[maker-devel] Maker crash with big protein evidence ?

[Carson Holt]

You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It’s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out).

—Carson


> On Jan 15, 2019, at 2:54 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi,
> 
> I run maker with mpi and default option. 
> It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this :
> 
> in cluster::shadow_cluster...
>  sorting hits in shadow cluster...
>  j_size:3   current j:0
>  j_size:3   current j:1
>  j_size:3   current j:2
> ...finished clustering.
> 
> Did you already face something similar ?
> 
> Thanks.
> 
> Patrick 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190117/695dd10f/attachment-0003.html>