[maker-devel] No genes predicted by Fgenesh in MAKER

[Chan Kuang Lim]

Dear MAKER developers,

I am using MAKER 2.31.8, with SNAP, AUGUSTUS and Fgenesh. I have tested my sequences, with many different parameters. MAKER output gives genes predicted by SNAP and AUGUSTUS, but no genes predicted by Fgenesh. I do not get any error message. The sequences FINISHED successful. May I know what are the possible mistake I have done?

Thank you.

Regards,

Chan KL

---

Come and join us on:

  

1. Journal of Oil Palm Research is now available free online at http://jopr.mpob.gov.my
2. 22nd MPOB Transfer of Technology Seminar 2016 (2 June 2016)
3. Persidangan Pekebun Kecil Sawit Kebangsaan 2016 (11 - 12 Oktober 2016)
   

Malaysian Palm Oil Board - http://www.mpob.gov.my
This email was sent using MPOB Webmail System.

[Daniel Ence]

Hi Chan, Fgenesh is a gene predictor that requires users to purchase parameter files from their company: http://www.softberry.com/. If you didn’t give a Fgenesh file, then you won’t get any predictions. 

~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

_______________________________________________
maker-devel mailing list
maker...@box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

[Carson Holt]

Also there is the chance that FgenesH has changed formats slightly for their output (it's happened a couple of times before), so if you are already running with a parameter file you purchased that could be the issues. Look at the STDERR report MAKER produces to see if FgenesH even ran and with what command.

—Carson