[maker-devel] Problem with Maker using GeneMark

[Carson Holt]

Could you try the attached version, and let me know if it resolves the issue (copy over the old one)? The probuild command I used is just one I stole from another GeneMark script, so I just borrowed the updated command from the SplitFasta subroutine in gmes_petap.pl.

—Carson



> On Mar 31, 2020, at 11:53 AM, Gagné, Patrick (NRCAN/RNCAN) <patrick.gagne at canada.ca> wrote:
> 
> Hi
>  
> I’ve come across a bug while using Maker. I’m trying to annotate a 560Mb Genome and I’m using Snap, GeneMark and Augustus in Maker.
> When Maker is executing the GeneMark command, it just failed (GeneMark Failed) without any error messages, so I’ve decided to debug it myself…So I launched every commands manually and found out that the gmhmm_wrap is causing the issue. The problem is in fact in the prebuild command; it doesn’t do anything (from what I understand, this command is supposed to split the fasta whre there is NNN to prevent GeneMark Crash). My genome got very long stretches of N (up to 14Kb)
>  
> After checking the prebuild help, I’ve found that the command used in gmhmm_wrap is not valid (half the options are not in probuild anymore, probably because of GeneMark updates)
>  
> I have tried different Probuild (those I could download from GeneMark site, they don’t give older versions except those that come with their program’s versions)
> 2.16
> 2.34
> 2.44 (lastest that come with GeneMark ES)
>  
> I’ve also tried to edit the gmhmm_wrap script and modify the prebuild command, but even when the fasta are splitted, I got another bug : ERROR: Logic error in getting offset. I’ve tried to replace the command for the offset extraction, which also worked, but now I got a bug when Maker try to get the ab-initio output :
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Calling translate without a seq argument!
>  
> Could you please tell me how to fix this, or tell me what probuild I should use (I will ask the GeneMark support for it)
>  
> Thanks in advance
>  
> P.S 
> Sorry for my English, It’s not my first language and I’m still learning
>  
> Patrick Gagné
> Spécialiste en bio-informatique / Bioinformatics specialist
> Service canadien des forêts / Canadian Forest Service
> Ressources naturelles Canada / Natural Resources Canada
> Gouvernement du Canada / Government of Canada
> Centre de foresterie des Laurentides/Laurentian Forestry Centre
> 1055, rue du P.E.P.S.
> C.P. 10380, succ. Sainte-Foy/P.O. Box 10380, Stn. Sainte-Foy
> Québec (Qc) G1V 4C7
> Laboratoire de pathologie forestière (Local 2.21)
> patrick.gagne at canada.ca <mailto:patrick.gagne at canada.ca> / tel : (418) 648-4443
>  
>  
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