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

[Chris Mungall]

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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