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

[Marc Höppner]

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_2927-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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140730/95f92f49/attachment-0002.html>