04 Aug 2023 10:31:22,116 DEBUG: Resetting Job ID: 53c7ef41-151a-103c-9905-fea6ddf5d37c
04 Aug 2023 10:31:22,140 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
04 Aug 2023 10:31:22,141 INFO : Starting to import Skyline document from AutoQC_2023-08-04_13-31-18.sky.zip
04 Aug 2023 10:31:22,141 INFO : Expanding AutoQC.skyd
04 Aug 2023 10:31:22,211 INFO : Expanding AutoQC.sky
04 Aug 2023 10:31:22,215 INFO : Expanding AutoQC.skyl
04 Aug 2023 10:31:22,217 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
04 Aug 2023 10:31:22,220 INFO : 1% Done
04 Aug 2023 10:31:22,239 DEBUG: Starting to load chromatogram headers
04 Aug 2023 10:31:22,241 DEBUG: Done loading chromatogram headers
04 Aug 2023 10:31:22,304 INFO : Inserting PFCA
04 Aug 2023 10:31:22,307 INFO : 2% Done
04 Aug 2023 10:31:22,322 INFO : 4% Done
04 Aug 2023 10:31:22,336 INFO : 5% Done
04 Aug 2023 10:31:22,349 INFO : 7% Done
04 Aug 2023 10:31:22,363 INFO : 8% Done
04 Aug 2023 10:31:22,377 INFO : 10% Done
04 Aug 2023 10:31:22,390 INFO : 11% Done
04 Aug 2023 10:31:22,403 INFO : 13% Done
04 Aug 2023 10:31:22,416 INFO : 14% Done
04 Aug 2023 10:31:22,429 INFO : 15% Done
04 Aug 2023 10:31:22,439 INFO : 17% Done
04 Aug 2023 10:31:22,452 INFO : 19% Done
04 Aug 2023 10:31:22,468 DEBUG: Total molecules inserted: 13
04 Aug 2023 10:31:22,468 INFO : Inserting PFSA
04 Aug 2023 10:31:22,470 INFO : 21% Done
04 Aug 2023 10:31:22,482 INFO : 22% Done
04 Aug 2023 10:31:22,489 INFO : 23% Done
04 Aug 2023 10:31:22,499 INFO : 24% Done
04 Aug 2023 10:31:22,506 INFO : 26% Done
04 Aug 2023 10:31:22,523 INFO : 28% Done
04 Aug 2023 10:31:22,538 DEBUG: Total molecules inserted: 8
04 Aug 2023 10:31:22,538 INFO : Inserting PFECA
04 Aug 2023 10:31:22,540 INFO : 29% Done
04 Aug 2023 10:31:22,546 INFO : 30% Done
04 Aug 2023 10:31:22,553 INFO : 31% Done
04 Aug 2023 10:31:22,560 INFO : 32% Done
04 Aug 2023 10:31:22,571 INFO : 33% Done
04 Aug 2023 10:31:22,579 INFO : 34% Done
04 Aug 2023 10:31:22,587 INFO : 35% Done
04 Aug 2023 10:31:22,604 INFO : 37% Done
04 Aug 2023 10:31:22,617 DEBUG: Total molecules inserted: 10
04 Aug 2023 10:31:22,617 INFO : Inserting PFESA
04 Aug 2023 10:31:22,620 INFO : 38% Done
04 Aug 2023 10:31:22,628 INFO : 39% Done
04 Aug 2023 10:31:22,636 INFO : 40% Done
04 Aug 2023 10:31:22,643 INFO : 41% Done
04 Aug 2023 10:31:22,657 DEBUG: Total molecules inserted: 5
04 Aug 2023 10:31:22,657 INFO : Inserting PFSAm
04 Aug 2023 10:31:22,659 INFO : 42% Done
04 Aug 2023 10:31:22,667 INFO : 43% Done
04 Aug 2023 10:31:22,676 INFO : 45% Done
04 Aug 2023 10:31:22,688 INFO : 46% Done
04 Aug 2023 10:31:22,701 INFO : 48% Done
04 Aug 2023 10:31:22,713 INFO : 49% Done
04 Aug 2023 10:31:22,724 DEBUG: Total molecules inserted: 6
04 Aug 2023 10:31:22,724 INFO : Inserting FTS
04 Aug 2023 10:31:22,726 INFO : 51% Done
04 Aug 2023 10:31:22,738 INFO : 53% Done
04 Aug 2023 10:31:22,750 INFO : 54% Done
04 Aug 2023 10:31:22,761 INFO : 56% Done
04 Aug 2023 10:31:22,772 DEBUG: Total molecules inserted: 4
04 Aug 2023 10:31:22,772 INFO : Inserting FTCA
04 Aug 2023 10:31:22,780 DEBUG: Total molecules inserted: 1
04 Aug 2023 10:31:22,780 INFO : Inserting diPAP
04 Aug 2023 10:31:22,782 INFO : 58% Done
04 Aug 2023 10:31:22,789 DEBUG: Total molecules inserted: 1
04 Aug 2023 10:31:22,789 INFO : Inserting Zwitterionic
04 Aug 2023 10:31:22,799 INFO : 59% Done
04 Aug 2023 10:31:22,806 INFO : 60% Done
04 Aug 2023 10:31:22,812 DEBUG: Total molecules inserted: 3
04 Aug 2023 10:31:22,814 INFO : Done parsing Skyline document.
04 Aug 2023 10:31:22,867 INFO : No group comparisons found.
04 Aug 2023 10:31:22,867 INFO : Calculating calibration curves
04 Aug 2023 10:31:22,867 DEBUG: Calculating calibration curve for PFCA, 1 of 9
04 Aug 2023 10:31:22,985 INFO : 61% Done
04 Aug 2023 10:31:22,985 DEBUG: Calculating calibration curve for PFSA, 2 of 9
04 Aug 2023 10:31:23,087 INFO : 62% Done
04 Aug 2023 10:31:23,088 DEBUG: Calculating calibration curve for PFECA, 3 of 9
04 Aug 2023 10:31:23,205 INFO : 63% Done
04 Aug 2023 10:31:23,205 DEBUG: Calculating calibration curve for PFESA, 4 of 9
04 Aug 2023 10:31:23,263 INFO : 64% Done
04 Aug 2023 10:31:23,263 DEBUG: Calculating calibration curve for PFSAm, 5 of 9
04 Aug 2023 10:31:23,322 DEBUG: Calculating calibration curve for FTS, 6 of 9
04 Aug 2023 10:31:23,352 INFO : 65% Done
04 Aug 2023 10:31:23,352 DEBUG: Calculating calibration curve for FTCA, 7 of 9
04 Aug 2023 10:31:23,365 INFO : 66% Done
04 Aug 2023 10:31:23,365 DEBUG: Calculating calibration curve for diPAP, 8 of 9
04 Aug 2023 10:31:23,378 INFO : 67% Done
04 Aug 2023 10:31:23,378 DEBUG: Calculating calibration curve for Zwitterionic, 9 of 9
04 Aug 2023 10:31:23,413 INFO : 68% Done
04 Aug 2023 10:31:23,420 INFO : Done calculating calibration curves.
04 Aug 2023 10:31:26,929 ERROR: Import failed
org.labkey.targetedms.parser.skyaudit.AuditLogException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineAuditLogManager.persistAuditLog(SkylineAuditLogManager.java:269)
at org.labkey.targetedms.SkylineAuditLogManager.importAuditLogFile(SkylineAuditLogManager.java:109)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:472)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:249)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
04 Aug 2023 10:31:26,957 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
04 Aug 2023 10:31:26,958 ERROR: Invalid audit log. Documents with same GUID should have same first audit log entry.
org.labkey.api.pipeline.PipelineJobException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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:833)
Caused by: org.labkey.targetedms.parser.skyaudit.AuditLogException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineAuditLogManager.persistAuditLog(SkylineAuditLogManager.java:269)
at org.labkey.targetedms.SkylineAuditLogManager.importAuditLogFile(SkylineAuditLogManager.java:109)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:472)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:249)
... 24 more