Maker Annotation Error: Unsupported characters

Question

[zgayk]

Hello,

We have installed the Maker2 pipeline on our small cluster. I would like to use it to start annotating an assembly we have produced. But when I run maker, I get the following error:

The nucleotide sequence file '/home/zgayk/MakerExample2/Gaviaimmerheader.fasta' appears to contain unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV]
Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically.
Invalid Character: 'R'

Would anyone know a quick way to get rid of all of these base designations that aren't supported by maker? The file size is close to 1 GB so manual replacement is not possible.

Thanks very much,
Zach

Answer 1

[GouthamAtla]

Use -fix_nucleotides option while running maker. This will replace IUPAC char. with 'N's