[maker-devel] Fwd: about running MAKER

[Yunxi Lin]

Hi Carson

Thank your for your help.

My genome estimated size is 250M base pairs. I ran it in 16cpu, but we
don't have the MPI so I cannot use it. I don't think I'm using the alt_est
option. I was following the tutorial to do that. I used TopHat and
Cufflinks to generate the ESTs from the assembly sequence based on RNA-seq.
I used that ESTs to run the MAKER.

I think I already got more than 10Mb data. The information you mentioned is
very helpful. I may go to use them to try to train the SNAP and Augustus.

Because this is my first time using the MAKER, I ran already a month, I was
wondering maybe the command I used in a wrong way.

Sincerely,
Yunxi



2013/6/24 Carson Holt <carsonhh at gmail.com>

> 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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