31 May 2022 16:35:41,475 INFO : Validating data for a ProteomeXchange submission.
31 May 2022 16:35:41,477 INFO : =======================================
31 May 2022 16:35:41,630 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask' at location 'webserver'
31 May 2022 16:35:41,631 INFO : Validating data for experiment Id: 1298, validation Id: 69
31 May 2022 16:35:41,753 INFO : Validating data for 12 Skyline documents in 1 folders
31 May 2022 16:35:41,953 INFO : Sample file validation for Skyline document: MRM analysis of two VP40 peptides for standard curve with VLPs_2021-04-28_10-51-43.sky.zip
31 May 2022 16:35:41,953 INFO : Found all sample files.
31 May 2022 16:35:42,094 INFO : Sample file validation for Skyline document: p24pep assay result for assay sensitivity and specificity_2021-04-28_17-25-32.sky.zip
31 May 2022 16:35:42,094 INFO : Found all sample files.
31 May 2022 16:35:42,163 INFO : Sample file validation for Skyline document: Other species PBS with virions_2021-10-04_10-39-31.sky.zip
31 May 2022 16:35:42,163 INFO : Found all sample files.
31 May 2022 16:35:42,287 INFO : Sample file validation for Skyline document: VP40 p12 variant_2021-10-04_10-30-51.sky.zip
31 May 2022 16:35:42,288 INFO : Found all sample files.
31 May 2022 16:35:42,376 INFO : Sample file validation for Skyline document: p24pep result for six HIV-1 and TB co-infected patients_2021-04-28_17-37-41.sky.zip
31 May 2022 16:35:42,376 INFO : Found all sample files.
31 May 2022 16:35:42,460 INFO : Sample file validation for Skyline document: p24pep assay using HIV-1 seroconversion panel of patient_2021-04-28_17-33-57.sky.zip
31 May 2022 16:35:42,461 INFO : Found all sample files.
31 May 2022 16:35:42,522 INFO : Sample file validation for Skyline document: p24pep standard curve using recombinant protein_2021-04-28_17-45-11.sky.zip
31 May 2022 16:35:42,522 INFO : Found all sample files.
31 May 2022 16:35:42,594 INFO : Sample file validation for Skyline document: VP40_peptide_12_EBOV_2021-04-28_14-41-14.sky.zip
31 May 2022 16:35:42,594 INFO : Found all sample files.
31 May 2022 16:35:42,682 INFO : Sample file validation for Skyline document: CFP-10pep result for six HIV-1 and TB co-infected patients_2021-04-28_17-57-22.sky.zip
31 May 2022 16:35:42,682 INFO : Found all sample files.
31 May 2022 16:35:42,968 INFO : Sample file validation for Skyline document: HIV-1 adult cohort for p24pep assay validation_2021-04-28_14-54-12.sky.zip
31 May 2022 16:35:42,968 INFO : Found all sample files.
31 May 2022 16:35:43,118 INFO : Sample file validation for Skyline document: VP40_peptide_12_SUDV_2021-04-28_14-43-06.sky.zip
31 May 2022 16:35:43,118 INFO : Found all sample files.
31 May 2022 16:35:43,193 INFO : Sample file validation for Skyline document: HIV-1 infant cohort for p24pep assay validation_2021-04-28_14-57-49.sky.zip
31 May 2022 16:35:43,193 INFO : Found all sample files.
31 May 2022 16:35:43,298 INFO : Modifications validation:
31 May 2022 16:35:43,298 INFO : VALID MODIFICATIONS:
31 May 2022 16:35:43,298 INFO : 264: Label:13C(6)15N(2) (C-term K):
31 May 2022 16:35:43,298 INFO : VP40_peptide_12_EBOV_2021-04-28_14-41-14.sky.zip
31 May 2022 16:35:43,298 INFO : VP40_peptide_12_SUDV_2021-04-28_14-43-06.sky.zip
31 May 2022 16:35:43,298 INFO : 265: Label:13C(6)15N(4) (R): UNIMOD:267 - Label:13C(6)15N(4)
31 May 2022 16:35:43,298 INFO : MRM analysis of two VP40 peptides for standard curve with VLPs_2021-04-28_10-51-43.sky.zip
31 May 2022 16:35:43,298 INFO : VP40 p12 variant_2021-10-04_10-30-51.sky.zip
31 May 2022 16:35:43,298 INFO : INVALID MODIFICATIONS (No Unimod ID):
31 May 2022 16:35:43,298 INFO : 266: Label:13C15N: No UNIMOD Id
31 May 2022 16:35:43,298 INFO : p24pep assay result for assay sensitivity and specificity_2021-04-28_17-25-32.sky.zip
31 May 2022 16:35:43,298 INFO : p24pep result for six HIV-1 and TB co-infected patients_2021-04-28_17-37-41.sky.zip
31 May 2022 16:35:43,299 INFO : p24pep standard curve using recombinant protein_2021-04-28_17-45-11.sky.zip
31 May 2022 16:35:43,299 INFO : p24pep assay using HIV-1 seroconversion panel of patient_2021-04-28_17-33-57.sky.zip
31 May 2022 16:35:43,299 INFO : CFP-10pep result for six HIV-1 and TB co-infected patients_2021-04-28_17-57-22.sky.zip
31 May 2022 16:35:43,299 INFO : HIV-1 adult cohort for p24pep assay validation_2021-04-28_14-54-12.sky.zip
31 May 2022 16:35:43,299 INFO : HIV-1 infant cohort for p24pep assay validation_2021-04-28_14-57-49.sky.zip
31 May 2022 16:35:43,494 FATAL:
31 May 2022 16:35:43,566 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 16:35:43,609 FATAL: Data validation failed
31 May 2022 16:35:43,651 INFO : Failed to complete task 'org.labkey.panoramapublic.pipeline.PxDataValidationTask'
31 May 2022 16:35:43,652 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