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blast execution in linux

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

alignment software-error next-gen blast
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updated by Ram Ram • written by seta seta

Have you moved all the executables to your bin directory?

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written by iraun iraun

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.

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written by seta seta

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)

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written by iraun iraun

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

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written by apelin20 apelin20

I tried it the output was:

bash: ./blastn: cannot execute binary file
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updated by Ram Ram • written by seta seta

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.

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updated by Ram Ram • written by prachessiit • prachessiit

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"

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written by Ram Ram

2 answers

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
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updated by Ram Ram • written by Siva Siva

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

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written by Ram Ram

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

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written by seta seta

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?

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written by Siva Siva

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

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written by Ram Ram

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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.

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written by Ram Ram

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?

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updated by Ram Ram • written by seta seta

Can you give us the output of which blastn please?

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written by Ram Ram

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

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written by seta seta

Then try this:

find ~ -name blastn
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written by Ram Ram

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

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written by seta seta

Then you might just wanna try that, like so:

/home/dps/ncbi-blast-2.2.30+/bin/blastn -v
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written by Ram Ram

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?

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updated by Ram Ram • written by seta seta

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
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written by Ram Ram

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?!

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updated by Ram Ram • written by seta seta

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