[maker-devel] Fwd: about running MAKER

[Carson Holt]

You are most likely only getting 1 cpu of performance.

You should just install MPICH2.  It's easy just to let MAKER do it for you:
Go to the …/maker/src/ directory
Run './Build mpich2'
Once it finishes installing, it will be in the …/maker/exe/mpich2/bin/ directory.

Setup MAKER again to use MPICH2:
Go to the …/maker/src/ directory
Run 'perl Build.PL'
Say yes to the "use MPI": question
Run './Build install'

Now run MAKER via 'mpiexec'.
Example --> …/maker/exe/mpich2/bin/mpiexec -n 16 maker

The –n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines.  You will get much better performance.

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, 24 June, 2013 7:11 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Fwd: about running MAKER

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

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

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

_______________________________________________ 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130625/6a11a5c2/attachment-0003.html>