Maker Annotation Error

Question

[hydra_questions]

Hi all,

It's my first time trying to annotate an assembly, and I have been struggling with one aspect of Maker. When I run maker, I get the following error:

The nucleotide sequence file '/home/name/ests.fasta' contains either protein sequence or unsupported characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV]. This message is to get you to look at your input files, and verify that there is not a mistake. Both an explanation of the cause and a solution are indicated in this message. Do not post it to the mailing list. Please manually check/fix the file before continuing, or set -fix_nucleotides on the command line to automatically replace invalid nucleotides with 'N'. Invalid Character: 'O'

I have tried to run the -fix_nucleotides as an option on the command line when running Maker:

maker -fix_nucleotides maker_exe.ctl maker_opts.ctl maker_bopts.ctl

Would anyone know an alternate way to run this code?

Thank you in advance

[Juke34]

Look at your sequence to see why you have the letter O. If it looks ok (actually part of the sequence) then replace it by N.

[hydra_questions]

There are quite a few sequences so I don't think it would be possible to visually remove them.. I'm not sure if you know of a very streamlined way to do so

[Juke34]

Use a sed command in a terminal

Answer 1

[hydra_questions]

I realized I had some non-ESTs in the FASTA file. Thanks for your help!