[maker-devel] genemark .mod file for yeast

[Jason Stajich]

Did you email the genemark authors? They would be a better source for help.
 I experienced the same problems with the yeast data to train from and didn't use genemark for those species  - it may be that it is expecting more introns and the files for training are empty on some rounds. 

Jason
On Apr 12, 2013, at 5:47 AM, xu zhang <xzhang at genome.wustl.edu> wrote:

> 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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> 
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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