[maker-devel] Maker annotation of large scaffolds

[Carson Holt]

Also you can run MPI within a single node and not across nodes. This will still give a performance bonus equal to the MPI process count

—Carson


> On Jun 23, 2017, at 2:25 AM, Aravind PRASAD <aravindp at imcb.a-star.edu.sg> wrote:
> 
> Hi All,
>  
> Thank you for your inputs. Currently, I’m not using the MPI version but running Maker in multiple instances. Previously, I tried to run the MPI version but failed. Though the installation had no issues with MPI-Maker.
>  
> Carson, Can you please explain what exactly does the blast_depth option does while running Maker?
>  
> Thank you all for your time!
>  
> Regards,
> Aravind.
>  
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Friday, 23 June, 2017 12:06 PM
> To: Seth Munholland
> Cc: Aravind PRASAD; maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Maker annotation of large scaffolds
>  
> If running under MPI, the only step that should take a long time would be a final clustering step (the clustering is not parallelized). It should run in well under 24 hours though, so perhaps it is a memory issue or a feature depth issue. You can try running the contig by itself and setting all the bast_depth parameters in maker_bopts.ctl to 10 to help both.
>  
> Otherwise making a large overlap for subdivided contigs (50-100kb) should be enough. Alternatively look for streches of NNNNNN’s in the contig and split on those.
>  
> —Carson
>  
>  
>  
> On Jun 22, 2017, at 9:43 AM, Seth Munholland <munholl at uwindsor.ca <mailto:munholl at uwindsor.ca>> wrote:
>  
> I would think splitting could work if you generate a sufficient overlap.  IE 1-100k, 50-150k, etc.  Reassembling the annotations for the overlap regions may be tricky if you get conflicting annotations though.
> 
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>  
> On Thu, Jun 22, 2017 at 2:39 AM, Aravind PRASAD <aravindp at imcb.a-star.edu.sg <mailto:aravindp at imcb.a-star.edu.sg>> wrote:
> Hi All,
>  
> I’m trying to annotate a fish genome using Maker pipeline. It could finish the annotation for maximum scaffolds except 5 of them which are of size around 100M base pairs. The current clusters in our institute has a time limit of 24hrs for a job and these scaffolds could not be annotated with in that time.
> Can you please suggest any other way of finishing the annotation for large scaffolds?
>  
> I thought of chunking up the scaffolds to run, but, I’m afraid that would split a gene into two.
> Thanks for your time.
>  
> Regards,
> Aravind PRASAD <mailto:aravindp at imcb.a-star.edu.sg> :: Research Officer :: Comparative and Medical Genomics Lab :: Institue of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)
> 61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID (+65) 6586 9573 <tel:+65%206586%209573> :: Fax (+65) 6779 1117 <tel:+65%206779%201117> :: http://www.imcb.a-star.edu.sg/ <http://www.imcb.a-star.edu.sg/>
>  
> <image002.png>     
>  
>  
> 
> 
> Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>  
> 
> 
> Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170626/93656baa/attachment-0003.html>