vcf data loading failed: "beginTransaction called, but already in transaction"

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vcf data loading failed: "beginTransaction called, but already in transaction"

Pengcheng Yang

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Daniela Butano-2

Hi Pengcheng,

try changing the configuration in the following way

<property name="src.data.file" location="/storage/FAWMine/VCF" />

<property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />


Daniela

On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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

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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Daniela Butano-2
In reply to this post by Pengcheng Yang

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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

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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Pengcheng Yang

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Daniela Butano-2

1. Checkout from my repo, the branch fix-vcf:

git add remote daniela https://github.com/danielabutano/intermine.git

git fetch daniela

git checkout daniela/fix-vcf

git checkout -b fix-vcf

2. Now install in your local maven only the bio-source-vcf:

cd intermine/bio/sources

./gradlew bio-source-vcf:install

3. integrate the vcf source and let me know :)

Daniela


On 11/02/2020 16:24, Pengcheng Yang wrote:

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Pengcheng Yang

Hi Daniela,

Thank you for your quickly updating. I  have tested the updated vcf but failed. The detailed information was pasted below.

After installing the updated vcf, I updated the project.xml by add the version number to "4.1.2" as found in ~/.m2/repository/org/intermine/bio-source-vcf/

                <source name="vcf1" type="vcf" dump="true" version="4.1.2">
                        <property name="src.data.file" location="/storage/FAWMine/VCF" />
                        <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>

Then I integrate the vcf with --info and --stacktrace and got the detailed information below.

The error message is different from previous and said "Caused by: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.".

Thank you and best,

pengcheng

========================= error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info
Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a729f84
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4239262e
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.001 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.028 secs.
:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.012 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.06 secs).

:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.085 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 3.727 secs.
:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.001 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.008 secs).

:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.012 secs.
:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.124 secs.
:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.002 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.17 secs).

:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 5.182 secs.
:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs.
:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.015 secs).

:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.019 secs.
:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.125 secs.
:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.392 secs.
:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.016 secs.
:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.774 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.
        at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:484)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:45)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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


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

BUILD FAILED in 28s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.


On 2020-2-12 0:45, Daniela Butano wrote:

1. Checkout from my repo, the branch fix-vcf:

git add remote daniela https://github.com/danielabutano/intermine.git

git fetch daniela

git checkout daniela/fix-vcf

git checkout -b fix-vcf

2. Now install in your local maven only the bio-source-vcf:

cd intermine/bio/sources

./gradlew bio-source-vcf:install

3. integrate the vcf source and let me know :)

Daniela


On 11/02/2020 16:24, Pengcheng Yang wrote:

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Daniela Butano-2

Sorry Pengcheng,

I hadn't realized you were using intermine 4.0.+. If you prefer, you can update the gradle.propeties to point to 4.1.+, so at that point you don't need  version="4.1.2" anymore.

About your error I think it's due to a wrong configuration.

src.data.file should be src.data.dir

Have a look here for an example.

Daniela

On 11/02/2020 18:14, Pengcheng Yang wrote:

Hi Daniela,

Thank you for your quickly updating. I  have tested the updated vcf but failed. The detailed information was pasted below.

After installing the updated vcf, I updated the project.xml by add the version number to "4.1.2" as found in ~/.m2/repository/org/intermine/bio-source-vcf/

                <source name="vcf1" type="vcf" dump="true" version="4.1.2">
                        <property name="src.data.file" location="/storage/FAWMine/VCF" />
                        <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>

Then I integrate the vcf with --info and --stacktrace and got the detailed information below.

The error message is different from previous and said "Caused by: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.".

Thank you and best,

pengcheng

========================= error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info
Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a729f84
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4239262e
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.001 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.028 secs.
:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.012 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.06 secs).

:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.085 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 3.727 secs.
:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.001 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.008 secs).

:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.012 secs.
:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.124 secs.
:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.002 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.17 secs).

:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 5.182 secs.
:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs.
:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.015 secs).

:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.019 secs.
:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.125 secs.
:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.392 secs.
:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.016 secs.
:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.774 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.
        at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:484)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:45)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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


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

BUILD FAILED in 28s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.


On 2020-2-12 0:45, Daniela Butano wrote:

1. Checkout from my repo, the branch fix-vcf:

git add remote daniela https://github.com/danielabutano/intermine.git

git fetch daniela

git checkout daniela/fix-vcf

git checkout -b fix-vcf

2. Now install in your local maven only the bio-source-vcf:

cd intermine/bio/sources

./gradlew bio-source-vcf:install

3. integrate the vcf source and let me know :)

Daniela


On 11/02/2020 16:24, Pengcheng Yang wrote:

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Pengcheng Yang

Hi Daniela,

Thanks for your suggestion. I have updated the gradle.properties to point 4.1.+

systemProp.imVersion=4.1.+
systemProp.bioVersion=4.1.+

and updated the setting in the project.xml file:

    <source name="vcf1" type="vcf" dump="true" version="4.1.2">
      <property name="src.data.dir" location="/storage/FAWMine/VCF" />
      <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
      <property name="vcf.vcfTaxonId" value="7108" />
      <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
      <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
    </source>

then I re-build the fawmine. But failed at the step loading vcf with the error message listed below. The error said "Caused by: : unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object". Please help me check how could I solve this problem.

Best,

Pengcheng


==================== error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info

Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@23d1e5d0
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@23d1e5d0
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@75ed9710
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c80e49b
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c80e49b
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@761e788f
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@10dfa7ef
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@75ed9710
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b4bd341
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b4bd341
:dbmodel:initConfig (Thread[main,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.0 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[main,5,main]) completed. Took 0.02 secs.
:dbmodel:processResources (Thread[main,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.011 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.047 secs).

:dbmodel:processResources (Thread[main,5,main]) completed. Took 0.069 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[main,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[main,5,main]) completed. Took 3.385 secs.
:dbmodel:copyMineProperties (Thread[main,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.002 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.01 secs).

:dbmodel:copyMineProperties (Thread[main,5,main]) completed. Took 0.015 secs.
:dbmodel:addSourceDependencies (Thread[main,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[main,5,main]) completed. Took 0.13 secs.
:dbmodel:copyGenomicModel (Thread[main,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[main,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[main,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[main,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[main,5,main]) completed. Took 0.003 secs.
:dbmodel:generateModel (Thread[main,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[main,5,main]) completed. Took 0.0 secs.
:dbmodel:compileJava (Thread[main,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.003 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.415 secs).

:dbmodel:compileJava (Thread[main,5,main]) completed. Took 5.424 secs.
:dbmodel:classes (Thread[main,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:jar (Thread[main,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.014 secs).

:dbmodel:jar (Thread[main,5,main]) completed. Took 0.017 secs.
:dbmodel:initIntegration (Thread[main,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[main,5,main]) completed. Took 0.111 secs.
:dbmodel:integrateMultipleSources (Thread[main,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[main,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[main,5,main]) completed. Took 7.028 secs.
:dbmodel:preRetrieveSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[main,5,main]) completed. Took 0.017 secs.
:dbmodel:retrieveSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[main,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [main] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [main] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[main,5,main]) completed. Took 7.56 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:60)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128)
        at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
        at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
        at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
        at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:311)
        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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:202)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:132)
        at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:107)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
        at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
        at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
        at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:45)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:29)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:71)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:45)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:51)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:58)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:33)
        at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:51)
        at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:287)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:260)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:33)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:253)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:182)
        at org.gradle.launcher.Main.doAction(Main.java:33)
        at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
        at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
        at org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:31)
        at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:108)
        at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
Caused by: : unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object
        at org.intermine.bio.dataconversion.VcfLoaderTask.processRecord(VcfLoaderTask.java:192)
        at org.intermine.bio.dataconversion.VcfLoaderTask.processFile(VcfLoaderTask.java:141)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:50)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:267)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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)
        ... 92 more


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

BUILD FAILED in 29s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.



On 2020-2-12 18:16, Daniela Butano wrote:

Sorry Pengcheng,

I hadn't realized you were using intermine 4.0.+. If you prefer, you can update the gradle.propeties to point to 4.1.+, so at that point you don't need  version="4.1.2" anymore.

About your error I think it's due to a wrong configuration.

src.data.file should be src.data.dir

Have a look here for an example.

Daniela

On 11/02/2020 18:14, Pengcheng Yang wrote:

Hi Daniela,

Thank you for your quickly updating. I  have tested the updated vcf but failed. The detailed information was pasted below.

After installing the updated vcf, I updated the project.xml by add the version number to "4.1.2" as found in ~/.m2/repository/org/intermine/bio-source-vcf/

                <source name="vcf1" type="vcf" dump="true" version="4.1.2">
                        <property name="src.data.file" location="/storage/FAWMine/VCF" />
                        <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>

Then I integrate the vcf with --info and --stacktrace and got the detailed information below.

The error message is different from previous and said "Caused by: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.".

Thank you and best,

pengcheng

========================= error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info
Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a729f84
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4239262e
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.001 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.028 secs.
:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.012 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.06 secs).

:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.085 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 3.727 secs.
:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.001 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.008 secs).

:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.012 secs.
:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.124 secs.
:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.002 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.17 secs).

:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 5.182 secs.
:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs.
:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.015 secs).

:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.019 secs.
:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.125 secs.
:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.392 secs.
:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.016 secs.
:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.774 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.
        at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:484)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:45)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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


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

BUILD FAILED in 28s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.


On 2020-2-12 0:45, Daniela Butano wrote:

1. Checkout from my repo, the branch fix-vcf:

git add remote daniela https://github.com/danielabutano/intermine.git

git fetch daniela

git checkout daniela/fix-vcf

git checkout -b fix-vcf

2. Now install in your local maven only the bio-source-vcf:

cd intermine/bio/sources

./gradlew bio-source-vcf:install

3. integrate the vcf source and let me know :)

Daniela


On 11/02/2020 16:24, Pengcheng Yang wrote:

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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Re: vcf data loading failed: "beginTransaction called, but already in transaction"

Daniela Butano-2

Hi Pengcheng,

When we parse the vcf files we expect (in the last column) something like:

dbSNP_138;TSA=SNV;E_Multiple_observations;E_......

where the value after the operator = has to be a class defined in the model.
From the error log you sent, it seems that this value (in your fil ) is not a class name defined in the model but a number.

Please send me the the line form the moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf file which contains 0075, so I can check if my deduction is correct.

Thank you!

On 12/02/2020 14:34, Pengcheng Yang wrote:

Hi Daniela,

Thanks for your suggestion. I have updated the gradle.properties to point 4.1.+

systemProp.imVersion=4.1.+
systemProp.bioVersion=4.1.+

and updated the setting in the project.xml file:

    <source name="vcf1" type="vcf" dump="true" version="4.1.2">
      <property name="src.data.dir" location="/storage/FAWMine/VCF" />
      <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
      <property name="vcf.vcfTaxonId" value="7108" />
      <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
      <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
    </source>

then I re-build the fawmine. But failed at the step loading vcf with the error message listed below. The error said "Caused by: : unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object". Please help me check how could I solve this problem.

Best,

Pengcheng


==================== error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info

Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@23d1e5d0
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@23d1e5d0
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@75ed9710
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c80e49b
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c80e49b
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@761e788f
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@10dfa7ef
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@75ed9710
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b4bd341
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b4bd341
:dbmodel:initConfig (Thread[main,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.0 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[main,5,main]) completed. Took 0.02 secs.
:dbmodel:processResources (Thread[main,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.011 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.047 secs).

:dbmodel:processResources (Thread[main,5,main]) completed. Took 0.069 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[main,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b32b129
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[main,5,main]) completed. Took 3.385 secs.
:dbmodel:copyMineProperties (Thread[main,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.002 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.01 secs).

:dbmodel:copyMineProperties (Thread[main,5,main]) completed. Took 0.015 secs.
:dbmodel:addSourceDependencies (Thread[main,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[main,5,main]) completed. Took 0.13 secs.
:dbmodel:copyGenomicModel (Thread[main,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[main,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[main,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[main,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[main,5,main]) completed. Took 0.003 secs.
:dbmodel:generateModel (Thread[main,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[main,5,main]) completed. Took 0.0 secs.
:dbmodel:compileJava (Thread[main,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.003 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.415 secs).

:dbmodel:compileJava (Thread[main,5,main]) completed. Took 5.424 secs.
:dbmodel:classes (Thread[main,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:jar (Thread[main,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.014 secs).

:dbmodel:jar (Thread[main,5,main]) completed. Took 0.017 secs.
:dbmodel:initIntegration (Thread[main,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[main,5,main]) completed. Took 0.111 secs.
:dbmodel:integrateMultipleSources (Thread[main,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[main,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[main,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[main,5,main]) completed. Took 7.028 secs.
:dbmodel:preRetrieveSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[main,5,main]) completed. Took 0.017 secs.
:dbmodel:retrieveSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[main,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[main,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [main] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [main] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[main,5,main]) completed. Took 7.56 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:60)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128)
        at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
        at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
        at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
        at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:311)
        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.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:202)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:132)
        at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:107)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
        at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
        at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
        at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:45)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:29)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:71)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:45)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:51)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:58)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:33)
        at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:51)
        at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:287)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:260)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:33)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:253)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:182)
        at org.gradle.launcher.Main.doAction(Main.java:33)
        at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
        at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
        at org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:31)
        at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:108)
        at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
Caused by: : unknown class: org.intermine.model.bio.0075 while creating new SequenceAlteration object
        at org.intermine.bio.dataconversion.VcfLoaderTask.processRecord(VcfLoaderTask.java:192)
        at org.intermine.bio.dataconversion.VcfLoaderTask.processFile(VcfLoaderTask.java:141)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:50)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:267)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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)
        ... 92 more


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

BUILD FAILED in 29s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.



On 2020-2-12 18:16, Daniela Butano wrote:

Sorry Pengcheng,

I hadn't realized you were using intermine 4.0.+. If you prefer, you can update the gradle.propeties to point to 4.1.+, so at that point you don't need  version="4.1.2" anymore.

About your error I think it's due to a wrong configuration.

src.data.file should be src.data.dir

Have a look here for an example.

Daniela

On 11/02/2020 18:14, Pengcheng Yang wrote:

Hi Daniela,

Thank you for your quickly updating. I  have tested the updated vcf but failed. The detailed information was pasted below.

After installing the updated vcf, I updated the project.xml by add the version number to "4.1.2" as found in ~/.m2/repository/org/intermine/bio-source-vcf/

                <source name="vcf1" type="vcf" dump="true" version="4.1.2">
                        <property name="src.data.file" location="/storage/FAWMine/VCF" />
                        <property name="vcf.includes" value="moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>

Then I integrate the vcf with --info and --stacktrace and got the detailed information below.

The error message is different from previous and said "Caused by: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.".

Thank you and best,

pengcheng

========================= error message ===============================

-bash-4.2$ /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1 --info
Initialized native services in: /home/pengchy/.gradle/native
Using 12 worker leases.
Creating new cache for fileHashes, path /home/pengchy/.gradle/caches/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for resourceHashesCache, path /home/pengchy/.gradle/caches/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@56aaaecd
Creating new cache for fileHashes, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for plugin-use-metadata, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/plugin-use-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Creating new cache for client-status, path /home/pengchy/.gradle/caches/4.1/plugin-resolution/client-status.bin, access org.gradle.cache.internal.DefaultCacheAccess@7829b776
Starting Build
Settings evaluated using settings file '/home/pengchy/soft/intermine.4.0/git/fawmine/settings.gradle'.
Projects loaded. Root project using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Included projects: [root project 'fawmine', project ':dbmodel', project ':webapp']

> Configure project :
Evaluating root project 'fawmine' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/build.gradle'.
Creating new cache for metadata-1.1/results, path /home/pengchy/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a729f84
Creating new cache for metadata-2.23/module-versions, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-versions.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/module-metadata, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Creating new cache for metadata-2.23/artifact-at-repository, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-repository.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Using properties file: '/home/pengchy/.intermine/fawmine.properties'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Configure project :dbmodel
Evaluating project ':dbmodel' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/build.gradle'.

> Configure project :webapp
Evaluating project ':webapp' using build file '/home/pengchy/soft/intermine.4.0/git/fawmine/webapp/build.gradle'.

All projects evaluated.
Selected primary task 'integrate' from project :
Creating new cache for annotation-processors, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4239262e
Tasks to be executed: [task ':dbmodel:initConfig', task ':dbmodel:processResources', task ':dbmodel:copyDefaultInterMineProperties', task ':dbmodel:copyMineProperties', task ':dbmodel:addSourceDependencies', task ':dbmodel:copyGenomicModel', task ':dbmodel:createSoModel', task ':dbmodel:mergeModels', task ':dbmodel:generateModel', task ':dbmodel:compileJava', task ':dbmodel:classes', task ':dbmodel:jar', task ':dbmodel:initIntegration', task ':dbmodel:integrateMultipleSources', task ':dbmodel:buildTgtItems', task ':dbmodel:preRetrieveSingleSource', task ':dbmodel:retrieveSingleSource', task ':dbmodel:loadSingleSource', task ':dbmodel:integrateSingleSource', task ':dbmodel:integrate']
Creating new cache for resourceHashesCache, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a791b66
Creating new cache for fileSnapshots, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/fileSnapshots.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
Creating new cache for taskHistory, path /home/pengchy/soft/intermine.4.0/git/fawmine/.gradle/4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@350bbd5d
:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initConfig
Putting task artifact state for task ':dbmodel:initConfig' into context took 0.001 secs.
Executing task ':dbmodel:initConfig' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initConfig (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.028 secs.
:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:processResources
Putting task artifact state for task ':dbmodel:processResources' into context took 0.012 secs.
Skipping task ':dbmodel:processResources' as it is up-to-date (took 0.06 secs).

:dbmodel:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.085 secs.
:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyDefaultInterMineProperties
Putting task artifact state for task ':dbmodel:copyDefaultInterMineProperties' into context took 0.0 secs.
Executing task ':dbmodel:copyDefaultInterMineProperties' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Creating new cache for metadata-2.23/artifact-at-url, path /home/pengchy/.gradle/caches/modules-2/metadata-2.23/artifact-at-url.bin, access org.gradle.cache.internal.DefaultCacheAccess@4fb392c4
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]

:dbmodel:copyDefaultInterMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 3.727 secs.
:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyMineProperties
Putting task artifact state for task ':dbmodel:copyMineProperties' into context took 0.001 secs.
Skipping task ':dbmodel:copyMineProperties' as it is up-to-date (took 0.008 secs).

:dbmodel:copyMineProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.012 secs.
:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:addSourceDependencies
Putting task artifact state for task ':dbmodel:addSourceDependencies' into context took 0.0 secs.
Executing task ':dbmodel:addSourceDependencies' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:addSourceDependencies (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.124 secs.
:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:copyGenomicModel
Skipping task ':dbmodel:copyGenomicModel' as task onlyIf is false.

:dbmodel:copyGenomicModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs.
:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:createSoModel
Skipping task ':dbmodel:createSoModel' as task onlyIf is false.

:dbmodel:createSoModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:mergeModels
Skipping task ':dbmodel:mergeModels' as task onlyIf is false.

:dbmodel:mergeModels (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:generateModel
Skipping task ':dbmodel:generateModel' as task onlyIf is false.

:dbmodel:generateModel (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:compileJava
Putting task artifact state for task ':dbmodel:compileJava' into context took 0.002 secs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
Skipping task ':dbmodel:compileJava' as it is up-to-date (took 5.17 secs).

:dbmodel:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 5.182 secs.
:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:classes
Skipping task ':dbmodel:classes' as it has no actions.

:dbmodel:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs.
:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:jar
Putting task artifact state for task ':dbmodel:jar' into context took 0.001 secs.
Skipping task ':dbmodel:jar' as it is up-to-date (took 0.015 secs).

:dbmodel:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.019 secs.
:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:initIntegration
Putting task artifact state for task ':dbmodel:initIntegration' into context took 0.0 secs.
Executing task ':dbmodel:initIntegration' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:initIntegration (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.125 secs.
:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:integrateMultipleSources
Skipping task ':dbmodel:integrateMultipleSources' as task onlyIf is false.

:dbmodel:integrateMultipleSources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs.
:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:buildTgtItems
Putting task artifact state for task ':dbmodel:buildTgtItems' into context took 0.0 secs.
Executing task ':dbmodel:buildTgtItems' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-model/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]

:dbmodel:buildTgtItems (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.392 secs.
:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:preRetrieveSingleSource
Putting task artifact state for task ':dbmodel:preRetrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:preRetrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.

:dbmodel:preRetrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.016 secs.
:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:retrieveSingleSource
Putting task artifact state for task ':dbmodel:retrieveSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:retrieveSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Retrieving vcf1 in a tgt items database

:dbmodel:retrieveSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.042 secs.
:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) started.

> Task :dbmodel:loadSingleSource
Putting task artifact state for task ':dbmodel:loadSingleSource' into context took 0.0 secs.
Executing task ':dbmodel:loadSingleSource' (up-to-date check took 0.0 secs) due to:
  Task has not declared any outputs.
Loading vcf1 tgt items into production DB
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-resources/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/bio-core/maven-metadata.xml]
Resource missing. [HTTP GET: https://clojars.org/repo/org/intermine/intermine-integrate/maven-metadata.xml]
file or directory '/home/pengchy/soft/intermine.4.0/git/fawmine/dbmodel/libs', not found
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Starting...
 [dataLoad] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.production - Start completed.

:dbmodel:loadSingleSource (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 6.774 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : /home/pengchy/soft/intermine.4.0/git/fawmine/null does not exist.
        at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:484)
        at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:45)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:123)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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


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

BUILD FAILED in 28s
12 actionable tasks: 8 executed, 4 up-to-date
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown initiated...
[Thread-33] INFO com.zaxxer.hikari.HikariDataSource - db.production - Shutdown completed.


On 2020-2-12 0:45, Daniela Butano wrote:

1. Checkout from my repo, the branch fix-vcf:

git add remote daniela https://github.com/danielabutano/intermine.git

git fetch daniela

git checkout daniela/fix-vcf

git checkout -b fix-vcf

2. Now install in your local maven only the bio-source-vcf:

cd intermine/bio/sources

./gradlew bio-source-vcf:install

3. integrate the vcf source and let me know :)

Daniela


On 11/02/2020 16:24, Pengcheng Yang wrote:

Dear Daniela,

Great! Thank you very much! Please show me how to install it locally.

Best,

Pengcheng


On 2020-2-11 23:16, Daniela Butano wrote:

Dear Pengcheng,

I have fixed the issue below (see https://github.com/intermine/intermine/issues/2204)

I'm going to release it in the next InterMine release (not scheduled yet).

Let me know if you need it before and I will show you how to install it locally.

Daniela


On 11/02/2020 09:12, Pengcheng Yang wrote:

Dear InterMiners,

I have to bother you again that I am stuck in VCF data loading.

The content in project.xml file related to vcf and the error message are listed below. The error message said that "Caused by: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction". I have searched against our archived mail list and the chat history content and did not find any information about this topic. Thank you!


                <source name="vcf1" type="vcf" dump="true">
                        <property name="src.data.file" location="/storage/FAWMine/VCF/moth_sen.raw_hardfil_true.SNP.2allelic.dp.AF.pl20.vcf" />
                        <property name="vcf.vcfTaxonId" value="7108" />
                        <property name="vcf.vcfDataSetTitle" value="FAW SNP data set" />
                        <property name="vcf.vcfDataSourceName" value="FAW Genome Project" />
                </source>



================ error message====================

Tue Feb 11 16:58:42 CST 2020

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=vcf1


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:loadSingleSource'.
> failed to store object

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:loadSingleSource'.
        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: : failed to store object
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:95)
        at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
        at org.intermine.bio.dataconversion.VcfLoaderTask.execute(VcfLoaderTask.java:117)
        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$_closure10.doCall(IntegrateUtils.groovy:265)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure9$_closure24.doCall(IntegratePlugin.groovy:222)
        at org.gradle.api.internal.AbstractTask$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: org.intermine.objectstore.ObjectStoreException: beginTransaction called, but already in transaction
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransactionWithConnection(ObjectStoreWriterInterMineImpl.java:1530)
        at org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.beginTransaction(ObjectStoreWriterInterMineImpl.java:1513)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.beginTransaction(IntegrationWriterAbstractImpl.java:599)
        at org.intermine.bio.dataconversion.VcfLoaderTask.process(VcfLoaderTask.java:90)
        ... 42 more


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

BUILD FAILED in 18s
Tue Feb 11 16:59:00 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=vcf1


=========================

Best,

Pengcheng


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