07 Jun 2019 13:47:00,974 INFO : Copying experiment "Developing a robust assay to monitor and quantify key players of metabolic pathways during adipogenesis by targeted proteomics" from folder /ISAS Dortmund - Ahrends Lab/Metabolic pathways targeted proteomics to /Panorama Public/2019/Ahrends Lab - Metabolic pathways targeted proteomics
07 Jun 2019 13:47:00,975 INFO : =======================================
07 Jun 2019 13:47:01,305 INFO : Starting to run task 'org.labkey.targetedms.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
07 Jun 2019 13:47:01,306 INFO :
07 Jun 2019 13:47:01,306 INFO : Exporting experiment.
07 Jun 2019 13:47:05,866 INFO :
07 Jun 2019 13:47:05,867 INFO : Experiment export completed successfully.
07 Jun 2019 13:47:05,867 INFO : Successfully completed task 'org.labkey.targetedms.pipeline.ExperimentExportTask'
07 Jun 2019 13:47:05,970 INFO : Starting to run task 'org.labkey.targetedms.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
07 Jun 2019 13:47:05,970 INFO :
07 Jun 2019 13:47:05,971 INFO : Importing experiment.
07 Jun 2019 13:47:05,977 INFO : Loading folder properties (folder type, settings and active modules)
07 Jun 2019 13:47:06,170 INFO : Done importing folder properties (folder type, settings and active modules)
07 Jun 2019 13:47:06,174 INFO : Loading xar
07 Jun 2019 13:47:06,972 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip'
07 Jun 2019 13:47:06,978 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Core'
07 Jun 2019 13:47:06,984 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Output'
07 Jun 2019 13:47:06,984 DEBUG: Protocol import complete
07 Jun 2019 13:47:07,010 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-5458:Developing+a+robust+assay+to+monitor+and+quantify++key+players+of+metabolic+pathways+during+adipogenesis+by+targeted+proteomics'
07 Jun 2019 13:47:07,010 DEBUG: Experiment/Run group import complete
07 Jun 2019 13:47:07,049 DEBUG: Protocol action set import complete
07 Jun 2019 13:47:07,066 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip'
07 Jun 2019 13:47:07,302 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-5458:213972d2-6800-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,316 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-5458:21397558-6800-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,317 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Core'
07 Jun 2019 13:47:07,326 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Output'
07 Jun 2019 13:47:07,328 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-5458:2139759d-6800-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,344 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip'
07 Jun 2019 13:47:07,361 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-5458:80df9ba4-67fe-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,399 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-5458:80df7da6-67fe-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,399 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Core'
07 Jun 2019 13:47:07,406 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-5458:TargetedMS.ImportSkyZip.Output'
07 Jun 2019 13:47:07,408 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-5458:80df9bcb-67fe-1037-b0bb-3013bb9b3bab'
07 Jun 2019 13:47:07,411 DEBUG: Trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final.sky.zip into the system
07 Jun 2019 13:47:07,416 INFO : Starting import from All pathways 2 prots each for quantification final.sky.zip
07 Jun 2019 13:47:07,429 INFO : Starting to import Skyline document from All pathways 2 prots each for quantification final.sky.zip
07 Jun 2019 13:47:07,442 INFO : Expanding Metabo Prots refined RT calc.irtdb
07 Jun 2019 13:47:07,443 INFO : Expanding complete-mouse-spectral final version 10.08.16.blib
07 Jun 2019 13:47:07,448 INFO : Expanding 2013_05_20_mouse_consensus_final_true_lib.blib
07 Jun 2019 13:47:07,449 INFO : Expanding All pathways 2 prots each for quantification final_for publication (20Prots).skyd
07 Jun 2019 13:47:07,900 INFO : Expanding All pathways 2 prots each for quantification final_for publication (20Prots).sky.view
07 Jun 2019 13:47:07,901 INFO : Expanding All pathways 2 prots each for quantification final_for publication (20Prots).sky
07 Jun 2019 13:47:09,386 INFO : Inserting sp|P19096|FAS_MOUSE
07 Jun 2019 13:47:10,773 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:11,071 INFO : Inserting sp|Q9Z2A7|DGAT1_MOUSE
07 Jun 2019 13:47:12,403 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:12,715 INFO : Inserting sp|Q8C0N2|GPAT3_MOUSE
07 Jun 2019 13:47:14,055 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:14,396 INFO : Inserting sp|Q8VDP6|CDIPT_MOUSE
07 Jun 2019 13:47:15,826 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:16,000 INFO : Inserting sp|P98191|CDS1_MOUSE
07 Jun 2019 13:47:16,770 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:16,826 INFO : Inserting sp|Q99L43|CDS2_MOUSE
07 Jun 2019 13:47:17,394 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:17,522 INFO : Inserting sp|P97363|SPTC2_MOUSE
07 Jun 2019 13:47:18,834 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:19,157 INFO : Inserting sp|Q924Z4|CERS2_MOUSE
07 Jun 2019 13:47:20,528 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:20,760 INFO : Inserting sp|P05064|ALDOA_MOUSE
07 Jun 2019 13:47:21,946 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:22,203 INFO : Inserting sp|P12382|K6PL_MOUSE
07 Jun 2019 13:47:23,536 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:23,804 INFO : Inserting sp|P14142|GTR4_MOUSE
07 Jun 2019 13:47:25,142 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:25,406 INFO : Inserting sp|P47968|RPIA_MOUSE
07 Jun 2019 13:47:27,244 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:27,573 INFO : Inserting sp|P40142|TKT_MOUSE
07 Jun 2019 13:47:28,692 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:29,015 INFO : Inserting sp|Q9CZU6|CISY_MOUSE
07 Jun 2019 13:47:30,389 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:30,542 INFO : Inserting sp|Q9D6R2|IDH3A_MOUSE
07 Jun 2019 13:47:31,853 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:32,084 INFO : Inserting sp|P81122|IRS2_MOUSE
07 Jun 2019 13:47:33,360 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:33,618 INFO : Inserting sp|Q08857|CD36_MOUSE
07 Jun 2019 13:47:35,476 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:35,793 INFO : Inserting sp|P53566|CEBPA_MOUSE
07 Jun 2019 13:47:36,665 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:36,819 INFO : Inserting sp|P28033|CEBPB_MOUSE
07 Jun 2019 13:47:38,104 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:38,374 INFO : Inserting sp|P04117|FABP4_MOUSE
07 Jun 2019 13:47:39,477 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:39,741 INFO : Inserting sp|P37238|PPARG_MOUSE
07 Jun 2019 13:47:41,723 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:43,854 INFO : Completed import of Skyline document from All pathways 2 prots each for quantification final.sky.zip
07 Jun 2019 13:47:43,858 DEBUG: Finished trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final.sky.zip into the system
07 Jun 2019 13:47:43,858 DEBUG: Trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final/All%20pathways%202%20prots%20each%20for%20quantification%20final_for%20publication%20(20Prots).skyd into the system
07 Jun 2019 13:47:43,860 DEBUG: Finished trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final/All%20pathways%202%20prots%20each%20for%20quantification%20final_for%20publication%20(20Prots).skyd into the system
07 Jun 2019 13:47:43,860 DEBUG: Trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd into the system
07 Jun 2019 13:47:43,861 DEBUG: Finished trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd into the system
07 Jun 2019 13:47:43,861 DEBUG: Trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/Calibration%20curves.sky.zip into the system
07 Jun 2019 13:47:43,864 INFO : Starting import from Calibration curves.sky.zip
07 Jun 2019 13:47:43,871 INFO : Starting to import Skyline document from Calibration curves.sky.zip
07 Jun 2019 13:47:43,872 INFO : Expanding Metabo Prots refined RT calc.irtdb
07 Jun 2019 13:47:43,872 INFO : Expanding complete-mouse-spectral final version 10.08.16.blib
07 Jun 2019 13:47:43,873 INFO : Expanding 2013_05_20_mouse_consensus_final_true_lib.blib
07 Jun 2019 13:47:43,873 INFO : Expanding All pathways 2 prots each for quantification final for calibration curve.skyd
07 Jun 2019 13:47:43,930 INFO : Expanding All pathways 2 prots each for quantification final for calibration curve.sky.view
07 Jun 2019 13:47:43,930 INFO : Expanding All pathways 2 prots each for quantification final for calibration curve.sky
07 Jun 2019 13:47:44,083 INFO : Calculated iRT regression line from full standard list.
07 Jun 2019 13:47:44,273 INFO : Inserting sp|P19096|FAS_MOUSE
07 Jun 2019 13:47:44,472 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:44,480 INFO : Inserting sp|Q9Z2A7|DGAT1_MOUSE
07 Jun 2019 13:47:44,679 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:44,687 INFO : Inserting sp|Q8C0N2|GPAT3_MOUSE
07 Jun 2019 13:47:44,863 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:44,872 INFO : Inserting sp|Q8VDP6|CDIPT_MOUSE
07 Jun 2019 13:47:45,065 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:45,073 INFO : Inserting sp|P98191|CDS1_MOUSE
07 Jun 2019 13:47:45,164 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:45,172 INFO : Inserting sp|Q99L43|CDS2_MOUSE
07 Jun 2019 13:47:45,250 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:45,258 INFO : Inserting sp|P97363|SPTC2_MOUSE
07 Jun 2019 13:47:45,439 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:45,599 INFO : Inserting sp|Q1A3B0|CERS3_MOUSE
07 Jun 2019 13:47:46,005 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:46,013 INFO : Inserting sp|Q924Z4|CERS2_MOUSE
07 Jun 2019 13:47:46,182 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:46,268 INFO : Inserting sp|Q9D6K9|CERS5_MOUSE
07 Jun 2019 13:47:46,370 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:46,379 INFO : Inserting sp|P05064|ALDOA_MOUSE
07 Jun 2019 13:47:46,537 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:46,600 INFO : Inserting sp|P47857|K6PF_MOUSE
07 Jun 2019 13:47:46,726 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:46,735 INFO : Inserting sp|P12382|K6PL_MOUSE
07 Jun 2019 13:47:46,901 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:47,004 INFO : Inserting sp|Q9WUA3|K6PP_MOUSE
07 Jun 2019 13:47:47,202 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:47,211 INFO : Inserting sp|P14142|GTR4_MOUSE
07 Jun 2019 13:47:47,381 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:47,388 INFO : Inserting sp|P47968|RPIA_MOUSE
07 Jun 2019 13:47:47,633 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:47,641 INFO : Inserting sp|P40142|TKT_MOUSE
07 Jun 2019 13:47:47,793 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:47,801 INFO : Inserting sp|Q9CZU6|CISY_MOUSE
07 Jun 2019 13:47:48,007 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:48,017 INFO : Inserting sp|Q9D6R2|IDH3A_MOUSE
07 Jun 2019 13:47:48,204 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:48,346 INFO : Inserting sp|P70404|IDHG1_MOUSE
07 Jun 2019 13:47:48,550 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:48,654 INFO : Inserting sp|P54071|IDHP_MOUSE
07 Jun 2019 13:47:48,931 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:49,075 INFO : Inserting sp|P35569|IRS1_MOUSE
07 Jun 2019 13:47:49,393 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:49,402 INFO : Inserting sp|P81122|IRS2_MOUSE
07 Jun 2019 13:47:49,675 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:49,684 INFO : Inserting sp|Q08857|CD36_MOUSE
07 Jun 2019 13:47:49,942 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:49,951 INFO : Inserting sp|P53566|CEBPA_MOUSE
07 Jun 2019 13:47:50,041 INFO : Total peptides inserted: 1
07 Jun 2019 13:47:50,049 INFO : Inserting sp|P28033|CEBPB_MOUSE
07 Jun 2019 13:47:50,233 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:50,242 INFO : Inserting sp|P04117|FABP4_MOUSE
07 Jun 2019 13:47:50,398 INFO : Total peptides inserted: 2
07 Jun 2019 13:47:50,406 INFO : Inserting sp|P37238|PPARG_MOUSE
07 Jun 2019 13:47:50,707 INFO : Total peptides inserted: 3
07 Jun 2019 13:47:52,620 INFO : Completed import of Skyline document from Calibration curves.sky.zip
07 Jun 2019 13:47:52,625 DEBUG: Finished trying to load data file file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/Calibration%20curves.sky.zip into the system
07 Jun 2019 13:47:52,646 INFO : Done importing xar
07 Jun 2019 13:47:52,649 INFO : Loading etl definitions
07 Jun 2019 13:47:52,651 INFO : Loading wikis
07 Jun 2019 13:47:52,653 INFO : 0 wikis imported
07 Jun 2019 13:47:52,653 INFO : Done importing wikis
07 Jun 2019 13:47:52,772 INFO : Loading pages and webpart properties
07 Jun 2019 13:47:52,906 INFO : Done importing pages and webpart properties
07 Jun 2019 13:47:52,907 INFO :
07 Jun 2019 13:47:52,907 INFO : Experiment import completed successfully.
07 Jun 2019 13:47:52,908 INFO : Successfully completed task 'org.labkey.targetedms.pipeline.ExperimentImportTask'
07 Jun 2019 13:47:52,970 INFO : Starting to run task 'org.labkey.targetedms.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
07 Jun 2019 13:47:52,971 INFO :
07 Jun 2019 13:47:52,971 INFO : Finishing up experiment copy.
07 Jun 2019 13:47:52,974 INFO : Creating a new TargetedMS experiment entry in targetedms.ExperimentAnnotations.
07 Jun 2019 13:47:53,211 INFO : Updating access URL to point to the new copy of the data.
07 Jun 2019 13:47:53,374 INFO : Setting the 'copied' timestamp on the JournalExperiment table.
07 Jun 2019 13:47:53,377 INFO : Removing copy permissions given to journal.
07 Jun 2019 13:47:53,517 INFO : Adding read permissions to all users that are folder admins in the source container.
07 Jun 2019 13:47:53,596 INFO : Setting the TargetedMS folder type to 'Experimental Data'
07 Jun 2019 13:47:53,610 INFO : Updating the 'Raw Data' tab configuration
07 Jun 2019 13:47:53,617 INFO : Updating dataFileUrls for run All pathways 2 prots each for quantification final.sky.zip; targetedms run ID 67700
07 Jun 2019 13:47:53,679 ERROR: Data path does not exist: /data/labkey/files/Panorama Public/2019/Ahrends Lab - Metabolic pathways targeted proteomics/@files/All pathways 2 prots each for quantification final/All pathways 2 prots each for quantification final.sky.zip
07 Jun 2019 13:47:54,032 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.CopyExperimentFinalTask'
07 Jun 2019 13:47:54,034 ERROR: Unable to update all data file paths.
org.labkey.api.pipeline.PipelineJobException: Unable to update all data file paths.
at org.labkey.targetedms.pipeline.CopyExperimentFinalTask.run(CopyExperimentFinalTask.java:99)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:795)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1026)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor2551.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865)
at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:835)
Caused by: org.labkey.api.pipeline.PipelineJobException: Unable to update all data file paths.
at org.labkey.targetedms.pipeline.CopyExperimentFinalTask.finishUp(CopyExperimentFinalTask.java:223)
at org.labkey.targetedms.pipeline.CopyExperimentFinalTask.run(CopyExperimentFinalTask.java:95)
... 23 more
07 Jun 2019 13:52:41,429 INFO : Retrying job.
07 Jun 2019 13:52:41,431 DEBUG: Database indicates active task ID is org.labkey.targetedms.pipeline.CopyExperimentFinalTask
07 Jun 2019 13:52:41,431 DEBUG: Retry details: Old Job ID: f61f9df6-6b92-1037-b0bb-3013bb9b3bab
07 Jun 2019 13:52:41,468 INFO : Starting to run task 'org.labkey.targetedms.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
07 Jun 2019 13:52:41,468 INFO :
07 Jun 2019 13:52:41,468 INFO : Finishing up experiment copy.
07 Jun 2019 13:52:41,471 INFO : Creating a new TargetedMS experiment entry in targetedms.ExperimentAnnotations.
07 Jun 2019 13:52:41,508 INFO : Updating access URL to point to the new copy of the data.
07 Jun 2019 13:52:41,518 INFO : Setting the 'copied' timestamp on the JournalExperiment table.
07 Jun 2019 13:52:41,521 INFO : Removing copy permissions given to journal.
07 Jun 2019 13:52:41,558 INFO : Adding read permissions to all users that are folder admins in the source container.
07 Jun 2019 13:52:41,601 INFO : Setting the TargetedMS folder type to 'Experimental Data'
07 Jun 2019 13:52:41,609 INFO : Updating the 'Raw Data' tab configuration
07 Jun 2019 13:52:41,616 INFO : Updating dataFileUrls for run All pathways 2 prots each for quantification final.sky.zip; targetedms run ID 67700
07 Jun 2019 13:52:41,617 INFO : Updating dataFileUrl...
07 Jun 2019 13:52:41,617 INFO : from: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final.sky.zip
07 Jun 2019 13:52:41,618 INFO : to: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/All%20pathways%202%20prots%20each%20for%20quantification%20final.sky.zip
07 Jun 2019 13:52:41,624 INFO : Updating dataFileUrl...
07 Jun 2019 13:52:41,625 INFO : from: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66842/All%20pathways%202%20prots%20each%20for%20quantification%20final/All%20pathways%202%20prots%20each%20for%20quantification%20final_for%20publication%20(20Prots).skyd
07 Jun 2019 13:52:41,625 INFO : to: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/All%20pathways%202%20prots%20each%20for%20quantification%20final/All%20pathways%202%20prots%20each%20for%20quantification%20final_for%20publication%20(20Prots).skyd
07 Jun 2019 13:52:41,645 INFO : Updating dataFileUrls for run Calibration curves.sky.zip; targetedms run ID 67701
07 Jun 2019 13:52:41,646 INFO : Adding ExpData for .skyd file
07 Jun 2019 13:52:41,647 INFO : Updating dataFileUrl...
07 Jun 2019 13:52:41,647 INFO : from: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd
07 Jun 2019 13:52:41,648 INFO : to: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd
07 Jun 2019 13:52:41,653 INFO : Updating dataFileUrl...
07 Jun 2019 13:52:41,653 INFO : from: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/Calibration%20curves.sky.zip
07 Jun 2019 13:52:41,654 INFO : to: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/Calibration%20curves.sky.zip
07 Jun 2019 13:52:41,659 INFO : Updating dataFileUrl...
07 Jun 2019 13:52:41,659 INFO : from: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/export/xar/experiments_and_runs.xar.exploded/Run66840/Calibration%20curves/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd
07 Jun 2019 13:52:41,660 INFO : to: file:///data/labkey/files/Panorama%20Public/2019/Ahrends%20Lab%20-%20Metabolic%20pathways%20targeted%20proteomics/@files/All%20pathways%202%20prots%20each%20for%20quantification%20final%20for%20calibration%20curve.skyd
07 Jun 2019 13:52:41,790 INFO : Successfully completed task 'org.labkey.targetedms.pipeline.CopyExperimentFinalTask'