Question: blast execution in linux
0
gravatar for seta
4.4 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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

ADD COMMENTlink modified 3.4 years ago by prachessiit0 • written 4.4 years ago by seta1.2k
1

Have you moved all the executables to your bin directory?

ADD REPLYlink written 4.4 years ago by iraun3.6k

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.

ADD REPLYlink written 4.4 years ago by seta1.2k
1

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)

ADD REPLYlink written 4.4 years ago by iraun3.6k

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

ADD REPLYlink written 4.4 years ago by apelin20470

I tried it the output was: bash: ./blastn: cannot execute binary file

ADD REPLYlink written 4.4 years ago by seta1.2k
3
gravatar for Siva
4.4 years ago by
Siva1.6k
United States
Siva1.6k wrote:

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
ADD COMMENTlink written 4.4 years ago by Siva1.6k

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

ADD REPLYlink written 4.4 years ago by RamRS22k

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

ADD REPLYlink written 4.4 years ago by seta1.2k

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?

ADD REPLYlink written 4.4 years ago by Siva1.6k

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: C: blast excutation in linux

ADD REPLYlink written 4.4 years ago by RamRS22k

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.

ADD REPLYlink written 4.4 years ago by Jean-Karim Heriche19k
1
gravatar for RamRS
4.4 years ago by
RamRS22k
Houston, TX
RamRS22k wrote:

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.

ADD COMMENTlink written 4.4 years ago by RamRS22k

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?

ADD REPLYlink modified 4.4 years ago by RamRS22k • written 4.4 years ago by seta1.2k

Can you give us the output of which blastn please?

ADD REPLYlink written 4.4 years ago by RamRS22k

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

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by seta1.2k

Then try this:

find ~ -name blastn
ADD REPLYlink written 4.4 years ago by RamRS22k

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

ADD REPLYlink written 4.4 years ago by seta1.2k

Then you might just wanna try that, like so:

/home/dps/ncbi-blast-2.2.30+/bin/blastn -v
ADD REPLYlink written 4.4 years ago by RamRS22k

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?

ADD REPLYlink written 4.4 years ago by seta1.2k

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
ADD REPLYlink written 4.4 years ago by RamRS22k

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?!

ADD REPLYlink written 4.4 years ago by seta1.2k
0
gravatar for prachessiit
3.4 years ago by
prachessiit0 wrote:
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 appreaciated.
ADD COMMENTlink written 3.4 years ago by prachessiit0

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"

ADD REPLYlink written 3.4 years ago by RamRS22k
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