31 May 2022 16:04:07,534 INFO : Validating data for a ProteomeXchange submission.
31 May 2022 16:04:07,535 INFO : =======================================
31 May 2022 16:04:07,691 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask' at location 'webserver'
31 May 2022 16:04:07,693 INFO : Validating data for experiment Id: 1339, validation Id: 53
31 May 2022 16:04:07,811 INFO : Validating data for 10 Skyline documents in 1 folders
31 May 2022 16:04:07,928 INFO : Sample file validation for Skyline document: CFP-10pep peak feature analysis in spiked-in samples_2021-11-10_10-57-06.sky.zip
31 May 2022 16:04:07,928 INFO : Found all sample files.
31 May 2022 16:04:08,052 INFO : Sample file validation for Skyline document: NHP TB plasma CFP10_MRM_2021-11-09_12-52-46.sky.zip
31 May 2022 16:04:08,052 INFO : Found all sample files.
31 May 2022 16:04:08,513 INFO : Sample file validation for Skyline document: 137 adult TB patient CFP10_2021-11-10_14-11-19.sky.zip
31 May 2022 16:04:08,513 INFO : Found all sample files.
31 May 2022 16:04:08,637 INFO : Sample file validation for Skyline document: 10 adult TB patient with repeating CFP10_2021-11-09_12-49-05.sky.zip
31 May 2022 16:04:08,637 INFO : Found all sample files.
31 May 2022 16:04:08,701 INFO : Sample file validation for Skyline document: PUSH pediatric cohort CFP10_MRM_2021-11-10_16-33-36.sky.zip
31 May 2022 16:04:08,701 INFO : Found all sample files.
31 May 2022 16:04:08,758 INFO : Sample file validation for Skyline document: 31 pediatric participants from Dominican Republic cohort_2021-11-09_12-50-10.sky.zip
31 May 2022 16:04:08,758 INFO : Found all sample files.
31 May 2022 16:04:08,865 INFO : Sample file validation for Skyline document: 18 adult TB patient with two sampling points CFP10_2021-11-09_12-49-48.sky.zip
31 May 2022 16:04:08,866 INFO : Found all sample files.
31 May 2022 16:04:08,922 INFO : Sample file validation for Skyline document: CFP-10 LOD estimation_2021-11-09_12-51-33.sky.zip
31 May 2022 16:04:08,922 INFO : Found all sample files.
31 May 2022 16:04:09,017 INFO : Sample file validation for Skyline document: NHP TB BAL CFP10_MRM_2021-11-09_12-52-18.sky.zip
31 May 2022 16:04:09,017 INFO : Found all sample files.
31 May 2022 16:04:09,072 INFO : Sample file validation for Skyline document: CFP-10 standard curve_2021-11-09_12-51-58.sky.zip
31 May 2022 16:04:09,072 INFO : Found all sample files.
31 May 2022 16:04:09,174 INFO : Modifications validation:
31 May 2022 16:04:09,174 INFO : VALID MODIFICATIONS:
31 May 2022 16:04:09,174 INFO : 216: Label:13C(6)15N(4) (R): UNIMOD:267 - Label:13C(6)15N(4)
31 May 2022 16:04:09,174 INFO : 137 adult TB patient CFP10_2021-11-10_14-11-19.sky.zip
31 May 2022 16:04:09,174 INFO : NHP TB plasma CFP10_MRM_2021-11-09_12-52-46.sky.zip
31 May 2022 16:04:09,174 INFO : PUSH pediatric cohort CFP10_MRM_2021-11-10_16-33-36.sky.zip
31 May 2022 16:04:09,174 INFO : 10 adult TB patient with repeating CFP10_2021-11-09_12-49-05.sky.zip
31 May 2022 16:04:09,174 INFO : 18 adult TB patient with two sampling points CFP10_2021-11-09_12-49-48.sky.zip
31 May 2022 16:04:09,174 INFO : 31 pediatric participants from Dominican Republic cohort_2021-11-09_12-50-10.sky.zip
31 May 2022 16:04:09,174 INFO : NHP TB BAL CFP10_MRM_2021-11-09_12-52-18.sky.zip
31 May 2022 16:04:09,174 INFO : CFP-10 LOD estimation_2021-11-09_12-51-33.sky.zip
31 May 2022 16:04:09,174 INFO : CFP-10 standard curve_2021-11-09_12-51-58.sky.zip
31 May 2022 16:04:09,174 INFO : CFP-10pep peak feature analysis in spiked-in samples_2021-11-10_10-57-06.sky.zip
31 May 2022 16:04:09,174 INFO : INVALID MODIFICATIONS (No Unimod ID):
31 May 2022 16:04:09,261 FATAL:
31 May 2022 16:04:09,330 FATAL: Error validating experiment data
java.lang.NullPointerException: Cannot invoke "java.lang.Comparable.compareTo(Object)" because the return value of "java.util.function.Function.apply(Object)" is null
at java.base/java.util.Comparator.lambda$comparing$77a9974f$1(Comparator.java:473)
at java.base/java.util.Comparator.lambda$thenComparing$36697e65$1(Comparator.java:220)
at java.base/java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
at java.base/java.util.TimSort.sort(TimSort.java:220)
at java.base/java.util.Arrays.sort(Arrays.java:1307)
at java.base/java.util.ArrayList.sort(ArrayList.java:1721)
at org.labkey.panoramapublic.proteomexchange.validator.SpecLibValidator.areSameSources(SpecLibValidator.java:191)
at org.labkey.panoramapublic.proteomexchange.validator.SpecLibValidator.validate(SpecLibValidator.java:125)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validateLibraries(DataValidator.java:89)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validate(DataValidator.java:72)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validateExperiment(DataValidator.java:63)
at org.labkey.panoramapublic.pipeline.PxDataValidationTask.doValidation(PxDataValidationTask.java:64)
at org.labkey.panoramapublic.pipeline.PxDataValidationTask.run(PxDataValidationTask.java:35)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:841)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1077)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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)
31 May 2022 16:04:09,375 FATAL: Data validation failed
31 May 2022 16:04:09,418 INFO : Failed to complete task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask'
31 May 2022 16:04:09,419 ERROR: Cannot invoke "java.lang.Comparable.compareTo(Object)" because the return value of "java.util.function.Function.apply(Object)" is null
org.labkey.panoramapublic.pipeline.PxDataValidationTask$1: Cannot invoke "java.lang.Comparable.compareTo(Object)" because the return value of "java.util.function.Function.apply(Object)" is null
at org.labkey.panoramapublic.pipeline.PxDataValidationTask.doValidation(PxDataValidationTask.java:82)
at org.labkey.panoramapublic.pipeline.PxDataValidationTask.run(PxDataValidationTask.java:35)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:841)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1077)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$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: java.lang.NullPointerException: Cannot invoke "java.lang.Comparable.compareTo(Object)" because the return value of "java.util.function.Function.apply(Object)" is null
at java.base/java.util.Comparator.lambda$comparing$77a9974f$1(Comparator.java:473)
at java.base/java.util.Comparator.lambda$thenComparing$36697e65$1(Comparator.java:220)
at java.base/java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
at java.base/java.util.TimSort.sort(TimSort.java:220)
at java.base/java.util.Arrays.sort(Arrays.java:1307)
at java.base/java.util.ArrayList.sort(ArrayList.java:1721)
at org.labkey.panoramapublic.proteomexchange.validator.SpecLibValidator.areSameSources(SpecLibValidator.java:191)
at org.labkey.panoramapublic.proteomexchange.validator.SpecLibValidator.validate(SpecLibValidator.java:125)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validateLibraries(DataValidator.java:89)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validate(DataValidator.java:72)
at org.labkey.panoramapublic.proteomexchange.validator.DataValidator.validateExperiment(DataValidator.java:63)
at org.labkey.panoramapublic.pipeline.PxDataValidationTask.doValidation(PxDataValidationTask.java:64)
... 23 more