Error on post-processing 2

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Error on post-processing 2

Paulo Nuin
Hi again

My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in the project.xml

        <post-process name="create-chromosome-locations-and-lengths"/>                                                                                                 │···············
        <post-process name="transfer-sequences"/>                                                                                                                      │···············
        <post-process name="do-sources”/>


and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is C elegans

Any help appreciated

Thanks
Paulo



postprocess:                                                                                                                                                           │···············
[postprocess] Found 7 post-processes                                                                                                                                   │···············
[postprocess] Performing postprocess: transfer-sequences                                                                                                               │···············
                                                                                                                                                                       │···············
BUILD FAILED                                                                                                                                                           │···············
/mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)                                                         │···············
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)                                                                              │···············
        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:606)                                                                                                            │···············
        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:392)                                                                                                        │···············
        at org.apache.tools.ant.Target.performTasks(Target.java:413)                                                                                                   │···············
        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:811)                                                                                                           │···············
        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:57)                                                                               │···············
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)                                                                       │···············
        at java.lang.reflect.Method.invoke(Method.java:606)                                                                                                            │···············
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)                                                                              │···············
        ... 17 more                                                                                                                                                    │···············
Caused by: Operation was:transfer-sequences                                                                                                                            │···············
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)                                                         │···············
        ... 22 more                                                                                                                                                    │···············
Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore os.production│···············
        at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)                                                                            │···············
        at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)                                                                              │···············
        at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)                                               │···············
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)                                                         │···············
        ... 22 more
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Re: Error on post-processing 2

Justin Clark-Casey-2
Hi Paulo.  Just to clarify, you're saying that when you manually look in the organism table in the database that C elegans is in fact there with ID 3000002?

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 13/06/16 22:45, Paulo Nuin wrote:

> Hi again
>
> My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in the project.xml
>
>          <post-process name="create-chromosome-locations-and-lengths"/>                                                                                                 │···············
>          <post-process name="transfer-sequences"/>                                                                                                                      │···············
>          <post-process name="do-sources”/>
>
>
> and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is C elegans
>
> Any help appreciated
>
> Thanks
> Paulo
>
>
>
> postprocess:                                                                                                                                                           │···············
> [postprocess] Found 7 post-processes                                                                                                                                   │···············
> [postprocess] Performing postprocess: transfer-sequences                                                                                                               │···············
>                                                                                                                                                                         │···············
> BUILD FAILED                                                                                                                                                           │···············
> /mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)                                                         │···············
>          at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)                                                                              │···············
>          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:606)                                                                                                            │···············
>          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:392)                                                                                                        │···············
>          at org.apache.tools.ant.Target.performTasks(Target.java:413)                                                                                                   │···············
>          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:811)                                                                                                           │···············
>          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:57)                                                                               │···············
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)                                                                       │···············
>          at java.lang.reflect.Method.invoke(Method.java:606)                                                                                                            │···············
>          at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)                                                                              │···············
>          ... 17 more                                                                                                                                                    │···············
> Caused by: Operation was:transfer-sequences                                                                                                                            │···············
>          at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)                                                         │···············
>          ... 22 more                                                                                                                                                    │···············
> Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore os.production│···············
>          at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)                                                                            │···············
>          at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)                                                                              │···············
>          at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)                                               │···············
>          at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)                                                         │···············
>          ... 22 more
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Error on post-processing 2

Justin Clark-Casey-2
In reply to this post by Paulo Nuin
(replying again since stack trace got chopped off in the first reply).

Hi Paulo.  Just to clarify, you're saying that when you manually look in the organism table in the database that C elegans is in fact there with ID 3000002?

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 13/06/16 22:45, Paulo Nuin wrote:

> Hi again
>
> My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in the project.xml
>
>          <post-process name="create-chromosome-locations-and-lengths"/>                                                                                                 │···············
>          <post-process name="transfer-sequences"/>                                                                                                                      │···············
>          <post-process name="do-sources”/>
>
>
> and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is C elegans
>
> Any help appreciated
>
> Thanks
> Paulo
>
>
>
> postprocess:                                                                                                                                                           │···············
> [postprocess] Found 7 post-processes                                                                                                                                   │···············
> [postprocess] Performing postprocess: transfer-sequences                                                                                                               │···············
>                                                                                                                                                                         │···············
> BUILD FAILED                                                                                                                                                           │···············
> /mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)                                                         │···············
>          at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)                                                                              │···············
>          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:606)                                                                                                            │···············
>          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:392)                                                                                                        │···············
>          at org.apache.tools.ant.Target.performTasks(Target.java:413)                                                                                                   │···············
>          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:811)                                                                                                           │···············
>          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:57)                                                                               │···············
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)                                                                       │···············
>          at java.lang.reflect.Method.invoke(Method.java:606)                                                                                                            │···············
>          at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)                                                                              │···············
>          ... 17 more                                                                                                                                                    │···············
> Caused by: Operation was:transfer-sequences                                                                                                                            │···············
>          at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)                                                         │···············
>          ... 22 more                                                                                                                                                    │···············
> Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore os.production│···············
>          at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)                                                                            │···············
>          at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)                                                                              │···············
>          at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)                                               │···············
>          at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)                                                         │···············
>          ... 22 more
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Re: Error on post-processing 2

Paulo Nuin
Hi Justin

That’s correct. Here is when I do select 

objectid | fieldname  |       sourcename       | version                                                                                                              │···············
----------+------------+------------------------+---------                                                                                                             │···············
  3000002 | shortName  | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | genus      | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | name       | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | species    | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | commonName | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | taxonId    | celegans-gff3-cds      |      38                                                                                                              │···············
  3000002 | shortName  | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | genus      | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | name       | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | species    | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | commonName | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | taxonId    | celegans-gff3-mrna     |      35                                                                                                              │···············
  3000002 | shortName  | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | genus      | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | name       | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | species    | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | commonName | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | taxonId    | celegans-gff3-gene     |      32                                                                                                              │···············
  3000002 | shortName  | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | genus      | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | name       | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | species    | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | commonName | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | taxonId    | celegans-protein-fasta |      31                                                                                                              │···············
  3000002 | shortName  | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | genus      | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | name       | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | species    | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | commonName | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | taxonId    | celegans-genome-fasta  |      30                                                                                                              │···············
  3000002 | shortName  | go-annotation          |      29                                                                                                              │···············
  3000002 | genus      | go-annotation          |      29                                                                                                              │···············
  3000002 | name       | go-annotation          |      29                                                                                                              │···············
  3000002 | species    | go-annotation          |      29                                                                                                              │···············
  3000002 | commonName | go-annotation          |      29                                                                                                              │···············
  3000002 | taxonId    | go-annotation          |      29                                                                                                              │···············
  3000002 | id         | go-annotation          |      29                                                                                                              │···············


Would this be connected to a GFF3 or FASTA error?

Thanks

Paulo


On Jun 14, 2016, at 8:00 AM, Justin Clark-Casey <[hidden email]> wrote:

(replying again since stack trace got chopped off in the first reply).

Hi Paulo.  Just to clarify, you're saying that when you manually look in the organism table in the database that C elegans is in fact there with ID 3000002?

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 13/06/16 22:45, Paulo Nuin wrote:
Hi again

My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in the project.xml

        <post-process name="create-chromosome-locations-and-lengths"/>                                                                                                 │···············
        <post-process name="transfer-sequences"/>                                                                                                                      │···············
        <post-process name="do-sources”/>


and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is C elegans

Any help appreciated

Thanks
Paulo



postprocess:                                                                                                                                                           │···············
[postprocess] Found 7 post-processes                                                                                                                                   │···············
[postprocess] Performing postprocess: transfer-sequences                                                                                                               │···············
                                                                                                                                                                       │···············
BUILD FAILED                                                                                                                                                           │···············
/mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)                                                         │···············
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)                                                                              │···············
        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:606)                                                                                                            │···············
        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:392)                                                                                                        │···············
        at org.apache.tools.ant.Target.performTasks(Target.java:413)                                                                                                   │···············
        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:811)                                                                                                           │···············
        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:57)                                                                               │···············
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)                                                                       │···············
        at java.lang.reflect.Method.invoke(Method.java:606)                                                                                                            │···············
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)                                                                              │···············
        ... 17 more                                                                                                                                                    │···············
Caused by: Operation was:transfer-sequences                                                                                                                            │···············
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)                                                         │···············
        ... 22 more                                                                                                                                                    │···············
Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore os.production│···············
        at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)                                                                            │···············
        at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)                                                                              │···············
        at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)                                               │···············
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)                                                         │···············
        ... 22 more
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Re: Error on post-processing 2

Justin Clark-Casey-2
Hi Paulo.  Whilst googling to see if anybody had hit this error before, I found that you posted exactly the same issue to this list almost exactly a year ago!
[1].  Could you see if the same issues apply this time or say where things are going wrong differently?  Thanks.

[1] https://lists.intermine.org/pipermail/dev/2015-June/003314.html

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 14/06/16 16:11, Paulo Nuin wrote:

> Hi Justin
>
> That’s correct. Here is when I do select
>
> objectid | fieldname  |       sourcename       | version                                                                                                              │···············
>
> ----------+------------+------------------------+---------                                                                                                             │···············
>
>    3000002 | shortName  | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | genus      | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | name       | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | species    | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | commonName | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | taxonId    | celegans-gff3-cds      |      38                                                                                                              │···············
>
>    3000002 | shortName  | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | genus      | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | name       | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | species    | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | commonName | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | taxonId    | celegans-gff3-mrna     |      35                                                                                                              │···············
>
>    3000002 | shortName  | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | genus      | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | name       | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | species    | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | commonName | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | taxonId    | celegans-gff3-gene     |      32                                                                                                              │···············
>
>    3000002 | shortName  | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | genus      | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | name       | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | species    | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | commonName | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | taxonId    | celegans-protein-fasta |      31                                                                                                              │···············
>
>    3000002 | shortName  | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | genus      | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | name       | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | species    | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | commonName | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | taxonId    | celegans-genome-fasta  |      30                                                                                                              │···············
>
>    3000002 | shortName  | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | genus      | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | name       | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | species    | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | commonName | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | taxonId    | go-annotation          |      29                                                                                                              │···············
>
>    3000002 | id         | go-annotation          |      29                                                                                                              │···············
>
>
>
> Would this be connected to a GFF3 or FASTA error?
>
> Thanks
>
> Paulo
>
>
>> On Jun 14, 2016, at 8:00 AM, Justin Clark-Casey <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> (replying again since stack trace got chopped off in the first reply).
>>
>> Hi Paulo.  Just to clarify, you're saying that when you manually look in the organism table in the database that C elegans is in fact there with ID 3000002?
>>
>> --
>> Justin Clark-Casey, Synbiomine/InterMine Developer
>> http://synbiomine.org
>> http://twitter.com/justincc
>>
>> On 13/06/16 22:45, Paulo Nuin wrote:
>>> Hi again
>>>
>>> My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in
>>> the project.xml
>>>
>>>         <post-process name="create-chromosome-locations-and-lengths"/>
>>>                                                                                                 │···············
>>>         <post-process name="transfer-sequences"/>
>>>                                                                                                                      │···············
>>>         <post-process name="do-sources”/>
>>>
>>>
>>> and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is
>>> C elegans
>>>
>>> Any help appreciated
>>>
>>> Thanks
>>> Paulo
>>>
>>>
>>>
>>> postprocess:
>>>                                                                                                                                                           │···············
>>> [postprocess] Found 7 post-processes
>>>                                                                                                                                   │···············
>>> [postprocess] Performing postprocess: transfer-sequences
>>>                                                                                                               │···············
>>>                                                                                                                                                                        │···············
>>> BUILD FAILED
>>>                                                                                                                                                           │···············
>>> /mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)
>>>                                                         │···············
>>>         at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
>>>                                                                              │···············
>>>         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:606)
>>>                                                                                                            │···············
>>>         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:392)
>>>                                                                                                        │···············
>>>         at org.apache.tools.ant.Target.performTasks(Target.java:413)
>>>                                                                                                   │···············
>>>         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:811)
>>>                                                                                                           │···············
>>>         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:57)
>>>                                                                               │···············
>>>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>                                                                       │···············
>>>         at java.lang.reflect.Method.invoke(Method.java:606)
>>>                                                                                                            │···············
>>>         at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
>>>                                                                              │···············
>>>         ... 17 more
>>>                                                                                                                                                    │···············
>>> Caused by: Operation was:transfer-sequences
>>>                                                                                                                            │···············
>>>         at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)
>>>                                                         │···············
>>>         ... 22 more
>>>                                                                                                                                                    │···············
>>> Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore
>>> os.production│···············
>>>         at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)
>>>                                                                            │···············
>>>         at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)
>>>                                                                              │···············
>>>         at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>                                               │···············
>>>         at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)
>>>                                                         │···············
>>>         ... 22 more
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Re: Error on post-processing 2

Paulo Nuin
Hi Justin

I checked the errors I had before and most of the things that Julie helped me at the time are not applicable now. I haven’t changed my keys files and I am using the same code to build WS253 that was used successfully to build WS251. 

Any other place I might be able to look?

Cheers
Paulo


On Jun 15, 2016, at 6:52 AM, Justin Clark-Casey <[hidden email]> wrote:

Hi Paulo.  Whilst googling to see if anybody had hit this error before, I found that you posted exactly the same issue to this list almost exactly a year ago! [1].  Could you see if the same issues apply this time or say where things are going wrong differently?  Thanks.

[1] https://lists.intermine.org/pipermail/dev/2015-June/003314.html

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 14/06/16 16:11, Paulo Nuin wrote:
Hi Justin

That’s correct. Here is when I do select

objectid | fieldname  |       sourcename       | version                                                                                                            │···············

----------+------------+------------------------+---------                                                                                                             │···············

  3000002 | shortName  | celegans-gff3-cds      |      38                                                                                                        │···············

  3000002 | genus      | celegans-gff3-cds      |      38                                                                                                           │···············

  3000002 | name       | celegans-gff3-cds      |      38                                                                                                           │···············

  3000002 | species    | celegans-gff3-cds      |      38                                                                                                           │···············

  3000002 | commonName | celegans-gff3-cds      |      38                                                                                                   │···············

  3000002 | taxonId    | celegans-gff3-cds      |      38                                                                                                           │···············

  3000002 | shortName  | celegans-gff3-mrna     |      35                                                                                                      │···············

  3000002 | genus      | celegans-gff3-mrna     |      35                                                                                                          │···············

  3000002 | name       | celegans-gff3-mrna     |      35                                                                                                          │···············

  3000002 | species    | celegans-gff3-mrna     |      35                                                                                                         │···············

  3000002 | commonName | celegans-gff3-mrna     |      35                                                                                                 │···············

  3000002 | taxonId    | celegans-gff3-mrna     |      35                                                                                                          │···············

  3000002 | shortName  | celegans-gff3-gene     |      32                                                                                                      │···············

  3000002 | genus      | celegans-gff3-gene     |      32                                                                                                          │···············

  3000002 | name       | celegans-gff3-gene     |      32                                                                                                          │···············

  3000002 | species    | celegans-gff3-gene     |      32                                                                                                          │···············

  3000002 | commonName | celegans-gff3-gene     |      32                                                                                                 │···············

  3000002 | taxonId    | celegans-gff3-gene     |      32                                                                                                          │···············

  3000002 | shortName  | celegans-protein-fasta |      31                                                                                                     │···············

  3000002 | genus      | celegans-protein-fasta |      31                                                                                                         │···············

  3000002 | name       | celegans-protein-fasta |      31                                                                                                         │···············

  3000002 | species    | celegans-protein-fasta |      31                                                                                                         │···············

  3000002 | commonName | celegans-protein-fasta |      31                                                                                                 │···············

  3000002 | taxonId    | celegans-protein-fasta |      31                                                                                                         │···············

  3000002 | shortName  | celegans-genome-fasta  |      30                                                                                                  │···············

  3000002 | genus      | celegans-genome-fasta  |      30                                                                                                      │···············

  3000002 | name       | celegans-genome-fasta  |      30                                                                                                      │···············

  3000002 | species    | celegans-genome-fasta  |      30                                                                                                      │···············

  3000002 | commonName | celegans-genome-fasta  |      30                                                                                              │···············

  3000002 | taxonId    | celegans-genome-fasta  |      30                                                                                                      │···············

  3000002 | shortName  | go-annotation          |      29                                                                                                          │···············

  3000002 | genus      | go-annotation          |      29                                                                                                              │···············

  3000002 | name       | go-annotation          |      29                                                                                                              │···············

  3000002 | species    | go-annotation          |      29                                                                                                             │···············

  3000002 | commonName | go-annotation          |      29                                                                                                     │···············

  3000002 | taxonId    | go-annotation          |      29                                                                                                              │···············

  3000002 | id         | go-annotation          |      29                                                                                                              │···············



Would this be connected to a GFF3 or FASTA error?

Thanks

Paulo


On Jun 14, 2016, at 8:00 AM, Justin Clark-Casey <[hidden email] <[hidden email]>> wrote:

(replying again since stack trace got chopped off in the first reply).

Hi Paulo.  Just to clarify, you're saying that when you manually look in the organism table in the database that C elegans is in fact there with ID 3000002?

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 13/06/16 22:45, Paulo Nuin wrote:
Hi again

My previous problem was solved (thanks Joe) and I am back to my original problem, where one the post-processing actions is failing. I have three actions in
the project.xml

       <post-process name="create-chromosome-locations-and-lengths"/>
                                                                                               │···············
       <post-process name="transfer-sequences"/>
                                                                                                                    │···············
       <post-process name="do-sources”/>


and the first and the last are working fine, while the transfer sequences is failing with the error at the bottom of this message. Object with ID 3000002 is
C elegans

Any help appreciated

Thanks
Paulo



postprocess:
                                                                                                                                                         │···············
[postprocess] Found 7 post-processes
                                                                                                                                 │···············
[postprocess] Performing postprocess: transfer-sequences
                                                                                                             │···············
                                                                                                                                                                      │···············
BUILD FAILED
                                                                                                                                                         │···············
/mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)
                                                       │···············
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
                                                                            │···············
       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:606)
                                                                                                          │···············
       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:392)
                                                                                                      │···············
       at org.apache.tools.ant.Target.performTasks(Target.java:413)
                                                                                                 │···············
       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:811)
                                                                                                         │···············
       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:57)
                                                                             │···············
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                                                                     │···············
       at java.lang.reflect.Method.invoke(Method.java:606)
                                                                                                          │···············
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
                                                                            │···············
       ... 17 more
                                                                                                                                                  │···············
Caused by: Operation was:transfer-sequences
                                                                                                                          │···············
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)
                                                       │···············
       ... 22 more
                                                                                                                                                  │···············
Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 3000002 for class org.intermine.model.bio.Organism from ObjectStore
os.production│···············
       at org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)
                                                                          │···············
       at org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)
                                                                            │···············
       at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
                                             │···············
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)
                                                       │···············
       ... 22 more
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Re: Error on post-processing 2

Julie Sullivan-2
Paulo,

This error is likely due to a missing key causing an integration error.
Your keys didn't change but your data certainly did. Can you go through
and check your data sources, and make sure there is a key for each data
type?

If you can put your latest code on github I can look too.

Julie

On 06/16/2016 10:39 PM, Paulo Nuin wrote:

> Hi Justin
>
> I checked the errors I had before and most of the things that Julie
> helped me at the time are not applicable now. I haven’t changed my keys
> files and I am using the same code to build WS253 that was used
> successfully to build WS251.
>
> Any other place I might be able to look?
>
> Cheers
> Paulo
>
>
>> On Jun 15, 2016, at 6:52 AM, Justin Clark-Casey
>> <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> Hi Paulo.  Whilst googling to see if anybody had hit this error
>> before, I found that you posted exactly the same issue to this list
>> almost exactly a year ago! [1].  Could you see if the same issues
>> apply this time or say where things are going wrong differently?  Thanks.
>>
>> [1]https://lists.intermine.org/pipermail/dev/2015-June/003314.html
>>
>> --
>> Justin Clark-Casey, Synbiomine/InterMine Developer
>> http://synbiomine.org <http://synbiomine.org/>
>> http://twitter.com/justincc
>>
>> On 14/06/16 16:11, Paulo Nuin wrote:
>>> Hi Justin
>>>
>>> That’s correct. Here is when I do select
>>>
>>> objectid | fieldname  |       sourcename       | version
>>>
>>> │···············
>>>
>>> ----------+------------+------------------------+---------
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | genus      | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | name       | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | species    | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | commonName | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | celegans-gff3-cds      |      38
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | genus      | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | name       | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | species    | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | commonName | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | celegans-gff3-mrna     |      35
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | genus      | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | name       | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | species    | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | commonName | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | celegans-gff3-gene     |      32
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | genus      | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | name       | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | species    | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | commonName | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | celegans-protein-fasta |      31
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | genus      | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | name       | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | species    | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | commonName | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | celegans-genome-fasta  |      30
>>>
>>> │···············
>>>
>>>   3000002 | shortName  | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | genus      | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | name       | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | species    | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | commonName | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | taxonId    | go-annotation          |      29
>>>
>>> │···············
>>>
>>>   3000002 | id         | go-annotation          |      29
>>>
>>> │···············
>>>
>>>
>>>
>>> Would this be connected to a GFF3 or FASTA error?
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>>> On Jun 14, 2016, at 8:00 AM, Justin Clark-Casey
>>>> <[hidden email]
>>>> <mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>>>
>>>> (replying again since stack trace got chopped off in the first reply).
>>>>
>>>> Hi Paulo.  Just to clarify, you're saying that when you manually
>>>> look in the organism table in the database that C elegans is in fact
>>>> there with ID 3000002?
>>>>
>>>> --
>>>> Justin Clark-Casey, Synbiomine/InterMine Developer
>>>> http://synbiomine.org
>>>> http://twitter.com/justincc
>>>>
>>>> On 13/06/16 22:45, Paulo Nuin wrote:
>>>>> Hi again
>>>>>
>>>>> My previous problem was solved (thanks Joe) and I am back to my
>>>>> original problem, where one the post-processing actions is failing.
>>>>> I have three actions in
>>>>> the project.xml
>>>>>
>>>>>        <post-process name="create-chromosome-locations-and-lengths"/>
>>>>>                                                                                                │···············
>>>>>        <post-process name="transfer-sequences"/>
>>>>>                                                                                                                     │···············
>>>>>        <post-process name="do-sources”/>
>>>>>
>>>>>
>>>>> and the first and the last are working fine, while the transfer
>>>>> sequences is failing with the error at the bottom of this message.
>>>>> Object with ID 3000002 is
>>>>> C elegans
>>>>>
>>>>> Any help appreciated
>>>>>
>>>>> Thanks
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>> postprocess:
>>>>>                                                                                                                                                          │···············
>>>>> [postprocess] Found 7 post-processes
>>>>>                                                                                                                                  │···············
>>>>> [postprocess] Performing postprocess: transfer-sequences
>>>>>                                                                                                              │···············
>>>>>
>>>>> │···············
>>>>> BUILD FAILED
>>>>>                                                                                                                                                          │···············
>>>>> /mnt/data/intermine_dev/imbuild/postprocess.xml:31: error running
>>>>> PostProcessTask (action: transfer-sequences)
>>>>>                                                        │···············
>>>>>        at
>>>>> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
>>>>>                                                                             │···············
>>>>>        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:606)
>>>>>                                                                                                           │···············
>>>>>        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:392)
>>>>>                                                                                                       │···············
>>>>>        at org.apache.tools.ant.Target.performTasks(Target.java:413)
>>>>>                                                                                                  │···············
>>>>>        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:811)
>>>>>                                                                                                          │···············
>>>>>        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:57)
>>>>>                                                                              │···············
>>>>>        at
>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>>>                                                                      │···············
>>>>>        at java.lang.reflect.Method.invoke(Method.java:606)
>>>>>                                                                                                           │···············
>>>>>        at
>>>>> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
>>>>>                                                                             │···············
>>>>>        ... 17 more
>>>>>                                                                                                                                                   │···············
>>>>> Caused by: Operation was:transfer-sequences
>>>>>                                                                                                                           │···············
>>>>>        at
>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:232)
>>>>>                                                        │···············
>>>>>        ... 22 more
>>>>>                                                                                                                                                   │···············
>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>> from proxy with ID 3000002 for class
>>>>> org.intermine.model.bio.Organism from ObjectStore
>>>>> os.production│···············
>>>>>        at
>>>>> org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.java:60)
>>>>>                                                                           │···············
>>>>>        at
>>>>> org.intermine.model.bio.ChromosomeShadow.getOrganism(ChromosomeShadow.java:98)
>>>>>                                                                             │···············
>>>>>        at
>>>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>>>                                              │···············
>>>>>        at
>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:125)
>>>>>                                                        │···············
>>>>>        ... 22 more
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>>>>>
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