[maker-devel] Fwd: about running MAKER

[Daniel Ence]

Hi Yunxi,

During the maker installation, there is an option to automatically install MPICH2, which would let you run maker parallelized. Try rerunning the perl Build.PL script in the "maker/src" directory, and when the option to install MPICH2 comes up, tell it yes. This will start an automated download and install onto your server.

You can also start more than one maker process. They will work on annotating the genome together. You can start as many as ten or more processes like this, but MPI is a better parallelizing option.

Hope that helps,
Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Yunxi Lin [lin11 at cougars.csusm.edu]
Sent: Monday, June 24, 2013 5:11 PM
To: Carson Holt
Cc: maker-devel at yandell-lab.org; Amelia Ireland
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

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