java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999_79.96633052074999-ATAA-5 from peptide YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999-ATAA-12_79.96633052074999-ATAA-5.

GitHub | jflucier | 2 months ago
  1. 0

    GitHub comment 56#251440488

    GitHub | 2 months ago | jflucier
    java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999_79.96633052074999-ATAA-5 from peptide YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999-ATAA-12_79.96633052074999-ATAA-5.
  2. 0

    Attempting to create duplicate peptide key

    GitHub | 4 months ago | paulstodghill
    java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: NAQMAEKPVVSMPSSTIK_15.99491461956 from peptide NAQMAEKPVVSMPSSTIK_15.99491461956-ATAA-12.
  3. 0

    Importing Data Canceled - Attempting to create duplicate peptide key

    GitHub | 1 year ago | GoogleCodeExporter
    java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: RIHMEKEMEMKK_15.994915-ATAA-4.
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  5. 0

    Peptide ILVISAVILVK presents no parent protein.

    GitHub | 1 year ago | GoogleCodeExporter
    java.lang.IllegalArgumentException: Peptide ILVISAVILVK presents no parent protein.
  6. 0

    JBAC had a hiccup and didn't spin up new elastic agents. Looking at the logs we've noticed the following exception: {noformat} 2015-02-10 07:28:48,486 ERROR [scheduler_Worker-4] [JobRunShell] Job elastic agent monitor job group.elastic agent monitor job threw an unhandled Exception: java.lang.IllegalArgumentException: duplicate key: QueuedResultKey{resultKey=J64SPT-UNIT2-UNIT-5, timestamp=53729201374254818} at com.google.common.base.Preconditions.checkArgument(Preconditions.java:115) at com.google.common.collect.RegularImmutableMap.<init>(RegularImmutableMap.java:72) at com.google.common.collect.ImmutableMap$Builder.fromEntryList(ImmutableMap.java:245) at com.google.common.collect.ImmutableMap$Builder.build(ImmutableMap.java:231) at com.google.common.collect.Maps.uniqueIndex(Maps.java:681) at com.google.common.collect.Maps.uniqueIndex(Maps.java:637) at com.atlassian.bamboo.v2.build.queue.QueueManagerView.getQueueView(QueueManagerView.java:68) at com.atlassian.bamboo.agent.elastic.schedule.ElasticRunningInstancesOptimizerImpl.getRequirementSetsOfQueuedExecutables(ElasticRunningInstancesOptimizerImpl.java:622) at com.atlassian.bamboo.agent.elastic.schedule.ElasticRunningInstancesOptimizerImpl.getImagesToStart(ElasticRunningInstancesOptimizerImpl.java:203) at sun.reflect.GeneratedMethodAccessor2545.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:483) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy139.getImagesToStart(Unknown Source) at com.atlassian.bamboo.agent.elastic.schedule.ElasticInstancesMonitorJob.execute(ElasticInstancesMonitorJob.java:47) at org.quartz.core.JobRunShell.run(JobRunShell.java:202) at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:49) at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:31) at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:20) at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:52) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:525) 2015-02-10 07:28:48,487 ERROR [scheduler_Worker-4] [ErrorLogger] Job (elastic agent monitor job group.elastic agent monitor job threw an exception. org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: java.lang.IllegalArgumentException: duplicate key: QueuedResultKey{resultKey=J64SPT-UNIT2-UNIT-5, timestamp=53729201374254818}] at org.quartz.core.JobRunShell.run(JobRunShell.java:213) at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:49) at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:31) at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:20) at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:52) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:525) Caused by: java.lang.IllegalArgumentException: duplicate key: QueuedResultKey{resultKey=J64SPT-UNIT2-UNIT-5, timestamp=53729201374254818} at com.google.common.base.Preconditions.checkArgument(Preconditions.java:115) at com.google.common.collect.RegularImmutableMap.<init>(RegularImmutableMap.java:72) at com.google.common.collect.ImmutableMap$Builder.fromEntryList(ImmutableMap.java:245) at com.google.common.collect.ImmutableMap$Builder.build(ImmutableMap.java:231) at com.google.common.collect.Maps.uniqueIndex(Maps.java:681) at com.google.common.collect.Maps.uniqueIndex(Maps.java:637) at com.atlassian.bamboo.v2.build.queue.QueueManagerView.getQueueView(QueueManagerView.java:68) at com.atlassian.bamboo.agent.elastic.schedule.ElasticRunningInstancesOptimizerImpl.getRequirementSetsOfQueuedExecutables(ElasticRunningInstancesOptimizerImpl.java:622) at com.atlassian.bamboo.agent.elastic.schedule.ElasticRunningInstancesOptimizerImpl.getImagesToStart(ElasticRunningInstancesOptimizerImpl.java:203) at sun.reflect.GeneratedMethodAccessor2545.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:483) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy139.getImagesToStart(Unknown Source) at com.atlassian.bamboo.agent.elastic.schedule.ElasticInstancesMonitorJob.execute(ElasticInstancesMonitorJob.java:47) at org.quartz.core.JobRunShell.run(JobRunShell.java:202) ... 5 more {noformat} According to the ui, the build mentioned in the exception finished about 4 hours ago. (5.8-m4 build 5860 - 04 Feb 15)

    Atlassian JIRA | 2 years ago | Martin Meinhold
    org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: java.lang.IllegalArgumentException: duplicate key: QueuedResultKey{resultKey=J64SPT-UNIT2-UNIT-5, timestamp=53729201374254818}]

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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Attempting to create duplicate peptide key: YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999_79.96633052074999-ATAA-5 from peptide YHGHSMSDPGVSYR_15.99491461956-ATAA-6_79.96633052074999-ATAA-12_79.96633052074999-ATAA-5.

      at eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs()
    2. eu.isas.peptideshaker
      PeptideShakerCLI.main
      1. eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs(PtmScorer.java:974)
      2. eu.isas.peptideshaker.ptm.PtmScorer.scorePeptidePtms(PtmScorer.java:1482)
      3. eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:496)
      4. eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)
      5. eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:158)
      6. eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:234)
      7. eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:732)
      8. eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:220)
      9. eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:945)
      9 frames