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SRA File Upload

File Transfer Protocol (FTP)

In order to upload your files to the NCBI server via FTP you need the following information:

  • Address
  • Username
  • Password

Figure 1: Credentials for file uploading in the Submission Portal

Start new SRA submission in Submission Portal

FTP Command Line Basics

File transfer can be initiated in Windows Command Prompt (Start -> Command Prompt), Mac Terminal (Finder -> Applications -> Utilities -> Terminal), Linux, and Unix.

Action Command line
Change into directory with your data files cd "U:\SRA\example-files"
Invoke FTP protocol ftp -i
Access NCBI FTP server open ftp-private.ncbi.nlm.nih.gov
Provide username on "User" prompt Username
Provide password on "Password" prompt Password
Create directory mkdir MYSUBMISSION
Change into that directory with arbitrary name cd MYSUBMISSION
Transfer all files mput *

Useful FTP commands:

Command Information
help, ? Either command prints list of commands
! Toggles back and forth between the operating system and ftp. Once back in the operating system, type 'exit' to get back to the FTP command line.
bye, quit These commands terminate the FTP session and exit
ls Lists files in the remote directory
put Send one file

FTP Command line Instructions for the SRA Submission Portal Wizard

After you connected to the NCBI FTP server:

  1. Navigate (use command cd) to your account folder uploads/user@email.com_xxxxx

  2. Create a submission folder (use command mkdir) for your data within your FTP account folder (uploads/user@email.com_xxxxx) and deposit your files into the submission folder. If you upload your files in the account folder directly or place the files into a nested folder, you will not be able to see or select the submission folder as instructed below. The submission folder is a temporary holding area and it will be removed after the whole submission is finished processing (the button Submit is clicked).

Using third party FTP clients

Many reliable FTP clients can be found on Internet. For example, Filezilla offsite image and NcFTP Client offsite image are free for download. Please refer to their documentation for usage instructions and troubleshooting tips.

Using FileZilla to transfer files when making submission in the SRA Submission Portal Wizard

When using FileZilla to upload files you need to paste your account folder's name into the Remote Site box on the right hand side of FileZilla interface (outlined in red) and hit Enter. Until you do this, you will see a message stating "550 /: Permission denied" or "Fail to read the directory listing". We prevent directory listing in the default sign in folder for security reasons. From within your account folder you can then create your submission folder(s) for your submission(s).

Figure 2


Aspera Connect

Aspera Connect is software that allows download and upload via a web plugin for popular browsers on machines running Linux, Windows, and Macintosh. The software also includes a command line tool (ascp) that allows scripted data transfer. The software client is free for users exchanging data with NCBI.

Aspera Connect Fast and Secure Protocol (FASP) uses User Datagram Protocol (UDP) that eliminates and overcomes many shortcomings of other FTP clients and we recommend it for all medium to large submissions and slow or unreliable connections (especially from abroad).

Download and install Aspera Connect software from: https://www.ibm.com/aspera/connect/ offsite image.

Aspera command line for the SRA Submission Portal Wizard

You may use the following command to upload files via Aspera command line:

<path to aspera executables> -i <path/to/key-file> -QT -l 100m -k1 -d <path/to/folder-with-file(s)> subasp@upload.ncbi.nlm.nih.gov:uploads/<user@email.com_xxxxx>

Aspera command line explanation:

  • <user@email.com_xxxxx> is your personal account SRA folder generated for you and is listed under the Aspera Command-Line upload link;
  • <path to aspera executables> or in many cases, simply, ascp:
    • Microsoft Windows: C:\Program Files\Aspera\Aspera Connect\bin\ascp.exe
    • Mac OS X: /Applications/Aspera/Connect.app/Contents/Resources/ascp (for admin's installation) or /Users/[username]/Applications/Aspera/Connect.app/Contents/Resources/ascp (for non-admin's installation)
    • Linux: /opt/aspera/bin/ascpor /home/[username]/aspera/connect/bin/ascp
  • i <path/to/key_file> - absolute path and file name of the private SSH key (e.g.: /home/keys/aspera.openssh)
  • <key-file> is provided upon your clicking on Get the key file link or sent upon request for direct SRA uploads
  • Q - for adaptive flow control (needed for disk throttling)
  • T - to disable encryption
  • k1 - enables resuming of partial transfers
  • d - <path/to/folder-with-file(s)> should include a directory name and so should not be '.' Or './'
  • l100m - designates maximum bandwidth of 100Mps, try 100m and move up if necessary to ensure good performance with unattended operations
  • <path/to/folder-with-file(s)> - names of files to transfer including path or path to a folder that contains all files

The environmental variable ASPERA_SCP_PASS can be used to store the private key path for a scripted series of bulk uploads.

Aspera Connect Download offsite image.

Tack A submission folder <folder-with-file(s)> will be created automatically by Aspera within your account folder <user@email.com_xxxxx> when the option -d is provided.

At the last step of your submission, the submission folder containing your files can be selected and the files will link to your submission.

Exclamation point Do not upload complex directory structures and files that do not contain sequence data!
Exclamation pointThe submission folder is a temporary holding area and it will be removed after the whole submission is finished processing (the button Submit is clicked).

Firewall Requirements

UDP (User Datagram Protocol for Aspera Connect) transfer must be enabled for the following IP ranges (please consult your local network admin if you are unsure): and TCP (Transmission Control Protocol for FTP) port 22 and UDP port 33001 must be open for our subnet.

Contact SRA staff

Email sra@ncbi.nlm.nih.gov for help.

Support Center

Last updated: 2023-08-01T12:49:42Z