Anyone run into this exception running the summarise-objectstore post-process?

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Anyone run into this exception running the summarise-objectstore post-process?

Sam Hokin-3
Could be the data source is mucked up, but usually these chado sources are pretty well-behaved.

2017-08-02 14:36:25 ERROR org.intermine.bio.postprocess.PostProcessOperationsTask     - Failed postprocess. Operation was:
summarise-objectstore
java.lang.RuntimeException: ObjectStore error has occurred (in get)
         at org.intermine.objectstore.query.Results.get(Results.java:233)
         at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
         at org.intermine.objectstore.ObjectStoreSummary.isReferenceEmpty(ObjectStoreSummary.java:508)
         at org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:222)
         at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:168)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:498)
         at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
         at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
         at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:498)
         at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
         at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
         at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
         at org.apache.tools.ant.Main.runBuild(Main.java:809)
         at org.apache.tools.ant.Main.startAnt(Main.java:217)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.objectstore.ObjectStoreException: Problem running SQL statement "SELECT 1 AS a1_ WHERE EXISTS(SELECT a2_.id
FROM Intron AS a1_, SequenceFeature AS a2_, OverlappingFeaturesSequenceFeature AS indirect0 WHERE a1_.id = indirect0.SequenceFeature
AND indirect0.OverlappingFeatures = a2_.id) LIMIT 1" while executing query "SELECT 1 AS a1_ WHERE (EXISTS (SELECT a2_ FROM
org.intermine.model.bio.Intron AS a1_, org.intermine.model.bio.SequenceFeature AS a2_ WHERE (a1_.overlappingFeatures CONTAINS a2_)))"
         at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1335)
         at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1131)
         at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(ObjectStoreInterMineImpl.java:1022)
         at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:193)
         at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:241)
         at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:146)
         at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
         at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
         at org.intermine.objectstore.query.Results.range(Results.java:197)
         at org.intermine.objectstore.query.Results.get(Results.java:226)
         ... 26 more
Caused by: org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound
         at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
         at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
         at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
         at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
         at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
         at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:303)
         at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:289)
         at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:266)
         at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:233)
         at com.zaxxer.hikari.proxy.StatementProxy.executeQuery(StatementProxy.java:99)
         at com.zaxxer.hikari.proxy.StatementJavassistProxy.executeQuery(StatementJavassistProxy.java)
         at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1230)
         ... 35 more
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Re: Anyone run into this exception running the summarise-objectstore post-process?

vkrishna
Hi Sam,

Have not encountered this error before, but here are some of my thoughts:

The error message "org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound" seems to indicate a SequenceFeature range that is of negative length (start > end).

Could it be due to an erroneous Intron feature (the class being referenced in the SQL in the stack trace) in your Chado DB? Or are you calculating the Introns, after the fact, using the IntronUtil.java post-process?

Thank you.
Vivek




On Wed, Aug 2, 2017 at 4:49 PM, Sam Hokin <[hidden email]> wrote:
Could be the data source is mucked up, but usually these chado sources are pretty well-behaved.

2017-08-02 14:36:25 ERROR org.intermine.bio.postprocess.PostProcessOperationsTask     - Failed postprocess. Operation was: summarise-objectstore
java.lang.RuntimeException: ObjectStore error has occurred (in get)
        at org.intermine.objectstore.query.Results.get(Results.java:233)
        at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
        at org.intermine.objectstore.ObjectStoreSummary.isReferenceEmpty(ObjectStoreSummary.java:508)
        at org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:222)
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:168)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.Main.runBuild(Main.java:809)
        at org.apache.tools.ant.Main.startAnt(Main.java:217)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.objectstore.ObjectStoreException: Problem running SQL statement "SELECT 1 AS a1_ WHERE EXISTS(SELECT a2_.id FROM Intron AS a1_, SequenceFeature AS a2_, OverlappingFeaturesSequenceFeature AS indirect0 WHERE a1_.id = indirect0.SequenceFeature AND indirect0.OverlappingFeatures = a2_.id) LIMIT 1" while executing query "SELECT 1 AS a1_ WHERE (EXISTS (SELECT a2_ FROM org.intermine.model.bio.Intron AS a1_, org.intermine.model.bio.SequenceFeature AS a2_ WHERE (a1_.overlappingFeatures CONTAINS a2_)))"
        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1335)
        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1131)
        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(ObjectStoreInterMineImpl.java:1022)
        at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:193)
        at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:241)
        at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:146)
        at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
        at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
        at org.intermine.objectstore.query.Results.range(Results.java:197)
        at org.intermine.objectstore.query.Results.get(Results.java:226)
        ... 26 more
Caused by: org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:303)
        at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:289)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:266)
        at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:233)
        at com.zaxxer.hikari.proxy.StatementProxy.executeQuery(StatementProxy.java:99)
        at com.zaxxer.hikari.proxy.StatementJavassistProxy.executeQuery(StatementJavassistProxy.java)
        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1230)
        ... 35 more
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Re: Anyone run into this exception running the summarise-objectstore post-process?

Sam Hokin-3
Calculating the introns using create-intron-features

On 08/02/2017 02:57 PM, Vivek Krishnakumar wrote:

> Hi Sam,
>
> Have not encountered this error before, but here are some of my thoughts:
>
> The error message "org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound"
> seems to indicate a SequenceFeature range that is of negative length (start > end).
>
> Could it be due to an erroneous Intron feature (the class being referenced in the SQL in the stack trace) in your Chado DB? Or are
> you calculating the Introns, after the fact, using the IntronUtil.java post-process?
>
> Thank you.
> Vivek
>
>
>
>
> On Wed, Aug 2, 2017 at 4:49 PM, Sam Hokin <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Could be the data source is mucked up, but usually these chado sources are pretty well-behaved.
>
>     2017-08-02 14:36:25 ERROR org.intermine.bio.postprocess.PostProcessOperationsTask     - Failed postprocess. Operation was:
>     summarise-objectstore
>     java.lang.RuntimeException: ObjectStore error has occurred (in get)
>              at org.intermine.objectstore.query.Results.get(Results.java:233)
>              at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
>              at org.intermine.objectstore.ObjectStoreSummary.isReferenceEmpty(ObjectStoreSummary.java:508)
>              at org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:222)
>              at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:168)
>              at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>              at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>              at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>              at java.lang.reflect.Method.invoke(Method.java:498)
>              at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
>              at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
>              at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>              at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>              at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>              at java.lang.reflect.Method.invoke(Method.java:498)
>              at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>              at org.apache.tools.ant.Task.perform(Task.java:348)
>              at org.apache.tools.ant.Target.execute(Target.java:390)
>              at org.apache.tools.ant.Target.pe <http://org.apache.tools.ant.Target.pe>rformTasks(Target.java:411)
>              at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
>              at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
>              at org.apache.tools.ant.helper.De
>     <http://org.apache.tools.ant.helper.De>faultExecutor.executeTargets(DefaultExecutor.java:41)
>              at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
>              at org.apache.tools.ant.Main.runBuild(Main.java:809)
>              at org.apache.tools.ant.Main.startAnt(Main.java:217)
>              at org.apache.tools.ant.launch.La <http://org.apache.tools.ant.launch.La>uncher.run(Launcher.java:280)
>              at org.apache.tools.ant.launch.La <http://org.apache.tools.ant.launch.La>uncher.main(Launcher.java:109)
>     Caused by: org.intermine.objectstore.ObjectStoreException: Problem running SQL statement "SELECT 1 AS a1_ WHERE EXISTS(SELECT
>     a2_.id FROM Intron AS a1_, SequenceFeature AS a2_, OverlappingFeaturesSequenceFeature AS indirect0 WHERE a1_.id =
>     indirect0.SequenceFeature AND indirect0.OverlappingFeatures = a2_.id) LIMIT 1" while executing query "SELECT 1 AS a1_ WHERE
>     (EXISTS (SELECT a2_ FROM org.intermine.model.bio.Intron AS a1_, org.intermine.model.bio.SequenceFeature AS a2_ WHERE
>     (a1_.overlappingFeatures CONTAINS a2_)))"
>              at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1335)
>              at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1131)
>              at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(ObjectStoreInterMineImpl.java:1022)
>              at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:193)
>              at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:241)
>              at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:146)
>              at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
>              at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
>              at org.intermine.objectstore.query.Results.range(Results.java:197)
>              at org.intermine.objectstore.query.Results.get(Results.java:226)
>              ... 26 more
>     Caused by: org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound
>              at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
>              at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
>              at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
>              at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
>              at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
>              at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:303)
>              at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:289)
>              at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:266)
>              at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:233)
>              at com.zaxxer.hikari.proxy.StatementProxy.executeQuery(StatementProxy.java:99)
>              at com.zaxxer.hikari.proxy.StatementJavassistProxy.executeQuery(StatementJavassistProxy.java)
>              at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1230)
>              ... 35 more
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>
>
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Re: Anyone run into this exception running the summarise-objectstore post-process?

vkrishna
Hi Sam -

Googling the error turned up this GitHub issue: https://github.com/intermine/intermine/issues/1095
Your initial assumption is probably right, the data is mucked up somewhere upstream, in the database, and likely also causing incorrect Introns to be calculated downstream.

Thank you.
Vivek

On Wed, Aug 2, 2017 at 4:59 PM, Sam Hokin <[hidden email]> wrote:
Calculating the introns using create-intron-features

On 08/02/2017 02:57 PM, Vivek Krishnakumar wrote:
Hi Sam,

Have not encountered this error before, but here are some of my thoughts:

The error message "org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound" seems to indicate a SequenceFeature range that is of negative length (start > end).

Could it be due to an erroneous Intron feature (the class being referenced in the SQL in the stack trace) in your Chado DB? Or are you calculating the Introns, after the fact, using the IntronUtil.java post-process?

Thank you.
Vivek




On Wed, Aug 2, 2017 at 4:49 PM, Sam Hokin <[hidden email] <mailto:[hidden email]>> wrote:

    Could be the data source is mucked up, but usually these chado sources are pretty well-behaved.

    2017-08-02 14:36:25 ERROR org.intermine.bio.postprocess.PostProcessOperationsTask     - Failed postprocess. Operation was:
    summarise-objectstore
    java.lang.RuntimeException: ObjectStore error has occurred (in get)
             at org.intermine.objectstore.query.Results.get(Results.java:233)
             at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
             at org.intermine.objectstore.ObjectStoreSummary.isReferenceEmpty(ObjectStoreSummary.java:508)
             at org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:222)
             at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:168)
             at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
             at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
             at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
             at java.lang.reflect.Method.invoke(Method.java:498)
             at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
             at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
             at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
             at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
             at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
             at java.lang.reflect.Method.invoke(Method.java:498)
             at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
             at org.apache.tools.ant.Task.perform(Task.java:348)
             at org.apache.tools.ant.Target.execute(Target.java:390)
             at org.apache.tools.ant.Target.pe <http://org.apache.tools.ant.Target.pe>rformTasks(Target.java:411)
             at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
             at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
             at org.apache.tools.ant.helper.De
    <http://org.apache.tools.ant.helper.De>faultExecutor.executeTargets(DefaultExecutor.java:41)
             at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
             at org.apache.tools.ant.Main.runBuild(Main.java:809)
             at org.apache.tools.ant.Main.startAnt(Main.java:217)
             at org.apache.tools.ant.launch.La <http://org.apache.tools.ant.launch.La>uncher.run(Launcher.java:280)
             at org.apache.tools.ant.launch.La <http://org.apache.tools.ant.launch.La>uncher.main(Launcher.java:109)

    Caused by: org.intermine.objectstore.ObjectStoreException: Problem running SQL statement "SELECT 1 AS a1_ WHERE EXISTS(SELECT
    a2_.id FROM Intron AS a1_, SequenceFeature AS a2_, OverlappingFeaturesSequenceFeature AS indirect0 WHERE a1_.id =
    indirect0.SequenceFeature AND indirect0.OverlappingFeatures = a2_.id) LIMIT 1" while executing query "SELECT 1 AS a1_ WHERE
    (EXISTS (SELECT a2_ FROM org.intermine.model.bio.Intron AS a1_, org.intermine.model.bio.SequenceFeature AS a2_ WHERE
    (a1_.overlappingFeatures CONTAINS a2_)))"
             at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1335)
             at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1131)
             at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(ObjectStoreInterMineImpl.java:1022)
             at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:193)
             at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:241)
             at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:146)
             at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
             at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
             at org.intermine.objectstore.query.Results.range(Results.java:197)
             at org.intermine.objectstore.query.Results.get(Results.java:226)
             ... 26 more
    Caused by: org.postgresql.util.PSQLException: ERROR: range lower bound must be less than or equal to range upper bound
             at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
             at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
             at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
             at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
             at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
             at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:303)
             at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:289)
             at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:266)
             at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:233)
             at com.zaxxer.hikari.proxy.StatementProxy.executeQuery(StatementProxy.java:99)
             at com.zaxxer.hikari.proxy.StatementJavassistProxy.executeQuery(StatementJavassistProxy.java)
             at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1230)
             ... 35 more
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Re: Anyone run into this exception running the summarise-objectstore post-process?

Sam Hokin-3
Ahh thanks, good work! I guess I'll have to throw some validation code into my chado-genomics data source. I'm loading a whole bunch
more organisms into LegumeMine (all the legumes we've got genomes for) so there's new data now, apparently not all conforming to
summarise-objectstore.

On 08/02/2017 03:06 PM, Vivek Krishnakumar wrote:
> Hi Sam -
>
> Googling the error turned up this GitHub issue: https://github.com/intermine/intermine/issues/1095
> Your initial assumption is probably right, the data is mucked up somewhere upstream, in the database, and likely also causing
> incorrect Introns to be calculated downstream.
>
> Thank you.
> Vivek
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