Uploading to NCBI/SRA directly from CLIMB user

[Munnj90]

Hi all,

I’m trying to upload files to NCBI, SRA. Can i do do this directly from CLIMB to avoid downloading and then uploading the files?

I’m on a UBUNTU 16 instance.

I’ve attempted this with Aspera command line tools (NCBI recommendation) with the following command:

ascp -i <path/to/key_file> -QT -l100m -k1 -d <path/to/folder/containing files> subasp@upload.ncbi.nlm.nih.gov:uploads/<user_specific>

I get this error:

Session Stop (Error: Client unable to connect to server (check UDP port and firewall))

Any help or advice on uploading directly from my user to SRA would be greatly appreciated!

Best wishes,
John.

[flashton]

Hello,

You can usually upload files via the command line from e.g. CLIMB to NCBI/EBI.

E.g. https://www.ncbi.nlm.nih.gov/sra/docs/submitfiles/

Usually the way it works is that you setup the submission via the web interface, and then upload via the command line.

Thanks,

Phil

[Munnj90]

Hi Phil,

Thanks for your advice, it was this pages advice i was following but as far as i can tell they have no mention of the error. As a result i’m just downloading the files locally for upload but would prefer a direct upload. Perhaps it is an issue on my user but i’m not sure what that would be, especially if no one else has had the same issue.

Cheers,
John.