Problem with Maker

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Problem with Maker

filipegoncalo
Good afternoon,

I am trying to run maker. But i am going through some difficulties...
I've already tried with eukaryotics and prokaryotics genomes, and the result, on Apollo, using the maker output.gff is always the same. A ton of start and stop codons, and lots of data  resulting from repeatmasker and repeatrunner. That is far from what is expected obviously.
I run the maker -CTL, and after gedit the conf files...But i have a problem with some programs that i can not find on my computer.

As an example, in the maker_exe.ctl file-->on the section "Ab-initio Gene Prediction", i do have GeneMark Es isntalled, but i don't have the gmhmmp executable...but i have the gmhmme3. Is there a way to find it somewhere, i've searched on the WEB and  nothing.

Another question, maker_opts.ctl on the section Gene Prediction, what should i include (if i am supposed to include something) on:
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species= #Augustus gene prediction species model
I have all those applications installed and running but i don't have the HMM files and prediction species model, concerning Aungustus.

I am sorry for such newbie questions, but it is hard to get this thing working without further experience. So I was wondering if i could get a tip!!

Thanks for your attention,
Filipe

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Re: Problem with Maker

filipegoncalo
I feel embarrassed, that was such a silly question!!! I already got it, how to put things working with maker. 
I was wondering if there is any document with detailed information about the maker.ctl files. It would be useful for me, if I could understand them correctly, and the effect of different configurations.

Sorry for bothering,
My regards,
Filipe

2011/6/15 Filipe Bregieiro <[hidden email]>
Good afternoon,

I am trying to run maker. But i am going through some difficulties...
I've already tried with eukaryotics and prokaryotics genomes, and the result, on Apollo, using the maker output.gff is always the same. A ton of start and stop codons, and lots of data  resulting from repeatmasker and repeatrunner. That is far from what is expected obviously.
I run the maker -CTL, and after gedit the conf files...But i have a problem with some programs that i can not find on my computer.

As an example, in the maker_exe.ctl file-->on the section "Ab-initio Gene Prediction", i do have GeneMark Es isntalled, but i don't have the gmhmmp executable...but i have the gmhmme3. Is there a way to find it somewhere, i've searched on the WEB and  nothing.

Another question, maker_opts.ctl on the section Gene Prediction, what should i include (if i am supposed to include something) on:
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species= #Augustus gene prediction species model
I have all those applications installed and running but i don't have the HMM files and prediction species model, concerning Aungustus.

I am sorry for such newbie questions, but it is hard to get this thing working without further experience. So I was wondering if i could get a tip!!

Thanks for your attention,
Filipe


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Re: Problem with Maker

Carson Hinton Holt
Re: [maker-devel] Problem with Maker Sorry, I didn’t answer your other e-mails quickly.  I have been away for almost two weeks, and am only now getting caught up with the MAKER e-mail list.

I’m glad you were able to figure out the issue with RepeatMasker and get started with MAKER.  The best MAKER documentation is here --> http://gmod.org/wiki/MAKER_Tutorial

There will be updated docs soon for MAKER2.  GMOD is undergoing a major staff transition, so the updates we made for the 2011 GMOD spring training course aren’t online yet.

Don’t be afraid to ask any questions you want about MAKER.  I usually answer them within a couple of hours (excluding my recent absence).

Thanks,
Carson



On 6/16/11 5:15 AM, "Filipe Bregieiro" <filipegoncalo.duarte@...> wrote:

I feel embarrassed, that was such a silly question!!! I already got it, how to put things working with maker. 
I was wondering if there is any document with detailed information about the maker.ctl files. It would be useful for me, if I could understand them correctly, and the effect of different configurations.

Sorry for bothering,
My regards,
Filipe

2011/6/15 Filipe Bregieiro <filipegoncalo.duarte@...>
Good afternoon,

I am trying to run maker. But i am going through some difficulties...
I've already tried with eukaryotics and prokaryotics genomes, and the result, on Apollo, using the maker output.gff is always the same. A ton of start and stop codons, and lots of data  resulting from repeatmasker and repeatrunner. That is far from what is expected obviously.
I run the maker -CTL, and after gedit the conf files...But i have a problem with some programs that i can not find on my computer.

As an example, in the maker_exe.ctl file-->on the section "Ab-initio Gene Prediction", i do have GeneMark Es isntalled, but i don't have the gmhmmp executable...but i have the gmhmme3. Is there a way to find it somewhere, i've searched on the WEB and  nothing.

Another question, maker_opts.ctl on the section Gene Prediction, what should i include (if i am supposed to include something) on:
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species= #Augustus gene prediction species model
I have all those applications installed and running but i don't have the HMM files and prediction species model, concerning Aungustus.

I am sorry for such newbie questions, but it is hard to get this thing working without further experience. So I was wondering if i could get a tip!!

Thanks for your attention,
Filipe



Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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