The latest version of BLAST+ breaks the CEGMA program because it no longer supports a word size of 5 in TBLASTN. This may or may not be a bug: I can't find any mention of this change in the BLAST+ release notes and previously you were allowed word sizes between 2 and 7.
More info on my ACGT blog:
http://www.acgt.me/blog/2015/2/13/bl...bi-blast-v2230
More info on my ACGT blog:
http://www.acgt.me/blog/2015/2/13/bl...bi-blast-v2230