Re: [maker-devel] maker-devel post from david.hughes@rothamsted.ac.uk requires approval

[Carson Holt]

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

—Carson

From: David Hughes <david....@rothamsted.ac.uk>

Subject: MAKER v3.0.0.

Date: October 23, 2019 at 8:24:24 AM MDT

To: "maker...@yandell-lab.org" <maker...@yandell-lab.org>

When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

 

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

 

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. 

[David Hughes]

Thanks Carson, very helpful.  We will investigate further.