[Ontology-editors] [Software-group] obo2obo failing

[Tanya Berardini]

Is there something I could be doing to help sort this out?  I did several
term obsoletions on both Thursday and Friday, following the protocol and
format outlined in http://geneontology.org/GO.usage.shtml#obs.  I was
editing and saving in OE1.101.

Cheers,

Tanya

On Mon, Feb 9, 2009 at 9:19 AM, Chris Mungall <cjm at berkeleybop.org> wrote:

>
> one possibility is that we have just gone over some kind of size threshold.
> If so we have to up the memory. This can be done directly in the obo2obo
> script
>
> however, I have a suspicion this may be some oddity to do with the
> -writecomments required for 1.2 to 1.0. On friday some obsoletions in the
> ontology were accidentally made 1.0-style, this may be confusing obo2obo.
> Let's sort that out first and see if that works
>
> On Feb 9, 2009, at 9:12 AM, Mike Cherry wrote:
>
>  Hi,
>>
>> the obo2obo command is failing.  It worked last week, specifically it
>> worked on version 1.185 of the gene_ontology.1_2.obo file.  With version
>> 1.188 it doesn't work.
>>
>> Here is the command.
>>
>> obo2obo -formatversion OBO_1_0 /tmp/gene_ontology.1_2.obo -writecomments
>> -o /tmp/gene_ontology.1_0.obo -runscript
>> /share/go/bin/oboedit/current/docs/examplescripts/strip_disjoint_and_replaced_by_tags.osl
>> ;
>>
>> The error message on failng is just:
>>
>> Exception in thread "main" java.lang.StackOverflowError
>>
>> It there something wrong with that OBO file?
>>
>> -Mike
>>
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>>
>>
>


-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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