A. baumannii Pasteur scheme not in BLAST database

[VGalata]

Dear Torsten,

It seems that the Pasteur A. baumannii scheme is not included in the BLAST database. Using the scheme abaumannii_2 returns no results:

bin/mlst --scheme abaumannii_2 <input FASTA> --debug

Retuned (after skipping matches for the Oxford A. baumannii scheme):

$VAR1 = [
          'abaumannii_2',
          '-',
          '-/-/-/-/-/-/-'
        ];

Also the inspection of the BLAST database returned no matches for the genes from the Pasteur scheme.

blastdbcmd -db db/blast/mlst.fa -entry all | grep 'Pas_.*'

Used version: mlst 2.5

[tseemann]

@VGalata you are right - for some reason my script https://github.com/tseemann/mlst/blob/master/scripts/mlst-make_blast_db
does not include schemes with _2 in them.

I suspect I had a good reason at the time but I am not sure why now!

I have fixed the problem. Thank you for the report. Please use the latest github version (git clone).