[dena.dinesh]

I am already in the directory where I stored all the files and then exceuted fasq-dump..is it right?

[GenoMax]

I am already in the directory where I stored all the files and then exceuted fasq-dump..is it right?

I know it does not make sense to provide the full path, but that seems to work in many cases. Like the example I tried from your dataset above (even though I was in the directory where the file was located).

[fkrueger]

We have also experienced these problems, and as a result always use a relative path to the file if we are in the directory already:

$ fastq-dump ./SRR1266967.sra

[dena.dinesh]

I tried giving relative path. then also the same error..how can i rectify it.

[dena.dinesh]

Dear Kruger,

Did it ran well for you? When I ran fastq-dump ./SRR1266967.sra, it failed immeditely where as for other files it ran for 3 seconds and throwed this error.

[fkrueger]

I just tested it, and it actually works well with or without prepending './'. I am using fastq-dump version 2.3.5 by the way.

[GenoMax]

I used sra-toolkit v.2.3.2.

[dena.dinesh]

Hi

I am using fastqdump 2.1.7. I downloaded the sratoolkit.2.4.2-ubuntu64 and later installed it suing sudo agt-get command. Inside the bin folder of sratoolkit.2.4.2 I am able find following version fastq-dump version:

fastq-dump.2.4.2; fastq-dump; fastq-dump.2

But I am not able to run the fastq-dump.2.4.2. Not only this file but also all other files of version 2.4.2 were higlighted in green color and I am not able to run those highlighted in green color.

Please guide me.

[Richard Finney]

This is why you don't need to re-invent sftp and gzip.

Just ... don't ... do it.

[GenoMax]

Hi

I am using fastqdump 2.1.7. I downloaded the sratoolkit.2.4.2-ubuntu64 and later installed it suing sudo agt-get command. Inside the bin folder of sratoolkit.2.4.2 I am able find following version fastq-dump version:

fastq-dump.2.4.2; fastq-dump; fastq-dump.2

But I am not able to run the fastq-dump.2.4.2. Not only this file but also all other files of version 2.4.2 were higlighted in green color and I am not able to run those highlighted in green color.

Please guide me.

Do the following to make that fastq-dump executable in the bin folder of sratoolkit-2.4.2:

$ chmod u+x fastq-dump*

Hopefully this is the only version on your machine now. Just to be safe provide the full path to this new file when you try to run it and see if it works.

[piet]

When I ran fastq-dump ./SRR1266967.sra, it failed immeditely

For curiosity I have also tried SRR1266967.sra and I could convert to fastq successfully. But notably, download of the the SRA file (about 430 Mb) was very slow and took about 30 minutes. Maybe you have downloaded the SRA file only partially?

wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR126/SRR1266967/SRR1266967.sra
md5sum SRR1266967.sra
  01c653175917848a60ad01f700793a49  SRR1266967.sra
fastq-dump -F SRR1266967.sra
grep ^@ SRR1266967.fastq | wc
  16557954 16557954 521453404

As expected I got 16557954 reads.

[hdashnow]

I had a similar error message. The problem in my case was that the temporary download directory was full. I resolved it by changing the download directory using vdb-config -i.

From: http://trace.ncbi.nlm.nih.gov/Traces..._doc&f=std#s-3

The default location for the "download repository" is:

Linux: /home/[user_name]/ncbi/public
Mac OS X: /Users/[user_name]/ncbi/public
Windows: C:\Users\[user_name]\ncbi\public

Here's hoping for some more helpful error messages in the next release!