[maker-devel] Maker GFF output with features of 0 length

[Carson Holt]

One more thing.  From the example you gave, is is important to note that the
terminal CDS (first or last) can be a single base pair in length (start and
end will be the same value). Augustus sometimes does this for example.  Do
you have non-CDS feature types where this happens, or any internal CDS's
where this happens?

--Carson


From:  Carson Holt <carsonhh at gmail.com>
Date:  Tuesday, August 5, 2014 at 2:21 PM
To:  Marc Höppner <mphoeppner at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Maker GFF output with features of 0 length

Were you using GFF3 pass-through or correct_est_fusion options? When you
rerun do the same features still have lengths of zero (I.e. is it random or
is it reproducable)?

--Carson


From:  Marc Höppner <mphoeppner at gmail.com>
Date:  Wednesday, July 30, 2014 at 4:44 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker GFF output with features of 0 length

Hi,

I’ve - more by accident - found that many of the gene builds I have
generated with Maker (2.31.3) contain features with identical start and stop
positions. 

For example:

scaffold_2927   maker   CDS     13013   13013   .       +       1
ID=maker-scaffold_2927-augustus-gene-0.8-mRNA-1:cds;Parent=maker-scaffold_29
27-augustus-gene-0.8-mRNA-1


This occurs seemingly randomly for all sorts of feature types and I have
only seen this when running Maker on full assemblies. Before I start turning
every stone, any ideas about possible explanations for this phenomenon? Is
this likely some MPI-related communication issue, or NFS problems with
synching data? Maker runs fine on our system, but that doesn’t mean that
there aren’t any cryptic issues that only on these occasions read their
head… Regarding the frequency, out of 450.000 GFF lines, 270 were affected
in the case that I looked into the most. So it is pretty rare, but still...

I am currently using Maker with openmpi-1.7.4 and the file system is mounter
of NFS4 and IPoIB. I now switched to Maker 2.31.6, but have no strong reason
to suspect that this will make a difference.

Regards,

Marc


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