blast execution in linux

Question

[seta]

Hi all,

I've recently install the ncbi-blast-2.2.30+ on ubuntu based on its user manual, but when I'm trying to test it with the blastn -help command, it says:

The program 'blastn' is currently not installed. You can install it by typing: sudo apt-get install ncbi-blast+

while I'm in ~/ncbi-blast-2.2.30+/bin that contains several programs like blastn. Please let me know what the wrong is and what the solution for it? thanks a lot

[iraun]

Have you moved all the executables to your bin directory?

[seta]

Hi airan, I downloaded the package, placed in home directory, then unzip that all excutable program was appeared in the corresponding bin folder inside ncbi-blast30+ and try to test it, but I failed.

[iraun]

If you want to run 'blastn' without specifying all the path, you've to copy all the executables included in "~/ncbi-blast-2.2.30+/bin$" to your bin dir (usr/local/bin normally). Otherwise, to run blastn, you should write the path to blastn bin folder (in your case ~/ncbi-blast-2.2.30+/bin/blastn)

[apelin20]

go to ~/ncbi-blast-2.2.30+/bin, and write ./blastn

[seta]

I tried it the output was:

bash: ./blastn: cannot execute binary file

[prachessiit]

Hi guys,

I have 32 bit dell inspiron. I want to install blast on my CentOS7. Could you tell which version of blast should I install. Urgent replies would be appreciated.

[Ram]

a. Please do not specify timelines, it's a bit rude.

b. It's a 32 bit machine, 32 bit binaries are the ones you're looking for. Google "ncbi blast+ 32 bit linux"

Answer 1

[Siva]

Could it be due to your system being 32-bit and you downloaded the 64-bit version of BLAST?

To find your system information, type

uname -a

To find the version of BLAST, type

file /home/dps/ncbi-blast-2.2.30+/bin/blastn

[Ram]

The x86/64 was something I did not think of. Thank you, Siva.

[seta]

thanks for your comment. I checked it, both of them are x86/64. the problem is still another place!

[Siva]

Hmm. What is the name of the zip file you downloaded from the NCBI FTP site? Also if you don't mind, can you post the output of the two commands I suggested?

[Ram]

Could it be that the dir on which OP is trying to work doesn't have wx permissions or OP is out of disk space? Check out OP's comment here: blast execution in linux

[Jean-Karim Heriche]

Another related thing to consider is the type of archicture. You seem to have blast compiled for an x86-type CPU but maybe your computer has another type of CPU e.g. ARM.

Answer 2

[Ram]

Try ~/ncbi-blast-2.2.30+/bin/blastn -help(if you do not wish to install to the central repo). Add ~/ncbi-blast-2.2.30+/bin to PATH to make this easier.

[seta]

thanks for all feedback. I tried ~/ncbi-blast-2.2.30+/bin/blastn and also /ncbi-blast-2.2.30+/bin/blastn -help, but the problem remained. I'm confused, the blastn and other program are available in the bin folder, please any suggestion?

[Ram]

Can you give us the output of which blastn please?

[seta]

Strange, there is no output, no error, I came bake to dps@dps-Inspiron-N5110:~$

[Ram]

Then try this:

find ~ -name blastn

[seta]

thanks for your help me, the out put of the above command is : /home/dps/ncbi-blast-2.2.30+/bin/blastn

[Ram]

Then you might just wanna try that, like so:

/home/dps/ncbi-blast-2.2.30+/bin/blastn -v

[seta]

thanks. I try it but not helpful, the output was:

bash: /home/dps/ncbi-blast-2.2.30+/bin/blastn: cannot execute binary file. 

However, it's executable (x) as I checked. Really, what happened?

[Ram]

Maybe you're not the owner. Can you give us the output of:

$ whoami
$ ls -l /home/dps/ncbi-blast-2.2.30+/bin/blastn

[seta]

Thanks RamRs, the output of of two above command were dps and

-rwxr-xr-x 1 dps dps 32501336 oct 28 00:52 /home/dps/ncbi-blast-2.2.30+/bin/blastn

respectively. so I'm owner and the program is also executable, isn't it. I'm getting crazy why there is still problem?!