

14 Jul 2023 17:40:44,023 INFO : Hiding the Data Pipeline tab.

14 Jul 2023 17:40:44,028 INFO : Creating a new versioned URL for the previous copy of the data: Peu1_v1

14 Jul 2023 17:40:44,033 INFO : Setting the permanent link on the previous copy to Peu1_v1

14 Jul 2023 17:40:44,033 INFO : Removing DOI from the previous copy

14 Jul 2023 17:40:44,036 INFO : Updating Submission. Setting copiedExperimentId to 1651

14 Jul 2023 17:40:44,088 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'