how to assign specific genome assembly version to go-annotation data model

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how to assign specific genome assembly version to go-annotation data model

Pengcheng Yang

Dear InterMiners,

In our FAWMine, I want to load multi genome assemblies. The data model was constructed following the suggestions (https://github.com/intermine/intermine/issues/1596). Accordingly, I have updated the key values of Organism from TaxonId to name (https://github.com/pengchy/fawmine-bio-sources). The data from self constructed data model could be loaded successfully. However, the self produced go-annotation data was failed and the error information was listed below. So, how to assign specific genome assembly version to the go-annotation data model?

Best,

Pengcheng Yang


============ log information==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=go-annotation


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:retrieveSingleSource'.
> java.lang.ArrayIndexOutOfBoundsException: 1

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:retrieveSingleSource'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : java.lang.ArrayIndexOutOfBoundsException: 1
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:128)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure3.doCall(IntegrateUtils.groovy:84)
        at org.intermine.plugin.integrate.IntegrateUtils.invokeMethod(IntegrateUtils.groovy)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure2.doCall(IntegrateUtils.groovy:47)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure7$_closure20.doCall(IntegratePlugin.groovy:179)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 27 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at org.intermine.bio.dataconversion.GoConverter.parseTaxonId(GoConverter.java:712)
        at org.intermine.bio.dataconversion.GoConverter.process(GoConverter.java:267)
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:116)
        ... 42 more


* Get more help at https://help.gradle.org

BUILD FAILED in 22s
Tue Feb  4 01:44:47 CST 2020

finished


ERROR: 256
failed with exit code 0: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=go-annotation



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Re: how to assign specific genome assembly version to go-annotation data model

Pengcheng Yang

Hi, this problem turned out to be caused by mistake of the format of go-annotation file.

Thank Sam Hokin for his provided information.

Best,

Pengcheng


On 2020-2-4 13:25, Pengcheng Yang wrote:

Dear InterMiners,

In our FAWMine, I want to load multi genome assemblies. The data model was constructed following the suggestions (https://github.com/intermine/intermine/issues/1596). Accordingly, I have updated the key values of Organism from TaxonId to name (https://github.com/pengchy/fawmine-bio-sources). The data from self constructed data model could be loaded successfully. However, the self produced go-annotation data was failed and the error information was listed below. So, how to assign specific genome assembly version to the go-annotation data model?

Best,

Pengcheng Yang


============ log information==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=go-annotation


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:retrieveSingleSource'.
> java.lang.ArrayIndexOutOfBoundsException: 1

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:retrieveSingleSource'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : java.lang.ArrayIndexOutOfBoundsException: 1
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:128)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure3.doCall(IntegrateUtils.groovy:84)
        at org.intermine.plugin.integrate.IntegrateUtils.invokeMethod(IntegrateUtils.groovy)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure2.doCall(IntegrateUtils.groovy:47)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure7$_closure20.doCall(IntegratePlugin.groovy:179)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 27 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at org.intermine.bio.dataconversion.GoConverter.parseTaxonId(GoConverter.java:712)
        at org.intermine.bio.dataconversion.GoConverter.process(GoConverter.java:267)
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:116)
        ... 42 more


* Get more help at https://help.gradle.org

BUILD FAILED in 22s
Tue Feb  4 01:44:47 CST 2020

finished


ERROR: 256
failed with exit code 0: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=go-annotation



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev