SRA Toolkit in ubuntu 12.04

[shrujan]

Hi, i have downloaded SRA Toolkit.2.3.2 and tried to run ./fastq-dump in shell or terminal but after executing it is showing error as cannot be executed please resolve this.

thank you.

[sklages]

Which version of Ubuntu? 32bit? 64bit?

What is the exact error message you get?

Here on 12.10 (64bit) using 2.3.2-4 I encounter no problems.

[shrujan]

Ubuntu 12.04

Ubuntu 12.04. 64 bit Error is that when i try to execute ./fastq-dump, cannot be executed is coming

[sklages]

Just like this (not real):

bin $ ./fastq-dump
Cannot be executed

Please post a correct error message along with your command you executed.

Is this also true for other programs in bin?

[shrujan]

erro message

shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
bash: ./fastq-dump: cannot execute binary file

[shrujan]

yes this type of error is coming for other bin files too.

[sklages]

hmm, looks like the sra toolkit which you have downloaded has not been compiled for your system.
I didn't see any 32bit SRA Toolkit archives, so I assume you have dowloaded the 64bit archive.

So your Ubuntu system is very likely a 32bit system; what do you get with:
uname -m

[shrujan]

i686 comes when i type uname -m

[shrujan]

yes i have downloaded 64 bit archive of SRA Toolkit 2.3.2

[shrujan]

Should i have to download 32 bit version ??

[sklages]

So you have a 32bit system (though you wrote to have a 64bit system).
You cannot execute 64bit software on 32bit systems. As there is no 32bit SRA toolkit binary available for download you could either try to compile the toolkit from source on your 32bit system (be prepared to run into problems) or simply set up a new system, Ubuntu 64bit.
When dealing with big datasets, or with software for big datasets, it is not a bad idea to have a 64bit system for your analyses.

addendum: I see that Ubuntu holds a 32bit version of an older version of SRA toolkit, http://packages.ubuntu.com/quantal/science/sra-toolkit. Might be of interest for you.

[shrujan]

Oh, thank you for your guide lines. But i have a doubt regarding reinstalling on a hard disk i.e., i heard that re-installing OS on a hard disk may effect hard disk. Is it true ? Because i have already installed twice. So please clarify this doubt. Thank you

[sklages]

Oh, thank you for your guide lines. But i have a doubt regarding reinstalling on a hard disk i.e., i heard that re-installing OS on a hard disk may effect hard disk. Is it true ? Because i have already installed twice. So please clarify this doubt. Thank you

That's funny, never heard about that :-)

Don't worry, this is simply not true. I install twice a year a new version of some linux on my notebook, .. it is still alive ;-)

[shrujan]

Thank you. Its a great pleasure sharing views and issues. I will try installing 64 bit version, if it doesn't work i will ping you up. Thanks again

[shrujan]

SRA Toolkit error

Hi, as you said earlier i have reinstalled with 64 bit ubuntu 12.04 LTS OS and tried to run SRAToolkit.2.3.2 again. But same error message is repeated as
shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
bash: ./fastq-dump: No such file or directory

Please resolve this.

Thank you.