[maker-devel] Maker error: Invalid nucleotide

[Carson Holt]

Try running the contig in question (scaffold-92) as a separate MAKER run. That may haelp indicate if the issue may be a corrupt intermediate file (if it is, you can set clean_try=1 to force deletion of intermediate files before rerun).

—Carson



> On Jan 24, 2017, at 7:06 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi everyone,
> 
> I’m getting an error with an ongoing Maker run that I’m trying to troubleshoot. This is on a 2nd Maker run, where I used the first to prepare gene models for augustus/snap training, and have incorporated those results into this Maker run. The issue appears to be with augustus, and I’m getting the following type of error message for each contig:
> 
> —
> Widget::augustus:
> /opt/maker/exe/augustus.2.5.5/bin/augustus --species=Boa_constrictor --UTR=off /tmp/maker_xnOJ4d/scaffold-92.abinit_masked.0 > /tmp/maker_xnOJ4d/scaffold-92.abinit_masked.0.Boa_constrictor.augustus
> #-------------------------------#
> 
> /opt/maker/exe/augustus.2.5.5/bin/augustus: ERROR
> 	Invalid nucleotide '8' encountered.
> 
> 
> /opt/maker/exe/augustus.2.5.5/bin/augustus: ERROR
> 	Invalid nucleotide '8' encountered.
> 
> ERROR: Augustus failed
> --> rank=7, hostname=moonunit0
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:scaffold-92
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold-92
> 
> examining contents of the fasta file and run log
> —
> 
> Augustus is apparently encountering ‘8’ nucleotides, which is weird. I’ve looked within the contig fasta file in /tmp/ and there are no ‘8’s anywhere except the header lines. Everything else appears to be running without issues.
> 
> Any guidance on how I might further interpret and solve this issue would be greatly appreciated. Can provide more information if necessary.
> 
> Thanks,
> Daren Card
> 
> UT-Arlington
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