08 Dec 2021 20:46:17,649 INFO : Copying experiment "Relative quantification of acetylated histone peptides in HAP1 cells after treatment with MS-275" from folder /Max Perutz Labs - MS Facility/Seiser - Histone acetylation in HAP cells to /Panorama Public/2021/Max Perutz Labs MS Facility - Seiser - Histone acetylation in HAP cells
08 Dec 2021 20:46:17,650 INFO : =======================================
08 Dec 2021 20:46:17,947 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
08 Dec 2021 20:46:17,947 INFO : 
08 Dec 2021 20:46:17,947 INFO : Exporting experiment.
08 Dec 2021 20:51:28,853 INFO : 
08 Dec 2021 20:51:28,853 INFO : Experiment export completed successfully.
08 Dec 2021 20:51:28,853 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
08 Dec 2021 20:51:29,001 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
08 Dec 2021 20:51:29,001 INFO : 
08 Dec 2021 20:51:29,001 INFO : Importing experiment.
08 Dec 2021 20:51:29,006 INFO : Loading folder properties (folder type, settings and active modules)
08 Dec 2021 20:51:29,094 INFO : Done importing folder properties (folder type, settings and active modules)
08 Dec 2021 20:51:29,097 INFO : Loading etl definitions
08 Dec 2021 20:51:29,100 INFO : Loading wikis
08 Dec 2021 20:51:29,101 INFO : 0 wikis imported
08 Dec 2021 20:51:29,101 INFO : Done importing wikis
08 Dec 2021 20:51:29,102 INFO : Starting to copy files
08 Dec 2021 20:53:35,935 INFO : 9 files copied, now copying 20210820_QExHFX1_RSLC4_Hess_SeiserextUni_MPL_PRM_6h_r2.raw
08 Dec 2021 20:55:45,497 INFO : 16 files copied, now copying 20210820_QExHFX1_RSLC4_Hess_SeiserextUni_MPL_PRM_c_r2.raw
08 Dec 2021 20:56:27,005 INFO : 19 files copied, now copying 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyl
08 Dec 2021 20:56:29,265 INFO : Copied 25 files
08 Dec 2021 20:56:29,265 INFO : Ensuring exp.data rows exist for imported files
08 Dec 2021 20:56:29,402 INFO : Starting Sample Type and Data Class import
08 Dec 2021 20:56:29,402 INFO : No types XAR file to process.
08 Dec 2021 20:56:29,402 INFO : Finished importing Sample Types and Data Classes
08 Dec 2021 20:56:29,404 INFO : Loading xar
08 Dec 2021 20:56:30,174 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip'
08 Dec 2021 20:56:30,177 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip.Core'
08 Dec 2021 20:56:30,179 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip.Output'
08 Dec 2021 20:56:30,179 DEBUG: Protocol import complete
08 Dec 2021 20:56:30,180 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9408:Relative+quantification+of+acetylated+histone+peptides+in+HAP1+cells+after+treatment+with+MS-275'
08 Dec 2021 20:56:30,180 DEBUG: Experiment/Run group import complete
08 Dec 2021 20:56:30,192 DEBUG: Protocol action set import complete
08 Dec 2021 20:56:30,206 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip'
08 Dec 2021 20:56:30,215 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9408:343e0678-364e-103a-8339-fea6ddf5e014'
08 Dec 2021 20:56:30,220 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9408:343e0656-364e-103a-8339-fea6ddf5e014'
08 Dec 2021 20:56:30,220 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip.Core'
08 Dec 2021 20:56:30,223 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9408:TargetedMS.ImportSkyZip.Output'
08 Dec 2021 20:56:30,224 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9408:343e06b0-364e-103a-8339-fea6ddf5e014'
08 Dec 2021 20:56:30,228 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45/20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyd into the system
08 Dec 2021 20:56:30,229 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45/20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyd into the system
08 Dec 2021 20:56:30,229 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip into the system
08 Dec 2021 20:56:30,230 INFO : Starting import from 20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip
08 Dec 2021 20:56:30,235 INFO : Starting to import Skyline document from 20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip
08 Dec 2021 20:56:30,237 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.blib
08 Dec 2021 20:56:30,524 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.redundant.blib
08 Dec 2021 20:56:31,643 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyd
08 Dec 2021 20:56:31,685 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.sky.view
08 Dec 2021 20:56:31,686 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.sky
08 Dec 2021 20:56:31,692 INFO : Expanding 20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyl
08 Dec 2021 20:56:31,700 WARN : The version of this Skyline document is 21.12. This is newer than the highest supported version 20.22
08 Dec 2021 20:56:31,715 INFO : 2% Done
08 Dec 2021 20:56:31,787 DEBUG: Starting to load chromatogram headers
08 Dec 2021 20:56:31,789 DEBUG: Done loading chromatogram headers
08 Dec 2021 20:56:31,887 INFO : Inserting sp|Q71UI9-2|H2AV-2_HUMAN
08 Dec 2021 20:56:31,904 INFO : 4% Done
08 Dec 2021 20:56:31,952 INFO : 6% Done
08 Dec 2021 20:56:31,999 INFO : 9% Done
08 Dec 2021 20:56:32,037 INFO : 11% Done
08 Dec 2021 20:56:32,061 DEBUG: Total peptides inserted: 4
08 Dec 2021 20:56:32,061 INFO : Inserting sp|Q71UI9-2|H2AV-2_HUMAN Peptide with N-term M-loss
08 Dec 2021 20:56:32,072 INFO : 13% Done
08 Dec 2021 20:56:32,102 DEBUG: Total peptides inserted: 1
08 Dec 2021 20:56:32,105 INFO : 14% Done
08 Dec 2021 20:56:32,108 INFO : Inserting sp|P10412|H14_HUMAN
08 Dec 2021 20:56:32,118 INFO : 16% Done
08 Dec 2021 20:56:32,151 INFO : 18% Done
08 Dec 2021 20:56:32,184 INFO : 21% Done
08 Dec 2021 20:56:32,208 DEBUG: Total peptides inserted: 3
08 Dec 2021 20:56:32,211 INFO : Inserting sp|Q92522|H1X_HUMAN
08 Dec 2021 20:56:32,218 INFO : 23% Done
08 Dec 2021 20:56:32,248 INFO : 25% Done
08 Dec 2021 20:56:32,277 INFO : 27% Done
08 Dec 2021 20:56:32,297 DEBUG: Total peptides inserted: 3
08 Dec 2021 20:56:32,300 INFO : Inserting sp|P84243|H33_HUMAN
08 Dec 2021 20:56:32,307 INFO : 29% Done
08 Dec 2021 20:56:32,335 INFO : 32% Done
08 Dec 2021 20:56:32,361 INFO : 34% Done
08 Dec 2021 20:56:32,387 INFO : 37% Done
08 Dec 2021 20:56:32,413 INFO : 39% Done
08 Dec 2021 20:56:32,441 INFO : 41% Done
08 Dec 2021 20:56:32,462 DEBUG: Total peptides inserted: 6
08 Dec 2021 20:56:32,464 INFO : 42% Done
08 Dec 2021 20:56:32,467 INFO : Inserting sp|P62805|H4_HUMAN
08 Dec 2021 20:56:32,474 INFO : 44% Done
08 Dec 2021 20:56:32,499 INFO : 46% Done
08 Dec 2021 20:56:32,525 INFO : 49% Done
08 Dec 2021 20:56:32,551 INFO : 51% Done
08 Dec 2021 20:56:32,576 INFO : 53% Done
08 Dec 2021 20:56:32,601 INFO : 56% Done
08 Dec 2021 20:56:32,626 INFO : 58% Done
08 Dec 2021 20:56:32,651 INFO : 61% Done
08 Dec 2021 20:56:32,675 INFO : 63% Done
08 Dec 2021 20:56:32,695 DEBUG: Total peptides inserted: 9
08 Dec 2021 20:56:32,699 INFO : Inserting sp|Q5QNW6|H2B2F_HUMAN
08 Dec 2021 20:56:32,705 INFO : 65% Done
08 Dec 2021 20:56:32,742 INFO : 68% Done
08 Dec 2021 20:56:32,771 INFO : 70% Done
08 Dec 2021 20:56:32,803 INFO : 73% Done
08 Dec 2021 20:56:32,835 INFO : 74% Done
08 Dec 2021 20:56:32,861 INFO : 76% Done
08 Dec 2021 20:56:32,888 INFO : 79% Done
08 Dec 2021 20:56:32,912 INFO : 81% Done
08 Dec 2021 20:56:32,936 INFO : 84% Done
08 Dec 2021 20:56:32,966 INFO : 86% Done
08 Dec 2021 20:56:32,989 DEBUG: Total peptides inserted: 10
08 Dec 2021 20:56:32,993 INFO : Inserting sp|O60814|H2B1K_HUMAN
08 Dec 2021 20:56:33,000 INFO : 89% Done
08 Dec 2021 20:56:33,030 INFO : 91% Done
08 Dec 2021 20:56:33,060 INFO : 93% Done
08 Dec 2021 20:56:33,091 INFO : 96% Done
08 Dec 2021 20:56:33,114 DEBUG: Total peptides inserted: 4
08 Dec 2021 20:56:33,114 INFO : Inserting H2B1K_HUMAN peptides with N-term M-loss
08 Dec 2021 20:56:33,119 INFO : 98% Done
08 Dec 2021 20:56:33,141 DEBUG: Total peptides inserted: 1
08 Dec 2021 20:56:33,142 INFO : Done parsing Skyline document.
08 Dec 2021 20:56:34,949 INFO : Creating and populating temp tables for Proportion values
08 Dec 2021 20:56:34,971 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
08 Dec 2021 20:56:35,001 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
08 Dec 2021 20:56:35,023 INFO : Cleaning up temp tables
08 Dec 2021 20:56:35,250 INFO : Completed import of Skyline document from 20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip
08 Dec 2021 20:56:35,253 INFO : 100% Done
08 Dec 2021 20:56:35,258 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip into the system
08 Dec 2021 20:56:35,265 INFO : Done importing xar
08 Dec 2021 20:56:35,268 INFO : Loading pages and webpart properties
08 Dec 2021 20:56:35,392 INFO : Done importing pages and webpart properties
08 Dec 2021 20:56:35,393 INFO : 
08 Dec 2021 20:56:35,393 INFO : Experiment import completed successfully.
08 Dec 2021 20:56:35,393 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
08 Dec 2021 20:56:35,492 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
08 Dec 2021 20:56:35,492 INFO : 
08 Dec 2021 20:56:35,492 INFO : Finishing up experiment copy.
08 Dec 2021 20:56:35,493 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
08 Dec 2021 20:56:35,496 INFO : Assigning a ProteomeXchange ID.
08 Dec 2021 20:56:35,968 INFO : Assigning a DOI.
08 Dec 2021 20:56:38,456 INFO : Assigned DOI: 10.6069/8p39-mv42
08 Dec 2021 20:56:38,459 INFO : Updating access URL to point to the new copy of the data.
08 Dec 2021 20:56:38,465 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
08 Dec 2021 20:56:38,472 INFO : Removing copy permissions given to journal.
08 Dec 2021 20:56:38,484 INFO : Adding read permissions to all users that are folder admins in the source container.
08 Dec 2021 20:56:38,492 INFO : Setting the TargetedMS folder type to 'Experimental Data'
08 Dec 2021 20:56:38,501 INFO : Updating the 'Raw Data' tab configuration
08 Dec 2021 20:56:38,503 INFO : Updating dataFileUrls for run 20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip; targetedms run ID 126754
08 Dec 2021 20:56:38,504 INFO : Updating dataFileUrl...
08 Dec 2021 20:56:38,504 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45/20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyd
08 Dec 2021 20:56:38,504 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells/@files/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45/20210831_Lena_Hess_MS275_samples_final_quan_3transitions.skyd
08 Dec 2021 20:56:38,506 INFO : Updating dataFileUrl...
08 Dec 2021 20:56:38,506 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells_ae265b1b-3ad6-103a-8339-fea6ddf5e014/_temp__2021-12-08_20-46-17/export/xar/experiments_and_runs.xar.exploded/Run122908/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip
08 Dec 2021 20:56:38,506 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/Max%20Perutz%20Labs%20MS%20Facility%20-%20Seiser%20-%20Histone%20acetylation%20in%20HAP%20cells/@files/20210831_Lena_Hess_MS275_samples_final_quan_3transitions_2021-12-03_11-03-45.sky.zip
08 Dec 2021 20:56:38,509 INFO : Creating a reviewer account.
08 Dec 2021 20:56:38,743 INFO : Created reviewer with email: User panorama+reviewer83@proteinms.net
08 Dec 2021 20:56:38,751 INFO : Hiding the Data Pipeline tab.
08 Dec 2021 20:56:38,836 INFO : Emailing submitter.
08 Dec 2021 20:56:38,940 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'