26 Mar 2023 19:50:35,389 DEBUG: Resetting Job ID: da31943a-ae77-103b-a3e9-fea6ddf59764
26 Mar 2023 19:50:35,407 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
26 Mar 2023 19:50:35,408 INFO : Starting to import Skyline document from final_sprg2019_all_charges_template2_tony_2023-03-26_22-50-21.sky.zip
26 Mar 2023 19:50:35,408 INFO : Expanding sprg2019_std_only_onefile.blib
26 Mar 2023 19:50:35,411 INFO : Expanding final_sprg2019_all_charges_template2_tony.skyd
26 Mar 2023 19:50:35,826 INFO : Expanding final_sprg2019_all_charges_template2_tony.sky.view
26 Mar 2023 19:50:35,831 INFO : Expanding final_sprg2019_all_charges_template2_tony.sky
26 Mar 2023 19:50:35,848 INFO : Expanding final_sprg2019_all_charges_template2_tony.skyl
26 Mar 2023 19:50:35,874 INFO : 1% Done
26 Mar 2023 19:50:36,640 DEBUG: Starting to load chromatogram headers
26 Mar 2023 19:50:36,642 DEBUG: Done loading chromatogram headers
26 Mar 2023 19:50:36,816 INFO : Inserting Library Peptides
26 Mar 2023 19:50:36,832 INFO : 2% Done
26 Mar 2023 19:50:36,962 INFO : 3% Done
26 Mar 2023 19:50:37,096 INFO : 5% Done
26 Mar 2023 19:50:37,232 INFO : 6% Done
26 Mar 2023 19:50:37,395 INFO : 7% Done
26 Mar 2023 19:50:37,479 INFO : 8% Done
26 Mar 2023 19:50:37,572 INFO : 10% Done
26 Mar 2023 19:50:37,726 INFO : 11% Done
26 Mar 2023 19:50:37,794 INFO : 12% Done
26 Mar 2023 19:50:37,938 INFO : 13% Done
26 Mar 2023 19:50:38,027 INFO : 14% Done
26 Mar 2023 19:50:38,099 INFO : 15% Done
26 Mar 2023 19:50:38,179 INFO : 16% Done
26 Mar 2023 19:50:38,267 INFO : 17% Done
26 Mar 2023 19:50:38,383 INFO : 18% Done
26 Mar 2023 19:50:38,497 INFO : 19% Done
26 Mar 2023 19:50:38,607 INFO : 21% Done
26 Mar 2023 19:50:38,755 INFO : 22% Done
26 Mar 2023 19:50:38,831 INFO : 23% Done
26 Mar 2023 19:50:38,941 INFO : 24% Done
26 Mar 2023 19:50:39,049 INFO : 25% Done
26 Mar 2023 19:50:39,175 INFO : 26% Done
26 Mar 2023 19:50:39,278 INFO : 27% Done
26 Mar 2023 19:50:39,421 INFO : 28% Done
26 Mar 2023 19:50:39,533 INFO : 29% Done
26 Mar 2023 19:50:39,604 INFO : 30% Done
26 Mar 2023 19:50:39,721 INFO : 31% Done
26 Mar 2023 19:50:39,792 INFO : 32% Done
26 Mar 2023 19:50:39,885 INFO : 33% Done
26 Mar 2023 19:50:40,004 INFO : 34% Done
26 Mar 2023 19:50:40,107 INFO : 35% Done
26 Mar 2023 19:50:40,213 INFO : 36% Done
26 Mar 2023 19:50:40,300 INFO : 37% Done
26 Mar 2023 19:50:40,442 INFO : 38% Done
26 Mar 2023 19:50:40,499 INFO : 39% Done
26 Mar 2023 19:50:40,664 INFO : 40% Done
26 Mar 2023 19:50:40,710 DEBUG: Inserted 50 peptides
26 Mar 2023 19:50:40,768 INFO : 41% Done
26 Mar 2023 19:50:40,856 INFO : 42% Done
26 Mar 2023 19:50:40,931 INFO : 43% Done
26 Mar 2023 19:50:41,029 INFO : 44% Done
26 Mar 2023 19:50:41,184 INFO : 45% Done
26 Mar 2023 19:50:41,286 INFO : 46% Done
26 Mar 2023 19:50:41,354 INFO : 47% Done
26 Mar 2023 19:50:41,475 INFO : 49% Done
26 Mar 2023 19:50:41,616 INFO : 50% Done
26 Mar 2023 19:50:41,781 INFO : 51% Done
26 Mar 2023 19:50:41,838 INFO : 52% Done
26 Mar 2023 19:50:41,943 INFO : 53% Done
26 Mar 2023 19:50:42,019 INFO : 54% Done
26 Mar 2023 19:50:42,181 INFO : 55% Done
26 Mar 2023 19:50:42,296 INFO : 56% Done
26 Mar 2023 19:50:42,360 INFO : 57% Done
26 Mar 2023 19:50:42,472 INFO : 58% Done
26 Mar 2023 19:50:42,578 INFO : 59% Done
26 Mar 2023 19:50:42,646 INFO : 60% Done
26 Mar 2023 19:50:42,717 INFO : 61% Done
26 Mar 2023 19:50:42,846 INFO : 62% Done
26 Mar 2023 19:50:42,912 INFO : 63% Done
26 Mar 2023 19:50:42,997 INFO : 64% Done
26 Mar 2023 19:50:43,132 INFO : 65% Done
26 Mar 2023 19:50:43,264 INFO : 67% Done
26 Mar 2023 19:50:43,402 INFO : 68% Done
26 Mar 2023 19:50:43,507 INFO : 69% Done
26 Mar 2023 19:50:43,634 INFO : 70% Done
26 Mar 2023 19:50:43,709 INFO : 71% Done
26 Mar 2023 19:50:43,780 INFO : 72% Done
26 Mar 2023 19:50:43,923 INFO : 73% Done
26 Mar 2023 19:50:43,992 INFO : 74% Done
26 Mar 2023 19:50:44,233 INFO : 75% Done
26 Mar 2023 19:50:44,369 INFO : 76% Done
26 Mar 2023 19:50:44,437 INFO : 77% Done
26 Mar 2023 19:50:44,517 INFO : 78% Done
26 Mar 2023 19:50:44,740 INFO : 79% Done
26 Mar 2023 19:50:44,829 INFO : 80% Done
26 Mar 2023 19:50:44,914 INFO : 81% Done
26 Mar 2023 19:50:44,914 DEBUG: Inserted 100 peptides
26 Mar 2023 19:50:44,998 INFO : 82% Done
26 Mar 2023 19:50:45,112 INFO : 83% Done
26 Mar 2023 19:50:45,202 INFO : 84% Done
26 Mar 2023 19:50:45,288 INFO : 86% Done
26 Mar 2023 19:50:45,475 INFO : 87% Done
26 Mar 2023 19:50:45,593 INFO : 88% Done
26 Mar 2023 19:50:45,716 INFO : 89% Done
26 Mar 2023 19:50:45,794 INFO : 90% Done
26 Mar 2023 19:50:45,915 INFO : 91% Done
26 Mar 2023 19:50:45,984 INFO : 92% Done
26 Mar 2023 19:50:46,072 INFO : 93% Done
26 Mar 2023 19:50:46,130 INFO : 94% Done
26 Mar 2023 19:50:46,250 INFO : 95% Done
26 Mar 2023 19:50:46,366 INFO : 96% Done
26 Mar 2023 19:50:46,459 INFO : 98% Done
26 Mar 2023 19:50:46,590 DEBUG: Total peptides inserted: 121
26 Mar 2023 19:50:46,591 INFO : Done parsing Skyline document.
26 Mar 2023 19:50:46,862 ERROR: Import failed
org.labkey.targetedms.parser.skyaudit.AuditLogException: Error when parsing audit log file.
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.<init>(SkylineAuditLogParser.java:108)
at org.labkey.targetedms.SkylineAuditLogManager.importAuditLogFile(SkylineAuditLogManager.java:106)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:470)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:248)
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:1074)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1748.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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 17; cvc-complex-type.4: Attribute 'format_version' must appear on element 'audit_log_root'.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.error(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.reportSchemaError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.addDefaultAttributes(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.handleStartElement(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.jaxp.validation.StreamValidatorHelper.validate(Unknown Source)
at org.apache.xerces.jaxp.validation.ValidatorImpl.validate(Unknown Source)
at java.xml/javax.xml.validation.Validator.validate(Validator.java:124)
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.validateXml(SkylineAuditLogParser.java:122)
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.<init>(SkylineAuditLogParser.java:104)
... 27 more
26 Mar 2023 19:50:46,869 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
26 Mar 2023 19:50:46,870 ERROR: Error when parsing audit log file.
org.labkey.api.pipeline.PipelineJobException: Error when parsing audit log file.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:275)
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:1074)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1748.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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: org.labkey.targetedms.parser.skyaudit.AuditLogException: Error when parsing audit log file.
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.<init>(SkylineAuditLogParser.java:108)
at org.labkey.targetedms.SkylineAuditLogManager.importAuditLogFile(SkylineAuditLogManager.java:106)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:470)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:248)
... 24 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 17; cvc-complex-type.4: Attribute 'format_version' must appear on element 'audit_log_root'.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.error(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.reportSchemaError(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.addDefaultAttributes(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.handleStartElement(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaValidator.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.jaxp.validation.StreamValidatorHelper.validate(Unknown Source)
at org.apache.xerces.jaxp.validation.ValidatorImpl.validate(Unknown Source)
at java.xml/javax.xml.validation.Validator.validate(Validator.java:124)
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.validateXml(SkylineAuditLogParser.java:122)
at org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser.<init>(SkylineAuditLogParser.java:104)
... 27 more