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

[Carson Holt]

If it happening only with GFF3 pass-through, then it may be something I saw
and fixed a while ago (there were some GFF3 passthrough fixes since 2.31.4).
Could you check and see if it still happens in 2.31.6.  Also if it is only
the first or last CDS/exon, then Augustus can do that and it's not actually
a bug.  Basically it is truncating the model to the start/stop codon so the
first or last exon/CDS may appear short, but it's really just incomplete.
If you can find any example of a non-CDS/exon feature then could you send it
to me?

Thanks,
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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