17 Feb 2023 09:55:40,526 INFO : Copying experiment "Correlative study using immuno-MRM in the Cancer Immunotherapy Trials Network (CITN-10) phase 2 clinical trial of pembrolizumab for the treatment of refractory or relapsed Mycosis fungoides (MF) and Sezary syndrome (SS)" from folder /Paulovich/Published_datasets/IO2 immunoMRM panel to /Panorama Public/2023/Paulovich - IO2 immunoMRM panel
17 Feb 2023 09:55:40,526 INFO : =======================================
17 Feb 2023 09:55:40,543 DEBUG: Resetting Job ID: d6fc2459-9118-103b-b327-fea6ddf5f3bc
17 Feb 2023 09:55:40,572 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
17 Feb 2023 09:55:40,572 INFO :
17 Feb 2023 09:55:40,572 INFO : Exporting experiment.
17 Feb 2023 09:55:50,913 INFO : Exporting files metadata.
17 Feb 2023 09:55:50,913 DEBUG: [/Paulovich/Published_datasets/IO2 immunoMRM panel] Writing files metadata to /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich - IO2 immunoMRM panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export
17 Feb 2023 09:55:50,915 INFO :
17 Feb 2023 09:55:50,915 INFO : Experiment export completed successfully.
17 Feb 2023 09:55:50,915 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
17 Feb 2023 09:55:50,937 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
17 Feb 2023 09:55:50,937 INFO :
17 Feb 2023 09:55:50,937 INFO : Importing experiment.
17 Feb 2023 09:55:50,938 DEBUG: [/Panorama Public/2023/Paulovich - IO2 immunoMRM panel] Importing folder properties from: /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich - IO2 immunoMRM panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export
17 Feb 2023 09:55:50,940 INFO : Loading folder properties (folder type, settings and active modules)
17 Feb 2023 09:55:50,940 DEBUG: [/Panorama Public/2023/Paulovich - IO2 immunoMRM panel] Folder type: Targeted MS
17 Feb 2023 09:55:50,940 DEBUG: [/Panorama Public/2023/Paulovich - IO2 immunoMRM panel] Active modules: Internal, API, Pipeline, Wiki, MS2, TargetedMS, Core, Issues, Experiment, Assay, FileContent, PanoramaPublic, Search, Announcements, Query
17 Feb 2023 09:55:51,020 INFO : Done importing folder properties (folder type, settings and active modules)
17 Feb 2023 09:55:51,022 INFO : Loading container specific module properties
17 Feb 2023 09:55:51,030 INFO : Done importing container specific module properties
17 Feb 2023 09:55:51,032 INFO : Loading queries
17 Feb 2023 09:55:51,046 INFO : 6 queries imported
17 Feb 2023 09:55:51,046 INFO : Done importing queries
17 Feb 2023 09:55:51,047 INFO : Loading etl definitions
17 Feb 2023 09:55:51,048 INFO : Loading wikis
17 Feb 2023 09:55:51,049 INFO : 0 wikis imported
17 Feb 2023 09:55:51,049 INFO : Done importing wikis
17 Feb 2023 09:55:51,049 INFO : Starting to copy files
17 Feb 2023 09:55:52,802 INFO : Copied 11 files
17 Feb 2023 09:55:52,802 INFO : Ensuring exp.data rows exist for imported files
17 Feb 2023 09:55:53,411 INFO : Starting Sample Type and Data Class import
17 Feb 2023 09:55:53,411 INFO : No types XAR file to process.
17 Feb 2023 09:55:53,411 INFO : Finished importing Sample Types and Data Classes
17 Feb 2023 09:55:53,412 INFO : Loading xar
17 Feb 2023 09:55:54,468 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip'
17 Feb 2023 09:55:54,470 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Core'
17 Feb 2023 09:55:54,472 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Output'
17 Feb 2023 09:55:54,472 DEBUG: Protocol import complete
17 Feb 2023 09:55:54,473 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-11129:Correlative+study+using+immuno-MRM+in+the+Cancer+Immunotherapy+Trials+Network+%28CITN-10%29+phase+2+clinical+trial+of+pembrolizumab+for+the+treatment+of+refractory+or+relapsed+Mycosis+fungoides+%28MF%29+an...'
17 Feb 2023 09:55:54,473 DEBUG: Experiment/Run group import complete
17 Feb 2023 09:55:54,481 DEBUG: Protocol action set import complete
17 Feb 2023 09:55:54,489 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip'
17 Feb 2023 09:55:54,497 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11129:431e5d41-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,500 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11129:431e5d20-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,500 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Core'
17 Feb 2023 09:55:54,502 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Output'
17 Feb 2023 09:55:54,503 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11129:431e5f36-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,508 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip'
17 Feb 2023 09:55:54,512 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-11129:ecb8e2c3-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,515 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-11129:ecb8e2a4-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,516 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Core'
17 Feb 2023 09:55:54,517 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-11129:TargetedMS.ImportSkyZip.Output'
17 Feb 2023 09:55:54,518 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-11129:ecb8e53e-9113-103b-b327-fea6ddf5f3bc'
17 Feb 2023 09:55:54,519 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52/IO1_Panel_CITN10_exploratory_study.skyd into the system
17 Feb 2023 09:55:54,519 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52/IO1_Panel_CITN10_exploratory_study.skyd into the system
17 Feb 2023 09:55:54,519 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip into the system
17 Feb 2023 09:55:54,520 INFO : Starting import from IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip
17 Feb 2023 09:55:54,523 INFO : Starting to import Skyline document from IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip
17 Feb 2023 09:55:54,533 INFO : Expanding CE_optim_Skyline_library_all_6500_09172022.optdb
17 Feb 2023 09:55:54,533 INFO : Expanding IO1_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:55:54,871 INFO : Expanding IO1_Panel_CITN10_exploratory_study.sky.view
17 Feb 2023 09:55:54,871 INFO : Expanding IO1_Panel_CITN10_exploratory_study.sky
17 Feb 2023 09:55:54,999 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
17 Feb 2023 09:55:55,007 INFO : 1% Done
17 Feb 2023 09:55:55,498 DEBUG: Starting to load chromatogram headers
17 Feb 2023 09:55:55,523 DEBUG: Done loading chromatogram headers
17 Feb 2023 09:55:56,011 INFO : Inserting sp|O43927|CXL13_HUMAN
17 Feb 2023 09:55:56,059 INFO : 3% Done
17 Feb 2023 09:55:56,638 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:56,638 INFO : Inserting sp|O75144|ICOSL_HUMAN
17 Feb 2023 09:55:56,687 INFO : 5% Done
17 Feb 2023 09:55:57,254 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:57,255 INFO : Inserting sp|P02778|CXL10_HUMAN
17 Feb 2023 09:55:57,297 INFO : 8% Done
17 Feb 2023 09:55:57,855 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:57,855 INFO : Inserting sp|P04083|ANXA1_HUMAN
17 Feb 2023 09:55:57,879 INFO : 9% Done
17 Feb 2023 09:55:58,201 INFO : 10% Done
17 Feb 2023 09:55:58,441 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:55:58,441 INFO : Inserting sp|P04233|HG2A_HUMAN
17 Feb 2023 09:55:58,479 INFO : 12% Done
17 Feb 2023 09:55:59,039 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:59,040 INFO : Inserting sp|P04406|G3P_HUMAN
17 Feb 2023 09:55:59,059 INFO : 13% Done
17 Feb 2023 09:55:59,302 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:59,302 INFO : Inserting sp|P05362|ICAM1_HUMAN
17 Feb 2023 09:55:59,331 INFO : 14% Done
17 Feb 2023 09:55:59,724 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:55:59,724 INFO : Inserting sp|P08571|CD14_HUMAN
17 Feb 2023 09:55:59,777 INFO : 17% Done
17 Feb 2023 09:56:00,336 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:00,336 INFO : Inserting sp|P08575|PTPRC_HUMAN
17 Feb 2023 09:56:00,365 INFO : 18% Done
17 Feb 2023 09:56:00,747 INFO : 20% Done
17 Feb 2023 09:56:01,053 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:01,053 INFO : Inserting sp|P09382|LEG1_HUMAN
17 Feb 2023 09:56:01,321 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:01,321 INFO : Inserting sp|P13501|CCL5_HUMAN
17 Feb 2023 09:56:01,346 INFO : 21% Done
17 Feb 2023 09:56:01,586 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:01,587 INFO : Inserting sp|P16284|PECA1_HUMAN
17 Feb 2023 09:56:01,621 INFO : 23% Done
17 Feb 2023 09:56:02,075 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:02,075 INFO : Inserting sp|P19320|VCAM1_HUMAN
17 Feb 2023 09:56:02,127 INFO : 25% Done
17 Feb 2023 09:56:02,779 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:02,779 INFO : Inserting sp|P20138|CD33_HUMAN
17 Feb 2023 09:56:02,831 INFO : 27% Done
17 Feb 2023 09:56:03,435 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:03,436 INFO : Inserting sp|P21589-2|5NTD_HUMAN
17 Feb 2023 09:56:03,480 INFO : 29% Done
17 Feb 2023 09:56:04,215 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:04,216 INFO : Inserting sp|P25445|TNR6_HUMAN
17 Feb 2023 09:56:04,265 INFO : 31% Done
17 Feb 2023 09:56:05,044 INFO : 33% Done
17 Feb 2023 09:56:05,548 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:05,548 INFO : Inserting sp|P25786|PSA1_HUMAN
17 Feb 2023 09:56:05,599 INFO : 36% Done
17 Feb 2023 09:56:06,218 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:06,218 INFO : Inserting sp|P25942|TNR5_HUMAN
17 Feb 2023 09:56:06,260 INFO : 38% Done
17 Feb 2023 09:56:06,858 INFO : 40% Done
17 Feb 2023 09:56:07,424 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:07,425 INFO : Inserting sp|P31997|CEAM8_HUMAN
17 Feb 2023 09:56:07,461 INFO : 42% Done
17 Feb 2023 09:56:07,904 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:07,905 INFO : Inserting sp|P32970|CD70_HUMAN
17 Feb 2023 09:56:07,956 INFO : 45% Done
17 Feb 2023 09:56:08,518 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:08,519 INFO : Inserting sp|P35354|PGH2_HUMAN
17 Feb 2023 09:56:08,568 INFO : 47% Done
17 Feb 2023 09:56:09,071 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:09,072 INFO : Inserting sp|P38570|ITAE_HUMAN
17 Feb 2023 09:56:09,109 INFO : 49% Done
17 Feb 2023 09:56:09,599 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:09,599 INFO : Inserting sp|P40763|STAT3_HUMAN
17 Feb 2023 09:56:09,637 INFO : 51% Done
17 Feb 2023 09:56:10,173 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:10,173 INFO : Inserting sp|P41273|TNFL9_HUMAN
17 Feb 2023 09:56:10,210 INFO : 53% Done
17 Feb 2023 09:56:10,663 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:10,663 INFO : Inserting sp|P42224|STAT1_HUMAN
17 Feb 2023 09:56:10,704 INFO : 55% Done
17 Feb 2023 09:56:11,225 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:11,225 INFO : Inserting sp|P42226-2|STAT6_HUMAN
17 Feb 2023 09:56:11,286 INFO : 57% Done
17 Feb 2023 09:56:11,875 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:11,875 INFO : Inserting sp|P49961|ENTP1_HUMAN
17 Feb 2023 09:56:11,912 INFO : 59% Done
17 Feb 2023 09:56:12,373 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:12,373 INFO : Inserting sp|P78423|X3CL1_HUMAN
17 Feb 2023 09:56:12,415 INFO : 61% Done
17 Feb 2023 09:56:12,878 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:12,878 INFO : Inserting sp|P78536|ADA17_HUMAN
17 Feb 2023 09:56:12,904 INFO : 62% Done
17 Feb 2023 09:56:13,204 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:13,204 INFO : Inserting sp|P78540|ARGI2_HUMAN
17 Feb 2023 09:56:13,249 INFO : 64% Done
17 Feb 2023 09:56:13,820 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:13,820 INFO : Inserting sp|Q00653|NFKB2_HUMAN
17 Feb 2023 09:56:13,850 INFO : 65% Done
17 Feb 2023 09:56:14,177 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:14,177 INFO : Inserting sp|Q02223|TNR17_HUMAN
17 Feb 2023 09:56:14,205 INFO : 67% Done
17 Feb 2023 09:56:14,614 INFO : 68% Done
17 Feb 2023 09:56:14,858 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:14,858 INFO : Inserting sp|Q03519|TAP2_HUMAN
17 Feb 2023 09:56:14,897 INFO : 70% Done
17 Feb 2023 09:56:15,429 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:15,429 INFO : Inserting sp|Q07011|TNR9_HUMAN
17 Feb 2023 09:56:15,465 INFO : 72% Done
17 Feb 2023 09:56:16,000 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:16,000 INFO : Inserting sp|Q08722|CD47_HUMAN
17 Feb 2023 09:56:16,033 INFO : 74% Done
17 Feb 2023 09:56:16,510 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:16,511 INFO : Inserting sp|Q13315|ATM_HUMAN
17 Feb 2023 09:56:16,576 INFO : 75% Done
17 Feb 2023 09:56:17,202 INFO : 77% Done
17 Feb 2023 09:56:17,686 INFO : 79% Done
17 Feb 2023 09:56:18,122 INFO : 80% Done
17 Feb 2023 09:56:18,359 DEBUG: Total peptides inserted: 4
17 Feb 2023 09:56:18,360 INFO : Inserting sp|Q14116|IL18_HUMAN
17 Feb 2023 09:56:18,383 INFO : 81% Done
17 Feb 2023 09:56:18,616 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:18,616 INFO : Inserting sp|Q5UIP0|RIF1_HUMAN
17 Feb 2023 09:56:18,644 INFO : 83% Done
17 Feb 2023 09:56:19,062 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:19,062 INFO : Inserting sp|Q7Z7D3|VTCN1_HUMAN
17 Feb 2023 09:56:19,088 INFO : 84% Done
17 Feb 2023 09:56:19,383 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:19,383 INFO : Inserting sp|Q86VB7|C163A_HUMAN
17 Feb 2023 09:56:19,417 INFO : 86% Done
17 Feb 2023 09:56:19,888 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:19,888 INFO : Inserting sp|Q8TDQ0|HAVR2_HUMAN
17 Feb 2023 09:56:19,918 INFO : 88% Done
17 Feb 2023 09:56:20,332 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:20,332 INFO : Inserting sp|Q92956|TNR14_HUMAN
17 Feb 2023 09:56:20,370 INFO : 90% Done
17 Feb 2023 09:56:20,911 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:20,911 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN
17 Feb 2023 09:56:20,948 INFO : 92% Done
17 Feb 2023 09:56:21,436 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:21,436 INFO : Inserting sp|Q9H400|LIME1_HUMAN
17 Feb 2023 09:56:21,470 INFO : 94% Done
17 Feb 2023 09:56:22,036 INFO : 96% Done
17 Feb 2023 09:56:22,650 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:22,650 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN
17 Feb 2023 09:56:22,688 INFO : 98% Done
17 Feb 2023 09:56:23,105 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:23,106 INFO : Done parsing Skyline document.
17 Feb 2023 09:56:23,108 INFO : Creating and populating temp tables for Proportion values
17 Feb 2023 09:56:23,297 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
17 Feb 2023 09:56:24,166 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
17 Feb 2023 09:56:24,434 INFO : Cleaning up temp tables
17 Feb 2023 09:56:24,715 INFO : Completed import of Skyline document from IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip
17 Feb 2023 09:56:24,717 INFO : 100% Done
17 Feb 2023 09:56:24,722 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip into the system
17 Feb 2023 09:56:24,722 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37/IO2_Panel_CITN10_exploratory_study.skyd into the system
17 Feb 2023 09:56:24,722 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37/IO2_Panel_CITN10_exploratory_study.skyd into the system
17 Feb 2023 09:56:24,722 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip into the system
17 Feb 2023 09:56:24,723 INFO : Starting import from IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip
17 Feb 2023 09:56:24,725 INFO : Starting to import Skyline document from IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip
17 Feb 2023 09:56:24,734 INFO : Expanding IO2_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:56:25,053 INFO : Expanding IO2_Panel_CITN10_exploratory_study.sky.view
17 Feb 2023 09:56:25,054 INFO : Expanding IO2_Panel_CITN10_exploratory_study.sky
17 Feb 2023 09:56:25,176 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
17 Feb 2023 09:56:25,181 INFO : 1% Done
17 Feb 2023 09:56:25,660 DEBUG: Starting to load chromatogram headers
17 Feb 2023 09:56:25,680 DEBUG: Done loading chromatogram headers
17 Feb 2023 09:56:26,192 INFO : Inserting <name:PVR>
17 Feb 2023 09:56:26,236 INFO : 3% Done
17 Feb 2023 09:56:26,808 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:26,808 INFO : Inserting TMEM173
17 Feb 2023 09:56:26,840 INFO : 4% Done
17 Feb 2023 09:56:27,265 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:27,265 INFO : Inserting CD4
17 Feb 2023 09:56:27,314 INFO : 7% Done
17 Feb 2023 09:56:27,840 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:27,840 INFO : Inserting sp|Q13740|CD166_HUMAN
17 Feb 2023 09:56:27,885 INFO : 9% Done
17 Feb 2023 09:56:28,407 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:28,407 INFO : Inserting sp|P05089|ARGI1_HUMAN
17 Feb 2023 09:56:28,448 INFO : 11% Done
17 Feb 2023 09:56:28,971 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:28,971 INFO : Inserting sp|Q07812|BAX_HUMAN
17 Feb 2023 09:56:29,017 INFO : 13% Done
17 Feb 2023 09:56:29,608 INFO : 16% Done
17 Feb 2023 09:56:30,114 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:30,115 INFO : Inserting sp|O95999|BCL10_HUMAN
17 Feb 2023 09:56:30,152 INFO : 18% Done
17 Feb 2023 09:56:30,658 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:30,658 INFO : Inserting sp|Q06187|BTK_HUMAN
17 Feb 2023 09:56:30,697 INFO : 20% Done
17 Feb 2023 09:56:31,205 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:31,205 INFO : Inserting sp|Q7Z6A9|BTLA_HUMAN
17 Feb 2023 09:56:31,240 INFO : 22% Done
17 Feb 2023 09:56:31,760 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:31,761 INFO : Inserting sp|P28907|CD38_HUMAN
17 Feb 2023 09:56:31,788 INFO : 23% Done
17 Feb 2023 09:56:32,078 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:32,078 INFO : Inserting sp|P09326|CD48_HUMAN
17 Feb 2023 09:56:32,115 INFO : 25% Done
17 Feb 2023 09:56:32,629 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:32,629 INFO : Inserting sp|P15509|CSF2R_HUMAN
17 Feb 2023 09:56:32,667 INFO : 27% Done
17 Feb 2023 09:56:33,220 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:33,220 INFO : Inserting sp|P18074|ERCC2_HUMAN
17 Feb 2023 09:56:33,258 INFO : 29% Done
17 Feb 2023 09:56:33,746 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:33,746 INFO : Inserting sp|Q12778|FOXO1_HUMAN
17 Feb 2023 09:56:33,788 INFO : 31% Done
17 Feb 2023 09:56:34,328 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:34,328 INFO : Inserting sp|P04406|G3P_HUMAN
17 Feb 2023 09:56:34,354 INFO : 32% Done
17 Feb 2023 09:56:34,643 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:34,643 INFO : Inserting sp|P01903|DRA_HUMAN
17 Feb 2023 09:56:34,685 INFO : 34% Done
17 Feb 2023 09:56:35,211 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:35,211 INFO : Inserting sp|P13747|HLAE_HUMAN
17 Feb 2023 09:56:35,248 INFO : 36% Done
17 Feb 2023 09:56:35,760 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:35,760 INFO : Inserting sp|P14902|I23O1_HUMAN
17 Feb 2023 09:56:35,786 INFO : 38% Done
17 Feb 2023 09:56:36,137 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:36,137 INFO : Inserting sp|P09914|IFIT1_HUMAN
17 Feb 2023 09:56:36,187 INFO : 40% Done
17 Feb 2023 09:56:36,719 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:36,719 INFO : Inserting sp|P09913|IFIT2_HUMAN
17 Feb 2023 09:56:36,761 INFO : 42% Done
17 Feb 2023 09:56:37,232 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:37,232 INFO : Inserting sp|O14879|IFIT3_HUMAN
17 Feb 2023 09:56:37,271 INFO : 44% Done
17 Feb 2023 09:56:37,769 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:37,769 INFO : Inserting sp|Q14005|IL16_HUMAN
17 Feb 2023 09:56:37,819 INFO : 46% Done
17 Feb 2023 09:56:38,414 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:38,414 INFO : Inserting sp|P01583|IL1A_HUMAN
17 Feb 2023 09:56:38,452 INFO : 48% Done
17 Feb 2023 09:56:38,891 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:38,891 INFO : Inserting sp|P31785|IL2RG_HUMAN
17 Feb 2023 09:56:38,929 INFO : 50% Done
17 Feb 2023 09:56:39,476 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:39,476 INFO : Inserting sp|P08887|IL6RA_HUMAN
17 Feb 2023 09:56:39,515 INFO : 52% Done
17 Feb 2023 09:56:40,069 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:40,070 INFO : Inserting sp|P20702|ITAX_HUMAN
17 Feb 2023 09:56:40,107 INFO : 54% Done
17 Feb 2023 09:56:40,713 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:40,713 INFO : Inserting sp|O00182|LEG9_HUMAN
17 Feb 2023 09:56:40,765 INFO : 57% Done
17 Feb 2023 09:56:41,375 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:41,375 INFO : Inserting sp|O60449|LY75_HUMAN
17 Feb 2023 09:56:41,423 INFO : 59% Done
17 Feb 2023 09:56:41,991 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:41,991 INFO : Inserting sp|Q07820|MCL1_HUMAN
17 Feb 2023 09:56:42,038 INFO : 61% Done
17 Feb 2023 09:56:42,704 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:42,704 INFO : Inserting sp|P16455|MGMT_HUMAN
17 Feb 2023 09:56:42,748 INFO : 63% Done
17 Feb 2023 09:56:43,516 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:43,516 INFO : Inserting sp|P46013|KI67_HUMAN
17 Feb 2023 09:56:43,552 INFO : 65% Done
17 Feb 2023 09:56:44,074 INFO : 67% Done
17 Feb 2023 09:56:44,882 INFO : 70% Done
17 Feb 2023 09:56:45,440 DEBUG: Total peptides inserted: 3
17 Feb 2023 09:56:45,441 INFO : Inserting sp|P05164|PERM_HUMAN
17 Feb 2023 09:56:45,483 INFO : 71% Done
17 Feb 2023 09:56:46,005 INFO : 74% Done
17 Feb 2023 09:56:46,512 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:46,513 INFO : Inserting sp|P52701|MSH6_HUMAN
17 Feb 2023 09:56:46,548 INFO : 75% Done
17 Feb 2023 09:56:47,118 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:47,118 INFO : Inserting sp|P26927|HGFL_HUMAN
17 Feb 2023 09:56:47,159 INFO : 77% Done
17 Feb 2023 09:56:47,727 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:47,727 INFO : Inserting sp|P54277|PMS1_HUMAN
17 Feb 2023 09:56:47,761 INFO : 78% Done
17 Feb 2023 09:56:48,045 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:48,045 INFO : Inserting sp|P28340|DPOD1_HUMAN
17 Feb 2023 09:56:48,078 INFO : 80% Done
17 Feb 2023 09:56:48,579 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:48,580 INFO : Inserting sp|P06400|RB_HUMAN
17 Feb 2023 09:56:48,606 INFO : 81% Done
17 Feb 2023 09:56:48,938 INFO : 83% Done
17 Feb 2023 09:56:49,353 DEBUG: Total peptides inserted: 2
17 Feb 2023 09:56:49,354 INFO : Inserting sp|Q9BZZ2|SN_HUMAN
17 Feb 2023 09:56:49,401 INFO : 85% Done
17 Feb 2023 09:56:49,936 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:49,936 INFO : Inserting sp|Q9Y286|SIGL7_HUMAN
17 Feb 2023 09:56:49,978 INFO : 87% Done
17 Feb 2023 09:56:50,587 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:50,587 INFO : Inserting sp|P10451|OSTP_HUMAN
17 Feb 2023 09:56:50,633 INFO : 90% Done
17 Feb 2023 09:56:51,335 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:51,335 INFO : Inserting sp|Q03518|TAP1_HUMAN
17 Feb 2023 09:56:51,381 INFO : 92% Done
17 Feb 2023 09:56:51,925 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:51,925 INFO : Inserting sp|O15533|TPSN_HUMAN
17 Feb 2023 09:56:51,961 INFO : 94% Done
17 Feb 2023 09:56:52,377 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:52,377 INFO : Inserting sp|P13010|XRCC5_HUMAN
17 Feb 2023 09:56:52,420 INFO : 96% Done
17 Feb 2023 09:56:52,945 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:52,946 INFO : Inserting sp|P43403|ZAP70_HUMAN
17 Feb 2023 09:56:52,979 INFO : 98% Done
17 Feb 2023 09:56:53,432 DEBUG: Total peptides inserted: 1
17 Feb 2023 09:56:53,433 INFO : Done parsing Skyline document.
17 Feb 2023 09:56:53,434 INFO : Creating and populating temp tables for Proportion values
17 Feb 2023 09:56:53,590 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
17 Feb 2023 09:56:54,232 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
17 Feb 2023 09:56:54,449 INFO : Cleaning up temp tables
17 Feb 2023 09:56:54,746 INFO : Completed import of Skyline document from IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip
17 Feb 2023 09:56:54,748 INFO : 100% Done
17 Feb 2023 09:56:54,752 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip into the system
17 Feb 2023 09:56:54,763 INFO : Done importing xar
17 Feb 2023 09:56:54,764 INFO : Loading pages and webpart properties
17 Feb 2023 09:56:54,847 INFO : Done importing 4 page(s) with 7 webpart(s)
17 Feb 2023 09:56:54,848 INFO : Loading File Browser config
17 Feb 2023 09:56:54,848 INFO : Done importing File Browser config
17 Feb 2023 09:56:54,849 INFO : Starting Sample Status Data import
17 Feb 2023 09:56:54,849 INFO : No sample types XAR file to process.
17 Feb 2023 09:56:54,849 INFO : Finished importing Sample Status Data
17 Feb 2023 09:56:54,855 INFO : Starting data import from QCAnnotationType.tsv into targetedms.QCAnnotationType
17 Feb 2023 09:56:54,857 INFO : A row containing [Description: 'null', Color: '800000', Name: 'Reagent Change'] values already exists. Skipping
17 Feb 2023 09:56:54,857 INFO : A row containing [Description: 'null', Color: 'FF0000', Name: 'Instrumentation Change'] values already exists. Skipping
17 Feb 2023 09:56:54,858 INFO : A row containing [Description: 'null', Color: '0000FF', Name: 'Technician Change'] values already exists. Skipping
17 Feb 2023 09:56:54,858 INFO : Finished importing 0 rows from QCAnnotationType.tsv into targetedms.QCAnnotationType
17 Feb 2023 09:56:54,858 INFO : Importing files metadata.
17 Feb 2023 09:56:54,858 DEBUG: [/Panorama Public/2023/Paulovich - IO2 immunoMRM panel] Reading files metadata from /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich - IO2 immunoMRM panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export
17 Feb 2023 09:56:54,858 INFO :
17 Feb 2023 09:56:54,858 INFO : Experiment import completed successfully.
17 Feb 2023 09:56:54,858 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
17 Feb 2023 09:56:54,880 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask' at location 'webserver-high-priority'
17 Feb 2023 09:56:54,880 INFO :
17 Feb 2023 09:56:54,880 INFO : Checking for library folders.
17 Feb 2023 09:56:54,882 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyLibraryStateTask'
17 Feb 2023 09:56:54,898 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
17 Feb 2023 09:56:54,898 INFO :
17 Feb 2023 09:56:54,898 INFO : Finishing up experiment copy.
17 Feb 2023 09:56:54,900 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
17 Feb 2023 09:56:54,901 INFO : Setting version on new experiment to 1
17 Feb 2023 09:56:54,901 INFO : Assigning a DOI.
17 Feb 2023 09:56:55,722 INFO : Assigned DOI: 10.6069/kah2-th19
17 Feb 2023 09:56:55,725 INFO : Updating access URL to point to the new copy of the data.
17 Feb 2023 09:56:55,730 INFO : Removing copy permissions given to Panorama Public
17 Feb 2023 09:56:55,745 INFO : Adding read permissions to all users that are folder admins in the source folder.
17 Feb 2023 09:56:55,754 INFO : Updating the 'Raw Data' tab configuration
17 Feb 2023 09:56:55,756 INFO : Updating dataFileUrls for run IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip; targetedms run ID 153042
17 Feb 2023 09:56:55,757 INFO : Updating dataFileUrl...
17 Feb 2023 09:56:55,757 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52/IO1_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:56:55,757 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Paulovich%20-%20IO2%20immunoMRM%20panel/@files/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52/IO1_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:56:55,758 INFO : Updating dataFileUrl...
17 Feb 2023 09:56:55,758 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151145/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip
17 Feb 2023 09:56:55,759 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Paulovich%20-%20IO2%20immunoMRM%20panel/@files/IO1_Panel_CITN10_exploratory_study_2023-02-17_09-05-52.sky.zip
17 Feb 2023 09:56:55,762 INFO : Updating dataFileUrls for run IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip; targetedms run ID 153043
17 Feb 2023 09:56:55,762 INFO : Updating dataFileUrl...
17 Feb 2023 09:56:55,762 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37/IO2_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:56:55,762 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Paulovich%20-%20IO2%20immunoMRM%20panel/@files/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37/IO2_Panel_CITN10_exploratory_study.skyd
17 Feb 2023 09:56:55,764 INFO : Updating dataFileUrl...
17 Feb 2023 09:56:55,764 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Paulovich%20-%20IO2%20immunoMRM%20panel_d6fc2446-9118-103b-b327-fea6ddf5f3bc/_temp__2023-02-17_09-55-40/export/xar/experiments_and_runs.xar.exploded/Run151146/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip
17 Feb 2023 09:56:55,764 INFO : to: file:///data/labkey/files/Panorama%20Public/2023/Paulovich%20-%20IO2%20immunoMRM%20panel/@files/IO2_Panel_CITN10_exploratory_study_2023-02-17_09-13-37.sky.zip
17 Feb 2023 09:56:55,769 INFO : Creating a reviewer account.
17 Feb 2023 09:56:55,978 INFO : Created reviewer with email: User panorama+reviewer171@proteinms.net
17 Feb 2023 09:56:55,987 INFO : Hiding the Data Pipeline tab.
17 Feb 2023 09:56:55,991 INFO : Updating Submission. Setting copiedExperimentId to 1578
17 Feb 2023 09:56:56,087 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'