The Genomics Sequencing Facility no longer makes result files for next-generation sequencing services available for download through our website. NGS results are now available from an IS-maintained file delivery server, which offers greater download speed, security, and flexibility than the old web-based method.

The username and password for the new download server are included in the automated messages you receive from dnacore@cchmc.org when sequencing results are ready. Please share these credentials with any collaborators with whom you wish to share access to your data.

There are multiple ways to retrieve GSF sequencing results:

• Using a graphical SFTP client (i.e., Windows desktops)
• Using a command-line SFTP client (i.e., CCHMC cluster or Linux/Mac desktops)
• Using rclone (allows parallel downloads)
• Using the ActiveMFT Website (not recommended)

Graphical SFTP client

The easiest way to download multiple files is with a graphical file transfer application. Windows users at CCHMC have easy access to WinSCP, so we provide instructions for that software. However, any similar tool will work.

1. Install WinSCP (if necessary) — Open the "Software Center" app on your CCHMC-provided Windows computer. Within the Software Center, find and install WinSCP (highlighted in yellow in the image). Programs installed from the Software Center do not require administrative access.

   

2. Configure the connection — Open the WinSCP software and open the Login dialog (it should open by default). Ensure that the Protocol is set to SFTP, the Host name is activemft.research.cchmc.org, and the Port number is 51022. Once these settings are configured, you can save this profile for future use.

   

3. Connect to the file server — Click the "Login" button to connect. When prompted, enter the username/password you received in the email from the DNA Core, not your CCHMC login credentials.
4. Download your files — Highlight the files you wish to download, and click the "Download" button.

For CCHMC-provided Mac users who would like to use a graphical SFTP client, there are no options in Self-Service (the Mac equivalent of Software Center). We would recommend downloading and installing FileZilla for Mac or Cyberduck for this purpose.

Command-line SFTP client

The sftp program is installed by default on Unix-like computers, including Macs and the cluster. You can connect to the download server using the following command line:

sftp -P 51022 <username>@activemft.research.cchmc.org

Where <username> is replaced with the numerical ID found in the email you received. If you get a "no matching key exchange method" error message at this step, see this FAQ.

Once you're connected, you can type

• help to see an overview of possible commands
• ls to view available files
• get <filename> to download a specific file
• get -R * to download all files, and
• exit to disconnect from the server and close the client.

Further commands can be found in the sftp manual page .

Using rclone for parallel downloads

Rclone, a command-line program for downloading from various web storage services, also supports the SFTP protocol. It has the advantage over the sftp command mentioned above of being able to perform multiple downloads in parallel.

Either download a version of rclone appropriate for your local system or load the rclone module if using the Children's HPC cluster. If you choose to download the program on your own, the rclone binary should be placed somewhere in the shell's search path.

Then perform the following setup steps:¹

# if on the Children's HPC cluster, load the 'rclone' module
module load rclone

# create a new "remote" named 'gsf'
rclone config create gsf sftp \
  host activemft.research.cchmc.org \
  port 51022 \
  ask_password true

# test the connection
# as noted above, <username> is a numeric ID sent via email
rclone ls --sftp-user=<username> gsf:

Backslashes are used to here to split long lines for readability; you may omit them and type the individual commands on a single line instead.²

Download all results from a submission to the current working directory (.) using the copy subcommand:

# `--dry-run` means preview the transfer without copying anything
rclone copy --sftp-user=<username> --dry-run gsf:/ .

# `-P` means "show transfer progress"
rclone copy --sftp-user=<username> -P gsf:/ .

Note that you must provide --sftp-user=<username> with the numeric username provided to you via email for each rclone invocation. If you forget this option, rclone will default to using your local username, and the login to the SFTP server will fail. Remember that the username and password change with each submission!

Further information may be found in the the help for the SFTP backend on rclone.org.

Website

The web interface for the download server is at https://activemft.research.cchmc.org. We do not recommend this method because it only lets you download a single file at a time, but it is available if no other options are suitable.

When logging into this website, ensure that you change the Domain to ResCore. Your login credentials will not work using the default domain.