[maker-devel] trouble using Maker

[Eugénie Pessia]

Dear Maker community,

Sorry to bother you again but I encountered 2 problems while using Maker 
and I don't understand them

- Apollo : the first time I launched Maker on one of my chromosomes, I 
only used the est2genome option to see if it worked. Then, I had been 
able to open the resulting .gff file with Apollo and to look at the 
genes found by maker. But now that I am running Maker with more options, 
Apollo is not able anymore to open the .gff file: it gets stuck in the 
"load file" window... Do you have any idea why? I join one of my 
maker_opts.ctl so that you can see which options I use
Here is also a link if you want to download one of my .gff files 
obtained: 
http://dl.ens-lyon.fr/bigfilesharing/files/981d3d4ae5de715c0476d0ff8d844ef2/supercont10.1.gff 


- I am having trouble while launching Maker with all the options that 
interest me (see the maker_opts.ctl file). First, half of my 6 species 
on which I launch Maker didn't succeed (Maker died) whereas I am using 
the exact same parameters and files for the 6 and moreover these 6 
species are very close to each other. I have no clue of why.
Second, for the 3 species where Maker succeeded to end, there is only 1 
partial gene that has been found by Genemark. Which is really not much! 
So I think there is a problem with Genemark. I join you the .mod file I 
am using, which I obtained by launching Genemark-ES on Neurospora crassa 
genome.

I thank you in advance for your help and wish you a very nice day,
Eugénie
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