04 Aug 2023 05:39:05,783 DEBUG: Resetting Job ID: 5c2b4be6-14f1-103c-9905-fea6ddf5d37c
04 Aug 2023 05:39:05,801 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
04 Aug 2023 05:39:05,802 INFO : Starting to import Skyline document from AutoQC_2023-08-04_08-39-01.sky.zip
04 Aug 2023 05:39:05,802 INFO : Expanding AutoQC.skyd
04 Aug 2023 05:39:05,865 INFO : Expanding AutoQC.sky
04 Aug 2023 05:39:05,869 INFO : Expanding AutoQC.skyl
04 Aug 2023 05:39:05,872 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
04 Aug 2023 05:39:05,875 INFO : 1% Done
04 Aug 2023 05:39:05,893 DEBUG: Starting to load chromatogram headers
04 Aug 2023 05:39:05,895 DEBUG: Done loading chromatogram headers
04 Aug 2023 05:39:05,948 INFO : Inserting PFCA
04 Aug 2023 05:39:05,951 INFO : 2% Done
04 Aug 2023 05:39:05,963 INFO : 4% Done
04 Aug 2023 05:39:05,973 INFO : 5% Done
04 Aug 2023 05:39:05,985 INFO : 7% Done
04 Aug 2023 05:39:05,995 INFO : 8% Done
04 Aug 2023 05:39:06,006 INFO : 10% Done
04 Aug 2023 05:39:06,017 INFO : 11% Done
04 Aug 2023 05:39:06,028 INFO : 13% Done
04 Aug 2023 05:39:06,039 INFO : 14% Done
04 Aug 2023 05:39:06,049 INFO : 15% Done
04 Aug 2023 05:39:06,056 INFO : 17% Done
04 Aug 2023 05:39:06,067 INFO : 19% Done
04 Aug 2023 05:39:06,082 DEBUG: Total molecules inserted: 13
04 Aug 2023 05:39:06,082 INFO : Inserting PFSA
04 Aug 2023 05:39:06,084 INFO : 21% Done
04 Aug 2023 05:39:06,096 INFO : 22% Done
04 Aug 2023 05:39:06,102 INFO : 23% Done
04 Aug 2023 05:39:06,114 INFO : 24% Done
04 Aug 2023 05:39:06,121 INFO : 26% Done
04 Aug 2023 05:39:06,137 INFO : 28% Done
04 Aug 2023 05:39:06,148 DEBUG: Total molecules inserted: 8
04 Aug 2023 05:39:06,148 INFO : Inserting PFECA
04 Aug 2023 05:39:06,150 INFO : 29% Done
04 Aug 2023 05:39:06,156 INFO : 30% Done
04 Aug 2023 05:39:06,163 INFO : 31% Done
04 Aug 2023 05:39:06,170 INFO : 32% Done
04 Aug 2023 05:39:06,181 INFO : 33% Done
04 Aug 2023 05:39:06,188 INFO : 34% Done
04 Aug 2023 05:39:06,195 INFO : 35% Done
04 Aug 2023 05:39:06,208 INFO : 37% Done
04 Aug 2023 05:39:06,219 DEBUG: Total molecules inserted: 10
04 Aug 2023 05:39:06,219 INFO : Inserting PFESA
04 Aug 2023 05:39:06,221 INFO : 38% Done
04 Aug 2023 05:39:06,228 INFO : 39% Done
04 Aug 2023 05:39:06,235 INFO : 40% Done
04 Aug 2023 05:39:06,242 INFO : 41% Done
04 Aug 2023 05:39:06,253 DEBUG: Total molecules inserted: 5
04 Aug 2023 05:39:06,253 INFO : Inserting PFSAm
04 Aug 2023 05:39:06,255 INFO : 42% Done
04 Aug 2023 05:39:06,261 INFO : 43% Done
04 Aug 2023 05:39:06,269 INFO : 45% Done
04 Aug 2023 05:39:06,279 INFO : 46% Done
04 Aug 2023 05:39:06,290 INFO : 48% Done
04 Aug 2023 05:39:06,301 INFO : 49% Done
04 Aug 2023 05:39:06,312 DEBUG: Total molecules inserted: 6
04 Aug 2023 05:39:06,312 INFO : Inserting FTS
04 Aug 2023 05:39:06,314 INFO : 51% Done
04 Aug 2023 05:39:06,326 INFO : 53% Done
04 Aug 2023 05:39:06,338 INFO : 54% Done
04 Aug 2023 05:39:06,350 INFO : 56% Done
04 Aug 2023 05:39:06,359 DEBUG: Total molecules inserted: 4
04 Aug 2023 05:39:06,359 INFO : Inserting FTCA
04 Aug 2023 05:39:06,366 DEBUG: Total molecules inserted: 1
04 Aug 2023 05:39:06,366 INFO : Inserting diPAP
04 Aug 2023 05:39:06,368 INFO : 58% Done
04 Aug 2023 05:39:06,374 DEBUG: Total molecules inserted: 1
04 Aug 2023 05:39:06,374 INFO : Inserting Zwitterionic
04 Aug 2023 05:39:06,382 INFO : 59% Done
04 Aug 2023 05:39:06,389 INFO : 60% Done
04 Aug 2023 05:39:06,395 DEBUG: Total molecules inserted: 3
04 Aug 2023 05:39:06,396 INFO : Done parsing Skyline document.
04 Aug 2023 05:39:06,448 INFO : No group comparisons found.
04 Aug 2023 05:39:06,448 INFO : Calculating calibration curves
04 Aug 2023 05:39:06,449 DEBUG: Calculating calibration curve for PFCA, 1 of 9
04 Aug 2023 05:39:06,562 INFO : 61% Done
04 Aug 2023 05:39:06,562 DEBUG: Calculating calibration curve for PFSA, 2 of 9
04 Aug 2023 05:39:06,661 INFO : 62% Done
04 Aug 2023 05:39:06,661 DEBUG: Calculating calibration curve for PFECA, 3 of 9
04 Aug 2023 05:39:06,776 INFO : 63% Done
04 Aug 2023 05:39:06,776 DEBUG: Calculating calibration curve for PFESA, 4 of 9
04 Aug 2023 05:39:06,838 INFO : 64% Done
04 Aug 2023 05:39:06,838 DEBUG: Calculating calibration curve for PFSAm, 5 of 9
04 Aug 2023 05:39:06,905 DEBUG: Calculating calibration curve for FTS, 6 of 9
04 Aug 2023 05:39:06,939 INFO : 65% Done
04 Aug 2023 05:39:06,939 DEBUG: Calculating calibration curve for FTCA, 7 of 9
04 Aug 2023 05:39:06,952 INFO : 66% Done
04 Aug 2023 05:39:06,953 DEBUG: Calculating calibration curve for diPAP, 8 of 9
04 Aug 2023 05:39:06,966 INFO : 67% Done
04 Aug 2023 05:39:06,966 DEBUG: Calculating calibration curve for Zwitterionic, 9 of 9
04 Aug 2023 05:39:07,008 INFO : 68% Done
04 Aug 2023 05:39:07,016 INFO : Done calculating calibration curves.
04 Aug 2023 05:39:10,529 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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
04 Aug 2023 05:39:10,554 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
04 Aug 2023 05:39:10,555 ERROR: Invalid audit log. Documents with same GUID should have same first audit log entry.
org.labkey.api.pipeline.PipelineJobException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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