04 Aug 2023 02:45:15,065 DEBUG: Resetting Job ID: 5a69ce1e-14d9-103c-9905-fea6ddf5d37c
04 Aug 2023 02:45:15,082 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
04 Aug 2023 02:45:15,084 INFO : Starting to import Skyline document from AutoQC_2023-08-04_05-45-11.sky.zip
04 Aug 2023 02:45:15,084 INFO : Expanding AutoQC.skyd
04 Aug 2023 02:45:15,149 INFO : Expanding AutoQC.sky
04 Aug 2023 02:45:15,153 INFO : Expanding AutoQC.skyl
04 Aug 2023 02:45:15,155 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
04 Aug 2023 02:45:15,158 INFO : 1% Done
04 Aug 2023 02:45:15,177 DEBUG: Starting to load chromatogram headers
04 Aug 2023 02:45:15,179 DEBUG: Done loading chromatogram headers
04 Aug 2023 02:45:15,236 INFO : Inserting PFCA
04 Aug 2023 02:45:15,239 INFO : 2% Done
04 Aug 2023 02:45:15,251 INFO : 4% Done
04 Aug 2023 02:45:15,261 INFO : 5% Done
04 Aug 2023 02:45:15,272 INFO : 7% Done
04 Aug 2023 02:45:15,282 INFO : 8% Done
04 Aug 2023 02:45:15,293 INFO : 10% Done
04 Aug 2023 02:45:15,303 INFO : 11% Done
04 Aug 2023 02:45:15,313 INFO : 13% Done
04 Aug 2023 02:45:15,324 INFO : 14% Done
04 Aug 2023 02:45:15,334 INFO : 15% Done
04 Aug 2023 02:45:15,341 INFO : 17% Done
04 Aug 2023 02:45:15,351 INFO : 19% Done
04 Aug 2023 02:45:15,366 DEBUG: Total molecules inserted: 13
04 Aug 2023 02:45:15,366 INFO : Inserting PFSA
04 Aug 2023 02:45:15,368 INFO : 21% Done
04 Aug 2023 02:45:15,379 INFO : 22% Done
04 Aug 2023 02:45:15,386 INFO : 23% Done
04 Aug 2023 02:45:15,396 INFO : 24% Done
04 Aug 2023 02:45:15,403 INFO : 26% Done
04 Aug 2023 02:45:15,420 INFO : 28% Done
04 Aug 2023 02:45:15,431 DEBUG: Total molecules inserted: 8
04 Aug 2023 02:45:15,431 INFO : Inserting PFECA
04 Aug 2023 02:45:15,433 INFO : 29% Done
04 Aug 2023 02:45:15,438 INFO : 30% Done
04 Aug 2023 02:45:15,445 INFO : 31% Done
04 Aug 2023 02:45:15,452 INFO : 32% Done
04 Aug 2023 02:45:15,462 INFO : 33% Done
04 Aug 2023 02:45:15,469 INFO : 34% Done
04 Aug 2023 02:45:15,475 INFO : 35% Done
04 Aug 2023 02:45:15,489 INFO : 37% Done
04 Aug 2023 02:45:15,501 DEBUG: Total molecules inserted: 10
04 Aug 2023 02:45:15,501 INFO : Inserting PFESA
04 Aug 2023 02:45:15,503 INFO : 38% Done
04 Aug 2023 02:45:15,510 INFO : 39% Done
04 Aug 2023 02:45:15,516 INFO : 40% Done
04 Aug 2023 02:45:15,522 INFO : 41% Done
04 Aug 2023 02:45:15,533 DEBUG: Total molecules inserted: 5
04 Aug 2023 02:45:15,533 INFO : Inserting PFSAm
04 Aug 2023 02:45:15,535 INFO : 42% Done
04 Aug 2023 02:45:15,542 INFO : 43% Done
04 Aug 2023 02:45:15,548 INFO : 45% Done
04 Aug 2023 02:45:15,559 INFO : 46% Done
04 Aug 2023 02:45:15,569 INFO : 48% Done
04 Aug 2023 02:45:15,580 INFO : 49% Done
04 Aug 2023 02:45:15,591 DEBUG: Total molecules inserted: 6
04 Aug 2023 02:45:15,591 INFO : Inserting FTS
04 Aug 2023 02:45:15,593 INFO : 51% Done
04 Aug 2023 02:45:15,604 INFO : 53% Done
04 Aug 2023 02:45:15,616 INFO : 54% Done
04 Aug 2023 02:45:15,626 INFO : 56% Done
04 Aug 2023 02:45:15,635 DEBUG: Total molecules inserted: 4
04 Aug 2023 02:45:15,635 INFO : Inserting FTCA
04 Aug 2023 02:45:15,642 DEBUG: Total molecules inserted: 1
04 Aug 2023 02:45:15,642 INFO : Inserting diPAP
04 Aug 2023 02:45:15,644 INFO : 58% Done
04 Aug 2023 02:45:15,650 DEBUG: Total molecules inserted: 1
04 Aug 2023 02:45:15,650 INFO : Inserting Zwitterionic
04 Aug 2023 02:45:15,658 INFO : 59% Done
04 Aug 2023 02:45:15,664 INFO : 60% Done
04 Aug 2023 02:45:15,670 DEBUG: Total molecules inserted: 3
04 Aug 2023 02:45:15,671 INFO : Done parsing Skyline document.
04 Aug 2023 02:45:15,721 INFO : No group comparisons found.
04 Aug 2023 02:45:15,721 INFO : Calculating calibration curves
04 Aug 2023 02:45:15,721 DEBUG: Calculating calibration curve for PFCA, 1 of 9
04 Aug 2023 02:45:15,823 INFO : 61% Done
04 Aug 2023 02:45:15,823 DEBUG: Calculating calibration curve for PFSA, 2 of 9
04 Aug 2023 02:45:15,902 INFO : 62% Done
04 Aug 2023 02:45:15,902 DEBUG: Calculating calibration curve for PFECA, 3 of 9
04 Aug 2023 02:45:16,005 INFO : 63% Done
04 Aug 2023 02:45:16,005 DEBUG: Calculating calibration curve for PFESA, 4 of 9
04 Aug 2023 02:45:16,064 INFO : 64% Done
04 Aug 2023 02:45:16,064 DEBUG: Calculating calibration curve for PFSAm, 5 of 9
04 Aug 2023 02:45:16,122 DEBUG: Calculating calibration curve for FTS, 6 of 9
04 Aug 2023 02:45:16,151 INFO : 65% Done
04 Aug 2023 02:45:16,151 DEBUG: Calculating calibration curve for FTCA, 7 of 9
04 Aug 2023 02:45:16,165 INFO : 66% Done
04 Aug 2023 02:45:16,165 DEBUG: Calculating calibration curve for diPAP, 8 of 9
04 Aug 2023 02:45:16,178 INFO : 67% Done
04 Aug 2023 02:45:16,178 DEBUG: Calculating calibration curve for Zwitterionic, 9 of 9
04 Aug 2023 02:45:16,214 INFO : 68% Done
04 Aug 2023 02:45:16,224 INFO : Done calculating calibration curves.
04 Aug 2023 02:45:19,722 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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
04 Aug 2023 02:45:19,748 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
04 Aug 2023 02:45:19,748 ERROR: Invalid audit log. Documents with same GUID should have same first audit log entry.
org.labkey.api.pipeline.PipelineJobException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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