[maker-devel] Trouble with gmhmme3 setup

[Carson Holt]

Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package.  You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.

Thanks,
Carson


> On Jun 8, 2015, at 11:13 PM, Aaron McKenna <aaronmck at uw.edu> wrote:
> 
> Hi Maker-dev list,
> 
> I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part.   The install script says this is optional:
> 
> **(OPTIONAL COMPONENTS)
> 
> 1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/ <http://bioinf.uni-greifswald.de/augustus/>
> 2. GeneMark-ES. Download from http://exon.biology.gatech.edu <http://exon.biology.gatech.edu/>
> ...
> 
> but if don't list a path in my exe file I get:
> 
> ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
> 
> If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:
> 
> error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
> ERROR: GeneMark Failed
> --> rank=NA, hostname=parvati.grid.gs.washington.edu <http://parvati.grid.gs.washington.edu/>
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> 
> Has anyone seen this before?  Thanks for any info you have.
> 
> - Aaron
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