|
Hi all, I’m sorry because I know this has been asked before, since
I found a bunch of messages describing this in the past. However, I never
seemed to get a straight answer on the source of this problem. I get errors similar to this on certain files I am trying to
mpiformatdb: [formatdb] WARNING: Sequence number 551226 (lcl|2_/home/raychan/public_html/db/Ne),
11 illegal characters were removed: 3 Es, 4 Is, 2 Ls, 2 Os I always do “—skip-reorder” to save time,
and this was one of the things suggested in the past to maybe avoid these
errors. This happens on some pretty well annotated and described FASTA
files I get from places like NCBI. Before, on my own personal FASTA files
during a formatdb, I used to accidentally forget the “>” for the
beginning of each line from time to time and got this error. Is carelessness/typos the root of this problem as well?
I’ve tried to trace back to all the places in my original file where there
was a reported error, but I do not see any obvious illegal characters or
missing “>”. Also, I would think these “reliable
sources” would not be so careless (maybe a few times, but not over 21,000+
errors which I’ve encountered in this case). You’ve all been so helpful in the past, I hope I can
get some advice. Sorry for annoyingly asking the same thing again, as I
know how that goes. Thanks again, Ray C. |
