I can not transfer files by using sftp

Confirm the following points.

Authentification is by using SSH key not by password.
A private key is pair of a public key registered in a DDBJ account. Manual
Make sure to specify a private key for authentification and not a private key for dataset encryption/decryption. Manual
A private key file has read permission.
A private key file permission is set as others cannot access. For example, rw——-.
A passphrase for private key is correctly entered.
The ssh connection with the port number 22 (DRA/GEA/DDBJ/MetaboBank) or 443 (JGA) is allowed in your network (Please ask your network administrator)

When transferring data files by using a private key generated in the other operating system, please check format of a private key. Convert private key

In Unix/Mac OS X: Convert a key in the Windows PuTTY file format into the OpenSSH.
In Windows WinSCP: Convert a key in the Unix/Mac OS X OpenSSH file format into the Windows PuTTY format.

When these are correct, because we do not support technical details regarding use of third-party softwares, please refer to websites of softwares or confirm your system administrators whether ssh, port 22 (DRA/GEA/DDBJ/MetaboBank) and 443 (JGA), is allowed or not.

Accounts newly created on the DDBJ Account system are immediately available for use via sftp. However, it may take about 15 minutes before they can be used in D-way/JGA. Please note this in advance.

Check if communication is allowed in the user environment

As requested, the DDBJ Center will investigate access logs to ftp-private.ddbj.nig.ac.jp. If there is no record in the access logs, it is possible that communication is not allowed in the user’s environment.
On April 10, 2025, the IP address of ftp-private.ddbj.nig.ac.jp was changed from 133.39.224.111 to 133.39.233.40. Due to this change, communication that was previously allowed in the user environment may now be blocked. Please ask your network administrator to confirm whether communication to 133.39.233.40 on port 22 is allowed.

JGA/AGD data transfer server is jga-gw.ddbj.nig.ac.jp 133.39.233.39

Check if the user home directory has been created

If you see the following error message, it is possible that the user home directory has not been created on ftp-private.ddbj.nig.ac.jp for DDBJ accounts newly created after April 10, 2025.
The DDBJ Center will create the user home directory on your behalf, so please contact us with your account name.

sftp -i id_rsa test07@ftp-private.ddbj.nig.ac.jp
Enter passphrase for key id_rsa':
client_loop: send disconnect:
Connection resetConnection closed

Checking key pair match

Check by command

You can display the corresponding public key for a private key (e.g., id_rsa) by running the following command:

ssh-keygen -y -f id_rsa

Compare the contents of both keys. If they match, the keys form a valid pair. If they do not match, the keys are not a pair. In that case, generate a new key pair, specify the private key for SFTP, and add the corresponding OpenSSH-format public key to your DDBJ account. You can register multiple public keys in your DDBJ account.

Check by WinSCP

WinSCP displays the public key that corresponds to a private key. You can also check the registered public key in your DDBJ account. By comparing the two keys, you can check whether the private and public keys are a pair.

In WinSCP, go to Advanced Site Settings > SSH > Authentication, and click Display Public Key. This will display the public key that pairs with the private key specified in the Private key file field.

Compare both keys. If they match, the keys form a valid pair. If they do not match, they are not a valid pair. In that case, generate a new key pair, specify the new private key in WinSCP, and add the corresponding OpenSSH-format public key to your DDBJ account. You can register multiple public keys to your DDBJ account.

client_loop: send disconnect: Broken pipe

client_loop: send disconnect: Broken pipe

If the above error appears when using sftp, please take the same measures as for “ssh connection is disconnected”.

ssh connection is disconnected

Please specify the following options with the sftp command.

sftp -o ServerAliveInterval=60 -o TCPKeepAlive=no -i id_rsa test07@ftp-private.ddbj.nig.ac.jp 

By adding the configuration to the .ssh/config file in your home directory, you can avoid having to specify the above options with each command.

Host ddbj-ftp
  ServerAliveInterval 60
  TCPKeepAlive no
  HostName ftp-private.ddbj.nig.ac.jp
  User test07
  IdentityFile ~/id_rsa

After adding the configuration, close the terminal once and reopen it before running the sftp command again.
With the above config settings, you can access sftp using a shortened command as shown below.

sftp ddbj-ftp

REMOTE HOST IDENTIFICATION HAS CHANGED

The BioProject/BioSample/DRA/GEA systems have been migrated to new supercomputer at 10th April 2025.
Due to this migration, access to ftp-private.ddbj.nig.ac.jp may be blocked by the remote host key identification warning.

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the ECDSA key sent by the remote host is
SHA256:LAPCiua8RAlPIZwE4MKWX7YHMY//rtyjfnUYBj/cnfk.
Please contact your system administrator.
Add correct host key in /Users/test07/.ssh/known_hosts to get rid
of this message.
Offending ECDSA key in /Users/test07/.ssh/known_hosts:2
Host key for ftp-private.ddbj.nig.ac.jp has changed and you have
requested strict checking.
Host key verification failed.
Connection closed

Delete a line where “ftp-private.ddbj.nig.ac.jp” or the IP address “133.39.224.111” are recorded from the known_hosts file under your home directory (for example, test07).
/home/test07/.ssh/known_hosts

You may know the line number to be deleted from the warning message (example below is 2).

Offending ECDSA key in /Users/test07/.ssh/known_hosts:2

After deleting the line of the known_hosts file, access to the server.
Because the access is regarded as a first time access, you are asked whether record the server key or not. Please select “yes” and access the server.

UNPROTECTED PRIVATE KEY FILE WARNING

If the private key access permission is too open, following error may be shown.

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@         WARNING: UNPROTECTED PRIVATE KEY FILE!          @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Permissions for './private-key-for-auth' are too open.
It is required that your private key files are NOT accessible by others.
This private key will be ignored.
Load key "./private-key-for-auth": bad permissions
test07@ftp-private.ddbj.nig.ac.jp: Permission denied (publickey,gssapi-keyex,gssapi-with-mic).
lost connection

Right-click the private key file and select the property.

Select detailed setting of the security tab.

Disable access permission entry inheritance to enable permission deletion.

Convert explicit access permission.

Delete all permissions.

Add access permission.

Add a Windows user (example, test07).

Allow full control to the Windows user.

Change the file permission.

Run sftp.

Using a submission ID as the username

sftp authentication is based on the account, not on individual submissions.
For example, when uploading data to the DRA submission “test07-0001”, the following command is incorrect and will fail to log in:

sftp -i id_rsa test07-0001@ftp-private.ddbj.nig.ac.jp

You will see an error message like this:

Using username "test07-0001".
Server refused our key.

The correct command is:

sftp -i id_rsa test07@ftp-private.ddbj.nig.ac.jp