03 May 2021 07:17:16,870 INFO : Copying experiment "C.auto_3gas_absquant: Anchor protein absolute quantification" from folder /U of Tartu - GasFermTEC/C.auto_3gas_absquant/Anchors to /Panorama Public/2021/U of Tartu GasFermTEC - Anchors
03 May 2021 07:17:16,870 INFO : =======================================
03 May 2021 07:17:16,982 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
03 May 2021 07:17:16,982 INFO :
03 May 2021 07:17:16,982 INFO : Exporting experiment.
03 May 2021 07:18:41,974 INFO :
03 May 2021 07:18:41,974 INFO : Experiment export completed successfully.
03 May 2021 07:18:41,974 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
03 May 2021 07:18:42,017 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
03 May 2021 07:18:42,017 INFO :
03 May 2021 07:18:42,017 INFO : Importing experiment.
03 May 2021 07:18:42,048 INFO : Loading folder properties (folder type, settings and active modules)
03 May 2021 07:18:42,144 INFO : Done importing folder properties (folder type, settings and active modules)
03 May 2021 07:18:42,148 INFO : Loading etl definitions
03 May 2021 07:18:42,152 INFO : Loading wikis
03 May 2021 07:18:42,162 INFO : 1 wiki imported
03 May 2021 07:18:42,162 INFO : Done importing wikis
03 May 2021 07:18:42,162 INFO : Starting to copy files
03 May 2021 07:18:57,206 INFO : Copied 8 files
03 May 2021 07:18:57,206 INFO : Ensuring exp.data rows exist for imported files
03 May 2021 07:18:57,324 INFO : Starting Sample Type and Data Class import
03 May 2021 07:18:57,325 INFO : No types XAR file to process.
03 May 2021 07:18:57,326 INFO : Finished importing Sample Types and Data Classes
03 May 2021 07:18:57,328 INFO : Loading xar
03 May 2021 07:19:05,575 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip'
03 May 2021 07:19:05,580 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip.Core'
03 May 2021 07:19:05,585 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip.Output'
03 May 2021 07:19:05,585 DEBUG: Protocol import complete
03 May 2021 07:19:05,644 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8471:C.auto_3gas_absquant%3A+Anchor+protein+absolute+quantification'
03 May 2021 07:19:05,644 DEBUG: Experiment/Run group import complete
03 May 2021 07:19:05,673 DEBUG: Protocol action set import complete
03 May 2021 07:19:05,700 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip'
03 May 2021 07:19:05,704 WARN : Unrecognized CpasType 'urn:lsid:uw.edu:.Folder-8461:' loaded for Data object.
03 May 2021 07:19:05,722 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8471:96d1b582-e546-1038-9455-3013bb9b8170'
03 May 2021 07:19:05,723 WARN : Unrecognized CpasType 'urn:lsid:uw.edu:.Folder-8461:' loaded for Data object.
03 May 2021 07:19:05,730 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8471:25b674a1-e542-1038-9455-3013bb9b8170'
03 May 2021 07:19:05,730 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip.Core'
03 May 2021 07:19:05,733 WARN : Unrecognized CpasType 'urn:lsid:uw.edu:.Folder-8461:' loaded for Data object.
03 May 2021 07:19:05,735 WARN : Unrecognized CpasType 'urn:lsid:uw.edu:.Folder-8461:' loaded for Data object.
03 May 2021 07:19:05,736 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8471:TargetedMS.ImportSkyZip.Output'
03 May 2021 07:19:05,738 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8471:5a50dbcb-e54b-1038-9455-3013bb9b8170'
03 May 2021 07:19:05,740 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd into the system
03 May 2021 07:19:05,741 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd into the system
03 May 2021 07:19:05,741 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14.sky.zip into the system
03 May 2021 07:19:05,743 INFO : Starting import from SILP CO, syngas, highH2, DS_qbelow0.01_2020-09-30_22-02-14.sky.zip
03 May 2021 07:19:05,748 INFO : Starting to import Skyline document from SILP CO, syngas, highH2, DS_qbelow0.01_2020-09-30_22-02-14.sky.zip
03 May 2021 07:19:05,748 INFO : Expanding Abs quant iRT2.irtdb
03 May 2021 07:19:05,772 INFO : Expanding Abs_quant_study.blib
03 May 2021 07:19:07,118 INFO : Expanding SILP CO, syngas, highH2, DS_qbelow0.01.skyd
03 May 2021 07:19:11,252 INFO : Expanding SILP CO, syngas, highH2, DS_qbelow0.01.sky.view
03 May 2021 07:19:11,253 INFO : Expanding SILP CO, syngas, highH2, DS_qbelow0.01.sky
03 May 2021 07:19:18,368 DEBUG: Starting to load chromatogram headers
03 May 2021 07:19:18,436 DEBUG: Done loading chromatogram headers
03 May 2021 07:19:23,447 INFO : Inserting CAETHG_RS14890
03 May 2021 07:19:24,051 INFO : 1% Done
03 May 2021 07:19:25,767 INFO : 2% Done
03 May 2021 07:19:27,062 INFO : 3% Done
03 May 2021 07:19:28,429 INFO : 4% Done
03 May 2021 07:19:29,180 DEBUG: Inserted 50 peptides
03 May 2021 07:19:29,706 INFO : 5% Done
03 May 2021 07:19:30,980 INFO : 6% Done
03 May 2021 07:19:32,199 INFO : 7% Done
03 May 2021 07:19:32,369 DEBUG: Total peptides inserted: 79
03 May 2021 07:19:32,371 INFO : Inserting CAETHG_RS07850
03 May 2021 07:19:33,239 INFO : 8% Done
03 May 2021 07:19:34,318 INFO : 9% Done
03 May 2021 07:19:35,453 INFO : 10% Done
03 May 2021 07:19:36,340 INFO : 11% Done
03 May 2021 07:19:36,950 DEBUG: Total peptides inserted: 44
03 May 2021 07:19:36,952 INFO : Inserting CAETHG_RS00440
03 May 2021 07:19:37,247 INFO : 12% Done
03 May 2021 07:19:38,542 INFO : 13% Done
03 May 2021 07:19:39,756 INFO : 14% Done
03 May 2021 07:19:40,678 INFO : 15% Done
03 May 2021 07:19:41,753 INFO : 16% Done
03 May 2021 07:19:42,040 DEBUG: Total peptides inserted: 46
03 May 2021 07:19:42,043 INFO : Inserting CAETHG_RS07815
03 May 2021 07:19:43,088 INFO : 17% Done
03 May 2021 07:19:44,071 INFO : 18% Done
03 May 2021 07:19:45,238 INFO : 19% Done
03 May 2021 07:19:45,336 DEBUG: Total peptides inserted: 28
03 May 2021 07:19:45,338 INFO : Inserting CAETHG_RS13725
03 May 2021 07:19:45,614 INFO : 20% Done
03 May 2021 07:19:46,005 INFO : 21% Done
03 May 2021 07:19:46,273 DEBUG: Total peptides inserted: 22
03 May 2021 07:19:46,275 INFO : Inserting CAETHG_RS16495
03 May 2021 07:19:46,308 INFO : 22% Done
03 May 2021 07:19:46,736 INFO : 23% Done
03 May 2021 07:19:47,136 DEBUG: Total peptides inserted: 22
03 May 2021 07:19:47,139 INFO : Inserting CAETHG_RS16490
03 May 2021 07:19:47,148 INFO : 24% Done
03 May 2021 07:19:47,413 INFO : 25% Done
03 May 2021 07:19:47,824 DEBUG: Total peptides inserted: 19
03 May 2021 07:19:47,826 INFO : Inserting CAETHG_RS13765
03 May 2021 07:19:48,285 INFO : 26% Done
03 May 2021 07:19:48,564 INFO : 27% Done
03 May 2021 07:19:48,851 DEBUG: Total peptides inserted: 27
03 May 2021 07:19:48,854 INFO : Inserting CAETHG_RS01830
03 May 2021 07:19:48,954 INFO : 28% Done
03 May 2021 07:19:49,370 INFO : 29% Done
03 May 2021 07:19:49,701 DEBUG: Total peptides inserted: 22
03 May 2021 07:19:49,703 INFO : Inserting CAETHG_RS00580
03 May 2021 07:19:49,824 INFO : 30% Done
03 May 2021 07:19:50,175 INFO : 31% Done
03 May 2021 07:19:50,214 DEBUG: Total peptides inserted: 16
03 May 2021 07:19:50,216 INFO : Inserting CAETHG_RS07840
03 May 2021 07:19:50,479 INFO : 32% Done
03 May 2021 07:19:50,743 DEBUG: Total peptides inserted: 13
03 May 2021 07:19:50,744 INFO : Inserting CAETHG_RS07830
03 May 2021 07:19:50,851 INFO : 33% Done
03 May 2021 07:19:51,205 INFO : 34% Done
03 May 2021 07:19:51,319 DEBUG: Total peptides inserted: 15
03 May 2021 07:19:51,321 INFO : Inserting CAETHG_RS02630
03 May 2021 07:19:51,633 INFO : 35% Done
03 May 2021 07:19:51,815 DEBUG: Total peptides inserted: 12
03 May 2021 07:19:51,816 INFO : Inserting CAETHG_RS07845
03 May 2021 07:19:52,053 INFO : 36% Done
03 May 2021 07:19:52,190 DEBUG: Total peptides inserted: 11
03 May 2021 07:19:52,193 INFO : Inserting CAETHG_RS09495
03 May 2021 07:19:52,540 INFO : 37% Done
03 May 2021 07:19:52,638 DEBUG: Total peptides inserted: 11
03 May 2021 07:19:52,640 INFO : Inserting CAETHG_RS00590
03 May 2021 07:19:53,058 INFO : 38% Done
03 May 2021 07:19:53,196 DEBUG: Total peptides inserted: 16
03 May 2021 07:19:53,198 INFO : Inserting CAETHG_RS14410
03 May 2021 07:19:53,551 INFO : 39% Done
03 May 2021 07:19:53,565 DEBUG: Total peptides inserted: 15
03 May 2021 07:19:53,567 INFO : Inserting CAETHG_RS18395
03 May 2021 07:19:54,189 INFO : 40% Done
03 May 2021 07:19:54,619 DEBUG: Total peptides inserted: 38
03 May 2021 07:19:54,621 INFO : Inserting CAETHG_RS07861
03 May 2021 07:19:54,731 INFO : 41% Done
03 May 2021 07:19:54,912 DEBUG: Total peptides inserted: 11
03 May 2021 07:19:54,913 INFO : Inserting Decoys
03 May 2021 07:19:55,101 INFO : 42% Done
03 May 2021 07:19:55,349 INFO : 43% Done
03 May 2021 07:19:55,571 INFO : 44% Done
03 May 2021 07:19:55,899 INFO : 45% Done
03 May 2021 07:19:56,101 INFO : 46% Done
03 May 2021 07:19:56,315 INFO : 47% Done
03 May 2021 07:19:56,527 INFO : 48% Done
03 May 2021 07:19:56,559 DEBUG: Inserted 50 peptides
03 May 2021 07:19:56,757 INFO : 49% Done
03 May 2021 07:19:57,005 INFO : 50% Done
03 May 2021 07:19:57,278 INFO : 51% Done
03 May 2021 07:19:57,550 INFO : 52% Done
03 May 2021 07:19:57,841 INFO : 53% Done
03 May 2021 07:19:58,096 INFO : 54% Done
03 May 2021 07:19:58,273 DEBUG: Inserted 100 peptides
03 May 2021 07:19:58,315 INFO : 55% Done
03 May 2021 07:19:58,587 INFO : 56% Done
03 May 2021 07:19:58,880 INFO : 57% Done
03 May 2021 07:19:59,081 INFO : 58% Done
03 May 2021 07:19:59,286 INFO : 59% Done
03 May 2021 07:19:59,507 INFO : 60% Done
03 May 2021 07:19:59,948 INFO : 61% Done
03 May 2021 07:19:59,948 DEBUG: Inserted 150 peptides
03 May 2021 07:20:00,236 INFO : 62% Done
03 May 2021 07:20:00,553 INFO : 63% Done
03 May 2021 07:20:00,837 INFO : 64% Done
03 May 2021 07:20:01,051 INFO : 65% Done
03 May 2021 07:20:01,383 INFO : 66% Done
03 May 2021 07:20:01,708 INFO : 67% Done
03 May 2021 07:20:01,863 DEBUG: Inserted 200 peptides
03 May 2021 07:20:01,935 INFO : 68% Done
03 May 2021 07:20:02,193 INFO : 69% Done
03 May 2021 07:20:02,407 INFO : 70% Done
03 May 2021 07:20:02,639 INFO : 71% Done
03 May 2021 07:20:02,950 INFO : 72% Done
03 May 2021 07:20:03,293 INFO : 73% Done
03 May 2021 07:20:03,625 INFO : 74% Done
03 May 2021 07:20:03,802 DEBUG: Inserted 250 peptides
03 May 2021 07:20:04,148 INFO : 75% Done
03 May 2021 07:20:04,359 INFO : 76% Done
03 May 2021 07:20:04,569 INFO : 77% Done
03 May 2021 07:20:04,851 INFO : 78% Done
03 May 2021 07:20:05,122 INFO : 79% Done
03 May 2021 07:20:05,314 INFO : 80% Done
03 May 2021 07:20:05,355 DEBUG: Inserted 300 peptides
03 May 2021 07:20:05,513 INFO : 81% Done
03 May 2021 07:20:05,757 INFO : 82% Done
03 May 2021 07:20:05,984 INFO : 83% Done
03 May 2021 07:20:06,183 INFO : 84% Done
03 May 2021 07:20:06,383 INFO : 85% Done
03 May 2021 07:20:06,610 INFO : 86% Done
03 May 2021 07:20:06,738 DEBUG: Inserted 350 peptides
03 May 2021 07:20:06,861 INFO : 87% Done
03 May 2021 07:20:07,048 INFO : 88% Done
03 May 2021 07:20:07,292 INFO : 89% Done
03 May 2021 07:20:07,495 INFO : 90% Done
03 May 2021 07:20:07,874 INFO : 91% Done
03 May 2021 07:20:08,137 INFO : 92% Done
03 May 2021 07:20:08,464 INFO : 93% Done
03 May 2021 07:20:08,504 DEBUG: Inserted 400 peptides
03 May 2021 07:20:08,700 INFO : 94% Done
03 May 2021 07:20:09,030 INFO : 95% Done
03 May 2021 07:20:09,223 INFO : 96% Done
03 May 2021 07:20:09,431 INFO : 97% Done
03 May 2021 07:20:09,648 INFO : 98% Done
03 May 2021 07:20:09,768 DEBUG: Total peptides inserted: 443
03 May 2021 07:20:09,769 INFO : None of the 461780 TransitionChromInfos in the file were imported because they exceed the limit of 100000
03 May 2021 07:23:34,672 INFO : Updated 53504 PrecursorChromInfos with transition chromatogram index information
03 May 2021 07:23:34,674 INFO : Done parsing Skyline document.
03 May 2021 07:23:34,676 INFO : Creating and populating temp tables for Proportion values
03 May 2021 07:23:35,072 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
03 May 2021 07:23:37,145 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
03 May 2021 07:23:37,731 INFO : Cleaning up temp tables
03 May 2021 07:23:38,188 INFO : Completed import of Skyline document from SILP CO, syngas, highH2, DS_qbelow0.01_2020-09-30_22-02-14.sky.zip
03 May 2021 07:23:38,195 INFO : 100% Done
03 May 2021 07:23:38,213 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14.sky.zip into the system
03 May 2021 07:23:38,226 INFO : Done importing xar
03 May 2021 07:23:38,231 INFO : Loading pages and webpart properties
03 May 2021 07:23:38,311 INFO : Done importing pages and webpart properties
03 May 2021 07:23:38,312 INFO :
03 May 2021 07:23:38,312 INFO : Experiment import completed successfully.
03 May 2021 07:23:38,312 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
03 May 2021 07:23:38,360 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
03 May 2021 07:23:38,360 INFO :
03 May 2021 07:23:38,360 INFO : Finishing up experiment copy.
03 May 2021 07:23:38,361 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
03 May 2021 07:23:38,365 INFO : Assigning a DOI.
03 May 2021 07:23:40,177 INFO : Assigned DOI: 10.6069/qwaj-ht11
03 May 2021 07:23:40,184 INFO : Updating access URL to point to the new copy of the data.
03 May 2021 07:23:40,192 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
03 May 2021 07:23:40,195 INFO : Removing copy permissions given to journal.
03 May 2021 07:23:40,216 INFO : Adding read permissions to all users that are folder admins in the source container.
03 May 2021 07:23:40,228 INFO : Setting the TargetedMS folder type to 'Experimental Data'
03 May 2021 07:23:40,241 INFO : Updating the 'Raw Data' tab configuration
03 May 2021 07:23:40,249 INFO : Updating dataFileUrls for run SILP CO, syngas, highH2, DS_qbelow0.01_2020-09-30_22-02-14.sky.zip; targetedms run ID 109944
03 May 2021 07:23:40,250 INFO : Adding ExpData for .skyd file
03 May 2021 07:23:40,250 INFO : Updating dataFileUrl...
03 May 2021 07:23:40,251 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd
03 May 2021 07:23:40,251 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Tartu%20GasFermTEC%20-%20Anchors/@files/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd
03 May 2021 07:23:40,256 INFO : Updating dataFileUrl...
03 May 2021 07:23:40,256 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14.sky.zip
03 May 2021 07:23:40,257 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Tartu%20GasFermTEC%20-%20Anchors/@files/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14.sky.zip
03 May 2021 07:23:40,260 INFO : Updating dataFileUrl...
03 May 2021 07:23:40,260 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/U%20of%20Tartu%20GasFermTEC%20-%20Anchors_1b8a4103-8e48-1039-a9d2-fea6ddf5fcf4/_temp__2021-05-03_07-17-16/export/xar/experiments_and_runs.xar.exploded/Run107631/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd
03 May 2021 07:23:40,260 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Tartu%20GasFermTEC%20-%20Anchors/@files/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01_2020-09-30_22-02-14/SILP%20CO,%20syngas,%20highH2,%20DS_qbelow0.01.skyd
03 May 2021 07:23:40,268 INFO : Creating a reviewer account.
03 May 2021 07:23:40,552 INFO : Created reviewer with email: User panorama+reviewer25@proteinms.net
03 May 2021 07:23:40,566 INFO : Hiding the Data Pipeline tab.
03 May 2021 07:23:40,644 INFO : Emailing submitter.
03 May 2021 07:23:40,796 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'