08 May 2020 14:52:41,328 INFO : Copying experiment "Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer" from folder /Protypia LLC/Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer to /Panorama Public/2020/Protypia - Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer
08 May 2020 14:52:41,328 INFO : =======================================
08 May 2020 14:52:41,419 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
08 May 2020 14:52:41,419 INFO :
08 May 2020 14:52:41,419 INFO : Exporting experiment.
08 May 2020 15:12:02,484 INFO :
08 May 2020 15:12:02,488 INFO : Experiment export completed successfully.
08 May 2020 15:12:02,489 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
08 May 2020 15:12:02,846 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
08 May 2020 15:12:02,847 INFO :
08 May 2020 15:12:02,847 INFO : Importing experiment.
08 May 2020 15:12:02,871 INFO : Loading folder properties (folder type, settings and active modules)
08 May 2020 15:12:03,050 INFO : Done importing folder properties (folder type, settings and active modules)
08 May 2020 15:12:03,057 INFO : Loading etl definitions
08 May 2020 15:12:03,113 INFO : Loading wikis
08 May 2020 15:12:03,164 INFO : 1 wiki imported
08 May 2020 15:12:03,165 INFO : Done importing wikis
08 May 2020 15:12:03,165 INFO : Starting to copy files
08 May 2020 15:14:51,102 INFO : 13 files copied, now copying Lilly pilot Ph1 batch 2 083118_2.sky.view
08 May 2020 15:16:01,126 INFO : 18 files copied, now copying Human RefSeq.protdb
08 May 2020 15:17:07,862 INFO : 23 files copied, now copying Human RefSeq.protdb
08 May 2020 15:18:32,577 INFO : 28 files copied, now copying V97_frac3+4.raw
08 May 2020 15:20:34,793 INFO : 76 files copied, now copying V46_frac1+2.raw
08 May 2020 15:22:36,100 INFO : 125 files copied, now copying SR13_77_frac7+8.raw
08 May 2020 15:24:30,660 INFO : Copied 165 files
08 May 2020 15:24:30,660 INFO : Ensuring exp.data rows exist for imported files
08 May 2020 15:24:34,162 INFO : Loading xar
08 May 2020 15:27:33,146 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip'
08 May 2020 15:27:33,151 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Core'
08 May 2020 15:27:33,208 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Output'
08 May 2020 15:27:33,208 DEBUG: Protocol import complete
08 May 2020 15:27:33,285 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-6947:Analysis+of+Immune+Checkpoint+Drug+Targets+and+Tumor+Proteotypes+in+Non-Small+Cell+Lung+Cancer'
08 May 2020 15:27:33,285 DEBUG: Experiment/Run group import complete
08 May 2020 15:27:33,457 DEBUG: Protocol action set import complete
08 May 2020 15:27:33,570 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip'
08 May 2020 15:27:33,663 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-6947:390483ee-7203-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,686 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-6947:3904821b-7203-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,686 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Core'
08 May 2020 15:27:33,744 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Output'
08 May 2020 15:27:33,745 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-6947:39048422-7203-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,786 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip'
08 May 2020 15:27:33,820 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-6947:2c29cc4b-71ef-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,827 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-6947:2c29ca9c-71ef-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,828 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Core'
08 May 2020 15:27:33,842 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Output'
08 May 2020 15:27:33,844 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-6947:2c29cc5e-71ef-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,858 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip'
08 May 2020 15:27:33,867 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-6947:ea6c1353-71e8-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,896 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-6947:ea6c1159-71e8-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,896 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Core'
08 May 2020 15:27:33,909 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Output'
08 May 2020 15:27:33,910 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-6947:ea6c1365-71e8-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,978 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip'
08 May 2020 15:27:33,988 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-6947:6986e64d-71e4-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,995 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-6947:6986e3db-71e4-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:33,995 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Core'
08 May 2020 15:27:33,999 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-6947:TargetedMS.ImportSkyZip.Output'
08 May 2020 15:27:34,000 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-6947:6986e67f-71e4-1038-92a8-3013bb9ba73d'
08 May 2020 15:27:34,002 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2.skyd into the system
08 May 2020 15:27:34,005 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2.skyd into the system
08 May 2020 15:27:34,005 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39.sky.zip into the system
08 May 2020 15:27:34,031 INFO : Starting import from All targets Lilly pilot ph1B batch 1_2 011219_2_2020-05-06_14-47-39.sky.zip
08 May 2020 15:27:34,065 INFO : Starting to import Skyline document from All targets Lilly pilot ph1B batch 1_2 011219_2_2020-05-06_14-47-39.sky.zip
08 May 2020 15:27:34,074 INFO : Expanding Human RefSeq.protdb
08 May 2020 15:27:46,263 INFO : Expanding human_hcd_selected.msp
08 May 2020 15:29:07,641 INFO : Expanding All targets Lilly pilot ph1B batch 1_2 011219_2.skyd
08 May 2020 15:29:07,791 INFO : Expanding All targets Lilly pilot ph1B batch 1_2 011219_2.sky.view
08 May 2020 15:29:07,791 INFO : Expanding All targets Lilly pilot ph1B batch 1_2 011219_2.sky
08 May 2020 15:29:07,825 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
08 May 2020 15:29:07,883 INFO : 3% Done
08 May 2020 15:29:08,792 INFO : Inserting sp|Q15116|PDCD1_HUMAN
08 May 2020 15:29:09,016 INFO : 11% Done
08 May 2020 15:29:10,212 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:10,213 INFO : 12% Done
08 May 2020 15:29:10,513 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN
08 May 2020 15:29:10,573 INFO : 21% Done
08 May 2020 15:29:11,119 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:11,243 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN
08 May 2020 15:29:11,310 INFO : 30% Done
08 May 2020 15:29:11,836 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:11,957 INFO : Inserting sp|P18627|LAG3_HUMAN
08 May 2020 15:29:12,001 INFO : 40% Done
08 May 2020 15:29:12,480 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:12,647 INFO : Inserting sp|Q8TDQ0|HAVR2_HUMAN
08 May 2020 15:29:12,705 INFO : 50% Done
08 May 2020 15:29:13,006 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:13,107 INFO : Inserting sp|P14902|I23O1_HUMAN
08 May 2020 15:29:13,167 INFO : 60% Done
08 May 2020 15:29:13,488 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:13,679 INFO : Inserting sp|Q9H7M9|VISTA_HUMAN
08 May 2020 15:29:13,750 INFO : 69% Done
08 May 2020 15:29:13,924 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:13,924 INFO : 70% Done
08 May 2020 15:29:14,018 INFO : Inserting sp|O75144|ICOSL_HUMAN
08 May 2020 15:29:14,071 INFO : 79% Done
08 May 2020 15:29:14,351 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:14,522 INFO : Inserting sp|Q9Y5U5|TNR18_HUMAN
08 May 2020 15:29:14,582 INFO : 88% Done
08 May 2020 15:29:15,125 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:15,508 INFO : Inserting sp|P25942|TNR5_HUMAN
08 May 2020 15:29:15,659 INFO : 98% Done
08 May 2020 15:29:16,014 DEBUG: Total peptides inserted: 1
08 May 2020 15:29:16,014 INFO : Done parsing Skyline document.
08 May 2020 15:29:16,015 INFO : Creating and populating temp tables for Proportion values
08 May 2020 15:29:16,389 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
08 May 2020 15:29:16,514 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
08 May 2020 15:29:16,547 INFO : Cleaning up temp tables
08 May 2020 15:29:16,634 INFO : Completed import of Skyline document from All targets Lilly pilot ph1B batch 1_2 011219_2_2020-05-06_14-47-39.sky.zip
08 May 2020 15:29:16,635 INFO : 100% Done
08 May 2020 15:29:16,640 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39.sky.zip into the system
08 May 2020 15:29:16,641 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59/Lilly%20pilot%20Ph1%20batch%203%20090418_2.skyd into the system
08 May 2020 15:29:16,643 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59/Lilly%20pilot%20Ph1%20batch%203%20090418_2.skyd into the system
08 May 2020 15:29:16,643 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59.sky.zip into the system
08 May 2020 15:29:16,647 INFO : Starting import from Lilly pilot Ph1 batch 3 090418_2_2020-05-06_12-50-59.sky.zip
08 May 2020 15:29:16,652 INFO : Starting to import Skyline document from Lilly pilot Ph1 batch 3 090418_2_2020-05-06_12-50-59.sky.zip
08 May 2020 15:29:16,678 INFO : Expanding Human RefSeq.protdb
08 May 2020 15:29:36,664 INFO : Expanding human_hcd_selected.msp
08 May 2020 15:31:13,789 INFO : Expanding Lilly pilot Ph1 batch 3 090418_2.skyd
08 May 2020 15:31:13,866 INFO : Expanding Lilly pilot Ph1 batch 3 090418_2.sky.view
08 May 2020 15:31:13,866 INFO : Expanding Lilly pilot Ph1 batch 3 090418_2.sky
08 May 2020 15:31:13,876 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
08 May 2020 15:31:13,878 INFO : 3% Done
08 May 2020 15:31:14,114 INFO : Inserting sp|Q15116|PDCD1_HUMAN
08 May 2020 15:31:14,120 INFO : 14% Done
08 May 2020 15:31:14,351 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:14,360 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN
08 May 2020 15:31:14,365 INFO : 24% Done
08 May 2020 15:31:14,615 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:14,623 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN
08 May 2020 15:31:14,628 INFO : 32% Done
08 May 2020 15:31:14,885 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:14,892 INFO : Inserting sp|P18627|LAG3_HUMAN
08 May 2020 15:31:14,894 INFO : 41% Done
08 May 2020 15:31:15,097 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:15,104 INFO : Inserting sp|Q8TDQ0|HAVR2_HUMAN
08 May 2020 15:31:15,106 INFO : 51% Done
08 May 2020 15:31:15,315 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:15,323 INFO : Inserting sp|P14902|I23O1_HUMAN
08 May 2020 15:31:15,328 INFO : 61% Done
08 May 2020 15:31:15,563 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:15,572 INFO : Inserting sp|Q9H7M9|VISTA_HUMAN
08 May 2020 15:31:15,577 INFO : 71% Done
08 May 2020 15:31:15,798 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:15,805 INFO : Inserting sp|O75144|ICOSL_HUMAN
08 May 2020 15:31:15,809 INFO : 79% Done
08 May 2020 15:31:16,134 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:16,143 INFO : Inserting sp|Q9Y5U5|TNR18_HUMAN
08 May 2020 15:31:16,146 INFO : 89% Done
08 May 2020 15:31:16,366 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:16,373 INFO : Inserting sp|P25942|TNR5_HUMAN
08 May 2020 15:31:16,375 INFO : 98% Done
08 May 2020 15:31:16,664 DEBUG: Total peptides inserted: 1
08 May 2020 15:31:16,664 INFO : Done parsing Skyline document.
08 May 2020 15:31:16,666 INFO : Creating and populating temp tables for Proportion values
08 May 2020 15:31:16,699 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
08 May 2020 15:31:16,821 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
08 May 2020 15:31:16,858 INFO : Cleaning up temp tables
08 May 2020 15:31:16,869 INFO : Completed import of Skyline document from Lilly pilot Ph1 batch 3 090418_2_2020-05-06_12-50-59.sky.zip
08 May 2020 15:31:16,870 INFO : 100% Done
08 May 2020 15:31:16,879 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59.sky.zip into the system
08 May 2020 15:31:16,879 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03/Lilly%20pilot%20Ph1%20batch%202%20083118_2.skyd into the system
08 May 2020 15:31:16,881 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03/Lilly%20pilot%20Ph1%20batch%202%20083118_2.skyd into the system
08 May 2020 15:31:16,881 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03.sky.zip into the system
08 May 2020 15:31:16,884 INFO : Starting import from Lilly pilot Ph1 batch 2 083118_2_2020-05-06_12-14-03.sky.zip
08 May 2020 15:31:16,889 INFO : Starting to import Skyline document from Lilly pilot Ph1 batch 2 083118_2_2020-05-06_12-14-03.sky.zip
08 May 2020 15:31:16,923 INFO : Expanding Human RefSeq.protdb
08 May 2020 15:31:26,885 INFO : Expanding human_hcd_selected.msp
08 May 2020 15:33:31,201 INFO : Expanding Lilly pilot Ph1 batch 2 083118_2.skyd
08 May 2020 15:33:31,338 INFO : Expanding Lilly pilot Ph1 batch 2 083118_2.sky.view
08 May 2020 15:33:31,338 INFO : Expanding Lilly pilot Ph1 batch 2 083118_2.sky
08 May 2020 15:33:31,347 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
08 May 2020 15:33:31,349 INFO : 3% Done
08 May 2020 15:33:31,523 INFO : Inserting sp|Q15116|PDCD1_HUMAN
08 May 2020 15:33:31,528 INFO : 13% Done
08 May 2020 15:33:31,752 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:31,753 INFO : 14% Done
08 May 2020 15:33:31,756 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN
08 May 2020 15:33:31,758 INFO : 23% Done
08 May 2020 15:33:31,952 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:31,956 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN
08 May 2020 15:33:31,958 INFO : 32% Done
08 May 2020 15:33:32,116 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,120 INFO : Inserting sp|P18627|LAG3_HUMAN
08 May 2020 15:33:32,122 INFO : 41% Done
08 May 2020 15:33:32,286 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,289 INFO : Inserting sp|Q8TDQ0|HAVR2_HUMAN
08 May 2020 15:33:32,293 INFO : 51% Done
08 May 2020 15:33:32,437 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,441 INFO : Inserting sp|P14902|I23O1_HUMAN
08 May 2020 15:33:32,444 INFO : 61% Done
08 May 2020 15:33:32,572 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,576 INFO : Inserting sp|Q9H7M9|VISTA_HUMAN
08 May 2020 15:33:32,578 INFO : 70% Done
08 May 2020 15:33:32,811 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,811 INFO : 71% Done
08 May 2020 15:33:32,815 INFO : Inserting sp|O75144|ICOSL_HUMAN
08 May 2020 15:33:32,817 INFO : 79% Done
08 May 2020 15:33:32,962 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:32,965 INFO : Inserting sp|Q9Y5U5|TNR18_HUMAN
08 May 2020 15:33:32,968 INFO : 89% Done
08 May 2020 15:33:33,080 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:33,083 INFO : Inserting sp|P25942|TNR5_HUMAN
08 May 2020 15:33:33,085 INFO : 98% Done
08 May 2020 15:33:33,205 DEBUG: Total peptides inserted: 1
08 May 2020 15:33:33,205 INFO : Done parsing Skyline document.
08 May 2020 15:33:33,206 INFO : Creating and populating temp tables for Proportion values
08 May 2020 15:33:33,221 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
08 May 2020 15:33:33,296 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
08 May 2020 15:33:33,372 INFO : Cleaning up temp tables
08 May 2020 15:33:33,374 INFO : Completed import of Skyline document from Lilly pilot Ph1 batch 2 083118_2_2020-05-06_12-14-03.sky.zip
08 May 2020 15:33:33,381 INFO : 100% Done
08 May 2020 15:33:33,386 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03.sky.zip into the system
08 May 2020 15:33:33,387 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26/Lilly%20pilot%20Ph1%20batch%201%20090218_2.skyd into the system
08 May 2020 15:33:33,388 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26/Lilly%20pilot%20Ph1%20batch%201%20090218_2.skyd into the system
08 May 2020 15:33:33,388 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26.sky.zip into the system
08 May 2020 15:33:33,391 INFO : Starting import from Lilly pilot Ph1 batch 1 090218_2_2020-05-06_11-27-26.sky.zip
08 May 2020 15:33:33,394 INFO : Starting to import Skyline document from Lilly pilot Ph1 batch 1 090218_2_2020-05-06_11-27-26.sky.zip
08 May 2020 15:33:33,416 INFO : Expanding Human RefSeq.protdb
08 May 2020 15:33:48,069 INFO : Expanding human_hcd_selected.msp
08 May 2020 15:36:32,043 INFO : Expanding Lilly pilot Ph1 batch 1 090218_2.skyd
08 May 2020 15:36:32,136 INFO : Expanding Lilly pilot Ph1 batch 1 090218_2.sky.view
08 May 2020 15:36:32,136 INFO : Expanding Lilly pilot Ph1 batch 1 090218_2.sky
08 May 2020 15:36:32,144 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
08 May 2020 15:36:32,146 INFO : 3% Done
08 May 2020 15:36:32,355 INFO : Inserting sp|Q15116|PDCD1_HUMAN
08 May 2020 15:36:32,360 INFO : 14% Done
08 May 2020 15:36:32,488 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:32,491 INFO : Inserting sp|Q9NZQ7|PD1L1_HUMAN
08 May 2020 15:36:32,494 INFO : 24% Done
08 May 2020 15:36:32,617 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:32,623 INFO : Inserting sp|Q9BQ51|PD1L2_HUMAN
08 May 2020 15:36:32,625 INFO : 32% Done
08 May 2020 15:36:32,738 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:32,742 INFO : Inserting sp|P18627|LAG3_HUMAN
08 May 2020 15:36:32,744 INFO : 41% Done
08 May 2020 15:36:32,930 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:32,930 INFO : 42% Done
08 May 2020 15:36:32,935 INFO : Inserting sp|Q8TDQ0|HAVR2_HUMAN
08 May 2020 15:36:32,937 INFO : 51% Done
08 May 2020 15:36:33,134 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,138 INFO : Inserting sp|P14902|I23O1_HUMAN
08 May 2020 15:36:33,140 INFO : 61% Done
08 May 2020 15:36:33,267 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,271 INFO : Inserting sp|Q9H7M9|VISTA_HUMAN
08 May 2020 15:36:33,273 INFO : 70% Done
08 May 2020 15:36:33,384 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,387 INFO : Inserting sp|O75144|ICOSL_HUMAN
08 May 2020 15:36:33,389 INFO : 79% Done
08 May 2020 15:36:33,505 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,509 INFO : Inserting sp|Q9Y5U5|TNR18_HUMAN
08 May 2020 15:36:33,511 INFO : 89% Done
08 May 2020 15:36:33,617 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,620 INFO : Inserting sp|P25942|TNR5_HUMAN
08 May 2020 15:36:33,622 INFO : 98% Done
08 May 2020 15:36:33,751 DEBUG: Total peptides inserted: 1
08 May 2020 15:36:33,752 INFO : Done parsing Skyline document.
08 May 2020 15:36:33,753 INFO : Creating and populating temp tables for Proportion values
08 May 2020 15:36:33,780 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
08 May 2020 15:36:33,842 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
08 May 2020 15:36:33,860 INFO : Cleaning up temp tables
08 May 2020 15:36:33,868 INFO : Completed import of Skyline document from Lilly pilot Ph1 batch 1 090218_2_2020-05-06_11-27-26.sky.zip
08 May 2020 15:36:33,869 INFO : 100% Done
08 May 2020 15:36:33,876 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26.sky.zip into the system
08 May 2020 15:36:34,018 INFO : Done importing xar
08 May 2020 15:36:34,058 INFO : Loading pages and webpart properties
08 May 2020 15:36:34,835 INFO : Done importing pages and webpart properties
08 May 2020 15:36:34,835 INFO :
08 May 2020 15:36:34,835 INFO : Experiment import completed successfully.
08 May 2020 15:36:34,836 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
08 May 2020 15:36:35,151 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
08 May 2020 15:36:35,151 INFO :
08 May 2020 15:36:35,151 INFO : Finishing up experiment copy.
08 May 2020 15:36:35,153 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
08 May 2020 15:36:35,331 INFO : Updating access URL to point to the new copy of the data.
08 May 2020 15:36:35,503 INFO : Setting the 'copied' timestamp on the JournalExperiment table.
08 May 2020 15:36:35,575 INFO : Removing copy permissions given to journal.
08 May 2020 15:36:35,746 INFO : Adding read permissions to all users that are folder admins in the source container.
08 May 2020 15:36:35,757 INFO : Setting the TargetedMS folder type to 'Experimental Data'
08 May 2020 15:36:35,818 INFO : Updating the 'Raw Data' tab configuration
08 May 2020 15:36:35,821 INFO : Updating dataFileUrls for run Lilly pilot Ph1 batch 1 090218_2_2020-05-06_11-27-26.sky.zip; targetedms run ID 86598
08 May 2020 15:36:35,822 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,822 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26/Lilly%20pilot%20Ph1%20batch%201%20090218_2.skyd
08 May 2020 15:36:35,822 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26/Lilly%20pilot%20Ph1%20batch%201%20090218_2.skyd
08 May 2020 15:36:35,825 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,825 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84484/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26.sky.zip
08 May 2020 15:36:35,825 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%201%20090218_2_2020-05-06_11-27-26.sky.zip
08 May 2020 15:36:35,838 INFO : Updating dataFileUrls for run Lilly pilot Ph1 batch 2 083118_2_2020-05-06_12-14-03.sky.zip; targetedms run ID 86597
08 May 2020 15:36:35,838 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,838 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03/Lilly%20pilot%20Ph1%20batch%202%20083118_2.skyd
08 May 2020 15:36:35,839 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03/Lilly%20pilot%20Ph1%20batch%202%20083118_2.skyd
08 May 2020 15:36:35,842 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,842 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84485/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03.sky.zip
08 May 2020 15:36:35,842 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%202%20083118_2_2020-05-06_12-14-03.sky.zip
08 May 2020 15:36:35,847 INFO : Updating dataFileUrls for run Lilly pilot Ph1 batch 3 090418_2_2020-05-06_12-50-59.sky.zip; targetedms run ID 86596
08 May 2020 15:36:35,847 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,847 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59.sky.zip
08 May 2020 15:36:35,847 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59.sky.zip
08 May 2020 15:36:35,850 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,850 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84488/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59/Lilly%20pilot%20Ph1%20batch%203%20090418_2.skyd
08 May 2020 15:36:35,850 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/Lilly%20pilot%20Ph1%20batch%203%20090418_2_2020-05-06_12-50-59/Lilly%20pilot%20Ph1%20batch%203%20090418_2.skyd
08 May 2020 15:36:35,854 INFO : Updating dataFileUrls for run All targets Lilly pilot ph1B batch 1_2 011219_2_2020-05-06_14-47-39.sky.zip; targetedms run ID 86595
08 May 2020 15:36:35,854 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,854 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2.skyd
08 May 2020 15:36:35,855 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2.skyd
08 May 2020 15:36:35,857 INFO : Updating dataFileUrl...
08 May 2020 15:36:35,857 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer_e109921c-73a3-1038-92a8-3013bb9ba73d/_temp__2020-05-08_14-52-40/export/xar/experiments_and_runs.xar.exploded/Run84493/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39.sky.zip
08 May 2020 15:36:35,857 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/Protypia%20-%20Analysis%20of%20Immune%20Checkpoint%20Drug%20Targets%20and%20Tumor%20Proteotypes%20in%20Non-Small%20Cell%20Lung%20Cancer/@files/All%20targets%20Lilly%20pilot%20ph1B%20batch%201_2%20011219_2_2020-05-06_14-47-39.sky.zip
08 May 2020 15:36:35,975 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'