[maker-devel] Further split genome questions

[Jeanne Wilbrandt]

aha, so this explains that. 
Daniel, the average is 5930.37 bp, but ranging from ~ 50 to more than 60,000, roughly
half of the sequences being shorter than 3,000 bp.

What do you think about this weird 'I am running but not really doing anything'-behavior?


Thanks a lot!
Jeanne



On Wed, 6 Aug 2014 14:16:52 +0000
 Carson Holt <carsonhh at gmail.com> wrote:
>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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