[maker-devel] Maker error: Invalid nucleotide

[Daren C. Card]

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