Networking and output locations on the NextSeq 1000/2000

Background Information:

Depending on the control software version there are multiple options for the run output folder location:

• External Drives: Server Message Block (SMB), Common Internet File Systems (CIFs), and Network File Systems (NFS) are the supported methods for a persistent mount of a network drive on the NextSeq 1000/2000. This is supported for all versions of the control software and allows runs to be output directly to the network drive.

• BaseSpace Sequence Hub: To set the output to BaseSpace Sequencing Hub, select "Proactive, Run Monitoring and Storage*". When this setting is selected, the "Default Output Folder" becomes optional.

• Local Storage: Illumina does not recommend saving runs on the instrument. This is because, runs must be manually deleted from the instrument as the build-up of completed runs in this location will negatively impact future sequencing runs. In control software version v1.5 or later, the available designated local output folder is /usr/local/Illumina/Images. In the control software version ≤1.4, this must be set manually. Saving to any other location will cause the run to fail.

Setting the Default Output folder:

1. Navigate to the menu in the top left corner and select settings.

2. If sending data to BaseSpace, select "Proactive, Run Monitoring and Storage*"

3. Choose the default folder location as either "Local Storage" or "External Storage"

   1. Note that control software versions ≤1.4, there is no distinction between local and external storage.

4. If using external storage, select the mounted network folder in the /mnt/ directory.

   1. For instructions on how to mount network drives, see below:

Mounting Network Drives:

Follow instructions for either SMB/CIFS or NFS mounting according to the type of network share configured.

SMB/CIFS Mounting Instructions

1. If NextSeq 1000/2000 Control Software is open, select Minimize Application.

2. Log into the ilmnadmin user account.

3. Select Applications.

4. Under Favorites, select Terminal.

5. Enter sudo touch /root/.smbcreds and then select Enter.

6. Enter the ilmnadmin password when prompted. The ilmnadmin password is required for each sudo command.

7. Enter sudo gedit /root/.smbcreds and then select Enter to open the text file named smbcreds

8. When the .smbcreds text file opens, enter the network log in credentials in the following format.username=[username] password=[password] domain=[domain name] Note: Brackets [] are not required for username, password, and domain name. Domain credential is only required if the remote account is part of a domain. If unsure of the domain, type SAMBA: Example, Figure 1:

9. Select Save and exit the file.

10. Identify the server name and share name for the SMB/CIFs server. The server name and share name cannot have spaces, for example:Server name: 192.168.500.100 or Myserver-myinstitute-03 Share name: /share111. In the terminal, enter sudo chmod 400 /root/.smbcreds and then select Enter to grant read only access to the .smbcreds text file.

11. Enter sudo mkdir /mnt/[local name]. This is the folder that the network output is linked to. [local name] is the name of the new directory in the network drive and can contain spaces. This directory appears on the instrument. [local name] can be replaced with any name.

12. Select Enter.

13. Enter sudo gedit /etc/fstab and then select Enter.

14. When the fstab file opens, enter the following to the end of the file, and then select Enter./// /mnt/[local name] cifs credentials=/root/.smbcreds,uid=ilmnadmin,gid=ilmnusers,dir_ mode=0775,file_mode=0775,_netdev,x-systemd.automount,sec=ntlmssp 0 0NOTE: As of Control Software v1.5 all mounts MUST be placed beneath /mnt/ in order to be used as an output location.

15. Select Save and exit the file.* The following warning will be displayed, this is normal; acknowledge it and proceed: ** (gedit:136244): WARNING **: 14:23:47.654: Set document metadata failed: Setting attribute metadata::gedit-spell-language not supported.

16. In the terminal, enter sudo mount -a -vvv and select Enter. The network drive is now mounted as /mnt/[local name].

17. To confirm if the mount was successful, enter df | grep [local name] and then select Enter. The name of the fileshare will appear.

18. Enter sudo mkdir /mnt/[local name]/[output directory] to create a subfolder within the local directory. The [output directory] represents the default output folder location. The NextSeq 1000/2000 Control Software requires at least two levels of nested folders to recognize the location as a mounted network drive.

19. Power cycle the instrument.

20. Set the persistent mounted network drive as the default output folder.

***

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Figure 1***: example FSTAB file with SMB/CIFS mount onto a folder on /mnt/ called "output"*** Updating SMB/CFS Mounting username and login information1. If NextSeq 1000/2000 Control Software is open, select Minimize Application.

1. Log into the ilmnadmin user account.

2. Select Applications.

3. Under Favorites, select Terminal.

4. Enter the command: sudo chmod 700 /root/.smbcreds and then select Enter.

5. Enter the ilmnadmin password when prompted. The ilmnadmin password is required for each sudo command.

6. Enter the command: sudo gedit /root/.smbcreds and then select Enter to open the text file named .smbcreds

7. When the .smbcreds text file opens, edit the username, password, or domain as needed.

8. Select Save and exit the file.

9. In the terminal, enter command sudo chmod 400 /root/.smbcreds and then select Enter.

10. In the terminal, enter command sudo mount -a -vvv and select Enter.

11. Power cycle the instrument.

NFS Mounting Instructions

1. If NextSeq 1000/2000 Control Software is open, select Minimize Application.

2. Log into ilmnadmin.

3. Identify the server name for the NFS server. The server name cannot have spaces, for example:Server name: 192.168.500.100 or Myserver-myinstitute-034. Select Applications.

4. Under Favorites, select Terminal.

5. Enter sudo mkdir /mnt/{local name} and then select Enter. {local name} is the name of the new directory in the network drive.

6. Enter sudo gedit /etc/fstab and then select Enter.

7. When the fstab file opens, enter the following, and then select Enter.Server name:/share //mnt/{local name} nfs x-systemd.automount,defaults 0 0NOTE: As of Control Software v1.5 all mounts MUST be placed beneath /mnt/ in order to be used as an output location.

8. Select Save and exit the file.* If the following warning is displayed, acknowledge it and proceed: ** (gedit:136244): WARNING **: 14:23:47.654: Set document metadata failed: Setting attribute metadata::gedit-spell-language not supported.

9. In the terminal, enter sudo mount -a -vvv and then select Enter. The network drive is now mounted in the /mnt/directory within the {local name} folder.

10. Create a new subfolder within the {local name} folder. The subfolder represents the default {output directory} location. The NextSeq 1000/2000 Control Software requires at least two levels of nested folders to recognize the location as a mounted network drive.

11. Power cycle the instrument.

12. Set the persistent mounted network drive as the default output folder.

For additional information, see the System Configuration Section of NextSeq 1000/2000 Product Documentation in English and other languages.

For information on mounting an External Drive, search for Knowledge Base article Setting external hard drives as the default output folder on NextSeq 1000/2000

For information on how to power cycle the instrument, search for Knowledge Base articles How to power cycle the NextSeq 1000/2000 andHow To Power Cycle NextSeq 1000/2000 Video.

For any feedback or questions regarding this article (Illumina Knowledge Article #3037), contact Illumina Technical Support [e-mail].