Genemark XXX.mod files

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Genemark XXX.mod files

Jennifer Anderson

Hello,

I am working on annotations for fungal genomes, using GenemarkES with —fungi for gene prediction.  In earlier attempts, I did not use the  training flag, and I did get the output gmhmm file.  Now I have tried with the training flag and do not get this file.  In the /run/ directory I do get mod files  ES_A.mod, ES_B.mod, and ES_C.mod, as well as ini.mod.  Does one of these files work as the ES.mod file as in 
"gmhmm=../train_genemark/es.mod #GeneMark HMM file” from http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained? I don’t find documentation of the genemarkES output online.

Thank you.

Jenni

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Re: Genemark XXX.mod files

Jason Stajich-4
the run/ES_C.mod should be the right one if it is there.
It is possible is crashing on one of the training / retraining?

Jason Stajich
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On Tue, Jul 3, 2018 at 11:05 AM Jennifer Anderson <[hidden email]> wrote:

Hello,

I am working on annotations for fungal genomes, using GenemarkES with —fungi for gene prediction.  In earlier attempts, I did not use the  training flag, and I did get the output gmhmm file.  Now I have tried with the training flag and do not get this file.  In the /run/ directory I do get mod files  ES_A.mod, ES_B.mod, and ES_C.mod, as well as ini.mod.  Does one of these files work as the ES.mod file as in 
"gmhmm=../train_genemark/es.mod #GeneMark HMM file” from http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained? I don’t find documentation of the genemarkES output online.

Thank you.

Jenni









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/om-uu/dataskydd-personuppgifter/
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