[maker-devel] Fwd: about running MAKER

[Carson Holt]

Run time is dependent on the size of your evidence dataset, genome size, and
number of processors you use.  If you have a large genome (Gb size) and you
are running on a single cpu then that could take a long time.  This is
especially true if you use the alt_est option for evidence as these are
aligned via tblastx  which is 3-4 times slower than protein alignments, and
10-20 time slower than standard EST alignments. 95% of MAKER's runtime is
BLAST alignment so your evidence dataset is the major factor.

Also you do not need results from the entire genome to train SNAP.  If you
get results from ~10Mb of the genome that is usually sufficient.  Also make
sure you are taking advantage of parallelization.  Launch via MPI to get
maximum performance.  I commonly launch on 16 and 32 cpu Linux servers which
can annotate most fungal genomes in a few hours and larger genomes in a few
days.

--Carson


From:  Amelia Ireland <amelia.ireland at gmod.org>
Date:  Sunday, 23 June, 2013 10:15 PM
To:  <maker-devel at yandell-lab.org>
Cc:  <lin11 at cougars.csusm.edu>
Subject:  [maker-devel] Fwd: about running MAKER

>From the GMOD helpdesk; please cc Lin, lin11 at cougars.csusm.edu.

---------- Forwarded message ----------
From: Yunxi Lin <lin11 at cougars.csusm.edu>
Date: Sun, Jun 23, 2013 at 4:14 PM
Subject: about running MAKER
To: "gmod-help at gmod.org" <help at gmod.org>


Hi 

I'm running a eukaryote project on our server. Because our server do not
have the GUI, is that still work for MAKER? And our command already ran more
than one month to try to generate the model use for the training of SNAP and
Augustus. Is that normal? I'm running on a 256G memory 64 Linux server.

Thank you. 

Sincerely,
Lin



-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

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