blastall with a GI list to limit the search - I got error messages doing that (Jun/14/2009 )
I setup a standalone blast server on Windows vista. It seems to work well except that I could not do a restricted search with a GI list.
The database is nr downloaded from NCBI and I formatdb it myself.
I also got the GI list (as attached) from NCBI entrez for Drosophila proteins and I put that file in the same folder with the nr and input file.
Somehow whenever I used -l Dm.gi.txt in the blastall command, I always got error messages "
...then some other warnings."
Could somebody give me some suggestions?
Thanks a lot.
Try providing the full path to the file after the command line switch -- you may have to quote it if there's spaces in the path. Or, try putting Dm.gi.txt in the same directory as the blastall executable.
HomeBrew on Jun 14 2009, 01:44 PM said:
I did. Actually, Dm.gi.txt is in the same directory with blastall.exe and nr data base. I still have no clue to fix it.