If BWA wants *.nt.ann file… (Rose)

Recently BWA (an alignment program) suddenly started giving a strange error message, indicating that a reference file ending in *.nt.ann was missing. This file type was unfamiliar to me, with good reason: it’s a colourspace reference file, which shouldn’t be generated when we index the fasta-based references we’re using (at least, I don’t know of anyone in our lab using SOLID data as a reference). DO NOT rebuild the reference with the -c (colourspace) flag, as you might see suggested on the web, because we don’t know what effect that might have on our alignments. DO rebuild it with the usual settings.