04 Aug 2023 10:26:03,960 DEBUG: Resetting Job ID: b335f4a4-1519-103c-9905-fea6ddf5d37c
04 Aug 2023 10:26:03,978 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
04 Aug 2023 10:26:03,979 INFO : Starting to import Skyline document from AutoQC_2023-08-04_13-25-59.sky.zip
04 Aug 2023 10:26:03,979 INFO : Expanding AutoQC.skyd
04 Aug 2023 10:26:04,044 INFO : Expanding AutoQC.sky
04 Aug 2023 10:26:04,049 INFO : Expanding AutoQC.skyl
04 Aug 2023 10:26:04,051 WARN : The version of this Skyline document is 22.2. This is newer than the highest supported version 22.13
04 Aug 2023 10:26:04,056 INFO : 1% Done
04 Aug 2023 10:26:04,074 DEBUG: Starting to load chromatogram headers
04 Aug 2023 10:26:04,076 DEBUG: Done loading chromatogram headers
04 Aug 2023 10:26:10,926 INFO : Inserting PFCA
04 Aug 2023 10:26:10,929 INFO : 2% Done
04 Aug 2023 10:26:10,943 INFO : 4% Done
04 Aug 2023 10:26:10,954 INFO : 5% Done
04 Aug 2023 10:26:10,964 INFO : 7% Done
04 Aug 2023 10:26:10,975 INFO : 8% Done
04 Aug 2023 10:26:10,985 INFO : 10% Done
04 Aug 2023 10:26:10,996 INFO : 11% Done
04 Aug 2023 10:26:11,006 INFO : 13% Done
04 Aug 2023 10:26:11,017 INFO : 14% Done
04 Aug 2023 10:26:11,027 INFO : 15% Done
04 Aug 2023 10:26:11,034 INFO : 17% Done
04 Aug 2023 10:26:11,045 INFO : 19% Done
04 Aug 2023 10:26:11,059 DEBUG: Total molecules inserted: 13
04 Aug 2023 10:26:11,059 INFO : Inserting PFSA
04 Aug 2023 10:26:11,061 INFO : 21% Done
04 Aug 2023 10:26:11,072 INFO : 22% Done
04 Aug 2023 10:26:11,079 INFO : 23% Done
04 Aug 2023 10:26:11,089 INFO : 24% Done
04 Aug 2023 10:26:11,095 INFO : 26% Done
04 Aug 2023 10:26:11,111 INFO : 28% Done
04 Aug 2023 10:26:11,122 DEBUG: Total molecules inserted: 8
04 Aug 2023 10:26:11,122 INFO : Inserting PFECA
04 Aug 2023 10:26:11,124 INFO : 29% Done
04 Aug 2023 10:26:11,129 INFO : 30% Done
04 Aug 2023 10:26:11,135 INFO : 31% Done
04 Aug 2023 10:26:11,142 INFO : 32% Done
04 Aug 2023 10:26:11,152 INFO : 33% Done
04 Aug 2023 10:26:11,159 INFO : 34% Done
04 Aug 2023 10:26:11,166 INFO : 35% Done
04 Aug 2023 10:26:11,179 INFO : 37% Done
04 Aug 2023 10:26:11,190 DEBUG: Total molecules inserted: 10
04 Aug 2023 10:26:11,190 INFO : Inserting PFESA
04 Aug 2023 10:26:11,192 INFO : 38% Done
04 Aug 2023 10:26:11,198 INFO : 39% Done
04 Aug 2023 10:26:11,205 INFO : 40% Done
04 Aug 2023 10:26:11,211 INFO : 41% Done
04 Aug 2023 10:26:11,222 DEBUG: Total molecules inserted: 5
04 Aug 2023 10:26:11,222 INFO : Inserting PFSAm
04 Aug 2023 10:26:11,224 INFO : 42% Done
04 Aug 2023 10:26:11,230 INFO : 43% Done
04 Aug 2023 10:26:11,237 INFO : 45% Done
04 Aug 2023 10:26:11,247 INFO : 46% Done
04 Aug 2023 10:26:11,257 INFO : 48% Done
04 Aug 2023 10:26:11,268 INFO : 49% Done
04 Aug 2023 10:26:11,278 DEBUG: Total molecules inserted: 6
04 Aug 2023 10:26:11,278 INFO : Inserting FTS
04 Aug 2023 10:26:11,281 INFO : 51% Done
04 Aug 2023 10:26:11,291 INFO : 53% Done
04 Aug 2023 10:26:11,303 INFO : 54% Done
04 Aug 2023 10:26:11,313 INFO : 56% Done
04 Aug 2023 10:26:11,322 DEBUG: Total molecules inserted: 4
04 Aug 2023 10:26:11,322 INFO : Inserting FTCA
04 Aug 2023 10:26:11,329 DEBUG: Total molecules inserted: 1
04 Aug 2023 10:26:11,329 INFO : Inserting diPAP
04 Aug 2023 10:26:11,331 INFO : 58% Done
04 Aug 2023 10:26:11,336 DEBUG: Total molecules inserted: 1
04 Aug 2023 10:26:11,336 INFO : Inserting Zwitterionic
04 Aug 2023 10:26:11,344 INFO : 59% Done
04 Aug 2023 10:26:11,350 INFO : 60% Done
04 Aug 2023 10:26:11,355 DEBUG: Total molecules inserted: 3
04 Aug 2023 10:26:11,359 INFO : Done parsing Skyline document.
04 Aug 2023 10:26:11,411 INFO : No group comparisons found.
04 Aug 2023 10:26:11,411 INFO : Calculating calibration curves
04 Aug 2023 10:26:11,412 DEBUG: Calculating calibration curve for PFCA, 1 of 9
04 Aug 2023 10:26:11,511 INFO : 61% Done
04 Aug 2023 10:26:11,511 DEBUG: Calculating calibration curve for PFSA, 2 of 9
04 Aug 2023 10:26:11,589 INFO : 62% Done
04 Aug 2023 10:26:11,589 DEBUG: Calculating calibration curve for PFECA, 3 of 9
04 Aug 2023 10:26:11,689 INFO : 63% Done
04 Aug 2023 10:26:11,689 DEBUG: Calculating calibration curve for PFESA, 4 of 9
04 Aug 2023 10:26:11,762 INFO : 64% Done
04 Aug 2023 10:26:11,762 DEBUG: Calculating calibration curve for PFSAm, 5 of 9
04 Aug 2023 10:26:11,843 DEBUG: Calculating calibration curve for FTS, 6 of 9
04 Aug 2023 10:26:11,877 INFO : 65% Done
04 Aug 2023 10:26:11,877 DEBUG: Calculating calibration curve for FTCA, 7 of 9
04 Aug 2023 10:26:11,891 INFO : 66% Done
04 Aug 2023 10:26:11,891 DEBUG: Calculating calibration curve for diPAP, 8 of 9
04 Aug 2023 10:26:11,904 INFO : 67% Done
04 Aug 2023 10:26:11,904 DEBUG: Calculating calibration curve for Zwitterionic, 9 of 9
04 Aug 2023 10:26:11,942 INFO : 68% Done
04 Aug 2023 10:26:11,949 INFO : Done calculating calibration curves.
04 Aug 2023 10:26:15,455 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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
04 Aug 2023 10:26:15,483 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
04 Aug 2023 10:26:15,484 ERROR: Invalid audit log. Documents with same GUID should have same first audit log entry.
org.labkey.api.pipeline.PipelineJobException: Invalid audit log. Documents with same GUID should have same first audit log entry.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1575.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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