[maker-devel] Maker with GeneMarkS

[Carson Holt]

The model file is the HMM file GeneMark uses to build gene predictions.  It is not a set of gene models.  GeneMark must be trained for each organism it runs on before it can produce any ab initio gene predictions.  One of the scripts in GeneMarkS can do self training.  You can also train based on preexisting gene models.  Either way you get an HMM file with a .mod extension as a result.  The self training GeneMark script will do self training and then skip forward and produce ab initio gene predictions based on the training without requiring the user to restart the program with the HMM file.  This hides a step from the user, and often leaves them unaware that the training file even exists or is necessary.  Unfortunately, by letting GeneMark do self training every time rather than reusing the existing training files you actually increase the runtime of the program by several fold and this would double or even triple the run time for MAKER.  As a result if you don't have a model file, you need to run the script for self training that comes with GeneMarkS once outside of MAKER.  Then take the resulting HMM training file and give it to MAKER (the file usually has the extension .mod).  That way when you make minor changes to the MAKER run you don't have to wait for re-training of GeneMark again and again.  Also self training only works on long contigs, so if you want to analyze a small dataset you will need to provide the HMM file or GeneMark will just fail, which is the other reason we require the user to supply the HMM file up front.

The error you are getting is related to an option in the maker_opt.ctl file, 'evalutate'.  You have it set to 1.  You need to set this to 0.  The program EVALUATOR is separate from MAKER, and is off by default because EVALUATOR is still an experimental program.

Also once you have an HMM file for GeneMark you can try our online version of MAKER at http://www.yandell-lab.org/software/mwas.html

Just let me know if there are other problems or suggestions.  Also we plan on adding support for Glimmer within the next month if you're interested in using multiple sets of ab initio gene predictions for your annotations.

Thanks,
Carson

On 1/13/10 7:17 AM, "Mihaela Angelova" <mihaela.angelova at tugraz.at> wrote:

Hello,
I would like to use Maker for gene annotation of a prokaryote. As I
read from the manual, with the option -predictor=genemark, I tell
Maker to use GeneMarkS. However, the program fails because there is no
model file, which should not be a problem, because GeneMarks does ab
initio prediction.
If i use a model file, the program still fails with the following
error message:
"Undefined subroutine &evaluator::evaluate::evaluate_maker_annotations called
ERROR: Failed while calculating annotations!!"
Could you, please, inform me how to use Maker with GeneMarkS.
Thank you!
Best regards,
Mihaela





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