[maker-devel] genemark .mod file for yeast

[xu zhang]

I know how to do that.  I tried different initial mod file and it 
worked  on my sequences with org_S1_55.0mtx initial mod. I don't know 
why. if somebody knows, please let me know.

Thanks,
Xu

On 04/10/2013 11:30 AM, xu zhang wrote:
> Hi All,
>
> Does anybody have genemark .mod file for yeast? I tried to create my 
> own model file using this command" gm_es.pl 
> S288C_reference_sequence_R64-1-1_20110203.fsa", where the sequence was 
> downloaded from ncbi". it failed with this error "
> warning, error in input file format:
> -3
> error reading parameter BRANCH_MAT
> error in model file 
> /gscmnt/gc2124/info/annotation/personal_dir/xzhang/yeast/s_cerevisiae/genemark/training2/mod/es.mod
> Error on system: prediction step" and "Error: unknown line format".
>
> and I tried the sample file(pythium_ultimum_scaffolds.fasta) from 
> Carson. a mod file was created, although it also had some error 
> information
> " warning, error in input file format:
> -13
> 5654 dna.fa.good.gb.acc.ph2
> first order for ACC 2
> Error: unknown line format
>        GC%    ntron".
>
> any suggestion and comments are appreciated
>
> Thanks,
> Xu
>
>
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