09 Jun 2020 10:52:18,832 INFO : Copying experiment "Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing" from folder /BayBioMS/Merits of proteomics for SARS-CoV2 research and testing to /Panorama Public/2020/BayBioMS - Merits of proteomics for SARS-CoV2 research and testing
09 Jun 2020 10:52:18,832 INFO : =======================================
09 Jun 2020 12:34:00,762 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
09 Jun 2020 12:34:00,772 INFO :
09 Jun 2020 12:34:00,772 INFO : Exporting experiment.
09 Jun 2020 12:51:15,402 INFO :
09 Jun 2020 12:51:15,416 INFO : Experiment export completed successfully.
09 Jun 2020 12:51:15,416 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
09 Jun 2020 13:02:52,588 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
09 Jun 2020 13:02:52,588 INFO :
09 Jun 2020 13:02:52,588 INFO : Importing experiment.
09 Jun 2020 13:02:52,686 INFO : Loading folder properties (folder type, settings and active modules)
09 Jun 2020 13:02:53,008 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jun 2020 13:02:53,028 INFO : Loading etl definitions
09 Jun 2020 13:02:53,035 INFO : Loading wikis
09 Jun 2020 13:02:53,181 INFO : 1 wiki imported
09 Jun 2020 13:02:53,181 INFO : Done importing wikis
09 Jun 2020 13:02:53,182 INFO : Starting to copy files
09 Jun 2020 13:02:59,601 INFO : Copied 8 files
09 Jun 2020 13:02:59,602 INFO : Ensuring exp.data rows exist for imported files
09 Jun 2020 13:03:00,021 INFO : Loading xar
09 Jun 2020 13:03:05,152 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-7162:Data%2C+reagents%2C+assays+and+merits+of+proteomics+for+SARS-CoV-2+research+and+testing'
09 Jun 2020 13:03:05,152 DEBUG: Experiment/Run group import complete
09 Jun 2020 13:03:05,153 INFO : Done importing xar
09 Jun 2020 13:03:05,160 INFO : Loading pages and webpart properties
09 Jun 2020 13:03:05,364 INFO : Done importing pages and webpart properties
09 Jun 2020 13:03:05,371 INFO : Loading subfolders and container tabs
09 Jun 2020 13:03:05,744 INFO : New container created with inherited permissions for Dilution series supernatant from SARS-CoV2-infected Vero E6 cells
09 Jun 2020 13:03:05,744 INFO : Loading folder archive for Dilution series supernatant from SARS-CoV2-infected Vero E6 cells
09 Jun 2020 13:03:05,751 INFO : Loading folder properties (folder type, settings and active modules)
09 Jun 2020 13:03:05,923 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jun 2020 13:03:05,930 INFO : Loading etl definitions
09 Jun 2020 13:03:05,936 INFO : Loading wikis
09 Jun 2020 13:03:05,960 INFO : 0 wikis imported
09 Jun 2020 13:03:05,960 INFO : Done importing wikis
09 Jun 2020 13:03:05,969 INFO : Starting to copy files
09 Jun 2020 13:04:45,548 INFO : Copied 31 files
09 Jun 2020 13:04:45,548 INFO : Ensuring exp.data rows exist for imported files
09 Jun 2020 13:04:46,176 INFO : Loading xar
09 Jun 2020 13:04:53,649 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip'
09 Jun 2020 13:04:53,654 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:04:53,659 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:04:53,659 DEBUG: Protocol import complete
09 Jun 2020 13:04:53,686 DEBUG: Protocol action set import complete
09 Jun 2020 13:04:53,740 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip'
09 Jun 2020 13:04:53,841 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7163:10e1ed34-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:04:53,852 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7163:10e1ecfd-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:04:53,852 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:04:53,858 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7163:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:04:53,859 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7163:10e1edb5-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:04:53,860 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow.skyd into the system
09 Jun 2020 13:04:53,862 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow.skyd into the system
09 Jun 2020 13:04:53,862 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29.sky.zip into the system
09 Jun 2020 13:04:53,872 INFO : Starting import from Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip
09 Jun 2020 13:04:53,881 INFO : Starting to import Skyline document from Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip
09 Jun 2020 13:04:53,884 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:04:56,788 INFO : Expanding Prosit_113SARS_plus_JPT_iRT_semitryptic.blib
09 Jun 2020 13:04:56,790 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.blib
09 Jun 2020 13:04:56,805 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:04:57,331 INFO : Expanding MaxQuant_DDA_113_SARS_Cov2_JPT_PepMix_099FDR_iRT.blib
09 Jun 2020 13:04:57,337 INFO : Expanding MaxQuant_DDA_113_SARS_Cov2_JPT_PepMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:04:57,392 INFO : Expanding Prosit_113_JPT_SARS_Cov2_PepMix_complete.blib
09 Jun 2020 13:04:57,394 INFO : Expanding Sky2 Dilution series SARS Cov2 nano and microflow.skyd
09 Jun 2020 13:04:57,495 INFO : Expanding Sky2 Dilution series SARS Cov2 nano and microflow.sky.view
09 Jun 2020 13:04:57,496 INFO : Expanding Sky2 Dilution series SARS Cov2 nano and microflow.sky
09 Jun 2020 13:04:57,505 INFO : Expanding Sky2 Dilution series SARS Cov2 nano and microflow.skyl
09 Jun 2020 13:04:57,522 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:04:57,524 INFO : 1% Done
09 Jun 2020 13:04:58,705 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:04:58,734 INFO : 5% Done
09 Jun 2020 13:04:59,252 INFO : 8% Done
09 Jun 2020 13:04:59,534 INFO : 11% Done
09 Jun 2020 13:04:59,863 INFO : 15% Done
09 Jun 2020 13:05:00,119 INFO : 18% Done
09 Jun 2020 13:05:00,319 INFO : 21% Done
09 Jun 2020 13:05:00,620 INFO : 25% Done
09 Jun 2020 13:05:00,918 INFO : 27% Done
09 Jun 2020 13:05:01,153 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:05:01,176 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:05:01,182 INFO : 31% Done
09 Jun 2020 13:05:01,441 INFO : 34% Done
09 Jun 2020 13:05:01,711 INFO : 38% Done
09 Jun 2020 13:05:02,005 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:05:02,059 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:05:02,065 INFO : 41% Done
09 Jun 2020 13:05:02,301 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:05:02,323 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:05:02,329 INFO : 45% Done
09 Jun 2020 13:05:02,573 INFO : 48% Done
09 Jun 2020 13:05:02,812 INFO : 52% Done
09 Jun 2020 13:05:03,046 INFO : 55% Done
09 Jun 2020 13:05:03,258 INFO : 56% Done
09 Jun 2020 13:05:03,382 INFO : 60% Done
09 Jun 2020 13:05:03,614 INFO : 63% Done
09 Jun 2020 13:05:03,887 DEBUG: Total peptides inserted: 7
09 Jun 2020 13:05:03,905 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:05:03,910 INFO : 66% Done
09 Jun 2020 13:05:04,152 INFO : 70% Done
09 Jun 2020 13:05:04,718 INFO : 73% Done
09 Jun 2020 13:05:04,943 INFO : 74% Done
09 Jun 2020 13:05:05,063 DEBUG: Total peptides inserted: 4
09 Jun 2020 13:05:05,063 INFO : Inserting Biognosys iRT peptide
09 Jun 2020 13:05:05,067 INFO : 76% Done
09 Jun 2020 13:05:05,165 INFO : 78% Done
09 Jun 2020 13:05:05,260 INFO : 80% Done
09 Jun 2020 13:05:05,352 INFO : 83% Done
09 Jun 2020 13:05:05,444 INFO : 85% Done
09 Jun 2020 13:05:05,536 INFO : 87% Done
09 Jun 2020 13:05:05,628 INFO : 89% Done
09 Jun 2020 13:05:05,720 INFO : 92% Done
09 Jun 2020 13:05:05,811 INFO : 94% Done
09 Jun 2020 13:05:05,903 INFO : 96% Done
09 Jun 2020 13:05:05,994 INFO : 98% Done
09 Jun 2020 13:05:06,083 DEBUG: Total peptides inserted: 11
09 Jun 2020 13:05:06,084 INFO : Done parsing Skyline document.
09 Jun 2020 13:05:10,819 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:05:10,911 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:05:11,140 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:05:11,233 INFO : Cleaning up temp tables
09 Jun 2020 13:05:11,714 INFO : Completed import of Skyline document from Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip
09 Jun 2020 13:05:11,716 INFO : 100% Done
09 Jun 2020 13:05:11,729 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29.sky.zip into the system
09 Jun 2020 13:05:11,769 INFO : Done importing xar
09 Jun 2020 13:05:11,776 INFO : Loading pages and webpart properties
09 Jun 2020 13:05:11,982 INFO : Done importing pages and webpart properties
09 Jun 2020 13:05:11,982 INFO : Done importing folder archive for Dilution series supernatant from SARS-CoV2-infected Vero E6 cells
09 Jun 2020 13:05:12,203 INFO : New container created with inherited permissions for Micro-flow 91 patient swab samples
09 Jun 2020 13:05:12,204 INFO : Loading folder archive for Micro-flow 91 patient swab samples
09 Jun 2020 13:05:12,211 INFO : Loading folder properties (folder type, settings and active modules)
09 Jun 2020 13:05:12,379 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jun 2020 13:05:12,386 INFO : Loading etl definitions
09 Jun 2020 13:05:12,392 INFO : Loading wikis
09 Jun 2020 13:05:12,415 INFO : 0 wikis imported
09 Jun 2020 13:05:12,416 INFO : Done importing wikis
09 Jun 2020 13:05:12,442 INFO : Starting to copy files
09 Jun 2020 13:07:14,559 INFO : 45 files copied, now copying 3974_BA8_COVID_PRM_P43835.raw
09 Jun 2020 13:09:16,689 INFO : 78 files copied, now copying 3976_BC4_COVID_PRM_P044022_R1.raw
09 Jun 2020 13:11:07,151 INFO : Copied 108 files
09 Jun 2020 13:11:07,152 INFO : Ensuring exp.data rows exist for imported files
09 Jun 2020 13:11:08,980 INFO : Loading xar
09 Jun 2020 13:11:20,062 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip'
09 Jun 2020 13:11:20,064 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:11:20,067 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:11:20,067 DEBUG: Protocol import complete
09 Jun 2020 13:11:20,083 DEBUG: Protocol action set import complete
09 Jun 2020 13:11:20,092 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip'
09 Jun 2020 13:11:20,115 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7164:57bd1c3e-842d-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,130 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7164:57bd19a0-842d-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,130 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:11:20,139 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:11:20,139 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7164:57bd1dd6-842d-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,144 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip'
09 Jun 2020 13:11:20,155 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7164:8faa7cf2-8428-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,160 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7164:47967dbf-8428-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,160 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:11:20,163 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7164:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:11:20,163 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7164:8faa7d99-8428-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:11:20,165 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41/Sky5%2091%20patients%20micro%20PRM-MS2%20raw.skyd into the system
09 Jun 2020 13:11:20,165 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41/Sky5%2091%20patients%20micro%20PRM-MS2%20raw.skyd into the system
09 Jun 2020 13:11:20,165 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41.sky.zip into the system
09 Jun 2020 13:11:20,167 INFO : Starting import from Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip
09 Jun 2020 13:11:20,172 INFO : Starting to import Skyline document from Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip
09 Jun 2020 13:11:20,210 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:11:24,160 INFO : Expanding MaxQuant_DDA_microflow_113_SARS_CoV2.blib
09 Jun 2020 13:11:24,169 INFO : Expanding Sky5 91 patients micro PRM-MS2 raw.skyd
09 Jun 2020 13:11:25,064 INFO : Expanding Sky5 91 patients micro PRM-MS2 raw.sky.view
09 Jun 2020 13:11:25,065 INFO : Expanding Sky5 91 patients micro PRM-MS2 raw.sky
09 Jun 2020 13:11:25,167 INFO : Expanding Sky5 91 patients micro PRM-MS2 raw.skyl
09 Jun 2020 13:11:25,215 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:11:25,222 INFO : 1% Done
09 Jun 2020 13:11:26,560 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:11:26,584 INFO : 5% Done
09 Jun 2020 13:11:28,169 INFO : 9% Done
09 Jun 2020 13:11:29,824 INFO : 13% Done
09 Jun 2020 13:11:31,185 INFO : 17% Done
09 Jun 2020 13:11:32,428 INFO : 21% Done
09 Jun 2020 13:11:33,847 INFO : 24% Done
09 Jun 2020 13:11:35,135 INFO : 28% Done
09 Jun 2020 13:11:36,706 INFO : 32% Done
09 Jun 2020 13:11:38,025 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:11:38,033 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:11:38,052 INFO : 35% Done
09 Jun 2020 13:11:39,333 INFO : 39% Done
09 Jun 2020 13:11:40,459 INFO : 43% Done
09 Jun 2020 13:11:41,752 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:11:41,760 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:11:41,778 INFO : 47% Done
09 Jun 2020 13:11:42,979 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:11:42,988 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:11:43,009 INFO : 51% Done
09 Jun 2020 13:11:44,329 INFO : 55% Done
09 Jun 2020 13:11:45,708 INFO : 59% Done
09 Jun 2020 13:11:46,834 INFO : 62% Done
09 Jun 2020 13:11:48,010 INFO : 66% Done
09 Jun 2020 13:11:49,318 INFO : 70% Done
09 Jun 2020 13:11:50,615 DEBUG: Total peptides inserted: 6
09 Jun 2020 13:11:50,622 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:11:50,643 INFO : 74% Done
09 Jun 2020 13:11:52,014 INFO : 78% Done
09 Jun 2020 13:11:53,336 INFO : 81% Done
09 Jun 2020 13:11:54,468 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:11:54,468 INFO : Inserting PROCAL Retention Time Standard Peptides
09 Jun 2020 13:11:54,481 INFO : 83% Done
09 Jun 2020 13:11:54,735 INFO : 84% Done
09 Jun 2020 13:11:54,999 INFO : 85% Done
09 Jun 2020 13:11:55,271 INFO : 86% Done
09 Jun 2020 13:11:55,544 INFO : 88% Done
09 Jun 2020 13:11:55,815 INFO : 89% Done
09 Jun 2020 13:11:56,087 INFO : 90% Done
09 Jun 2020 13:11:56,359 INFO : 92% Done
09 Jun 2020 13:11:56,631 INFO : 93% Done
09 Jun 2020 13:11:56,957 INFO : 94% Done
09 Jun 2020 13:11:57,257 INFO : 95% Done
09 Jun 2020 13:11:57,528 INFO : 97% Done
09 Jun 2020 13:11:57,817 INFO : 98% Done
09 Jun 2020 13:11:58,083 DEBUG: Total peptides inserted: 13
09 Jun 2020 13:11:58,083 INFO : Done parsing Skyline document.
09 Jun 2020 13:12:03,201 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:12:03,345 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:12:04,136 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:12:04,326 INFO : Cleaning up temp tables
09 Jun 2020 13:12:04,328 INFO : Completed import of Skyline document from Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip
09 Jun 2020 13:12:04,342 INFO : 100% Done
09 Jun 2020 13:12:04,350 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41.sky.zip into the system
09 Jun 2020 13:12:04,350 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined.skyd into the system
09 Jun 2020 13:12:04,352 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined.skyd into the system
09 Jun 2020 13:12:04,352 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04.sky.zip into the system
09 Jun 2020 13:12:04,355 INFO : Starting import from Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip
09 Jun 2020 13:12:04,361 INFO : Starting to import Skyline document from Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip
09 Jun 2020 13:12:04,371 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:12:08,002 INFO : Expanding MaxQuant_DDA_microflow_113_SARS_CoV2.blib
09 Jun 2020 13:12:08,012 INFO : Expanding Sky6 11 positive patients micro PRM-MS2 refined.skyd
09 Jun 2020 13:12:08,105 INFO : Expanding Sky6 11 positive patients micro PRM-MS2 refined.sky.view
09 Jun 2020 13:12:08,106 INFO : Expanding Sky6 11 positive patients micro PRM-MS2 refined.sky
09 Jun 2020 13:12:08,110 INFO : Expanding Sky6 11 positive patients micro PRM-MS2 refined.skyl
09 Jun 2020 13:12:08,133 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:12:08,135 INFO : 2% Done
09 Jun 2020 13:12:08,308 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:12:08,314 INFO : 5% Done
09 Jun 2020 13:12:08,429 INFO : 8% Done
09 Jun 2020 13:12:08,553 INFO : 13% Done
09 Jun 2020 13:12:08,708 INFO : 16% Done
09 Jun 2020 13:12:08,834 INFO : 20% Done
09 Jun 2020 13:12:08,998 INFO : 23% Done
09 Jun 2020 13:12:09,127 INFO : 26% Done
09 Jun 2020 13:12:09,262 INFO : 29% Done
09 Jun 2020 13:12:09,371 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:12:09,378 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:12:09,382 INFO : 33% Done
09 Jun 2020 13:12:09,518 INFO : 37% Done
09 Jun 2020 13:12:09,672 INFO : 40% Done
09 Jun 2020 13:12:09,818 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:12:09,818 INFO : 41% Done
09 Jun 2020 13:12:09,824 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:12:09,846 INFO : 44% Done
09 Jun 2020 13:12:09,994 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:12:10,002 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:12:10,006 INFO : 49% Done
09 Jun 2020 13:12:10,171 INFO : 53% Done
09 Jun 2020 13:12:10,339 INFO : 57% Done
09 Jun 2020 13:12:10,530 INFO : 61% Done
09 Jun 2020 13:12:10,683 INFO : 65% Done
09 Jun 2020 13:12:10,848 INFO : 69% Done
09 Jun 2020 13:12:10,995 DEBUG: Total peptides inserted: 6
09 Jun 2020 13:12:11,002 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:12:11,006 INFO : 73% Done
09 Jun 2020 13:12:11,154 INFO : 76% Done
09 Jun 2020 13:12:11,263 INFO : 79% Done
09 Jun 2020 13:12:11,372 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:12:11,373 INFO : Inserting PROCAL Retention Time Standard Peptides
09 Jun 2020 13:12:11,375 INFO : 80% Done
09 Jun 2020 13:12:11,415 INFO : 82% Done
09 Jun 2020 13:12:11,456 INFO : 83% Done
09 Jun 2020 13:12:11,497 INFO : 85% Done
09 Jun 2020 13:12:11,536 INFO : 86% Done
09 Jun 2020 13:12:11,575 INFO : 88% Done
09 Jun 2020 13:12:11,613 INFO : 89% Done
09 Jun 2020 13:12:11,653 INFO : 91% Done
09 Jun 2020 13:12:11,692 INFO : 92% Done
09 Jun 2020 13:12:11,732 INFO : 94% Done
09 Jun 2020 13:12:11,771 INFO : 95% Done
09 Jun 2020 13:12:11,810 INFO : 97% Done
09 Jun 2020 13:12:11,848 INFO : 98% Done
09 Jun 2020 13:12:11,886 DEBUG: Total peptides inserted: 13
09 Jun 2020 13:12:11,886 INFO : Done parsing Skyline document.
09 Jun 2020 13:12:17,638 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:12:17,671 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:12:17,779 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:12:17,829 INFO : Cleaning up temp tables
09 Jun 2020 13:12:18,612 INFO : Completed import of Skyline document from Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip
09 Jun 2020 13:12:18,614 INFO : 100% Done
09 Jun 2020 13:12:18,627 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04.sky.zip into the system
09 Jun 2020 13:12:18,653 INFO : Done importing xar
09 Jun 2020 13:12:18,660 INFO : Loading pages and webpart properties
09 Jun 2020 13:12:18,876 INFO : Done importing pages and webpart properties
09 Jun 2020 13:12:18,876 INFO : Done importing folder archive for Micro-flow 91 patient swab samples
09 Jun 2020 13:12:19,152 INFO : New container created with inherited permissions for Nano-flow 52 patient swab samples
09 Jun 2020 13:12:19,152 INFO : Loading folder archive for Nano-flow 52 patient swab samples
09 Jun 2020 13:12:19,159 INFO : Loading folder properties (folder type, settings and active modules)
09 Jun 2020 13:12:19,323 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jun 2020 13:12:19,329 INFO : Loading etl definitions
09 Jun 2020 13:12:19,335 INFO : Loading wikis
09 Jun 2020 13:12:19,347 INFO : 0 wikis imported
09 Jun 2020 13:12:19,348 INFO : Done importing wikis
09 Jun 2020 13:12:19,349 INFO : Starting to copy files
09 Jun 2020 13:14:23,774 INFO : 27 files copied, now copying BBM_284_P159_08_CHL_003.raw
09 Jun 2020 13:16:29,378 INFO : 42 files copied, now copying BBM_284_P159_08_CHL_061.raw
09 Jun 2020 13:18:34,161 INFO : 57 files copied, now copying BBM_284_P159_08_CHL_020.raw
09 Jun 2020 13:20:05,740 INFO : 68 files copied, now copying MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:20:10,844 INFO : Copied 76 files
09 Jun 2020 13:20:10,844 INFO : Ensuring exp.data rows exist for imported files
09 Jun 2020 13:20:11,717 INFO : Loading xar
09 Jun 2020 13:20:22,944 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip'
09 Jun 2020 13:20:22,950 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:20:22,955 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:20:22,955 DEBUG: Protocol import complete
09 Jun 2020 13:20:22,982 DEBUG: Protocol action set import complete
09 Jun 2020 13:20:23,005 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip'
09 Jun 2020 13:20:23,049 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7165:097fd510-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,062 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7165:097fd4a1-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,062 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:20:23,069 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:20:23,071 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7165:097fd53b-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,083 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip'
09 Jun 2020 13:20:23,096 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7165:097fb9ff-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,107 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7165:097fb9a5-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,107 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:20:23,114 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7165:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:20:23,115 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7165:097fbb08-842b-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:20:23,118 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined.skyd into the system
09 Jun 2020 13:20:23,119 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined.skyd into the system
09 Jun 2020 13:20:23,119 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02.sky.zip into the system
09 Jun 2020 13:20:23,123 INFO : Starting import from Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip
09 Jun 2020 13:20:23,147 INFO : Starting to import Skyline document from Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip
09 Jun 2020 13:20:23,151 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:20:26,454 INFO : Expanding Prosit_113_JPT_SARS_Cov2_PepMix_complete.blib
09 Jun 2020 13:20:26,456 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.blib
09 Jun 2020 13:20:26,471 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:20:27,002 INFO : Expanding Sky4 5 positive patients nano PRM-MS2 refined.skyd
09 Jun 2020 13:20:27,027 INFO : Expanding Sky4 5 positive patients nano PRM-MS2 refined.sky.view
09 Jun 2020 13:20:27,027 INFO : Expanding Sky4 5 positive patients nano PRM-MS2 refined.sky
09 Jun 2020 13:20:27,030 INFO : Expanding Sky4 5 positive patients nano PRM-MS2 refined.skyl
09 Jun 2020 13:20:27,045 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:20:27,046 INFO : 2% Done
09 Jun 2020 13:20:27,367 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:20:27,371 INFO : 6% Done
09 Jun 2020 13:20:27,419 INFO : 10% Done
09 Jun 2020 13:20:27,490 INFO : 14% Done
09 Jun 2020 13:20:27,542 INFO : 18% Done
09 Jun 2020 13:20:27,613 INFO : 22% Done
09 Jun 2020 13:20:27,660 INFO : 25% Done
09 Jun 2020 13:20:27,729 INFO : 28% Done
09 Jun 2020 13:20:27,845 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:20:27,846 INFO : 29% Done
09 Jun 2020 13:20:27,850 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:20:27,855 INFO : 33% Done
09 Jun 2020 13:20:27,920 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:20:27,920 INFO : 34% Done
09 Jun 2020 13:20:27,925 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:20:27,927 INFO : 37% Done
09 Jun 2020 13:20:27,971 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:20:27,976 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:20:27,978 INFO : 41% Done
09 Jun 2020 13:20:28,042 INFO : 45% Done
09 Jun 2020 13:20:28,095 INFO : 49% Done
09 Jun 2020 13:20:28,160 INFO : 53% Done
09 Jun 2020 13:20:28,211 INFO : 57% Done
09 Jun 2020 13:20:28,263 INFO : 60% Done
09 Jun 2020 13:20:28,302 DEBUG: Total peptides inserted: 7
09 Jun 2020 13:20:28,306 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:20:28,309 INFO : 64% Done
09 Jun 2020 13:20:28,363 INFO : 67% Done
09 Jun 2020 13:20:28,402 INFO : 70% Done
09 Jun 2020 13:20:28,442 INFO : 73% Done
09 Jun 2020 13:20:28,482 DEBUG: Total peptides inserted: 4
09 Jun 2020 13:20:28,482 INFO : 74% Done
09 Jun 2020 13:20:28,482 INFO : Inserting Biognosys iRT peptide
09 Jun 2020 13:20:28,484 INFO : 75% Done
09 Jun 2020 13:20:28,511 INFO : 77% Done
09 Jun 2020 13:20:28,532 INFO : 79% Done
09 Jun 2020 13:20:28,553 INFO : 82% Done
09 Jun 2020 13:20:28,573 INFO : 84% Done
09 Jun 2020 13:20:28,607 INFO : 87% Done
09 Jun 2020 13:20:28,628 INFO : 89% Done
09 Jun 2020 13:20:28,649 INFO : 91% Done
09 Jun 2020 13:20:28,669 INFO : 94% Done
09 Jun 2020 13:20:28,700 INFO : 96% Done
09 Jun 2020 13:20:28,720 INFO : 98% Done
09 Jun 2020 13:20:28,911 DEBUG: Total peptides inserted: 11
09 Jun 2020 13:20:28,911 INFO : Done parsing Skyline document.
09 Jun 2020 13:20:32,202 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:20:32,336 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:20:32,577 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:20:32,607 INFO : Cleaning up temp tables
09 Jun 2020 13:20:32,615 INFO : Completed import of Skyline document from Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip
09 Jun 2020 13:20:32,617 INFO : 100% Done
09 Jun 2020 13:20:32,627 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02.sky.zip into the system
09 Jun 2020 13:20:32,627 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21/Sky3%2052%20patients%20nano%20PRM-MS2%20raw.skyd into the system
09 Jun 2020 13:20:32,628 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21/Sky3%2052%20patients%20nano%20PRM-MS2%20raw.skyd into the system
09 Jun 2020 13:20:32,628 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21.sky.zip into the system
09 Jun 2020 13:20:32,632 INFO : Starting import from Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip
09 Jun 2020 13:20:32,638 INFO : Starting to import Skyline document from Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip
09 Jun 2020 13:20:32,651 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:20:35,695 INFO : Expanding Prosit_113_JPT_SARS_Cov2_PepMix_complete.blib
09 Jun 2020 13:20:35,697 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.blib
09 Jun 2020 13:20:35,713 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:20:36,287 INFO : Expanding Sky3 52 patients nano PRM-MS2 raw.skyd
09 Jun 2020 13:20:36,579 INFO : Expanding Sky3 52 patients nano PRM-MS2 raw.sky.view
09 Jun 2020 13:20:36,580 INFO : Expanding Sky3 52 patients nano PRM-MS2 raw.sky
09 Jun 2020 13:20:36,614 INFO : Expanding Sky3 52 patients nano PRM-MS2 raw.skyl
09 Jun 2020 13:20:36,629 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:20:36,632 INFO : 1% Done
09 Jun 2020 13:20:37,111 INFO : Calculated iRT regression line from full standard list.
09 Jun 2020 13:20:37,311 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:20:37,319 INFO : 4% Done
09 Jun 2020 13:20:37,829 INFO : 8% Done
09 Jun 2020 13:20:38,301 INFO : 11% Done
09 Jun 2020 13:20:38,695 INFO : 15% Done
09 Jun 2020 13:20:39,075 INFO : 18% Done
09 Jun 2020 13:20:39,431 INFO : 22% Done
09 Jun 2020 13:20:39,775 INFO : 25% Done
09 Jun 2020 13:20:40,213 INFO : 28% Done
09 Jun 2020 13:20:40,560 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:20:40,564 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:20:40,570 INFO : 31% Done
09 Jun 2020 13:20:40,958 INFO : 35% Done
09 Jun 2020 13:20:41,347 INFO : 38% Done
09 Jun 2020 13:20:41,736 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:20:41,739 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:20:41,745 INFO : 42% Done
09 Jun 2020 13:20:42,117 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:20:42,122 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:20:42,128 INFO : 45% Done
09 Jun 2020 13:20:42,470 INFO : 49% Done
09 Jun 2020 13:20:42,810 INFO : 52% Done
09 Jun 2020 13:20:43,134 INFO : 55% Done
09 Jun 2020 13:20:43,513 INFO : 59% Done
09 Jun 2020 13:20:43,889 INFO : 62% Done
09 Jun 2020 13:20:44,293 INFO : 66% Done
09 Jun 2020 13:20:44,634 DEBUG: Total peptides inserted: 7
09 Jun 2020 13:20:44,637 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:20:44,642 INFO : 69% Done
09 Jun 2020 13:20:45,000 INFO : 73% Done
09 Jun 2020 13:20:45,343 INFO : 75% Done
09 Jun 2020 13:20:45,689 INFO : 78% Done
09 Jun 2020 13:20:46,011 DEBUG: Total peptides inserted: 4
09 Jun 2020 13:20:46,011 INFO : Inserting Biognosys iRT peptide
09 Jun 2020 13:20:46,014 INFO : 80% Done
09 Jun 2020 13:20:46,121 INFO : 82% Done
09 Jun 2020 13:20:46,240 INFO : 84% Done
09 Jun 2020 13:20:46,343 INFO : 86% Done
09 Jun 2020 13:20:46,452 INFO : 87% Done
09 Jun 2020 13:20:46,556 INFO : 89% Done
09 Jun 2020 13:20:46,661 INFO : 91% Done
09 Jun 2020 13:20:46,766 INFO : 93% Done
09 Jun 2020 13:20:46,886 INFO : 94% Done
09 Jun 2020 13:20:46,993 INFO : 96% Done
09 Jun 2020 13:20:47,105 INFO : 98% Done
09 Jun 2020 13:20:47,208 DEBUG: Total peptides inserted: 11
09 Jun 2020 13:20:47,208 INFO : Done parsing Skyline document.
09 Jun 2020 13:20:50,112 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:20:50,154 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:20:50,420 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:20:50,624 INFO : Cleaning up temp tables
09 Jun 2020 13:20:50,959 INFO : Completed import of Skyline document from Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip
09 Jun 2020 13:20:50,961 INFO : 100% Done
09 Jun 2020 13:20:50,971 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21.sky.zip into the system
09 Jun 2020 13:20:50,994 INFO : Done importing xar
09 Jun 2020 13:20:51,058 INFO : Loading pages and webpart properties
09 Jun 2020 13:20:51,269 INFO : Done importing pages and webpart properties
09 Jun 2020 13:20:51,269 INFO : Done importing folder archive for Nano-flow 52 patient swab samples
09 Jun 2020 13:20:51,494 INFO : New container created with inherited permissions for Synthetic SARS-CoV2 peptide mix (98 PRM assays)
09 Jun 2020 13:20:51,494 INFO : Loading folder archive for Synthetic SARS-CoV2 peptide mix (98 PRM assays)
09 Jun 2020 13:20:51,500 INFO : Loading folder properties (folder type, settings and active modules)
09 Jun 2020 13:20:51,624 INFO : Done importing folder properties (folder type, settings and active modules)
09 Jun 2020 13:20:51,629 INFO : Loading etl definitions
09 Jun 2020 13:20:51,634 INFO : Loading wikis
09 Jun 2020 13:20:51,660 INFO : 0 wikis imported
09 Jun 2020 13:20:51,660 INFO : Done importing wikis
09 Jun 2020 13:20:51,681 INFO : Starting to copy files
09 Jun 2020 13:21:44,474 INFO : Copied 21 files
09 Jun 2020 13:21:44,474 INFO : Ensuring exp.data rows exist for imported files
09 Jun 2020 13:21:44,769 INFO : Loading xar
09 Jun 2020 13:21:56,017 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip'
09 Jun 2020 13:21:56,020 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:21:56,023 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:21:56,023 DEBUG: Protocol import complete
09 Jun 2020 13:21:56,037 DEBUG: Protocol action set import complete
09 Jun 2020 13:21:56,057 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip'
09 Jun 2020 13:21:56,074 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-7166:10e1f2a2-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:21:56,080 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-7166:10e1f200-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:21:56,080 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip.Core'
09 Jun 2020 13:21:56,084 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-7166:TargetedMS.ImportSkyZip.Output'
09 Jun 2020 13:21:56,084 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-7166:10e1f362-8429-1038-9976-3013bb9ba8d4'
09 Jun 2020 13:21:56,086 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library.skyd into the system
09 Jun 2020 13:21:56,087 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library.skyd into the system
09 Jun 2020 13:21:56,087 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22.sky.zip into the system
09 Jun 2020 13:21:56,089 INFO : Starting import from Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip
09 Jun 2020 13:21:56,094 INFO : Starting to import Skyline document from Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip
09 Jun 2020 13:21:56,149 INFO : Expanding Human_plus_SARS_COV_2.protdb
09 Jun 2020 13:21:59,058 INFO : Expanding Prosit_113_SARS_Cov2_JPT_peptideMix_iRTs.blib
09 Jun 2020 13:21:59,059 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.blib
09 Jun 2020 13:21:59,074 INFO : Expanding MaxQuant_PRM_113_SARS_Cov2_JPT_peptideMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:21:59,625 INFO : Expanding MaxQuant_DDA_113_SARS_Cov2_JPT_PepMix_099FDR_iRT.blib
09 Jun 2020 13:21:59,631 INFO : Expanding MaxQuant_DDA_113_SARS_Cov2_JPT_PepMix_099FDR_iRT.redundant.blib
09 Jun 2020 13:21:59,687 INFO : Expanding Prosit_113_JPT_SARS_Cov2_PepMix_complete.blib
09 Jun 2020 13:21:59,689 INFO : Expanding Sky1 Synthetic SARS-CoV2 proteome library.skyd
09 Jun 2020 13:22:01,638 INFO : Expanding Sky1 Synthetic SARS-CoV2 proteome library.sky.view
09 Jun 2020 13:22:01,638 INFO : Expanding Sky1 Synthetic SARS-CoV2 proteome library.sky
09 Jun 2020 13:22:01,641 INFO : Expanding Sky1 Synthetic SARS-CoV2 proteome library.skyl
09 Jun 2020 13:22:01,648 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
09 Jun 2020 13:22:01,650 INFO : 4% Done
09 Jun 2020 13:22:02,169 INFO : 6% Done
09 Jun 2020 13:22:02,174 INFO : Inserting sp|P0DTC2|SPIKE_WCPV
09 Jun 2020 13:22:02,256 INFO : 7% Done
09 Jun 2020 13:22:02,322 INFO : 8% Done
09 Jun 2020 13:22:02,368 INFO : 9% Done
09 Jun 2020 13:22:02,384 INFO : 10% Done
09 Jun 2020 13:22:02,412 INFO : 11% Done
09 Jun 2020 13:22:02,451 INFO : 12% Done
09 Jun 2020 13:22:02,478 INFO : 13% Done
09 Jun 2020 13:22:02,508 INFO : 14% Done
09 Jun 2020 13:22:02,556 INFO : 15% Done
09 Jun 2020 13:22:02,584 INFO : 16% Done
09 Jun 2020 13:22:02,616 INFO : 17% Done
09 Jun 2020 13:22:02,647 INFO : 18% Done
09 Jun 2020 13:22:02,678 INFO : 19% Done
09 Jun 2020 13:22:02,694 INFO : 20% Done
09 Jun 2020 13:22:02,758 INFO : 21% Done
09 Jun 2020 13:22:02,774 INFO : 22% Done
09 Jun 2020 13:22:02,790 INFO : 23% Done
09 Jun 2020 13:22:02,835 INFO : 24% Done
09 Jun 2020 13:22:02,910 INFO : 25% Done
09 Jun 2020 13:22:02,972 INFO : 26% Done
09 Jun 2020 13:22:03,001 INFO : 27% Done
09 Jun 2020 13:22:03,017 INFO : 28% Done
09 Jun 2020 13:22:03,064 INFO : 29% Done
09 Jun 2020 13:22:03,096 INFO : 30% Done
09 Jun 2020 13:22:03,127 INFO : 31% Done
09 Jun 2020 13:22:03,207 INFO : 32% Done
09 Jun 2020 13:22:03,224 INFO : 33% Done
09 Jun 2020 13:22:03,224 DEBUG: Inserted 50 peptides
09 Jun 2020 13:22:03,241 INFO : 34% Done
09 Jun 2020 13:22:03,275 INFO : 35% Done
09 Jun 2020 13:22:03,309 INFO : 36% Done
09 Jun 2020 13:22:03,339 INFO : 37% Done
09 Jun 2020 13:22:03,425 DEBUG: Total peptides inserted: 58
09 Jun 2020 13:22:03,425 INFO : 38% Done
09 Jun 2020 13:22:03,440 INFO : Inserting sp|P0DTC9|NCAP_WCPV
09 Jun 2020 13:22:03,471 INFO : 39% Done
09 Jun 2020 13:22:03,488 INFO : 40% Done
09 Jun 2020 13:22:03,594 INFO : 41% Done
09 Jun 2020 13:22:03,630 INFO : 42% Done
09 Jun 2020 13:22:03,662 INFO : 43% Done
09 Jun 2020 13:22:03,693 INFO : 44% Done
09 Jun 2020 13:22:03,768 INFO : 45% Done
09 Jun 2020 13:22:03,786 INFO : 46% Done
09 Jun 2020 13:22:03,833 INFO : 47% Done
09 Jun 2020 13:22:03,867 INFO : 48% Done
09 Jun 2020 13:22:03,898 INFO : 49% Done
09 Jun 2020 13:22:03,940 INFO : 50% Done
09 Jun 2020 13:22:03,989 INFO : 51% Done
09 Jun 2020 13:22:04,064 INFO : 52% Done
09 Jun 2020 13:22:04,080 INFO : 53% Done
09 Jun 2020 13:22:04,141 DEBUG: Total peptides inserted: 29
09 Jun 2020 13:22:04,146 INFO : Inserting sp|P0DTC5|VME1_WCPV
09 Jun 2020 13:22:04,147 INFO : 54% Done
09 Jun 2020 13:22:04,164 INFO : 55% Done
09 Jun 2020 13:22:04,197 INFO : 56% Done
09 Jun 2020 13:22:04,247 INFO : 57% Done
09 Jun 2020 13:22:04,281 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:22:04,281 INFO : 58% Done
09 Jun 2020 13:22:04,285 INFO : Inserting sp|P0DTD2|ORF9B_WCPV
09 Jun 2020 13:22:04,304 INFO : 59% Done
09 Jun 2020 13:22:04,340 INFO : 60% Done
09 Jun 2020 13:22:04,375 INFO : 61% Done
09 Jun 2020 13:22:04,392 INFO : 62% Done
09 Jun 2020 13:22:04,472 INFO : 63% Done
09 Jun 2020 13:22:04,507 DEBUG: Total peptides inserted: 11
09 Jun 2020 13:22:04,540 INFO : Inserting sp|P0DTC3|AP3A_WCPV
09 Jun 2020 13:22:04,542 INFO : 64% Done
09 Jun 2020 13:22:04,559 INFO : 65% Done
09 Jun 2020 13:22:04,606 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:22:04,618 INFO : Inserting sp|P0DTC4|VEMP_WCPV
09 Jun 2020 13:22:04,638 DEBUG: Total peptides inserted: 1
09 Jun 2020 13:22:04,662 INFO : Inserting sp|P0DTC6|NS6_WCPV
09 Jun 2020 13:22:04,666 INFO : 66% Done
09 Jun 2020 13:22:04,690 INFO : 67% Done
09 Jun 2020 13:22:04,723 INFO : 68% Done
09 Jun 2020 13:22:04,739 DEBUG: Total peptides inserted: 8
09 Jun 2020 13:22:04,758 INFO : Inserting sp|P0DTC7|NS7A_WCPV
09 Jun 2020 13:22:04,779 INFO : 69% Done
09 Jun 2020 13:22:04,813 DEBUG: Total peptides inserted: 4
09 Jun 2020 13:22:04,813 INFO : 70% Done
09 Jun 2020 13:22:04,817 INFO : Inserting sp|P0DTC8|NS8_WCPV
09 Jun 2020 13:22:04,850 INFO : 71% Done
09 Jun 2020 13:22:04,897 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:22:04,909 INFO : Inserting tr|A0A663DJA2|A0A663DJA2_9BETC
09 Jun 2020 13:22:04,932 INFO : 72% Done
09 Jun 2020 13:22:04,937 INFO : 73% Done
09 Jun 2020 13:22:04,953 DEBUG: Total peptides inserted: 4
09 Jun 2020 13:22:04,967 INFO : Inserting sp|P0DTD3|Y14_WCPV
09 Jun 2020 13:22:04,987 INFO : 74% Done
09 Jun 2020 13:22:05,018 DEBUG: Total peptides inserted: 3
09 Jun 2020 13:22:05,019 INFO : Inserting Biognosys iRT peptide
09 Jun 2020 13:22:05,020 INFO : 76% Done
09 Jun 2020 13:22:05,066 INFO : 78% Done
09 Jun 2020 13:22:05,103 INFO : 80% Done
09 Jun 2020 13:22:05,144 INFO : 83% Done
09 Jun 2020 13:22:05,181 INFO : 85% Done
09 Jun 2020 13:22:05,218 INFO : 87% Done
09 Jun 2020 13:22:05,254 INFO : 89% Done
09 Jun 2020 13:22:05,290 INFO : 92% Done
09 Jun 2020 13:22:05,326 INFO : 94% Done
09 Jun 2020 13:22:05,361 INFO : 96% Done
09 Jun 2020 13:22:05,397 INFO : 98% Done
09 Jun 2020 13:22:05,440 DEBUG: Total peptides inserted: 11
09 Jun 2020 13:22:05,440 INFO : Done parsing Skyline document.
09 Jun 2020 13:22:05,903 INFO : Creating and populating temp tables for Proportion values
09 Jun 2020 13:22:05,918 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Jun 2020 13:22:05,936 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Jun 2020 13:22:05,949 INFO : Cleaning up temp tables
09 Jun 2020 13:22:06,314 INFO : Completed import of Skyline document from Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip
09 Jun 2020 13:22:06,315 INFO : 100% Done
09 Jun 2020 13:22:06,322 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22.sky.zip into the system
09 Jun 2020 13:22:06,330 INFO : Done importing xar
09 Jun 2020 13:22:06,334 INFO : Loading pages and webpart properties
09 Jun 2020 13:22:06,698 INFO : Done importing pages and webpart properties
09 Jun 2020 13:22:06,699 INFO : Done importing folder archive for Synthetic SARS-CoV2 peptide mix (98 PRM assays)
09 Jun 2020 13:22:06,699 INFO : Done importing subfolders and container tabs
09 Jun 2020 13:22:06,699 INFO :
09 Jun 2020 13:22:06,699 INFO : Experiment import completed successfully.
09 Jun 2020 13:22:06,699 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
09 Jun 2020 13:28:27,088 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
09 Jun 2020 13:28:27,089 INFO :
09 Jun 2020 13:28:27,089 INFO : Finishing up experiment copy.
09 Jun 2020 13:28:27,095 INFO : Adding runs imported in subfolders.
09 Jun 2020 13:28:27,134 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
09 Jun 2020 13:28:27,229 INFO : Updating access URL to point to the new copy of the data.
09 Jun 2020 13:28:27,325 INFO : Setting the 'copied' timestamp on the JournalExperiment table.
09 Jun 2020 13:28:27,342 INFO : Removing copy permissions given to journal.
09 Jun 2020 13:28:27,559 INFO : Adding read permissions to all users that are folder admins in the source container.
09 Jun 2020 13:28:27,571 INFO : Setting the TargetedMS folder type to 'Experimental Data'
09 Jun 2020 13:28:27,615 INFO : Updating the 'Raw Data' tab configuration
09 Jun 2020 13:28:27,631 INFO : Updating dataFileUrls for run Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip; targetedms run ID 88788
09 Jun 2020 13:28:27,631 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,631 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29.sky.zip
09 Jun 2020 13:28:27,631 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/@files/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29.sky.zip
09 Jun 2020 13:28:27,638 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,638 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/xar/experiments_and_runs.xar.exploded/Run86330/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow.skyd
09 Jun 2020 13:28:27,638 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Dilution%20series%20supernatant%20from%20SARS-CoV2-infected%20Vero%20E6%20cells/@files/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow_2020-05-30_00-30-29/Sky2%20Dilution%20series%20SARS%20Cov2%20nano%20and%20microflow.skyd
09 Jun 2020 13:28:27,654 INFO : Updating dataFileUrls for run Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip; targetedms run ID 88790
09 Jun 2020 13:28:27,655 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,655 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04.sky.zip
09 Jun 2020 13:28:27,655 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Micro-flow%2091%20patient%20swab%20samples/@files/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04.sky.zip
09 Jun 2020 13:28:27,660 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,660 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86328/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined.skyd
09 Jun 2020 13:28:27,660 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Micro-flow%2091%20patient%20swab%20samples/@files/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined_2020-05-30_00-19-04/Sky6%2011%20positive%20patients%20micro%20PRM-MS2%20refined.skyd
09 Jun 2020 13:28:27,673 INFO : Updating dataFileUrls for run Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip; targetedms run ID 88789
09 Jun 2020 13:28:27,674 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,674 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41.sky.zip
09 Jun 2020 13:28:27,674 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Micro-flow%2091%20patient%20swab%20samples/@files/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41.sky.zip
09 Jun 2020 13:28:27,679 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,679 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Micro-flow%2091%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86335/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41/Sky5%2091%20patients%20micro%20PRM-MS2%20raw.skyd
09 Jun 2020 13:28:27,679 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Micro-flow%2091%20patient%20swab%20samples/@files/Sky5%2091%20patients%20micro%20PRM-MS2%20raw_2020-05-30_00-57-41/Sky5%2091%20patients%20micro%20PRM-MS2%20raw.skyd
09 Jun 2020 13:28:27,686 INFO : Updating dataFileUrls for run Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip; targetedms run ID 88792
09 Jun 2020 13:28:27,686 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,687 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21/Sky3%2052%20patients%20nano%20PRM-MS2%20raw.skyd
09 Jun 2020 13:28:27,687 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Nano-flow%2052%20patient%20swab%20samples/@files/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21/Sky3%2052%20patients%20nano%20PRM-MS2%20raw.skyd
09 Jun 2020 13:28:27,691 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,691 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86332/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21.sky.zip
09 Jun 2020 13:28:27,691 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Nano-flow%2052%20patient%20swab%20samples/@files/Sky3%2052%20patients%20nano%20PRM-MS2%20raw_2020-05-30_00-38-21.sky.zip
09 Jun 2020 13:28:27,704 INFO : Updating dataFileUrls for run Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip; targetedms run ID 88791
09 Jun 2020 13:28:27,705 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,705 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined.skyd
09 Jun 2020 13:28:27,705 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Nano-flow%2052%20patient%20swab%20samples/@files/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined.skyd
09 Jun 2020 13:28:27,709 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,709 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Nano-flow%2052%20patient%20swab%20samples/xar/experiments_and_runs.xar.exploded/Run86333/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02.sky.zip
09 Jun 2020 13:28:27,710 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Nano-flow%2052%20patient%20swab%20samples/@files/Sky4%205%20positive%20patients%20nano%20PRM-MS2%20refined_2020-05-30_00-52-02.sky.zip
09 Jun 2020 13:28:27,717 INFO : Updating dataFileUrls for run Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip; targetedms run ID 88793
09 Jun 2020 13:28:27,717 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,717 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22.sky.zip
09 Jun 2020 13:28:27,717 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/@files/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22.sky.zip
09 Jun 2020 13:28:27,722 INFO : Updating dataFileUrl...
09 Jun 2020 13:28:27,722 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing_ccd16db4-8ca6-1038-9976-3013bb9ba8d4/_temp__2020-06-09_10-52-18/export/subfolders/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/xar/experiments_and_runs.xar.exploded/Run86331/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library.skyd
09 Jun 2020 13:28:27,722 INFO : to: file:///data/labkey/files/Panorama%20Public/2020/BayBioMS%20-%20Merits%20of%20proteomics%20for%20SARS-CoV2%20research%20and%20testing/Synthetic%20SARS-CoV2%20peptide%20mix%20(98%20PRM%20assays)/@files/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library_2020-05-30_00-33-22/Sky1%20Synthetic%20SARS-CoV2%20proteome%20library.skyd
09 Jun 2020 13:28:27,735 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'