/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....

Question

[Manju]

Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the database(BLASTDB )path .ncbirc file. but when i am running fst blast command in terminal i.e blastn -help it showing me error that bash: /home/abc/ncbi-blast-2.2.25+/bin/blastn: No such file or directory

Its working fine in other system but not in my system. How can it possible i have check that this path is correct..but still its not finding that path..

I am working in Ubuntu 10.10.

I h've also search in google but didnt find any solution related to this. Pls help me in this.

Thanks Manju Rawat..

[Pierre Lindenbaum]

can you see the path to blast when you write "echo $PATH" ?

[Michael]

and what happens if you just run in a terminal: $ /home/abc/ncbi-blast-2.2.25+/bin/blastn -help

[Hranjeev]

You should rephrase your title

[Steve Moss]

What do you get when you do a "which blastn" and "whereis ?

[Steve Moss]

What do you get when you do a "which blastn" and "whereis blastn" from the terminal?

[Steve Moss]

What have you added to .bashrc? It should be export PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin! Also, are the binaries executable? What do you get from ls -al in the bin directory? You may need to chmod a+x the relevant binaries?

[Steve Moss]

Also try doing "file blastn" and "readelf -a blastn" and paste the output? Along with "uname -a"

[Steve Moss]

Also, why go through this in the first place? Aptitude has an ncbi-blast+ package! Do apt-cache search blast+ and then apt-get install!

Answer 1

[Daniel Standage]

I had a similar problem recently using a binary compiled for the wrong architecture. It's more likely that you have a path issues (as others have suggested), but this is worth checking as well. For example, when I download the wrong version of the SRA toolkit to my system, I get the same error when I try to execute the binaries.

standage@gremlin4:~$ wget http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.1.6-ubuntu32.tar.gz
standage@gremlin4:~$ tar xzf sratoolkit.2.1.6-ubuntu32.tar.gz
standage@gremlin4:~$ cd sratoolkit.2.1.6-ubuntu32/
standage@gremlin4:~/sratoolkit.2.1.6-ubuntu32$ ls -l fastq-dump.2.1.6
-rwxr-xr-x 1 standage standage 1633589 2011-09-12 11:11 fastq-dump.2.1.6
standage@gremlin4:~/sratoolkit.2.1.6-ubuntu32$ ./fastq-dump.2.1.6 
-bash: ./fastq-dump.2.1.6: No such file or directory

If I compile from the source code, the program executes successfully. If your path is correct, I would check whether the binaries were compiled for the correct architecture.

[Steve Moss]

I think you're right, I think this is a the result of trying to run a 32bit binary on a 64bit system! uname -a, file blastn and readelf -a blastn should confirm!

Answer 2

[Neilfws]

"No such file or directory" typically means that the executable (blastn in this case) was not found in the directory from which you tried to run it. So it's likely that $PATH does not include /home/abc/ncbi-blast-2.2.25+/bin/blastn.

Try this. Edit a file named .profile in your home directory and add these lines:

if [ -d "/home/abc/ncbi-blast-2.2.25+/bin" ] ; then
    PATH="/home/abc/ncbi-blast-2.2.25+/bin:$PATH"
fi

Note that the path points to the BLAST bin directory, not the blastn executable.

Then in the terminal run:

source ~/.profile

(only this time - the file will be read next time you log in.)

Then try blastn with no arguments (in the same terminal) to check that it is found.

EDIT: based on your response, another possibility is that blastn is not executable. What does:

ls -lrt /home/abc/ncbi-blast-2.2.25+/bin/blastn

show you?

Answer 3

[Manju]

I h've set everything.echo $PATH command giving me this output /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/abc/ncbi-blast-2.2.25+/bin..

And when i am running blastn command wothout any comment or with complete path /home/abc/ncbi-blast-2.2.25+/bin/blastn -help In both case it showing me the same error that bash: /home/abc/ncbi-blast-2.2.25+/bin/blastn: No such file or directory...

I am doing the same thing in other system and its working fine...But not in my system...

Thanks Manju Rawat.

[Neilfws]

This is not an answer; please paste it as a comment under the relevant answer and remove from here.