Something changed in the latest version of NCBI BLAST+ which breaks our CEGMA software. Compare the behavior of this simple TBLASTN command in v2.2.29+ and v2.2.30+ (from October 2014):

v2.2.29+

tblastn -db sample.dna -query sequence.prot -word_size 5

TBLASTN 2.2.29+

Database: sample.dna
           1 sequences; 2,499,950 total letters

Query= 7292122___KOG0292

Length=1234
                                                 Score     E
Sequences producing significant alignments:      (Bits)  Value

CHROMOSOME_I 1 15072418                           38.9    0.002

v2.2.30+

tblastn -db sample.dna -query sequence.aa -word_size 5

BLAST query/options error: Compressed alphabet lookup table requires word size 6 or 7
Please refer to the BLAST+ user manual.

One step in the CEGMA pipeline involves running TBLASTN with a word size of 5. This no longer works in the latest version and the error message suggests that only a word size of 6 or 7 is permitted. I can confirm that this is the case by looking at the latest source code for the blast_option.c file:


else if (options->lut_type == eCompressedAaLookupTable &&
         options->word_size != 6 && options->word_size != 7) {
         Blast_MessageWrite(blast_msg, eBlastSevError, kBlastMessageNoContext,
               "Compressed alphabet lookup table requires "
               "word size 6 or 7");
         return BLASTERR_OPTION_VALUE_INVALID;
}

The error message suggests I look at the BLAST+ user manual. I did this, and according to Table C5:

tblastn application options:

option = word_size    
type = integer
default value  = 3 
description and notes = "Valid word sizes are 2-7."

There also seems to be no mention of this change in the release notes, all of which makes me think that this is a bug. So I will report this to the NCBI, but any CEGMA users out there may wish to hold off updating to v.2.2.30+.