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

[Carson Holt]

NR will likly create problems on more genes than it will help recover in comparison to swiss-prot. The AED cutoff can be a convenient way to remove models when you expect too much or poor quality evidence (but it’s more of a sledgehammer than a scalpel).  So using NR to get better sensitivity and then using AED to reduce sensitivity will likely just make all models worse in general while not adding many missed models.

—Carson



> On Jan 18, 2019, at 10:09 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> 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 <mailto:carsonhh at gmail.com>>
> Sent: Thursday, January 17, 2019 10:31:17 PM
> To: Patrick Tran Van
> Cc: maker-devel at yandell-lab.org <mailto: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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