error - load breaks during create-bioseg-location-index

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error - load breaks during create-bioseg-location-index

Jayaraman, Pushkala

I updated from the master this morning ( I think and sincerely hope from the master branch..) and then tried to run my load as usual.. and the bioseg-location-index postprocess step broke..

Any idea where im going wrong or what changed in the code

 

BUILD FAILED

/home/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-bioseg-location-index)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)

        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        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: java.lang.reflect.InvocationTargetException

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)

        ... 17 more

Caused by: Operation was:create-bioseg-location-index

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)

        ... 22 more

Caused by: org.postgresql.util.PSQLException: ERROR: bad bioseg representation

  Detail: lower limit of range greater than upper

        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)

        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)

        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:302)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        at org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnection.java:455)

        at $Proxy3.executeUpdate(Unknown Source)

        at org.intermine.bio.postprocess.BiosegIndexTask.createIndex(BiosegIndexTask.java:58)

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:278)

        ... 22 more

 

Total time: 8 seconds

Thu Sep 26 00:00:36 CDT 2013

 

finished

 

 

ERROR: 256

failed with exit code 0: ant -v -Daction=create-bioseg-location-index

 

check log: pbuild.log

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 


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Re: error - load breaks during create-bioseg-location-index

Julie Sullivan
From the error message:

>   Detail: lower limit of range greater than upper

Can you verify that all your feature start lengths are greater than your
end lengths? And your feature.lengths are correct? If everything looks
fine, can you make a ticket?

I think this is a bug - I got another report of this happening a couple of
months ago. There must be a specific (rare!) case which causes the math to
be wrong. However, we aren't able to reproduce this bug. Is there a way
for you to make this database dump available to me? It's probably too
large I suppose. If you could get that error message to output which
object caused that error that would give me a better idea of what's going
on.

In the meantime you can skip this post-process for now.

> I updated from the master this morning ( I think and sincerely hope from
> the master branch..) and then tried to run my load as usual.. and the
> bioseg-location-index postprocess step broke..
> Any idea where im going wrong or what changed in the code
>
> BUILD FAILED
> /home/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error
> running PostProcessTask (action: create-bioseg-location-index)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)
>         at
> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         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: java.lang.reflect.InvocationTargetException
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)
>         ... 17 more
> Caused by: Operation was:create-bioseg-location-index
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>         ... 22 more
> Caused by: org.postgresql.util.PSQLException: ERROR: bad bioseg
> representation
>   Detail: lower limit of range greater than upper
>         at
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)
>         at
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)
>         at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:302)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnection.java:455)
>         at $Proxy3.executeUpdate(Unknown Source)
>         at
> org.intermine.bio.postprocess.BiosegIndexTask.createIndex(BiosegIndexTask.java:58)
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:278)
>         ... 22 more
>
> Total time: 8 seconds
> Thu Sep 26 00:00:36 CDT 2013
>
> finished
>
>
> ERROR: 256
> failed with exit code 0: ant -v -Daction=create-bioseg-location-index
>
> check log: pbuild.log
>
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: error - load breaks during create-bioseg-location-index

Jayaraman, Pushkala
Found the problem to be in our data..
A bunch of mouse qtls in a region had start position greater than stop position.. have reported this bug to the powers that be..






Sent via the Samsung Galaxy S™II Skyrocket™ an AT&T 4G LTE smartphone.

[hidden email] wrote:
From the error message:

>   Detail: lower limit of range greater than upper

Can you verify that all your feature start lengths are greater than your
end lengths? And your feature.lengths are correct? If everything looks
fine, can you make a ticket?

I think this is a bug - I got another report of this happening a couple of
months ago. There must be a specific (rare!) case which causes the math to
be wrong. However, we aren't able to reproduce this bug. Is there a way
for you to make this database dump available to me? It's probably too
large I suppose. If you could get that error message to output which
object caused that error that would give me a better idea of what's going
on.

In the meantime you can skip this post-process for now.

> I updated from the master this morning ( I think and sincerely hope from
> the master branch..) and then tried to run my load as usual.. and the
> bioseg-location-index postprocess step broke..
> Any idea where im going wrong or what changed in the code
>
> BUILD FAILED
> /home/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error
> running PostProcessTask (action: create-bioseg-location-index)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)
>         at
> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         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: java.lang.reflect.InvocationTargetException
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)
>         ... 17 more
> Caused by: Operation was:create-bioseg-location-index
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>         ... 22 more
> Caused by: org.postgresql.util.PSQLException: ERROR: bad bioseg
> representation
>   Detail: lower limit of range greater than upper
>         at
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)
>         at
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)
>         at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
>         at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:302)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnection.java:455)
>         at $Proxy3.executeUpdate(Unknown Source)
>         at
> org.intermine.bio.postprocess.BiosegIndexTask.createIndex(BiosegIndexTask.java:58)
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:278)
>         ... 22 more
>
> Total time: 8 seconds
> Thu Sep 26 00:00:36 CDT 2013
>
> finished
>
>
> ERROR: 256
> failed with exit code 0: ant -v -Daction=create-bioseg-location-index
>
> check log: pbuild.log
>
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev