18 Feb 2021 19:33:26,235 INFO : Copying experiment "Mouse Heart SS31 Targeted Proteomics" from folder /MacCoss/Collaborations/Whitson-Rab-Lab/SS31-PTM to /Panorama Public/2021/MacCoss - SS31-PTM
18 Feb 2021 19:33:26,235 INFO : =======================================
18 Feb 2021 19:35:25,137 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
18 Feb 2021 19:35:25,138 INFO :
18 Feb 2021 19:35:25,138 INFO : Exporting experiment.
18 Feb 2021 19:49:03,475 INFO :
18 Feb 2021 19:49:03,476 INFO : Experiment export completed successfully.
18 Feb 2021 19:49:03,476 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
18 Feb 2021 19:50:09,199 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
18 Feb 2021 19:50:09,199 INFO :
18 Feb 2021 19:50:09,199 INFO : Importing experiment.
18 Feb 2021 19:50:09,220 INFO : Loading folder properties (folder type, settings and active modules)
18 Feb 2021 19:50:09,772 INFO : Done importing folder properties (folder type, settings and active modules)
18 Feb 2021 19:50:09,779 INFO : Loading etl definitions
18 Feb 2021 19:50:09,786 INFO : Loading wikis
18 Feb 2021 19:50:09,806 INFO : 0 wikis imported
18 Feb 2021 19:50:09,807 INFO : Done importing wikis
18 Feb 2021 19:50:09,807 INFO : Starting to copy files
18 Feb 2021 19:52:13,783 INFO : 40 files copied, now copying 03March2020-Loomis-JW-PRM-pool-2-tubeSTD2-batch2.mzid
18 Feb 2021 19:54:23,033 INFO : 57 files copied, now copying 03March2020-Loomis-JW-PRM-JW23-LF-tube9-batch2.mzid
18 Feb 2021 19:56:26,471 INFO : 73 files copied, now copying 03March2020-Loomis-JW-PRM-JW36-RF-tube71-batch1.mzid
18 Feb 2021 19:58:33,097 INFO : 91 files copied, now copying 03March2020-Loomis-JW-PRM-MS-YM8-tube45-batch2.mzid
18 Feb 2021 20:00:36,930 INFO : 107 files copied, now copying 03March2020-Loomis-JW-PRM-JW24-LF-tube13-batch1.mzML
18 Feb 2021 20:02:41,038 INFO : 121 files copied, now copying 03March2020-Loomis-JW-PRM-JW37-LF-tube64-batch2.mzML
18 Feb 2021 20:03:07,043 INFO : Copied 124 files
18 Feb 2021 20:03:07,043 INFO : Ensuring exp.data rows exist for imported files
18 Feb 2021 20:03:09,783 INFO : Loading xar
18 Feb 2021 20:03:15,431 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip'
18 Feb 2021 20:03:15,437 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip.Core'
18 Feb 2021 20:03:15,444 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip.Output'
18 Feb 2021 20:03:15,444 DEBUG: Protocol import complete
18 Feb 2021 20:03:15,516 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8238:Mouse+Heart+SS31+Targeted+Proteomics'
18 Feb 2021 20:03:15,516 DEBUG: Experiment/Run group import complete
18 Feb 2021 20:03:15,578 DEBUG: Protocol action set import complete
18 Feb 2021 20:03:15,634 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip'
18 Feb 2021 20:03:15,760 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8238:5fc6f6ad-5456-1039-9674-3013bb9b91fd'
18 Feb 2021 20:03:15,802 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8238:5fc6fab3-5456-1039-9674-3013bb9b91fd'
18 Feb 2021 20:03:15,802 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip.Core'
18 Feb 2021 20:03:15,844 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8238:TargetedMS.ImportSkyZip.Output'
18 Feb 2021 20:03:15,846 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8238:5fc6fb3a-5456-1039-9674-3013bb9b91fd'
18 Feb 2021 20:03:15,849 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2.sky.zip into the system
18 Feb 2021 20:03:15,852 INFO : Starting import from PRM-JW-full-enolase-set1-MSamanda-2.sky.zip
18 Feb 2021 20:03:15,861 INFO : Starting to import Skyline document from PRM-JW-full-enolase-set1-MSamanda-2.sky.zip
18 Feb 2021 20:03:15,871 INFO : Expanding mouse-uniprot-enolase.protdb
18 Feb 2021 20:03:19,892 INFO : Expanding PRM-JW-full-enolase-set1-MSamanda-2.blib
18 Feb 2021 20:03:20,005 INFO : Expanding PRM-JW-full-enolase-set1-MSamanda-2.redundant.blib
18 Feb 2021 20:03:22,794 INFO : Expanding PRM-JW-full-enolase-set1-MSamanda-2.skyd
18 Feb 2021 20:03:22,893 INFO : Expanding PRM-JW-full-enolase-set1-MSamanda-2.sky.view
18 Feb 2021 20:03:22,894 INFO : Expanding PRM-JW-full-enolase-set1-MSamanda-2.sky
18 Feb 2021 20:03:22,986 INFO : 5% Done
18 Feb 2021 20:03:23,196 DEBUG: Starting to load chromatogram headers
18 Feb 2021 20:03:23,199 DEBUG: Done loading chromatogram headers
18 Feb 2021 20:03:23,647 INFO : 7% Done
18 Feb 2021 20:03:23,813 INFO : Inserting sp|A2ASS6|TITIN_MOUSE
18 Feb 2021 20:03:23,864 INFO : 9% Done
18 Feb 2021 20:03:24,563 INFO : 12% Done
18 Feb 2021 20:03:25,053 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:25,130 INFO : Inserting sp|Q99KI0|ACON_MOUSE
18 Feb 2021 20:03:25,261 INFO : 15% Done
18 Feb 2021 20:03:25,615 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:25,929 INFO : Inserting sp|Q9JI91|ACTN2_MOUSE
18 Feb 2021 20:03:25,961 INFO : 17% Done
18 Feb 2021 20:03:26,352 INFO : 20% Done
18 Feb 2021 20:03:26,520 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:27,135 INFO : Inserting sp|P29699|FETUA_MOUSE
18 Feb 2021 20:03:27,175 INFO : 22% Done
18 Feb 2021 20:03:27,458 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:27,501 INFO : Inserting tr|A0A0A6YXW8|A0A0A6YXW8_MOUSE
18 Feb 2021 20:03:27,544 INFO : 25% Done
18 Feb 2021 20:03:28,178 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:28,256 INFO : Inserting sp|Q9JLV1|BAG3_MOUSE
18 Feb 2021 20:03:28,273 INFO : 26% Done
18 Feb 2021 20:03:28,679 INFO : 29% Done
18 Feb 2021 20:03:29,050 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:29,121 INFO : Inserting sp|P07310|KCRM_MOUSE
18 Feb 2021 20:03:29,138 INFO : 31% Done
18 Feb 2021 20:03:29,418 INFO : 34% Done
18 Feb 2021 20:03:29,752 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:29,845 INFO : Inserting sp|E9Q557|DESP_MOUSE
18 Feb 2021 20:03:29,857 INFO : 36% Done
18 Feb 2021 20:03:30,180 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:30,284 INFO : Inserting sp|Q5EBG6|HSPB6_MOUSE
18 Feb 2021 20:03:30,327 INFO : 38% Done
18 Feb 2021 20:03:30,671 INFO : 41% Done
18 Feb 2021 20:03:31,077 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:31,183 INFO : Inserting sp|Q6PCP5|MFF_MOUSE
18 Feb 2021 20:03:31,224 INFO : 43% Done
18 Feb 2021 20:03:31,574 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:31,673 INFO : Inserting sp|O70468|MYPC3_MOUSE
18 Feb 2021 20:03:31,705 INFO : 46% Done
18 Feb 2021 20:03:32,142 INFO : 49% Done
18 Feb 2021 20:03:32,538 INFO : 51% Done
18 Feb 2021 20:03:32,905 DEBUG: Total peptides inserted: 3
18 Feb 2021 20:03:32,981 INFO : Inserting sp|Q9JIF9|MYOTI_MOUSE
18 Feb 2021 20:03:33,014 INFO : 53% Done
18 Feb 2021 20:03:33,436 INFO : 56% Done
18 Feb 2021 20:03:33,819 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:33,928 INFO : Inserting sp|P61014|PPLA_MOUSE
18 Feb 2021 20:03:33,952 INFO : 58% Done
18 Feb 2021 20:03:34,292 INFO : 61% Done
18 Feb 2021 20:03:34,645 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:34,716 INFO : Inserting sp|Q8BG95|MYPT2_MOUSE
18 Feb 2021 20:03:34,733 INFO : 64% Done
18 Feb 2021 20:03:35,141 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:35,216 INFO : Inserting sp|Q99MR9|PPR3A_MOUSE
18 Feb 2021 20:03:35,244 INFO : 66% Done
18 Feb 2021 20:03:35,602 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:35,663 INFO : Inserting sp|Q5EG47|AAPK1_MOUSE
18 Feb 2021 20:03:35,679 INFO : 69% Done
18 Feb 2021 20:03:36,026 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:36,129 INFO : Inserting sp|O70622|RTN2_MOUSE
18 Feb 2021 20:03:36,144 INFO : 72% Done
18 Feb 2021 20:03:36,482 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:36,571 INFO : Inserting sp|Q62407|SPEG_MOUSE
18 Feb 2021 20:03:36,646 INFO : 74% Done
18 Feb 2021 20:03:36,967 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:37,052 INFO : Inserting sp|P48787|TNNI3_MOUSE
18 Feb 2021 20:03:37,074 INFO : 75% Done
18 Feb 2021 20:03:37,352 INFO : 78% Done
18 Feb 2021 20:03:37,715 DEBUG: Total peptides inserted: 2
18 Feb 2021 20:03:37,792 INFO : Inserting sp|O70373|XIRP1_MOUSE
18 Feb 2021 20:03:37,806 INFO : 80% Done
18 Feb 2021 20:03:38,166 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:38,298 INFO : Inserting sp|Q9DAZ9|ANCHR_MOUSE
18 Feb 2021 20:03:38,313 INFO : 83% Done
18 Feb 2021 20:03:38,694 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:38,776 INFO : Inserting sp|P00924|ENO1_YEAST
18 Feb 2021 20:03:38,803 INFO : 85% Done
18 Feb 2021 20:03:39,140 INFO : 88% Done
18 Feb 2021 20:03:39,498 INFO : 90% Done
18 Feb 2021 20:03:39,875 INFO : 93% Done
18 Feb 2021 20:03:40,234 INFO : 95% Done
18 Feb 2021 20:03:40,566 DEBUG: Total peptides inserted: 5
18 Feb 2021 20:03:40,664 INFO : Inserting sp|Q149B8|PERM1_MOUSE
18 Feb 2021 20:03:40,695 INFO : 98% Done
18 Feb 2021 20:03:41,095 DEBUG: Total peptides inserted: 1
18 Feb 2021 20:03:41,097 INFO : Done parsing Skyline document.
18 Feb 2021 20:03:41,100 INFO : Creating and populating temp tables for Proportion values
18 Feb 2021 20:03:41,226 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
18 Feb 2021 20:03:41,700 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
18 Feb 2021 20:03:41,972 INFO : Cleaning up temp tables
18 Feb 2021 20:03:41,986 INFO : Completed import of Skyline document from PRM-JW-full-enolase-set1-MSamanda-2.sky.zip
18 Feb 2021 20:03:41,993 INFO : 100% Done
18 Feb 2021 20:03:42,004 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2.sky.zip into the system
18 Feb 2021 20:03:42,005 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2/PRM-JW-full-enolase-set1-MSamanda-2.skyd into the system
18 Feb 2021 20:03:42,007 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2/PRM-JW-full-enolase-set1-MSamanda-2.skyd into the system
18 Feb 2021 20:03:42,025 INFO : Done importing xar
18 Feb 2021 20:03:42,032 INFO : Loading pages and webpart properties
18 Feb 2021 20:03:42,356 INFO : Done importing pages and webpart properties
18 Feb 2021 20:03:42,356 INFO :
18 Feb 2021 20:03:42,356 INFO : Experiment import completed successfully.
18 Feb 2021 20:03:42,357 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
18 Feb 2021 20:03:42,433 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
18 Feb 2021 20:03:42,433 INFO :
18 Feb 2021 20:03:42,434 INFO : Finishing up experiment copy.
18 Feb 2021 20:03:42,438 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
18 Feb 2021 20:03:42,442 INFO : Assigning a ProteomeXchange ID.
18 Feb 2021 20:03:42,858 INFO : Updating access URL to point to the new copy of the data.
18 Feb 2021 20:03:42,884 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
18 Feb 2021 20:03:42,908 INFO : Removing copy permissions given to journal.
18 Feb 2021 20:03:42,963 INFO : Adding read permissions to all users that are folder admins in the source container.
18 Feb 2021 20:03:42,992 INFO : Setting the TargetedMS folder type to 'Experimental Data'
18 Feb 2021 20:03:43,019 INFO : Updating the 'Raw Data' tab configuration
18 Feb 2021 20:03:43,027 INFO : Updating dataFileUrls for run PRM-JW-full-enolase-set1-MSamanda-2.sky.zip; targetedms run ID 104142
18 Feb 2021 20:03:43,028 INFO : Updating dataFileUrl...
18 Feb 2021 20:03:43,028 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2/PRM-JW-full-enolase-set1-MSamanda-2.skyd
18 Feb 2021 20:03:43,029 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SS31-PTM/@files/PRM-JW-full-enolase-set1-MSamanda-2/PRM-JW-full-enolase-set1-MSamanda-2.skyd
18 Feb 2021 20:03:43,034 INFO : Updating dataFileUrl...
18 Feb 2021 20:03:43,034 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/MacCoss%20-%20SS31-PTM_831f9848-548f-1039-9674-3013bb9b91fd/_temp__2021-02-18_19-33-25/export/xar/experiments_and_runs.xar.exploded/Run101883/PRM-JW-full-enolase-set1-MSamanda-2.sky.zip
18 Feb 2021 20:03:43,035 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/MacCoss%20-%20SS31-PTM/@files/PRM-JW-full-enolase-set1-MSamanda-2.sky.zip
18 Feb 2021 20:03:43,042 INFO : Creating a reviewer account.
18 Feb 2021 20:03:44,141 INFO : Created reviewer with email: User panorama+maccoss9@proteinms.net
18 Feb 2021 20:03:44,163 INFO : Hiding the Data Pipeline tab.
18 Feb 2021 20:03:44,483 INFO : Emailing submitter.
18 Feb 2021 20:03:45,299 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'