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

[Patrick Tran Van]

Thanks Carson.

I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction.


but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ?


Cheers.


Patrick
________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: Thursday, January 17, 2019 10:31:17 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org
Subject: Re: Maker crash with big protein evidence ?

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<mailto: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

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