[maker-devel] Maker problem

[Carson Holt]

If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example —> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke (mario.stanke at uni-greifswald.de <mailto:mario.stanke at uni-greifswald.de>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

—Carson


> On Oct 12, 2017, at 1:37 AM, Jan FABI <jan.nagel at fabi.up.ac.za> wrote:
> 
> Dear Maker team
> 
> I am experiencing a problem while running maker and cannot find a solution to it online. 
> 
> I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. 
> 
> This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. 
> 
> I include the relevant portion of the log below. Could you help me determine the cause of this error.
> 
> 
> 
> setting up GFF3 output and fasta chunks
> preparing ab-inits
> running  augustus.
> #--------- command -------------#
> Widget::augustus:
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx-VirtualBox
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 
> 
> -- 
> Regards 
> Jan Nagel
> ----------------------------------------------------------------------
> PhD Genetics student
> Department of Genetics
> Forestry and Agricultural Biotechnology Institute (FABI) 
> FABI 1, Room 1-55
> University of Pretoria
> 74 Lunnon Rd. Hillcrest
> 0002
> Gauteng Province
> South Africa
> 
> Email : jan.nagel at fabi.up.ac.za <mailto:jan.nagel at fabi.up.ac.za>
> 
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