[maker-devel] Further split genome questions

[Carson Holt]

If you are starting and restarting, or running multiple jobs then the log can be partially rebuilt.  On rebuild only the FINISHED entries are added.  If there is a GFF3 result file for the contig, then it is FINISHED. FASTA files will only exist for the contigs that have gene models. Small contigs will rarely contain models.

--Carson

Sent from my iPhone

> On Aug 6, 2014, at 6:40 AM, "Jeanne Wilbrandt" <j.wilbrandt at zfmk.de> wrote:
> 
> 
> Hi Carson, 
> 
> I ran into more conspicuous behavior running maker 2.31 on a genome which is split into
> 20 parts, using the -g flag and the same basename.
> Most of the jobs ran simultaneously on the same node, 17 seemed to finish normally, while
> the remaining three seemed to be stalled and produced 0B of output. Do you have any
> suggestion why this is happening?
> 
> After I stopped these stalled jobs, I checked the index.log and found that of 38.384
> mentioned scaffolds, 154 appear only once in the log. The surprise is, that 2/3 of these
> only appear as FINISHED (the rest only started). There are no models for these 'finished'
> scaffolds stored in the .db and they are distributed over all parts of the genome (i.e.,
> each of the 20 jobs contained scaffolds that 'did not start' but 'finished')
> Should this be an issue of concern?
> It might be a NFS lock problem, as NFS is heavily loaded, but the NFS files look good, so
> we suspect something fishy going on...
> 
> Hope you can help,
> best wishes,
> Jeanne Wilbrandt
> 
> zmb // ZFMK // University of Bonn
> 
> 
> 
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