04 Aug 2023 03:00:52,235 DEBUG: Resetting Job ID: 713b4394-14db-103c-9905-fea6ddf5d37c
04 Aug 2023 03:00:52,255 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
04 Aug 2023 03:00:52,256 INFO : Starting to import Skyline document from AutoQC_2023-08-04_06-00-48.sky.zip
04 Aug 2023 03:00:52,256 INFO : Expanding AutoQC.skyd
04 Aug 2023 03:00:52,322 INFO : Expanding AutoQC.sky
04 Aug 2023 03:00:52,326 INFO : Expanding AutoQC.skyl
04 Aug 2023 03:00:52,328 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
04 Aug 2023 03:00:52,334 INFO : 1% Done
04 Aug 2023 03:00:52,356 DEBUG: Starting to load chromatogram headers
04 Aug 2023 03:00:52,358 DEBUG: Done loading chromatogram headers
04 Aug 2023 03:00:52,412 INFO : Inserting PFCA
04 Aug 2023 03:00:52,416 INFO : 2% Done
04 Aug 2023 03:00:52,429 INFO : 4% Done
04 Aug 2023 03:00:52,439 INFO : 5% Done
04 Aug 2023 03:00:52,451 INFO : 7% Done
04 Aug 2023 03:00:52,462 INFO : 8% Done
04 Aug 2023 03:00:52,473 INFO : 10% Done
04 Aug 2023 03:00:52,485 INFO : 11% Done
04 Aug 2023 03:00:52,497 INFO : 13% Done
04 Aug 2023 03:00:52,507 INFO : 14% Done
04 Aug 2023 03:00:52,518 INFO : 15% Done
04 Aug 2023 03:00:52,526 INFO : 17% Done
04 Aug 2023 03:00:52,537 INFO : 19% Done
04 Aug 2023 03:00:52,552 DEBUG: Total molecules inserted: 13
04 Aug 2023 03:00:52,552 INFO : Inserting PFSA
04 Aug 2023 03:00:52,555 INFO : 21% Done
04 Aug 2023 03:00:52,567 INFO : 22% Done
04 Aug 2023 03:00:52,574 INFO : 23% Done
04 Aug 2023 03:00:52,584 INFO : 24% Done
04 Aug 2023 03:00:52,591 INFO : 26% Done
04 Aug 2023 03:00:52,607 INFO : 28% Done
04 Aug 2023 03:00:52,619 DEBUG: Total molecules inserted: 8
04 Aug 2023 03:00:52,619 INFO : Inserting PFECA
04 Aug 2023 03:00:52,621 INFO : 29% Done
04 Aug 2023 03:00:52,626 INFO : 30% Done
04 Aug 2023 03:00:52,632 INFO : 31% Done
04 Aug 2023 03:00:52,639 INFO : 32% Done
04 Aug 2023 03:00:52,650 INFO : 33% Done
04 Aug 2023 03:00:52,657 INFO : 34% Done
04 Aug 2023 03:00:52,664 INFO : 35% Done
04 Aug 2023 03:00:52,676 INFO : 37% Done
04 Aug 2023 03:00:52,687 DEBUG: Total molecules inserted: 10
04 Aug 2023 03:00:52,687 INFO : Inserting PFESA
04 Aug 2023 03:00:52,690 INFO : 38% Done
04 Aug 2023 03:00:52,697 INFO : 39% Done
04 Aug 2023 03:00:52,704 INFO : 40% Done
04 Aug 2023 03:00:52,711 INFO : 41% Done
04 Aug 2023 03:00:52,723 DEBUG: Total molecules inserted: 5
04 Aug 2023 03:00:52,723 INFO : Inserting PFSAm
04 Aug 2023 03:00:52,726 INFO : 42% Done
04 Aug 2023 03:00:52,733 INFO : 43% Done
04 Aug 2023 03:00:52,769 INFO : 45% Done
04 Aug 2023 03:00:52,784 INFO : 46% Done
04 Aug 2023 03:00:52,797 INFO : 48% Done
04 Aug 2023 03:00:52,812 INFO : 49% Done
04 Aug 2023 03:00:52,825 DEBUG: Total molecules inserted: 6
04 Aug 2023 03:00:52,825 INFO : Inserting FTS
04 Aug 2023 03:00:52,828 INFO : 51% Done
04 Aug 2023 03:00:52,842 INFO : 53% Done
04 Aug 2023 03:00:52,858 INFO : 54% Done
04 Aug 2023 03:00:52,872 INFO : 56% Done
04 Aug 2023 03:00:52,883 DEBUG: Total molecules inserted: 4
04 Aug 2023 03:00:52,883 INFO : Inserting FTCA
04 Aug 2023 03:00:52,891 DEBUG: Total molecules inserted: 1
04 Aug 2023 03:00:52,891 INFO : Inserting diPAP
04 Aug 2023 03:00:52,895 INFO : 58% Done
04 Aug 2023 03:00:52,933 DEBUG: Total molecules inserted: 1
04 Aug 2023 03:00:52,933 INFO : Inserting Zwitterionic
04 Aug 2023 03:00:52,946 INFO : 59% Done
04 Aug 2023 03:00:52,959 INFO : 60% Done
04 Aug 2023 03:00:52,969 DEBUG: Total molecules inserted: 3
04 Aug 2023 03:00:52,972 INFO : Done parsing Skyline document.
04 Aug 2023 03:00:53,031 INFO : No group comparisons found.
04 Aug 2023 03:00:53,031 INFO : Calculating calibration curves
04 Aug 2023 03:00:53,032 DEBUG: Calculating calibration curve for PFCA, 1 of 9
04 Aug 2023 03:00:53,153 INFO : 61% Done
04 Aug 2023 03:00:53,153 DEBUG: Calculating calibration curve for PFSA, 2 of 9
04 Aug 2023 03:00:53,250 INFO : 62% Done
04 Aug 2023 03:00:53,250 DEBUG: Calculating calibration curve for PFECA, 3 of 9
04 Aug 2023 03:00:53,390 INFO : 63% Done
04 Aug 2023 03:00:53,390 DEBUG: Calculating calibration curve for PFESA, 4 of 9
04 Aug 2023 03:00:53,471 INFO : 64% Done
04 Aug 2023 03:00:53,471 DEBUG: Calculating calibration curve for PFSAm, 5 of 9
04 Aug 2023 03:00:53,543 DEBUG: Calculating calibration curve for FTS, 6 of 9
04 Aug 2023 03:00:53,578 INFO : 65% Done
04 Aug 2023 03:00:53,578 DEBUG: Calculating calibration curve for FTCA, 7 of 9
04 Aug 2023 03:00:53,597 INFO : 66% Done
04 Aug 2023 03:00:53,598 DEBUG: Calculating calibration curve for diPAP, 8 of 9
04 Aug 2023 03:00:53,615 INFO : 67% Done
04 Aug 2023 03:00:53,615 DEBUG: Calculating calibration curve for Zwitterionic, 9 of 9
04 Aug 2023 03:00:53,658 INFO : 68% Done
04 Aug 2023 03:00:53,666 INFO : Done calculating calibration curves.
04 Aug 2023 03:00:57,297 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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
04 Aug 2023 03:00:57,323 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
04 Aug 2023 03:00:57,324 ERROR: Invalid audit log. Documents with same GUID should have same first audit log entry.
org.labkey.api.pipeline.PipelineJobException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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