[maker-devel] Maker annotation of large scaffolds

[Aravind PRASAD]

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]
Sent: Friday, 23 June, 2017 12:06 PM
To: Seth Munholland
Cc: Aravind PRASAD; 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/

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