29 May 2022 15:20:07,612 INFO : Validating data for a ProteomeXchange submission.
29 May 2022 15:20:07,614 INFO : =======================================
29 May 2022 15:20:07,772 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask' at location 'webserver'
29 May 2022 15:20:07,773 INFO : Validating data for experiment Id: 1437, validation Id: 10
29 May 2022 15:20:07,848 INFO : Validating data for 3 Skyline documents in 1 folders
29 May 2022 15:20:07,897 INFO : Sample file validation for Skyline document: Fig2B_centroid_CIA_PRM_v4_MS2only_unique_protein_5640_9606_IOP1_20200214_v1.1_2022-04-27_15-36-21.sky.zip
29 May 2022 15:20:07,897 INFO : Found all sample files.
29 May 2022 15:20:07,946 INFO : Sample file validation for Skyline document: Fig1C_centroid_CIA_PRM_v5_MS2only_unique_protein_5640_9606_20210910_v1.1_2022-04-27_15-57-33.sky.zip
29 May 2022 15:20:07,947 INFO : Found all sample files.
29 May 2022 15:20:07,993 INFO : Sample file validation for Skyline document: Fig4BtoD_centroid_CIA_PRM_v3_MS2only_unique_protein_5640_9606_20190515_v1.1_2022-04-27_17-08-05.sky.zip
29 May 2022 15:20:07,993 INFO : Found all sample files.
29 May 2022 15:20:08,132 INFO : Modifications validation:
29 May 2022 15:20:08,133 INFO : VALID MODIFICATIONS:
29 May 2022 15:20:08,133 INFO : 20: Carbamidomethyl (C): UNIMOD:4 - Carbamidomethyl
29 May 2022 15:20:08,133 INFO : Fig4BtoD_centroid_CIA_PRM_v3_MS2only_unique_protein_5640_9606_20190515_v1.1_2022-04-27_17-08-05.sky.zip
29 May 2022 15:20:08,133 INFO : Fig2B_centroid_CIA_PRM_v4_MS2only_unique_protein_5640_9606_IOP1_20200214_v1.1_2022-04-27_15-36-21.sky.zip
29 May 2022 15:20:08,133 INFO : Fig1C_centroid_CIA_PRM_v5_MS2only_unique_protein_5640_9606_20210910_v1.1_2022-04-27_15-57-33.sky.zip
29 May 2022 15:20:08,133 INFO : INVALID MODIFICATIONS (No Unimod ID):
29 May 2022 15:20:09,261 FATAL:
29 May 2022 15:20:09,344 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)
29 May 2022 15:20:09,388 FATAL: Data validation failed
29 May 2022 15:20:09,430 INFO : Failed to complete task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask'
29 May 2022 15:20:09,431 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