Networking and output locations on the NextSeq 1000/2000

A run output folder location must be specified unless BaseSpace Sequence Hub is configured for Proactive, Run Monitoring, and Storage. External Drives, Server Message Block (SMB), Common Internet File Systems (CIFs), and Network File System (NFS) are the only supported methods for persistent mounting of a network drive on the NextSeq 1000/2000. The release of NextSeq 1000/2000 control software v1.5 also supports the local output of runs.

In NextSeq 1000/2000 control software version ≤1.4, Illumina does not recommend outputting the run locally (on the instrument). In control software version v1.5, the available designated local output folder is /usr/local/Illumina/Images. This output location is manually curated, and completed runs must be manually deleted from this folder as the build-up of completed runs in this location will negatively impact future sequencing runs.

SMB/CFS 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 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 (see Figure 2).

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Figure 2***: example FSTAB file with SMB/CIFS mount onto a folder on /mnt/ called "output"***

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 (see below).

Specify the Persistent Network Drive as the Default Output Folder

1. Login into ilmnuser.

2. From the NextSeq 1000/2000 Control Software menu, select Settings.

3. Under Default Output Folder, select the persistent network drive mount located at /mnt/{local name}/{output directory}.

4. [Optional] If the Run Mode is set as Online Run Setup, select an option from the Hosting Location drop-down menu.

5. Select Save.

For additional information, see the System Configuration Section of Sequencing Systems Guide 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 NextSeq 1000/2000 and How 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].