Problem with Maker using GeneMark

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Problem with Maker using GeneMark

Gagné, Patrick (NRCAN/RNCAN)

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)

[hidden email] / tel : (418) 648-4443

 

 


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Re: Problem with Maker using GeneMark

Carson Holt-2
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) <[hidden email]> 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)
[hidden email] / tel : (418) 648-4443
 
 
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gmhmm_wrap (9K) Download Attachment