[sklages]

Please enter

ls -l

hmm, and

uname -m

[shrujan]

shrujan@ubuntu:~/Programs/sratoolkit.2.3.2-4-ubuntu64/bin$ ls
abi-dump ncbi sra-stat.2
abi-dump.2 nenctool sra-stat.2.3.2
abi-dump.2.3.2 nenctool.2 sratoolkit.jar
abi-load nenctool.2.3.2 srf-load
abi-load.2 pacbio-load srf-load.2
abi-load.2.3.2 pacbio-load.2 srf-load.2.3.2
align-info pacbio-load.2.3.2 SRR072111_1.fastq
align-info.2 prefetch SRR072111_2.fastq
align-info.2.3.2 prefetch.2 SRR072111.sra
bam-load prefetch.2.3.2 test-sra
bam-load.2 rcexplain test-sra.2
bam-load.2.3.2 rcexplain.2 test-sra.2.3.2
cg-load rcexplain.2.3.2 vdb-config
cg-load.2 refseq-load vdb-config.2
cg-load.2.3.2 refseq-load.2 vdb-config.2.3.2
configuration-assistant.perl refseq-load.2.3.2 vdb-copy
fastq-dump sam-dump vdb-copy.2
fastq-dump.2 sam-dump.2 vdb-copy.2.3.2
fastq-dump.2.3.2 sam-dump.2.3.2 vdb-decrypt
fastq-load sff-dump vdb-decrypt.2
fastq-load.2 sff-dump.2 vdb-decrypt.2.3.2
fastq-load.2.3.2 sff-dump.2.3.2 vdb-dump
helicos-load sff-load vdb-dump.2
helicos-load.2 sff-load.2 vdb-dump.2.3.2
helicos-load.2.3.2 sff-load.2.3.2 vdb-encrypt
illumina-dump sra-dbcc vdb-encrypt.2
illumina-dump.2 sra-dbcc.2 vdb-encrypt.2.3.2
illumina-dump.2.3.2 sra-dbcc.2.3.2 vdb-lock
illumina-load sra-kar vdb-lock.2
illumina-load.2 sra-kar.2 vdb-lock.2.3.2
illumina-load.2.3.2 sra-kar.2.3.2 vdb-passwd
kar srapath vdb-passwd.2
kar.2 srapath.2 vdb-passwd.2.3.2
kar.2.3.2 srapath.2.3.2 vdb-unlock
kdbmeta sra-pileup vdb-unlock.2
kdbmeta.2 sra-pileup.2 vdb-unlock.2.3.2
kdbmeta.2.3.2 sra-pileup.2.3.2 vdb-validate
libcurl.so sra-sort vdb-validate.2
libcurl.so.4 sra-sort.2 vdb-validate.2.3.2
libcurl.so.4.3.0 sra-sort.2.3.2
libvdb_jni.so sra-stat

[sklages]

shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
bash: ./fastq-dump: No such file or directory

That is not the same error. As GenoMax wrote, post the content of your bin folder.

cd ~/Programs/sratoolkit.2.3.2/bin
ls -l

[GenoMax]

Can you post a listing of the bin directory?

ls -l

[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.

[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

[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]

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]

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]

Should i have to download 32 bit version ??

[shrujan]

yes i have downloaded 64 bit archive of SRA Toolkit 2.3.2

[shrujan]

i686 comes when i type uname -m

[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]

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

[shrujan]

erro message

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