Question: Blast Execution Problem
0
gravatar for somethingfromnothing
7.3 years ago by
somethingfromnothing0 wrote:

Hi,

I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong.

So here are the things I did so far:

1) I downloaded the Win-32 executable file from NCBI/blast/latest (2.2.26). Double-click and install the files under "C:\blast"

2) I went to Environmental Variables window and created variable BLAST with value "C:\blast\bin\", BLASTDB with "C:\blast\db\" and added "C:\blast\bin" to the variable Path

3) Under "C:\blast", I have three folders: bin, doc and db folder that I created to put the fasta database.

4) I downloaded pre-formatted non-redundant (nr) fasta database from NCBI ftp and put it under C:\blast\db

5) I used "formatdb -i nr -p T" command to create index files.

6) Now C:\blast\db has the following files: nr.00.phr, nr.00.pin, nr.00.psq, [...], nr.06.phr, nr.06.pin, nr.06.psq

7) Next I wanted to perform a protein blast search using this command:

C:>blastall -p blastp -d nr -i /users/lab512/Desktop/sequence.fas -o /users/lab512/Desktop/blast_output.txt

Unfortunately, I get the following error:

[blastall 2.2.24] WARNING: Unable to open nr.pin [blastall 2.2.24] WARNING: Unable to open nr.pin [blastall 2.2.24] WARNING: Unable to open nr.pin [blastall 2.2.24] WARNING: Unable to open nr.pin [blastall 2.2.24] WARNING: homosapiens: Unable to open nr.pin [blastall 2.2.24] WARNING: homosapiens: Unable to open nr.pin [blastall 2.2.24] WARNING: homosapiens: Unable to open nr.pin [blastall 2.2.24] WARNING: homosapiens: Unable to open nr.pin

My understanding is that it complains that it cannot locate the nr database. However, I already point to the correct directory when I set it in the environmental variables.

Moreover, when I try to write the path explicitly as "-d /blast/db/nr", this time I get this error:

[blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.02.pin [blastall 2.2.24] WARNING: Unable to open nr.02.pin [blastall 2.2.24] WARNING: Unable to open nr.02.pin [blastall 2.2.24] WARNING: Unable to open nr.02.pin [blastall 2.2.24] WARNING: Unable to open nr.03.pin [blastall 2.2.24] WARNING: Unable to open nr.03.pin [blastall 2.2.24] WARNING: Unable to open nr.03.pin [blastall 2.2.24] WARNING: Unable to open nr.03.pin [blastall 2.2.24] WARNING: Unable to open nr.04.pin [blastall 2.2.24] WARNING: Unable to open nr.04.pin [blastall 2.2.24] WARNING: Unable to open nr.04.pin [blastall 2.2.24] WARNING: Unable to open nr.04.pin [blastall 2.2.24] WARNING: Unable to open nr.05.pin [blastall 2.2.24] WARNING: Unable to open nr.05.pin [blastall 2.2.24] WARNING: Unable to open nr.05.pin [blastall 2.2.24] WARNING: Unable to open nr.05.pin [blastall 2.2.24] WARNING: Unable to open nr.06.pin [blastall 2.2.24] WARNING: Unable to open nr.06.pin [blastall 2.2.24] WARNING: Unable to open nr.06.pin [blastall 2.2.24] WARNING: Unable to open nr.06.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.00.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [blastall 2.2.24] WARNING: Unable to open nr.01.pin [...]

What is the problem here?

By the way, I have no idea why it prints blastall 2.2.24 in the error when I do not have that version on my computer but have the latest 2.2.26 version.

blast • 4.7k views
ADD COMMENTlink written 7.3 years ago by somethingfromnothing0
0
gravatar for Istvan Albert
7.3 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

The problem is with your path. Keep trying.

For example make sure that the paths are properly set and that you are not mixing paths with forward slashes (Unix style) with backward slashes (Windows style) as you do in your example. While technically it should be allowed, in practice (and especially with blast) this often leads to weird problems. Make sure that you set the environment variable in a global way, and that you open a command prompt AFTER the global environment was set, and that the variable is actually visible from both the command and a new shell as well.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Istvan Albert ♦♦ 81k
0
gravatar for kevin.l.neff
7.3 years ago by
kevin.l.neff210
Mayo Clinic College of Medicine
kevin.l.neff210 wrote:

make sure you have nr.nal in the current directory or specify it at the command line. I think you can say -db ./db/nt or something like that.

ADD COMMENTlink written 7.3 years ago by kevin.l.neff210

thank you. I was missing the nr.nal file after I transferred the data to a new directory. very helfpul

ADD REPLYlink written 6.0 years ago by eigoken0
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