Reg:GBrowse

[it]

Hi all,

        When we are trying to configure gbrowse to our mine, it replies following error :

BUILD FAILED
java.lang.RuntimeException: no chromosomes found
    at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:274)

But we are having chromosomes in our database.

Any thoughts?

Thanks and Regards,

Lenin

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[Julie Sullivan]

Hi Lenin

The query that is run to find the chromosomes is in
`org.intermine.bio.util.BioQueries.findLocationAndObjects()` and it's failing.
I think that method makes certain (dumb) assumptions so even though you may have
chromosome the query has a couple constraints that are causing it to return no
results.

That query is using chromosomeLocation - a shortcut field created in the
`create-chromosome-locations-and-lengths` post process.

        See: http://intermine.org/wiki/PostProcessing

Have you run that postprocess?

Also that query seems to be expecting the feature length to be non-null.  Is
that true in your mine?

If you make sure you have those 2 items (chromosomeLocations and non-null
feature lengths), then the write gff3 task should work.

Cheers
Julie

On 01/08/12 05:34, [hidden email] wrote:

> Hi all,
> When we are trying to configure gbrowse to our mine, it replies following error :
>
> BUILD FAILED
> java.lang.RuntimeException: no chromosomes found
> at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:274)
>
> But we are having chromosomes in our database.
>
> Any thoughts?
>
> Thanks and Regards,
> Lenin
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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