17 Feb 2021 18:11:50,720 INFO : Copying experiment "Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium" from folder /U of Pennsylvania - Garcia Lab/dictyostelium_histone_ptms to /Panorama Public/2021/U of Pennsylvania Garcia Lab - dictyostelium_histone_ptms
17 Feb 2021 18:11:50,721 INFO : =======================================
17 Feb 2021 19:42:47,577 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
17 Feb 2021 19:42:47,590 INFO : 
17 Feb 2021 19:42:47,591 INFO : Exporting experiment.
17 Feb 2021 19:49:32,251 INFO : 
17 Feb 2021 19:49:32,270 INFO : Experiment export completed successfully.
17 Feb 2021 19:49:32,270 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
17 Feb 2021 19:51:56,089 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
17 Feb 2021 19:51:56,089 INFO : 
17 Feb 2021 19:51:56,089 INFO : Importing experiment.
17 Feb 2021 19:51:56,132 INFO : Loading folder properties (folder type, settings and active modules)
17 Feb 2021 19:51:56,667 INFO : Done importing folder properties (folder type, settings and active modules)
17 Feb 2021 19:51:56,672 INFO : Loading etl definitions
17 Feb 2021 19:51:56,676 INFO : Loading wikis
17 Feb 2021 19:51:56,918 INFO : 1 wiki imported
17 Feb 2021 19:51:56,918 INFO : Done importing wikis
17 Feb 2021 19:51:56,918 INFO : Starting to copy files
17 Feb 2021 19:54:02,680 INFO : 48 files copied, now copying 20201123_LKP_QEHF_greer_06_DIA_025.raw
17 Feb 2021 19:56:10,563 INFO : 67 files copied, now copying 20201123_LKP_QEHF_greer_08_DIA_022.raw
17 Feb 2021 19:58:06,182 INFO : Copied 112 files
17 Feb 2021 19:58:06,182 INFO : Ensuring exp.data rows exist for imported files
17 Feb 2021 19:58:09,094 INFO : Loading xar
17 Feb 2021 19:58:15,555 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip'
17 Feb 2021 19:58:15,559 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip.Core'
17 Feb 2021 19:58:15,564 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip.Output'
17 Feb 2021 19:58:15,564 DEBUG: Protocol import complete
17 Feb 2021 19:58:15,663 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-8236:Role+of+Epigenetics+in+Unicellular+to+Multicellular+Transition+in+Dictyostelium'
17 Feb 2021 19:58:15,664 DEBUG: Experiment/Run group import complete
17 Feb 2021 19:58:15,697 DEBUG: Protocol action set import complete
17 Feb 2021 19:58:15,732 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip'
17 Feb 2021 19:58:15,778 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-8236:9e51c2e8-3679-1039-b990-3013bb9b12b3'
17 Feb 2021 19:58:15,785 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-8236:9e51b6da-3679-1039-b990-3013bb9b12b3'
17 Feb 2021 19:58:15,785 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip.Core'
17 Feb 2021 19:58:15,790 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-8236:TargetedMS.ImportSkyZip.Output'
17 Feb 2021 19:58:15,792 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-8236:9e51c4f8-3679-1039-b990-3013bb9b12b3'
17 Feb 2021 19:58:15,807 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49/histone_garcia_v0-9-2_greer_onlyhistlibrary.skyd into the system
17 Feb 2021 19:58:15,808 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49/histone_garcia_v0-9-2_greer_onlyhistlibrary.skyd into the system
17 Feb 2021 19:58:15,808 DEBUG: Trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip into the system
17 Feb 2021 19:58:15,840 INFO : Starting import from histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip
17 Feb 2021 19:58:15,857 INFO : Starting to import Skyline document from histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip
17 Feb 2021 19:58:15,885 INFO : Expanding dicty.protdb
17 Feb 2021 19:58:17,983 INFO : Expanding dicty_dda.blib
17 Feb 2021 19:58:18,097 INFO : Expanding dicty_dda.redundant.blib
17 Feb 2021 19:58:20,981 INFO : Expanding histone_garcia_v0-9-2_greer_onlyhistlibrary.skyd
17 Feb 2021 19:58:21,285 INFO : Expanding histone_garcia_v0-9-2_greer_onlyhistlibrary.sky.view
17 Feb 2021 19:58:21,286 INFO : Expanding histone_garcia_v0-9-2_greer_onlyhistlibrary.sky
17 Feb 2021 19:58:22,932 DEBUG: Starting to load chromatogram headers
17 Feb 2021 19:58:22,937 DEBUG: Done loading chromatogram headers
17 Feb 2021 19:58:24,234 INFO : 1% Done
17 Feb 2021 19:58:24,234 INFO : Inserting sp|P54671|H1_DICDI,sp|Q76NW2|H4_DICDI
17 Feb 2021 19:58:24,790 DEBUG: Total peptides inserted: 1
17 Feb 2021 19:58:25,099 INFO : Inserting sp|Q54LP8|H2BV3_DICDI
17 Feb 2021 19:58:25,720 INFO : 2% Done
17 Feb 2021 19:58:26,817 INFO : 3% Done
17 Feb 2021 19:58:27,046 INFO : 4% Done
17 Feb 2021 19:58:27,642 INFO : 5% Done
17 Feb 2021 19:58:28,015 INFO : 6% Done
17 Feb 2021 19:58:29,002 INFO : 7% Done
17 Feb 2021 19:58:29,237 INFO : 8% Done
17 Feb 2021 19:58:29,673 INFO : 9% Done
17 Feb 2021 19:58:29,930 INFO : 10% Done
17 Feb 2021 19:58:30,451 INFO : 11% Done
17 Feb 2021 19:58:30,752 INFO : 12% Done
17 Feb 2021 19:58:31,271 INFO : 13% Done
17 Feb 2021 19:58:31,725 INFO : 14% Done
17 Feb 2021 19:58:33,041 INFO : 15% Done
17 Feb 2021 19:58:33,274 INFO : 16% Done
17 Feb 2021 19:58:33,474 DEBUG: Total peptides inserted: 25
17 Feb 2021 19:58:33,553 INFO : Inserting sp|Q54WG6|H2AX_DICDI
17 Feb 2021 19:58:33,929 INFO : 17% Done
17 Feb 2021 19:58:34,651 INFO : 18% Done
17 Feb 2021 19:58:35,563 INFO : 19% Done
17 Feb 2021 19:58:36,278 INFO : 20% Done
17 Feb 2021 19:58:36,887 INFO : 21% Done
17 Feb 2021 19:58:37,487 INFO : 22% Done
17 Feb 2021 19:58:38,299 INFO : 23% Done
17 Feb 2021 19:58:38,960 INFO : 24% Done
17 Feb 2021 19:58:39,781 INFO : 25% Done
17 Feb 2021 19:58:40,133 INFO : 26% Done
17 Feb 2021 19:58:40,962 INFO : 27% Done
17 Feb 2021 19:58:41,187 INFO : 28% Done
17 Feb 2021 19:58:41,600 INFO : 29% Done
17 Feb 2021 19:58:41,911 DEBUG: Total peptides inserted: 27
17 Feb 2021 19:58:41,912 INFO : Inserting sp|O15819|H33A_DICDI,sp|Q55BN9|H33B_DICDI
17 Feb 2021 19:58:41,948 INFO : 30% Done
17 Feb 2021 19:58:42,599 INFO : 31% Done
17 Feb 2021 19:58:42,818 INFO : 32% Done
17 Feb 2021 19:58:43,286 INFO : 33% Done
17 Feb 2021 19:58:43,698 INFO : 34% Done
17 Feb 2021 19:58:44,367 INFO : 35% Done
17 Feb 2021 19:58:44,507 INFO : 36% Done
17 Feb 2021 19:58:44,786 INFO : 37% Done
17 Feb 2021 19:58:44,990 INFO : 38% Done
17 Feb 2021 19:58:45,336 DEBUG: Total peptides inserted: 18
17 Feb 2021 19:58:45,475 INFO : Inserting sp|P14794|RL40_DICDI
17 Feb 2021 19:58:45,543 INFO : 39% Done
17 Feb 2021 19:58:45,891 INFO : 40% Done
17 Feb 2021 19:58:46,011 DEBUG: Total peptides inserted: 3
17 Feb 2021 19:58:46,148 INFO : Inserting sp|Q76NW2|H4_DICDI
17 Feb 2021 19:58:46,185 INFO : 41% Done
17 Feb 2021 19:58:46,476 INFO : 42% Done
17 Feb 2021 19:58:47,017 INFO : 43% Done
17 Feb 2021 19:58:47,297 INFO : 44% Done
17 Feb 2021 19:58:47,782 INFO : 45% Done
17 Feb 2021 19:58:48,241 INFO : 46% Done
17 Feb 2021 19:58:48,819 INFO : 47% Done
17 Feb 2021 19:58:49,126 INFO : 48% Done
17 Feb 2021 19:58:49,402 INFO : 49% Done
17 Feb 2021 19:58:49,873 INFO : 50% Done
17 Feb 2021 19:58:50,293 INFO : 51% Done
17 Feb 2021 19:58:50,518 INFO : 52% Done
17 Feb 2021 19:58:50,805 INFO : 53% Done
17 Feb 2021 19:58:51,017 INFO : 54% Done
17 Feb 2021 19:58:53,493 INFO : 55% Done
17 Feb 2021 19:58:54,134 INFO : 56% Done
17 Feb 2021 19:58:55,891 INFO : 57% Done
17 Feb 2021 19:58:56,370 INFO : 58% Done
17 Feb 2021 19:58:56,999 INFO : 59% Done
17 Feb 2021 19:58:57,403 INFO : 61% Done
17 Feb 2021 19:58:57,694 INFO : 62% Done
17 Feb 2021 19:58:58,154 INFO : 63% Done
17 Feb 2021 19:58:58,689 INFO : 64% Done
17 Feb 2021 19:58:59,042 INFO : 65% Done
17 Feb 2021 19:58:59,353 INFO : 66% Done
17 Feb 2021 19:58:59,907 INFO : 67% Done
17 Feb 2021 19:59:00,201 INFO : 68% Done
17 Feb 2021 19:59:00,516 INFO : 69% Done
17 Feb 2021 19:59:00,859 INFO : 70% Done
17 Feb 2021 19:59:01,406 INFO : 71% Done
17 Feb 2021 19:59:01,631 INFO : 72% Done
17 Feb 2021 19:59:01,830 INFO : 73% Done
17 Feb 2021 19:59:02,111 DEBUG: Total peptides inserted: 49
17 Feb 2021 19:59:02,222 INFO : Inserting sp|P16168|RL11_DICDI
17 Feb 2021 19:59:02,506 INFO : 74% Done
17 Feb 2021 19:59:02,843 DEBUG: Total peptides inserted: 3
17 Feb 2021 19:59:02,908 INFO : Inserting sp|Q54LA5|H2AZ_DICDI
17 Feb 2021 19:59:02,934 INFO : 75% Done
17 Feb 2021 19:59:03,396 INFO : 76% Done
17 Feb 2021 19:59:03,881 DEBUG: Total peptides inserted: 3
17 Feb 2021 19:59:03,942 INFO : Inserting sp|O15819|H33A_DICDI
17 Feb 2021 19:59:03,963 INFO : 77% Done
17 Feb 2021 19:59:04,507 INFO : 78% Done
17 Feb 2021 19:59:05,001 DEBUG: Total peptides inserted: 4
17 Feb 2021 19:59:05,065 INFO : Inserting sp|Q55BN9|H33B_DICDI
17 Feb 2021 19:59:05,207 INFO : 79% Done
17 Feb 2021 19:59:05,418 INFO : 80% Done
17 Feb 2021 19:59:05,623 DEBUG: Total peptides inserted: 3
17 Feb 2021 19:59:05,625 INFO : Done parsing Skyline document.
17 Feb 2021 19:59:05,629 INFO : Calculating fold changes
17 Feb 2021 19:59:05,629 DEBUG: Calculating fold change for group comparison mound vs vegetative, 1 of 3
17 Feb 2021 19:59:17,288 INFO : 86% Done
17 Feb 2021 19:59:17,288 DEBUG: Calculating fold change for group comparison streaming vs vegetative, 2 of 3
17 Feb 2021 19:59:29,770 INFO : 92% Done
17 Feb 2021 19:59:29,770 DEBUG: Calculating fold change for group comparison fruiting vs vegetative, 3 of 3
17 Feb 2021 19:59:47,535 INFO : 98% Done
17 Feb 2021 19:59:47,535 INFO : Done calculating fold changes.
17 Feb 2021 19:59:47,538 INFO : Creating and populating temp tables for Proportion values
17 Feb 2021 19:59:47,677 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
17 Feb 2021 19:59:48,219 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
17 Feb 2021 19:59:48,387 INFO : Cleaning up temp tables
17 Feb 2021 19:59:48,778 INFO : Completed import of Skyline document from histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip
17 Feb 2021 19:59:48,782 INFO : 100% Done
17 Feb 2021 19:59:48,787 DEBUG: Finished trying to load data file file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip into the system
17 Feb 2021 19:59:48,808 INFO : Done importing xar
17 Feb 2021 19:59:48,811 INFO : Loading pages and webpart properties
17 Feb 2021 19:59:48,975 INFO : Done importing pages and webpart properties
17 Feb 2021 19:59:48,975 INFO : 
17 Feb 2021 19:59:48,975 INFO : Experiment import completed successfully.
17 Feb 2021 19:59:48,976 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
17 Feb 2021 19:59:49,028 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
17 Feb 2021 19:59:49,028 INFO : 
17 Feb 2021 19:59:49,028 INFO : Finishing up experiment copy.
17 Feb 2021 19:59:49,029 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
17 Feb 2021 19:59:49,045 INFO : Assigning a ProteomeXchange ID.
17 Feb 2021 19:59:50,557 INFO : Updating access URL to point to the new copy of the data.
17 Feb 2021 19:59:50,707 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
17 Feb 2021 19:59:50,770 INFO : Removing copy permissions given to journal.
17 Feb 2021 19:59:50,922 INFO : Adding read permissions to all users that are folder admins in the source container.
17 Feb 2021 19:59:50,942 INFO : Setting the TargetedMS folder type to 'Experimental Data'
17 Feb 2021 19:59:50,963 INFO : Updating the 'Raw Data' tab configuration
17 Feb 2021 19:59:50,966 INFO : Updating dataFileUrls for run histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip; targetedms run ID 104076
17 Feb 2021 19:59:50,966 INFO : Updating dataFileUrl...
17 Feb 2021 19:59:50,966 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip
17 Feb 2021 19:59:50,967 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms/@files/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49.sky.zip
17 Feb 2021 19:59:50,970 INFO : Updating dataFileUrl...
17 Feb 2021 19:59:50,970 INFO : from: file:///data/apache-tomcat/temp/Pipeline_temp/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms_baa000b6-53ba-1039-9674-3013bb9b91fd/_temp__2021-02-17_18-11-49/export/xar/experiments_and_runs.xar.exploded/Run97793/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49/histone_garcia_v0-9-2_greer_onlyhistlibrary.skyd
17 Feb 2021 19:59:50,970 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/U%20of%20Pennsylvania%20Garcia%20Lab%20-%20dictyostelium_histone_ptms/@files/histone_garcia_v0-9-2_greer_onlyhistlibrary_2021-01-11_15-29-49/histone_garcia_v0-9-2_greer_onlyhistlibrary.skyd
17 Feb 2021 19:59:50,987 INFO : Creating a reviewer account.
17 Feb 2021 19:59:52,475 INFO : Created reviewer with email: User panorama+garcia1@proteinms.net
17 Feb 2021 19:59:52,486 INFO : Hiding the Data Pipeline tab.
17 Feb 2021 19:59:54,260 INFO : Emailing submitter.
17 Feb 2021 19:59:54,999 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'