25 Oct 2021 12:35:29,672 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
25 Oct 2021 12:35:29,679 INFO : Starting to import Skyline document from plasma_combined_whole-EVs_2021-10-25_12-34-15.sky.zip
25 Oct 2021 12:35:29,680 INFO : Expanding Human_canonical_uniprot_June2019.protdb
25 Oct 2021 12:35:32,460 INFO : Expanding plasma_combined_whole-EVs.elib
25 Oct 2021 12:35:32,681 INFO : Expanding plasma_combined_whole-EVs.skyd
25 Oct 2021 12:35:38,923 INFO : Expanding plasma_combined_whole-EVs.sky.view
25 Oct 2021 12:35:40,205 INFO : Expanding plasma_combined_whole-EVs.sky
25 Oct 2021 12:35:44,404 INFO : Expanding plasma_combined_whole-EVs.skyl
25 Oct 2021 12:35:44,411 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
25 Oct 2021 12:36:21,954 DEBUG: Starting to load chromatogram headers
25 Oct 2021 12:36:22,672 DEBUG: Done loading chromatogram headers
25 Oct 2021 12:36:22,800 INFO : Inserting sp|A0A075B6H9|LV469_HUMAN
25 Oct 2021 12:36:23,056 DEBUG: Total peptides inserted: 3
25 Oct 2021 12:36:23,059 INFO : Inserting sp|A0A075B6I0|LV861_HUMAN
25 Oct 2021 12:36:23,265 DEBUG: Total peptides inserted: 3
25 Oct 2021 12:36:23,268 INFO : Inserting sp|A0A075B6I4|LVX54_HUMAN
25 Oct 2021 12:36:23,321 DEBUG: Total peptides inserted: 1
25 Oct 2021 12:36:23,325 INFO : Inserting sp|A0A075B6I9|LV746_HUMAN
25 Oct 2021 12:36:23,529 DEBUG: Total peptides inserted: 4
25 Oct 2021 12:36:23,534 INFO : Inserting sp|A0A075B6J1|LV537_HUMAN
25 Oct 2021 12:36:23,539 DEBUG: Total peptides inserted: 1
25 Oct 2021 12:36:23,542 INFO : Inserting sp|A0A075B6J9|LV218_HUMAN
25 Oct 2021 12:36:23,741 DEBUG: Total peptides inserted: 4
25 Oct 2021 12:36:23,745 INFO : Inserting sp|A0A075B6K0|LV316_HUMAN
25 Oct 2021 12:36:23,964 DEBUG: Total peptides inserted: 4
25 Oct 2021 12:36:23,966 INFO : Inserting sp|A0A075B6K2|LV312_HUMAN
25 Oct 2021 12:36:24,073 DEBUG: Total peptides inserted: 2
25 Oct 2021 12:36:24,075 INFO : Inserting sp|A0A075B6K4|LV310_HUMAN
25 Oct 2021 12:36:24,648 ERROR: Import failed
org.labkey.targetedms.PanoramaBadDataException: Duplicate precursor found: KYAYWYQQK, charge 2, mz 639.319305. Documents uploaded to a peptide library folder should contain unique precursors.
at org.labkey.targetedms.SkylineDocImporter.insertPrecursor(SkylineDocImporter.java:1598)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1418)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:1299)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:396)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:246)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1613.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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:831)
25 Oct 2021 12:36:24,695 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
25 Oct 2021 12:36:24,697 ERROR: Duplicate precursor found: KYAYWYQQK, charge 2, mz 639.319305. Documents uploaded to a peptide library folder should contain unique precursors.
org.labkey.api.pipeline.PipelineJobException: Duplicate precursor found: KYAYWYQQK, charge 2, mz 639.319305. Documents uploaded to a peptide library folder should contain unique precursors.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:270)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1613.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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:831)
Caused by: org.labkey.targetedms.PanoramaBadDataException: Duplicate precursor found: KYAYWYQQK, charge 2, mz 639.319305. Documents uploaded to a peptide library folder should contain unique precursors.
at org.labkey.targetedms.SkylineDocImporter.insertPrecursor(SkylineDocImporter.java:1598)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1418)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:1299)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:396)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:246)
... 24 more