01 May 2021 02:27:36,892 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
01 May 2021 02:27:36,896 INFO : Starting to import Skyline document from METRIC_Exploris_Dabney_Tox_All_QCs_2021-05-01_05-20-02.sky.zip
01 May 2021 02:27:36,897 INFO : Expanding METRIC_Exploris_Dabney_Tox_All_QCs.skyd
01 May 2021 02:27:37,378 INFO : Expanding METRIC_Exploris_Dabney_Tox_All_QCs.sky.view
01 May 2021 02:27:37,403 INFO : Expanding METRIC_Exploris_Dabney_Tox_All_QCs.sky
01 May 2021 02:27:37,463 WARN : The version of this Skyline document is 20.22. This is newer than the highest supported version 20.2
01 May 2021 02:27:37,515 INFO : 2% Done
01 May 2021 02:27:37,628 DEBUG: Starting to load chromatogram headers
01 May 2021 02:27:37,630 DEBUG: Done loading chromatogram headers
01 May 2021 02:27:38,101 INFO : Inserting gi|162648|gb|AAA51411.1|
01 May 2021 02:27:38,168 INFO : 9% Done
01 May 2021 02:27:38,351 INFO : 19% Done
01 May 2021 02:27:38,544 INFO : 26% Done
01 May 2021 02:27:38,725 INFO : 37% Done
01 May 2021 02:27:38,964 INFO : 48% Done
01 May 2021 02:27:39,185 INFO : 60% Done
01 May 2021 02:27:39,329 DEBUG: Total peptides inserted: 6
01 May 2021 02:27:39,331 INFO : Done parsing Skyline document.
01 May 2021 02:27:39,336 INFO : No group comparisons found.
01 May 2021 02:27:39,336 INFO : Calculating calibration curves
01 May 2021 02:27:39,337 DEBUG: Calculating calibration curve for gi|162648|gb|AAA51411.1|, 1 of 1
01 May 2021 02:29:26,206 INFO : 68% Done
01 May 2021 02:29:26,209 INFO : Done calculating calibration curves.
01 May 2021 02:29:28,287 DEBUG: Updating previously imported data for sample file D:\QC\QC_RAW_Files\20210325_BSA_QC-002.raw in QC folder. 1 of 63
01 May 2021 02:31:28,290 ERROR: Failed to set status to 'RUNNING, 69%' for '/data/labkey/files/NCSU - METRIC/METRIC Internal/METRIC QC/Exploris_Dabney/@files/METRIC_Exploris_Dabney_Tox_All_QCs_2021-05-01_05-20-02.sky_2021-05-01_02-27-36.log'.
org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1013)
at org.labkey.api.data.DbScope.beginTransaction(DbScope.java:544)
at org.labkey.api.data.DbScope.ensureTransaction(DbScope.java:490)
at org.labkey.pipeline.api.PipelineStatusManager.updateStatusFile(PipelineStatusManager.java:259)
at org.labkey.pipeline.api.PipelineStatusManager.setStatusFile(PipelineStatusManager.java:201)
at org.labkey.pipeline.api.PipelineServiceImpl.setStatus(PipelineServiceImpl.java:657)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:606)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:590)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:571)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.doUpdate(SkylineDocImporter.java:2803)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.updateProgress(SkylineDocImporter.java:2794)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor$ProgressPart.updateProgress(SkylineDocImporter.java:2841)
at org.labkey.targetedms.SkylineDocImporter.deleteOldSampleFiles(SkylineDocImporter.java:602)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:442)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:244)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1652.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.sql.SQLException: Cannot get a connection, pool error Timeout waiting for idle object
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:142)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:734)
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1009)
... 38 more
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:442)
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:352)
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:134)
... 40 more
01 May 2021 02:31:28,629 ERROR: Import failed
org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1013)
at org.labkey.api.data.DbScope.beginTransaction(DbScope.java:544)
at org.labkey.api.data.DbScope.ensureTransaction(DbScope.java:490)
at org.labkey.pipeline.api.PipelineStatusManager.updateStatusFile(PipelineStatusManager.java:259)
at org.labkey.pipeline.api.PipelineStatusManager.setStatusFile(PipelineStatusManager.java:201)
at org.labkey.pipeline.api.PipelineServiceImpl.setStatus(PipelineServiceImpl.java:657)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:606)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:590)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:571)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.doUpdate(SkylineDocImporter.java:2803)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.updateProgress(SkylineDocImporter.java:2794)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor$ProgressPart.updateProgress(SkylineDocImporter.java:2841)
at org.labkey.targetedms.SkylineDocImporter.deleteOldSampleFiles(SkylineDocImporter.java:602)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:442)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:244)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1652.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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:832)
Caused by: java.sql.SQLException: Cannot get a connection, pool error Timeout waiting for idle object
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:142)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:734)
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1009)
... 38 more
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:442)
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:352)
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:134)
... 40 more
01 May 2021 02:31:28,735 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
01 May 2021 02:31:28,737 ERROR: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1013)
at org.labkey.api.data.DbScope.beginTransaction(DbScope.java:544)
at org.labkey.api.data.DbScope.ensureTransaction(DbScope.java:490)
at org.labkey.pipeline.api.PipelineStatusManager.updateStatusFile(PipelineStatusManager.java:259)
at org.labkey.pipeline.api.PipelineStatusManager.setStatusFile(PipelineStatusManager.java:201)
at org.labkey.pipeline.api.PipelineServiceImpl.setStatus(PipelineServiceImpl.java:657)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:606)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:590)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:571)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.doUpdate(SkylineDocImporter.java:2803)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.updateProgress(SkylineDocImporter.java:2794)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor$ProgressPart.updateProgress(SkylineDocImporter.java:2841)
at org.labkey.targetedms.SkylineDocImporter.deleteOldSampleFiles(SkylineDocImporter.java:602)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:442)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:244)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1652.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
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$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.sql.SQLException: Cannot get a connection, pool error Timeout waiting for idle object
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:142)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:734)
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1009)
... 38 more
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:442)
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:352)
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:134)
... 40 more
01 May 2021 02:31:29,035 ERROR: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.tomcat.dbcp.dbcp2.BasicDataSource@136de93a
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1013)
at org.labkey.api.data.DbScope.beginTransaction(DbScope.java:544)
at org.labkey.api.data.DbScope.ensureTransaction(DbScope.java:490)
at org.labkey.pipeline.api.PipelineStatusManager.updateStatusFile(PipelineStatusManager.java:259)
at org.labkey.pipeline.api.PipelineStatusManager.setStatusFile(PipelineStatusManager.java:201)
at org.labkey.pipeline.api.PipelineServiceImpl.setStatus(PipelineServiceImpl.java:657)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:606)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:590)
at org.labkey.api.pipeline.PipelineJob.setStatus(PipelineJob.java:571)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.doUpdate(SkylineDocImporter.java:2803)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor.updateProgress(SkylineDocImporter.java:2794)
at org.labkey.targetedms.SkylineDocImporter$ProgressMonitor$ProgressPart.updateProgress(SkylineDocImporter.java:2841)
at org.labkey.targetedms.SkylineDocImporter.deleteOldSampleFiles(SkylineDocImporter.java:602)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:442)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:244)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1652.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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:832)
Caused by: java.sql.SQLException: Cannot get a connection, pool error Timeout waiting for idle object
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:142)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:734)
at org.labkey.api.data.DbScope.getPooledConnection(DbScope.java:1009)
... 38 more
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:442)
at org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:352)
at org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:134)
... 40 more