[maker-devel] fix nucleotides option on MWAS

[Humann, Jodi Lynn]

Hello,

I was wondering if there was any way to enable the '-fix_nucleotides' option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or 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: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu


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