Error: Executable for makeblastdb not found

[mohamedbahru]

Hi,
I tried to run this command 'makeblastdb(Ref_file, dbtype = 'nucl')' and it got the following error:

Error: Executable for makeblastdb not found! Please make sure that the software is correctly installed and, if necessary, path variables are set.

[mhahsler]

Hi, most likely you do not have the executable makeblastdb in your search path.

Did you check this from ? makeblastdb

Sys.which("makeblastdb")
makeblastdb
"/usr/bin/makeblastdb"

[mohamedbahru]

Hi, Thanks for your reply. I checked and the path was empty. Please guide me, what I should do.
Sys.which("makeblastdb")
makeblastdb

[mhahsler]

This is from ? blast

The blast+ software has to be installed:

    • For Linux (Debian/Ubuntu)install package: ncbi-blast+

    • For Windows or OS X install the software from
      <https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/>.

 R needs to be able to find the executable (mostly an issue with
 Windows). Try ‘Sys.which("blastn")’ to see if the program is
 properly installed. If not, then you probably need to set the
 environment variable called PATH using something like
 ‘Sys.setenv(PATH = paste(Sys.getenv("PATH"), "path_to_BLAST", sep=
 .Platform$path.sep))’. You can use Sys.getenv("PATH") first to see
 what is currently in the search path.

 You will also need a database. NCBI BLAST databases are updated
 daily and may be downloaded via FTP from
 <https://ftp.ncbi.nlm.nih.gov/blast/db/>.