blastformat function

I get the following error when trying to run blastformat:

Error using blastformat (line 154) FORMATDB produced the following error(s): /bin/bash: formatdb: command not found

I am running ncbi-blast-2.2.25+, and there is no command in the directory titled blastdb. I believe older versions used this command. Is there a workaround or should I just revert to an older, preferred version of ncbi-blast.

Thanks

Answer 1

[Didier]

I got the same problem just recently. In fact you have to tell Matlab where to find the executable formatdb using the setenv command.

In my case I just typed at the prompt in the command window: setenv('PATH', [getenv('PATH') ':/Users/DC/Documents/MATLAB/blast-2.2.26/bin']); This the Mac type of command. For Windows you have to change : to ;

And then you have to put the entire path to the .fna file you are using: blastformat('Inputdb','/Users/DC/Documents/MATLAB/Data/Bacteria/Ecoli_data/NC_004431.fna')

[Raffael]

I have the same problem but i don’t know which type of blast I use. What would the code look like then?

I’m using Matlab 2014b

%%BLAST Script für die Erstellung eines Core genomes

clc
clear

% cd ('/Users/ringlin/polybox/Fasta import Matlab/NT-Fasta');

%%Erstellen einer BLAST Datenbank

blastformat('Inputdb','/Users/ringlin/polybox/Fasta import Matlab/NT-Fasta/RI_009_gene.fa')

My Error looks like this:

Error using blastformat (line 154)
FORMATDB produced the following error(s): /bin/bash: formatdb: command not found

Error in Core_Genome_BLAST (line 10)
blastformat('Inputdb','/Users/ringlin/polybox/Fasta import Matlab/NT-Fasta/RI_009_gene.fa')

Answer 2

[Shlomo Geva]

I had the same problem, using Windows. I installed the NCBI blast suite. In the \bin file where it is installed there is a command called blast_formatter.exe You can specify this in matlab when you call formatdb, by adding the arguments pair identifying the program to invoke. In my case the additional call arguments look like this:

blastformat('Inputdb', 'foo.fasta','Protein',false,... 'FORMATPATH', 'C:\Program Files\NCBI\blast-2.6.0+\bin\blast_formatter.exe');

[Shlomo Geva]

You may actually mean to run the NCBI function makeblastdb.exe (NCBI formatdb was deprecated and this is the replacement, I think). It appears that the bioinformatics toolbox needs updating. The arguments naming had changed in the NCBI commnad (e.g. -i should be -in, -p should be -dbtype. It is wrong in MATLAB's implementation of blastformat.m