Transfer sequence problem

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Transfer sequence problem

Paulo Nuin
Hi

I am having an error at the tail end of the building process for WormMine, on the transfer sequence process. I found some reference in the list archives, but I have no idea where to start looking for the process. The error I am getting is

starting command: ant -v -Daction=transfer-sequences


BUILD FAILED
/mnt/data/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)
       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: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:146)
       ... 17 more
Caused by: Operation was:transfer-sequences
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
       ... 22 more
Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 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:91)
       at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
       ... 22 more

I know the most important bit of the output is


Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 for class org.intermine.model.bio.Organism from ObjectStore os.production


but the explanation I found is a little vague. Any help is appreciated.

Thanks in advance

Paulo
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Re: Transfer sequence problem

Julie Sullivan
Hi Paulo

The error message means some organism entries are referenced by other
objects but are not in the database. This is usually caused by merging
errors.

Take a look at the keys for the sources you're using and see if any of
them are loading organisms but are missing the organism primary key.

If your code is accessible somewhere, e.g. github, I can take a look too.

Julie

PS. Your predecessor had the same issue:

        http://mail.intermine.org/pipermail/dev/2013-April/002195.html



On 16/06/15 06:33, Paulo Nuin wrote:

> Hi
>
> I am having an error at the tail end of the building process for WormMine, on the transfer sequence process. I found some reference in the list archives, but I have no idea where to start looking for the process. The error I am getting is
>
> starting command: ant -v -Daction=transfer-sequences
>
>
> BUILD FAILED
> /mnt/data/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)
>         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: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:146)
>         ... 17 more
> Caused by: Operation was:transfer-sequences
>         at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>         ... 22 more
> Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 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:91)
>         at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>         at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>         ... 22 more
>
> I know the most important bit of the output is
>
>
> Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 for class org.intermine.model.bio.Organism from ObjectStore os.production
>
>
> but the explanation I found is a little vague. Any help is appreciated.
>
> Thanks in advance
>
> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: Transfer sequence problem

Paulo Nuin
Hi Julie  

That’s the exact message I found. My questions basically are:

- where are keys for the sources? Any specific database or location in the code?
- and where should I check for merging errors?

We are using the code on 


with some modifications in the redeployment script and file locations.

Thanks a lot

Paulo




On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]> wrote:

Hi Paulo

The error message means some organism entries are referenced by other objects but are not in the database. This is usually caused by merging errors.

Take a look at the keys for the sources you're using and see if any of them are loading organisms but are missing the organism primary key.

If your code is accessible somewhere, e.g. github, I can take a look too.

Julie

PS. Your predecessor had the same issue:

http://mail.intermine.org/pipermail/dev/2013-April/002195.html



On 16/06/15 06:33, Paulo Nuin wrote:
Hi

I am having an error at the tail end of the building process for WormMine, on the transfer sequence process. I found some reference in the list archives, but I have no idea where to start looking for the process. The error I am getting is

starting command: ant -v -Daction=transfer-sequences


BUILD FAILED
/mnt/data/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: transfer-sequences)
       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: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:146)
       ... 17 more
Caused by: Operation was:transfer-sequences
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
       ... 22 more
Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 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:91)
       at org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
       ... 22 more

I know the most important bit of the output is


Caused by: java.lang.NullPointerException: Error retrieving object from proxy with ID 4000000 for class org.intermine.model.bio.Organism from ObjectStore os.production


but the explanation I found is a little vague. Any help is appreciated.

Thanks in advance

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



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Re: Transfer sequence problem

Julie Sullivan
The keys are in the resources directory.

I checked your sources and organism has a key in each source but they
are using different fields. This one uses organism.name to merge:

https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-acedb/resources/wormbase-acedb_keys.properties

As does your FASTA source:

https://github.com/WormBase/intermine/blob/dev/bio/sources/fasta/resources/fasta_keys.properties

The GFF3 source uses organism.taxonId to merge objects:

https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-gff3-core/resources/wormbase-gff3-core_keys.properties#L4

Can you confirm those keys are correct? e.g the FASTA and acedb sources
use organism.name and not taxon ID.

On 16/06/15 17:04, Paulo Nuin wrote:

> Hi Julie
>
> That’s the exact message I found. My questions basically are:
>
> - where are keys for the sources? Any specific database or location in
> the code?
> - and where should I check for merging errors?
>
> We are using the code on
>
> https://github.com/WormBase/website-intermine.git
>
> with some modifications in the redeployment script and file locations.
>
> Thanks a lot
>
> Paulo
>
>
>
>
>> On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Hi Paulo
>>
>> The error message means some organism entries are referenced by other
>> objects but are not in the database. This is usually caused by merging
>> errors.
>>
>> Take a look at the keys for the sources you're using and see if any of
>> them are loading organisms but are missing the organism primary key.
>>
>> If your code is accessible somewhere, e.g. github, I can take a look too.
>>
>> Julie
>>
>> PS. Your predecessor had the same issue:
>>
>> http://mail.intermine.org/pipermail/dev/2013-April/002195.html
>>
>>
>>
>> On 16/06/15 06:33, Paulo Nuin wrote:
>>> Hi
>>>
>>> I am having an error at the tail end of the building process for
>>> WormMine, on the transfer sequence process. I found some reference in
>>> the list archives, but I have no idea where to start looking for the
>>> process. The error I am getting is
>>>
>>> starting command: ant -v -Daction=transfer-sequences
>>>
>>>
>>> BUILD FAILED
>>> /mnt/data/intermine/imbuild/postprocess.xml:31: error running
>>> PostProcessTask (action: transfer-sequences)
>>>        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: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:146)
>>>        ... 17 more
>>> Caused by: Operation was:transfer-sequences
>>>        at
>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>>>        ... 22 more
>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>> from proxy with ID 4000000 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:91)
>>>        at
>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>        at
>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>>>        ... 22 more
>>>
>>> I know the most important bit of the output is
>>>
>>>
>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>> from proxy with ID 4000000 for class org.intermine.model.bio.Organism
>>> from ObjectStore os.production
>>>
>>>
>>> but the explanation I found is a little vague. Any help is appreciated.
>>>
>>> Thanks in advance
>>>
>>> Paulo
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>

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Re: Transfer sequence problem

Paulo Nuin
Hi Julie

Indeed the gaff properties file have taxonID as the organism key. I found 3 of these gff3 files in my source, and tried modifying them to name and restarted the build with the same error as a result. Should I recreate DBs and other things? Or change the other files to taxon ID? On my organisms table, I have a entry with id 24000001, where the name (and other fields)  is empty.

Thanks a lot for your reply, it helped me learn little bit more about Intermine.

Cheers
Paulo


> On Jun 17, 2015, at 4:29 AM, Julie Sullivan <[hidden email]> wrote:
>
> The keys are in the resources directory.
>
> I checked your sources and organism has a key in each source but they are using different fields. This one uses organism.name to merge:
>
> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-acedb/resources/wormbase-acedb_keys.properties
>
> As does your FASTA source:
>
> https://github.com/WormBase/intermine/blob/dev/bio/sources/fasta/resources/fasta_keys.properties
>
> The GFF3 source uses organism.taxonId to merge objects:
>
> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-gff3-core/resources/wormbase-gff3-core_keys.properties#L4
>
> Can you confirm those keys are correct? e.g the FASTA and acedb sources use organism.name and not taxon ID.
>
> On 16/06/15 17:04, Paulo Nuin wrote:
>> Hi Julie
>>
>> That’s the exact message I found. My questions basically are:
>>
>> - where are keys for the sources? Any specific database or location in
>> the code?
>> - and where should I check for merging errors?
>>
>> We are using the code on
>>
>> https://github.com/WormBase/website-intermine.git
>>
>> with some modifications in the redeployment script and file locations.
>>
>> Thanks a lot
>>
>> Paulo
>>
>>
>>
>>
>>> On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>> Hi Paulo
>>>
>>> The error message means some organism entries are referenced by other
>>> objects but are not in the database. This is usually caused by merging
>>> errors.
>>>
>>> Take a look at the keys for the sources you're using and see if any of
>>> them are loading organisms but are missing the organism primary key.
>>>
>>> If your code is accessible somewhere, e.g. github, I can take a look too.
>>>
>>> Julie
>>>
>>> PS. Your predecessor had the same issue:
>>>
>>> http://mail.intermine.org/pipermail/dev/2013-April/002195.html
>>>
>>>
>>>
>>> On 16/06/15 06:33, Paulo Nuin wrote:
>>>> Hi
>>>>
>>>> I am having an error at the tail end of the building process for
>>>> WormMine, on the transfer sequence process. I found some reference in
>>>> the list archives, but I have no idea where to start looking for the
>>>> process. The error I am getting is
>>>>
>>>> starting command: ant -v -Daction=transfer-sequences
>>>>
>>>>
>>>> BUILD FAILED
>>>> /mnt/data/intermine/imbuild/postprocess.xml:31: error running
>>>> PostProcessTask (action: transfer-sequences)
>>>>       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: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:146)
>>>>       ... 17 more
>>>> Caused by: Operation was:transfer-sequences
>>>>       at
>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>>>>       ... 22 more
>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>> from proxy with ID 4000000 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:91)
>>>>       at
>>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>>       at
>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>>>>       ... 22 more
>>>>
>>>> I know the most important bit of the output is
>>>>
>>>>
>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>> from proxy with ID 4000000 for class org.intermine.model.bio.Organism
>>>> from ObjectStore os.production
>>>>
>>>>
>>>> but the explanation I found is a little vague. Any help is appreciated.
>>>>
>>>> Thanks in advance
>>>>
>>>> Paulo
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>
>>


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Re: Transfer sequence problem

Julie Sullivan
Hi Paulo!

What about the FASTA and Acedb sources? Can you confirm they use
organism "name" and NOT the "taxon ID"? Meaning the source creates an
organism object and then gives that organism a unique value. Do those
sources set the "name" or the "taxon ID"?

Whichever value the source sets is what you want to merge on.

If you don't know what the source does, you can use both fields for
safety. So update your keys to look like this for the sources (GFF3,
FASTA or acedb) where you don't know the actual key:

        Organism.key_taxonid=taxonId
        Organism.key_name=name

The build system will use the correct integration key. (But it would be
better if we knew what those sources are doing of course!)

After you update the keys files, run the "clean" target (ant clean-all)
and restart the build from the beginning. You should start as normal
with an empty database.

Let me know if that doesn't work!

Cheers
Julie


On 18/06/15 04:57, Paulo Nuin wrote:
> Hi Julie
>
> Indeed the gaff properties file have taxonID as the organism key. I found 3 of these gff3 files

  in my source, and tried modifying them to name and restarted the build
with the same error

  as a result. Should I recreate DBs and other things? Or change the
other files to taxon ID?

On my organisms table, I have a entry with id 24000001, where the name
(and other fields)

is empty.

>
> Thanks a lot for your reply, it helped me learn little bit more about Intermine.
>
> Cheers
> Paulo
>
>
>> On Jun 17, 2015, at 4:29 AM, Julie Sullivan <[hidden email]> wrote:
>>
>> The keys are in the resources directory.
>>
>> I checked your sources and organism has a key in each source but they are using different fields. This one uses organism.name to merge:
>>
>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-acedb/resources/wormbase-acedb_keys.properties
>>
>> As does your FASTA source:
>>
>> https://github.com/WormBase/intermine/blob/dev/bio/sources/fasta/resources/fasta_keys.properties
>>
>> The GFF3 source uses organism.taxonId to merge objects:
>>
>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-gff3-core/resources/wormbase-gff3-core_keys.properties#L4
>>
>> Can you confirm those keys are correct? e.g the FASTA and acedb sources use organism.name and not taxon ID.
>>
>> On 16/06/15 17:04, Paulo Nuin wrote:
>>> Hi Julie
>>>
>>> That’s the exact message I found. My questions basically are:
>>>
>>> - where are keys for the sources? Any specific database or location in
>>> the code?
>>> - and where should I check for merging errors?
>>>
>>> We are using the code on
>>>
>>> https://github.com/WormBase/website-intermine.git
>>>
>>> with some modifications in the redeployment script and file locations.
>>>
>>> Thanks a lot
>>>
>>> Paulo
>>>
>>>
>>>
>>>
>>>> On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi Paulo
>>>>
>>>> The error message means some organism entries are referenced by other
>>>> objects but are not in the database. This is usually caused by merging
>>>> errors.
>>>>
>>>> Take a look at the keys for the sources you're using and see if any of
>>>> them are loading organisms but are missing the organism primary key.
>>>>
>>>> If your code is accessible somewhere, e.g. github, I can take a look too.
>>>>
>>>> Julie
>>>>
>>>> PS. Your predecessor had the same issue:
>>>>
>>>> http://mail.intermine.org/pipermail/dev/2013-April/002195.html
>>>>
>>>>
>>>>
>>>> On 16/06/15 06:33, Paulo Nuin wrote:
>>>>> Hi
>>>>>
>>>>> I am having an error at the tail end of the building process for
>>>>> WormMine, on the transfer sequence process. I found some reference in
>>>>> the list archives, but I have no idea where to start looking for the
>>>>> process. The error I am getting is
>>>>>
>>>>> starting command: ant -v -Daction=transfer-sequences
>>>>>
>>>>>
>>>>> BUILD FAILED
>>>>> /mnt/data/intermine/imbuild/postprocess.xml:31: error running
>>>>> PostProcessTask (action: transfer-sequences)
>>>>>        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: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:146)
>>>>>        ... 17 more
>>>>> Caused by: Operation was:transfer-sequences
>>>>>        at
>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>>>>>        ... 22 more
>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>> from proxy with ID 4000000 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:91)
>>>>>        at
>>>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>>>        at
>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>>>>>        ... 22 more
>>>>>
>>>>> I know the most important bit of the output is
>>>>>
>>>>>
>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>> from proxy with ID 4000000 for class org.intermine.model.bio.Organism
>>>>> from ObjectStore os.production
>>>>>
>>>>>
>>>>> but the explanation I found is a little vague. Any help is appreciated.
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>> Paulo
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>
>>>
>
>

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Re: Transfer sequence problem

Paulo Nuin
Hi Julie

Thanks again for your help. I restarted the build yesterday after changing all files with these names to the keys you suggested. I cleaned the build, on

<intermine>/wormmine/dbmodel

It’s currently re-building and I let you know my results when it ends.

Thanks

Paulo
 

> On Jun 18, 2015, at 2:14 AM, Julie Sullivan <[hidden email]> wrote:
>
> Hi Paulo!
>
> What about the FASTA and Acedb sources? Can you confirm they use organism "name" and NOT the "taxon ID"? Meaning the source creates an organism object and then gives that organism a unique value. Do those sources set the "name" or the "taxon ID"?
>
> Whichever value the source sets is what you want to merge on.
>
> If you don't know what the source does, you can use both fields for safety. So update your keys to look like this for the sources (GFF3, FASTA or acedb) where you don't know the actual key:
>
> Organism.key_taxonid=taxonId
> Organism.key_name=name
>
> The build system will use the correct integration key. (But it would be better if we knew what those sources are doing of course!)
>
> After you update the keys files, run the "clean" target (ant clean-all) and restart the build from the beginning. You should start as normal with an empty database.
>
> Let me know if that doesn't work!
>
> Cheers
> Julie
>
>
> On 18/06/15 04:57, Paulo Nuin wrote:
>> Hi Julie
>>
>> Indeed the gaff properties file have taxonID as the organism key. I found 3 of these gff3 files
>
> in my source, and tried modifying them to name and restarted the build with the same error
>
> as a result. Should I recreate DBs and other things? Or change the other files to taxon ID?
>
> On my organisms table, I have a entry with id 24000001, where the name (and other fields)
>
> is empty.
>>
>> Thanks a lot for your reply, it helped me learn little bit more about Intermine.
>>
>> Cheers
>> Paulo
>>
>>
>>> On Jun 17, 2015, at 4:29 AM, Julie Sullivan <[hidden email]> wrote:
>>>
>>> The keys are in the resources directory.
>>>
>>> I checked your sources and organism has a key in each source but they are using different fields. This one uses organism.name to merge:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-acedb/resources/wormbase-acedb_keys.properties
>>>
>>> As does your FASTA source:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/fasta/resources/fasta_keys.properties
>>>
>>> The GFF3 source uses organism.taxonId to merge objects:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-gff3-core/resources/wormbase-gff3-core_keys.properties#L4
>>>
>>> Can you confirm those keys are correct? e.g the FASTA and acedb sources use organism.name and not taxon ID.
>>>
>>> On 16/06/15 17:04, Paulo Nuin wrote:
>>>> Hi Julie
>>>>
>>>> That’s the exact message I found. My questions basically are:
>>>>
>>>> - where are keys for the sources? Any specific database or location in
>>>> the code?
>>>> - and where should I check for merging errors?
>>>>
>>>> We are using the code on
>>>>
>>>> https://github.com/WormBase/website-intermine.git
>>>>
>>>> with some modifications in the redeployment script and file locations.
>>>>
>>>> Thanks a lot
>>>>
>>>> Paulo
>>>>
>>>>
>>>>
>>>>
>>>>> On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]
>>>>> <mailto:[hidden email]>> wrote:
>>>>>
>>>>> Hi Paulo
>>>>>
>>>>> The error message means some organism entries are referenced by other
>>>>> objects but are not in the database. This is usually caused by merging
>>>>> errors.
>>>>>
>>>>> Take a look at the keys for the sources you're using and see if any of
>>>>> them are loading organisms but are missing the organism primary key.
>>>>>
>>>>> If your code is accessible somewhere, e.g. github, I can take a look too.
>>>>>
>>>>> Julie
>>>>>
>>>>> PS. Your predecessor had the same issue:
>>>>>
>>>>> http://mail.intermine.org/pipermail/dev/2013-April/002195.html
>>>>>
>>>>>
>>>>>
>>>>> On 16/06/15 06:33, Paulo Nuin wrote:
>>>>>> Hi
>>>>>>
>>>>>> I am having an error at the tail end of the building process for
>>>>>> WormMine, on the transfer sequence process. I found some reference in
>>>>>> the list archives, but I have no idea where to start looking for the
>>>>>> process. The error I am getting is
>>>>>>
>>>>>> starting command: ant -v -Daction=transfer-sequences
>>>>>>
>>>>>>
>>>>>> BUILD FAILED
>>>>>> /mnt/data/intermine/imbuild/postprocess.xml:31: error running
>>>>>> PostProcessTask (action: transfer-sequences)
>>>>>>       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: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:146)
>>>>>>       ... 17 more
>>>>>> Caused by: Operation was:transfer-sequences
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>>>>>>       ... 22 more
>>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>>> from proxy with ID 4000000 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:91)
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>>>>>>       ... 22 more
>>>>>>
>>>>>> I know the most important bit of the output is
>>>>>>
>>>>>>
>>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>>> from proxy with ID 4000000 for class org.intermine.model.bio.Organism
>>>>>> from ObjectStore os.production
>>>>>>
>>>>>>
>>>>>> but the explanation I found is a little vague. Any help is appreciated.
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>> Paulo
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>>
>>>>
>>
>>


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Re: Transfer sequence problem

Paulo Nuin
In reply to this post by Julie Sullivan
Hi Julie

Worked like a charm, thanks a lot for all the help. I ended up learning quite a bit more about Intermine.

Cheers
Paulo


> On Jun 18, 2015, at 2:14 AM, Julie Sullivan <[hidden email]> wrote:
>
> Hi Paulo!
>
> What about the FASTA and Acedb sources? Can you confirm they use organism "name" and NOT the "taxon ID"? Meaning the source creates an organism object and then gives that organism a unique value. Do those sources set the "name" or the "taxon ID"?
>
> Whichever value the source sets is what you want to merge on.
>
> If you don't know what the source does, you can use both fields for safety. So update your keys to look like this for the sources (GFF3, FASTA or acedb) where you don't know the actual key:
>
> Organism.key_taxonid=taxonId
> Organism.key_name=name
>
> The build system will use the correct integration key. (But it would be better if we knew what those sources are doing of course!)
>
> After you update the keys files, run the "clean" target (ant clean-all) and restart the build from the beginning. You should start as normal with an empty database.
>
> Let me know if that doesn't work!
>
> Cheers
> Julie
>
>
> On 18/06/15 04:57, Paulo Nuin wrote:
>> Hi Julie
>>
>> Indeed the gaff properties file have taxonID as the organism key. I found 3 of these gff3 files
>
> in my source, and tried modifying them to name and restarted the build with the same error
>
> as a result. Should I recreate DBs and other things? Or change the other files to taxon ID?
>
> On my organisms table, I have a entry with id 24000001, where the name (and other fields)
>
> is empty.
>>
>> Thanks a lot for your reply, it helped me learn little bit more about Intermine.
>>
>> Cheers
>> Paulo
>>
>>
>>> On Jun 17, 2015, at 4:29 AM, Julie Sullivan <[hidden email]> wrote:
>>>
>>> The keys are in the resources directory.
>>>
>>> I checked your sources and organism has a key in each source but they are using different fields. This one uses organism.name to merge:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-acedb/resources/wormbase-acedb_keys.properties
>>>
>>> As does your FASTA source:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/fasta/resources/fasta_keys.properties
>>>
>>> The GFF3 source uses organism.taxonId to merge objects:
>>>
>>> https://github.com/WormBase/intermine/blob/dev/bio/sources/wormbase-gff3-core/resources/wormbase-gff3-core_keys.properties#L4
>>>
>>> Can you confirm those keys are correct? e.g the FASTA and acedb sources use organism.name and not taxon ID.
>>>
>>> On 16/06/15 17:04, Paulo Nuin wrote:
>>>> Hi Julie
>>>>
>>>> That’s the exact message I found. My questions basically are:
>>>>
>>>> - where are keys for the sources? Any specific database or location in
>>>> the code?
>>>> - and where should I check for merging errors?
>>>>
>>>> We are using the code on
>>>>
>>>> https://github.com/WormBase/website-intermine.git
>>>>
>>>> with some modifications in the redeployment script and file locations.
>>>>
>>>> Thanks a lot
>>>>
>>>> Paulo
>>>>
>>>>
>>>>
>>>>
>>>>> On Jun 16, 2015, at 2:27 AM, Julie Sullivan <[hidden email]
>>>>> <mailto:[hidden email]>> wrote:
>>>>>
>>>>> Hi Paulo
>>>>>
>>>>> The error message means some organism entries are referenced by other
>>>>> objects but are not in the database. This is usually caused by merging
>>>>> errors.
>>>>>
>>>>> Take a look at the keys for the sources you're using and see if any of
>>>>> them are loading organisms but are missing the organism primary key.
>>>>>
>>>>> If your code is accessible somewhere, e.g. github, I can take a look too.
>>>>>
>>>>> Julie
>>>>>
>>>>> PS. Your predecessor had the same issue:
>>>>>
>>>>> http://mail.intermine.org/pipermail/dev/2013-April/002195.html
>>>>>
>>>>>
>>>>>
>>>>> On 16/06/15 06:33, Paulo Nuin wrote:
>>>>>> Hi
>>>>>>
>>>>>> I am having an error at the tail end of the building process for
>>>>>> WormMine, on the transfer sequence process. I found some reference in
>>>>>> the list archives, but I have no idea where to start looking for the
>>>>>> process. The error I am getting is
>>>>>>
>>>>>> starting command: ant -v -Daction=transfer-sequences
>>>>>>
>>>>>>
>>>>>> BUILD FAILED
>>>>>> /mnt/data/intermine/imbuild/postprocess.xml:31: error running
>>>>>> PostProcessTask (action: transfer-sequences)
>>>>>>       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: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:146)
>>>>>>       ... 17 more
>>>>>> Caused by: Operation was:transfer-sequences
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)
>>>>>>       ... 22 more
>>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>>> from proxy with ID 4000000 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:91)
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.TransferSequences.transferToLocatedSequenceFeatures(TransferSequences.java:121)
>>>>>>       at
>>>>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:134)
>>>>>>       ... 22 more
>>>>>>
>>>>>> I know the most important bit of the output is
>>>>>>
>>>>>>
>>>>>> Caused by: java.lang.NullPointerException: Error retrieving object
>>>>>> from proxy with ID 4000000 for class org.intermine.model.bio.Organism
>>>>>> from ObjectStore os.production
>>>>>>
>>>>>>
>>>>>> but the explanation I found is a little vague. Any help is appreciated.
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>> Paulo
>>>>>> _______________________________________________
>>>>>> 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