error: BLAST database name is missing. Please edit provean.sh file to add the name.

Question

[elham]

Hi, I'm trying to install provean and use it on my local machine. I get the following error.

error: BLAST database name is missing. Please edit provean.sh file to add the name.

I am configuring provean by this command line:

./configure --prefix=/home/elham123456/linux/provean-1.1.5 PSIBLAST=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/psiblast BLASTDBCMD=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/blastdbcmd CDHIT=/home/elham123456/linux/provean-1.1.5/cd-hit/bin/cd-hit BLAST_DB=/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr

and it is my provean.sh file

BLAST_DB="/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr"
PSIBLAST="/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/psiblast"
CD_HIT="/home/elham123456/linux/provean-1.1.5/cd-hit/bin/cd-hit"
BLASTDBCMD="/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/blastdbcmd"

[Mensur Dlakic]

You already asked the same question here. This post is just a bit cleaner.

Like I told you, it would appear that BLAST database is defined as BLAST_DB variable. If that's not the case, I suggest you look through the code and find out what the problem is

[GenoMax]

You need to define BLAST_DB to point to directory that contains your index files. So try

BLAST_DB="/home/elham123456/linux/provean-1.1.5/nr_sep_2012/"

[elham]

thank you for the answer, but it is not work. can i get you a little more information, i hope you can solve the problem with this information...

nr_sep_2012$ ls
nr

and

nr$ ls
nr.00.phd  nr.01.pni  nr.02.psi  nr.04.pin  nr.05.ppi  nr.07.phi
nr.00.phi  nr.01.pog  nr.02.psq  nr.04.pnd  nr.05.psd  nr.07.phr
nr.00.phr  nr.01.ppd  nr.03.phd  nr.04.pni  nr.05.psi  nr.07.pin
nr.00.pin  nr.01.ppi  nr.03.phi  nr.04.pog  nr.05.psq  nr.07.pnd
nr.00.pni  nr.01.psi  nr.03.pin  nr.04.ppi  nr.06.phi  nr.07.pog
nr.00.pog  nr.01.psq  nr.03.pnd  nr.04.psd  nr.06.phr  nr.07.ppd
nr.00.ppd  nr.02.phd  nr.03.pni  nr.04.psi  nr.06.pin  nr.07.ppi
nr.00.ppi  nr.02.phi  nr.03.pog  nr.04.psq  nr.06.pnd  nr.07.psd
nr.00.psd  nr.02.phr  nr.03.ppd  nr.05.phd  nr.06.pni  nr.07.psi
nr.00.psi  nr.02.pin  nr.03.ppi  nr.05.phi  nr.06.pog  nr.07.psq
nr.00.psq  nr.02.pnd  nr.03.psd  nr.05.phr  nr.06.ppd  nr.pal
nr.01.phd  nr.02.pni  nr.03.psi  nr.05.pin  nr.06.ppi
nr.01.phi  nr.02.pog  nr.03.psq  nr.05.pnd  nr.06.psd
nr.01.phr  nr.02.ppd  nr.04.phd  nr.05.pni  nr.06.psi
nr.01.pin  nr.02.ppi  nr.04.phi  nr.05.pog  nr.06.psq
nr.01.pnd  nr.02.psd  nr.04.phr  nr.05.ppd  nr.07.phd

according theses, this code is correct for BLAST_DB

BLAST_DB="/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr"

i right?

[elham]

and one more point, in bash file write,

if [ -z "$BLAST_DB" ] ; then
    echo "error: BLAST database name is missing. Please edit provean.sh file to add the name."
    exit 1;

assuredly if [ -z "$BLAST_DB" ] is the solution but i do not understand it ...

[GenoMax]

It is possible the provean was written a long time ago when the blast databases were in v.4.x They are now in a new version called v.5.x. That may be the reason why this is not working.

If that is the case you are not going to be able to use provean with the indexes you downloaded from NCBI. You may need to create your own v.4.x indexes (after installed an OLD version of blast).

If true you may want to look for an alternative option to provean.sh.

[Mensur Dlakic]

Judging by the number of nr indices (8) and by name (nr_sep_2012), this sounds like an old database. So I would flip your argument and conclude that the OP's BLAST version is more recent than the database. If correct, that would mean downloading older BLAST or a newer nr database.

[GenoMax]

Agreed. If OP can justify using a 10+ year old database then trying to get old blast installed will be the way to go.

Otherwise finding an alternative to provean may be a better choice.

I vaguely recall a prior exchange with another poster about provean and I don't think it can use the new blast.