illumina DRAGEN User manual

Illumina DRAGEN Server
Installation Guide
Introduction 1
Racking the Server 2
Cabling 7
Installing USB License Key 7
BMC/iDRACConfigurations 8
Network Configuration 8
DNS Configuration 9
Set Server Time 9
External Storage 10
License Activation 11
Running the System Check 12
Shutting Down the Server 13
Advance Exchange 13
Revision History 17
Technical Assistance 19
Document # 1000000075000 v01
September 2019
ILLUMINA PROPRIETARY
For Research Use Only. Not for use in diagnostic procedures.

This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for
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does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third
parties by this document.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in
order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be
fully read and understood prior to using such product(s).
FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAY
RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGE
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Introduction
The Illumina DRAGEN™ Server is preconfigured to be seamlessly integrated into bioinformatics workflows. IT
runs the Bio-IT Platform, based on the highly reconfigurable DRAGEN Bio-IT Processor, which is integrated
on a Field Programmable Gate Array (FPGA) card. The platform can be loaded with highly optimized
algorithms for many different Next Generation Sequencing (NGS)secondary analysis pipelines, including the
following:
uWhole genome
uExome
uRNA-Seq
uMethylome
uMicrobiome
uCancer
All user interaction is accomplished via DRAGEN software that runs on the DRAGEN server and manages all
communication with the DRAGEN board.
This user guide summarizes the technical aspects of the system, and provides detailed information for all
DRAGEN command line options.
Before You Begin
The DRAGEN Server includes an Intel X710 DP 10 Gb DA/SFP+, +1350 DP 1 Gb Ethernet NIC. Illumina
recommends that the DRAGEN Server is connected to an attached storage system with a 10 Gb link, using
either copper or fiber cables. For fiber, transceivers might be necessary. As long as DRAGEN has a sustained
IO of 400 Mb/sec, it can stream samples and write output files without any need to copy to/from NAS.
Refer to the Terms &Conditions for further information regarding acceptable use of the server and covered
warranty.
Before installing your Illumina DRAGEN Server, make sure that you have received the following items in the
box with the server:
u10 GB SFP Optical Adapters (2)
uDRAGEN License USB Key
uPower Cables (2)
uRack rails (2)
Also required for installation (not included):
u10 GB copper (or fiber) cable for network connection to your DRAGEN Server
uRJ45 Cat5 (or better) for network connection to the iDRAC
[Optional] accessories for installation (not included):
uMonitor
uKeyboard
uMouse
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Hardware Specifications
Component Specification
Processor Dual Intel Xeon Gold 6126 2.6 G, 12 C/24 T
Memory 256 GB
Scratch drive 2 TB Intel NVMEP4600
OSdrives 2x120 GBSSDin Raid 1
FPGA card DRAGEN
Remote access iDRAC8 Enterprise, integrated Dell Remote Access
Controller, Enterprise
Operating system CentOS 7.5
Networking Intel X710 DP10GBDA?SFP+, +1350 DP1GBEthernet
Form factor 2Urack
Dimensions H8.73 cm (3.44 in), W 44.4 cm (17.49 in), D 68.4 cm (26.92
in)
Power supply Dual, hot-plug, redundant power supply (1 +1), 1100 W
Table 1 DRAGENServer Hardware Specifications
Racking the Server
NOTE
Install sliding rails onto rack so the sliding rails extend forward.
1 Attach the first sliding rail to the back of rack by attaching the bracket (at the rear of the sliding rail) to the
rack.
Figure 1 Server Rack and Sliding Rail
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2 Pull the entire sliding rail past the front of the rack and snap it back into place.
Figure 2 Sliding Rail Snapped onto Server Rack
3 Install the second rail at the same level on the other side of the rack.
Figure 3 Server Rack and Both Sliding Rails
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4 Extend the sliding rails completely.
Figure 4 DRAGEN Server, Sliding Rails (Extended) and Server Rack
5 Facing the front of the rack, use two people (one on either side) to lift the server in between the two
extended rails, with the front of the server facing out.
Figure 5 DRAGEN Server Lowered Between Extended Sliding Rails
6 Locate the eight flat black screws on the server (four on either side).
7 Line up the eight black flat screws with the corresponding notches in the sliding rails.
8 Attach the rear of the server onto the rails first, and then snap all eight into place.
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9 Make sure that all eight screws are fully seated and locked.
Figure 6 Black Flat Screw Seated in Notch
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Figure 7 Flat Black Screw in Notch - Unlocked
Figure 8 Flat Black Screw in Notch - Locked
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10 Slide the server back onto the rack.
Figure 9 DRAGENServer Installed on Server Rack
Cabling
Figure 10 Rear of DRAGEN Server
A iDRAC
B Monitor
C 10 GB SFP Port 1
D 10 GB SFP Port 2
E RJ45 1 GB Port 1
F RJ45 1 GB Port 2
G Power Supply (2)
Installing USB License Key
1 Locate the USBlicense key in the delivery box.
2 Plug the USBlicense key into any USB port on the back of the server.
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3 Turn on the server.
NOTE
The USBkey must remain plugged into the server at all times.
BMC/iDRACConfigurations
1 Connect a monitor, keyboard, and mouse (optional) to the server.
2 Connect an Ethernet cable (RJ45) to the BMC/iDRAC network port at the back of the server.
3 Turn on the system. The DRAGEN splash page appears on the monitor.
4 Press F2 to enter BIOS.
5 Under iDRAC Settings Network, scroll down to IPV4 Settings
6 Under IPV4 Settings, do the following:
uDisable DHCP.
uEnter IP address.
uEnter gateway.
uEnter subnet mask.
uSelect Back.
7 Select Finish. A prompt to save changes appears.
8 After changes have been saved, the prompt reads Success.
9 At the main window, select Exit in the top right corner.
10 Confirm that you want to exit to reboot the server.
Network Configuration
1 After the server has rebooted, log in using the credentials provided to you by your Illumina customer
service representative. If you have not received login credentials, contact [e-mail].
2 Change the root password before continuing with any configuration. Enter:
passwd
3 Enter:
cd /etc/sysconfig/network-scripts/
4 Several files appear. Locate filename:
ifcfg-eth0
5 Edit the file using vi, enter:
vi ifcfg-eth0
6 Enter the following information. Enter “static” for bootproto and refer to the pre-installation form (or
contact your IT department) for the ip address, netmask and gateway:
BOOTPROTO="static"
IPADDR=
NETMASK=
GATEWAY=
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7 Save the file, enter:
:wq!
8 Enter systemctl restart network to restart network to apply the changes.
9 After restarting the network service, verify the IPaddress.
DNS Configuration
1 Log in as root.
2 Add the DNSserver by editing /etc/resolv.config using vi, enter:
vi/etc/resolv.conf
3 Enter the DNSserver IPaddress provided by customer IT.
Example:
nameserver 192.168.1.1
nameserver 192.168.1.2
4 Save the file, enter:
:wq!
5 Restart the network to apply changes using this command:
systemctl restart network
6 Ping an external URLsite to make sure that name resolution is working.
Example:
ping www.illumina.com
Set Server Time
Set Server Time to Local Time Zone
1 Log in as root.
2 Check if the current server time reflects the local time zone using the date command. Enter:
date
3 Using the timedatectl command, check for a nearby city with the correct time zone.
For example, searching time zones in Asia:
timedatectl list-timezones | grep Asia
4 Change the server time to local time.
Example:
timedatectl set-timezone Asia/Singapore
5 Make sure that the server time has changed using the date command. Enter:
date
ls -l /etc/localtime
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Synchronize Server Time to NTP Server
1 Log in as root.
2 Check if ntp daemon is running, enter:
systemctl enable ntpd
3 If the result from the previous command shows inactive or dead, enable the ntp daemon, enter:
systemctl enable ntpd
4 Start the daemon, enter:
systemctl start ntpd
5 Edit /etc/ntp using vi, enter:
vi /etc/ntp.conf
6 Replace the default NTP server settings to the local NTPserver.
Example:
<original default settings>
server 0.centos.pool.ntp.org iburst
server 1.centos.pool.ntp.org iburst
server 2.centos.pool.ntp.org iburst
server 3.centos.pool.ntp.org iburst
<settings to use local NTPserver/s>
server 192.168.1.1 iburst
server 192.168.1.2 iburst
7 Save the file, enter:
:wq!
8 Restart the ntp daemon, enter:
systemctl restart ntpd
9 Check the health of the local to me server, enter:
ntpq -p
10 Make sure that Dragen can synchronize with the local NTPserver using the ntpdate command.
Example:
ntpdate -q 192.168.1.1
External Storage
Mounting NFS on DRAGEN Server
1 Locate your NFS Server and share name.
Example:
uServer: 192.168.100.100
uShare name: /share
2 This example would be 192.168.100.100:/share.
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3 To map this share to /mnt on the DRAGEN server, run the following command as root on your system:
mount -t nfs 192.168.100.100:/share /mnt
4 Share is mounted at 192.168.100.100:/share to the local file system under /mnt.
Mounting SMB/CIFS on DRAGEN Server
1 Locate your SMB/CIFS server and share name.
Example:
uServer: 192.168.100.100
uShare name: /share
2 Locate the username and password required to access this share (if applicable).
Example:
uUsername: sbsuser
uPassword: sbs123
3 This example would be //192.168.100.100/share.
4 To map this share to /mnt on the DRAGEN server, run the following command as root on your local
system:
mount -t cifs -o user=sbsuser //192.168.100.100/share /mnt
5 Enter password when prompted.
6 Share is mounted at //192.168.100.100/share to the local file system under /mnt.
Adding NFS or SMB mount to /etc/fstab
1 Add the network share to /etc/fstab so that the mount is permanent across reboots. Using the
previous examples in Mounting NFS on DRAGEN Server on page 10 and Mounting SMB/CIFS on
DRAGEN Server on page 11, this is what a basic entry in your /etc/fstab would look for a NFS or SMB
mount:
NFS:
192.168.100.100:/share /mnt nfs rsize=8192,wsize=8192 0 0
SMB:
//192.168.100.100/share /mnt cifs user=sbsuser,pass=sbs123 0 0
License Activation
The DRAGEN server ships with temporary short-term licenses. The license activation process differs
depending on whether the server is connected to the internet or is offline. Root/sudo access is needed to run
the commands below. For assistance with the various command line options, contact Technical Support at
[e-mail]. Follow the instructions below to activate your licenses.
Online Servers
For servers connected to the internet, license information can be activated as follows.
1 Test and confirm that the server is connected to the internet.
Example:
uPing www.illumina.com
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2 To activate the license, enter:
/opt/edico/bin/dragen_lic -i auto
3 Confirm that the license has been updated. Enter:
/opt/edico/bin/dragen_lic
Offline Servers
For offline servers not connected to the internet, Illumina Customer Service provides the necessary license
files to activate the license on the server locally. If you have not received these license files, contact
[e-mail].
After you have the necessary license files, activate the license as follows.
1 Copy the license files to the server.
2 Run the following commands:
sudo rm /var/lib/edico/*.gbin
sudo /opt/edico/bin/dragen_lic -i license_genome.bin
sudo /opt/edico/bin/dragen_lic -i license_somatic.bin
sudo /opt/edico/bin/dragen_lic -i license_cnv.bin
sudo /opt/edico/bin/dragen_lic -P license.dat
3 Confirm that the license has been updated. Enter:
/opt/edico/bin/dragen_lic
Running the System Check
After turning on the server, you can make sure that your DRAGEN server is functioning properly by running
/opt/edico/self_test/self_test.sh, which does the following:
uAutomatically indexes chromosome M from the hg19 reference genome
uLoads the reference genome and index
uMaps and aligns a set of reads
uSaves the aligned reads in a BAM file
uAsserts that the alignments exactly match the expected results
Each server ships with the test input FASTQ data for this script, which is located in /opt/edico/self_test. The
system check takes approximately 25–30 minutes.
The following example shows how to run the script and shows the output from a successful test.
[root@edico2 ~]# /opt/edico/self_test/self_test.sh
---------------------------------
test hash creating
test hash created
---------------------------------
reference loading /opt/edico/self_test/ref_data/chrM/hg19_chrM
reference loaded
---------------------------------
real0m0.640s
user0m0.047s
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sys0m0.604s
not properly paired and unmapped input records percentages: PASS
---------------------------------
md5sum check dbam sorted: PASS
---------------------------------
SELF TEST COMPLETED
SELF TEST RESULT : PASS
If the output BAM file does not match expected results, then the last line of the above text is as follows:
SELF TEST RESULT : FAIL
If you experience a FAIL result after running this test script immediately after turning on your DRAGEN server,
contact Illumina Technical Support.
Shutting Down the Server
Shutdown DRAGEN Server From Command Line
1 Log in as root.
2 To initiate system shutdown, enter:
poweroff
3 Wait a few minutes until the server comes to a complete shutdown.
Shutdown DRAGEN Server From iDRAC Web Console
1 Open a browser and log in to the iDRACweb console by typing https://<ip-address>.
For example: https://192.168.1.101
NOTE
This iDRACIPaddress is configured during installation based on network settings information provided by
customer ITsupport. The default login account for iDRACis root and the default password is calvin. The
password can be changed during the installation process. For more information, see
BMC/iDRACConfigurations on page 8.
2 From the right side of the Dashboard, select Launch Virtual Console.
3 Select Power.
4 Select Graceful Shutdown to initiate server shutdown.
5 Wait a few minutes until the server comes to a complete shutdown. The monitor displays No Signal
when the server is successfully shut down.
Advance Exchange
Service Model
The DRAGEN server is serviced using the Illumina Advance Exchange replacement model where damaged or
defective DRAGEN servers still under warranty are exchanged with a replacement server. To check the
warranty status of your current server, contact customer service at [e-mail].
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Illumina support performs troubleshooting to determine whether a server needs to be exchanged. We
recommend you contact [e-mail] as soon as you notice an issue with your system. Once
the system has been determined to be damaged or defective, Illumina ships out a replacement server before
the original is shipped back. This is done to minimize the downtime customer experience with their system.
The actual time it takes to ship the replacement can vary by region.
Regional Applicability
Advance Exchange is available in all regions.
Receive a Replacement System
1 After a system check and other troubleshooting efforts have failed, contact Illumina Technical Support.
uMake system check results available to Technical Support.
2 If Technical Support cannot resolve the issue remotely, a return is initiated and an order is placed for a
replacement system.
3 When you receive the replacement server:
u Save all the packaging , which is used to package the original server for return.
uSet aside the return documents, which include a UPSreturn label and commercial invoice (for
international shipments).
uVerify receipt and condition of the server.
Prepare the Original Server for Return
Return the original server to Illumina within 30 days of receiving the replacement.
Shut Down and Disconnect
If the system is on, follow steps 1–3to save and clear data before safely shutting down the server. Follow the
remaining steps to disconnect cords and cables.
1 Back up all your data.
2 Delete any files and folders you do not want to share with Illumina.
3 Make sure that the server is not being used before shutting down the server.
For shutdown instructions, see Shutting Down the Server on page 13.
4 Disconnect all power and Ethernet network cords from the back of the server.
5 If applicable:
uDisconnect monitor, keyboard, mouse, and cables from the server.
uRemove hard drives.
NOTE
Customers can retain hard drives at their discretion. However, hard drives cannot be installed in the
replacement server. Doing so results in nonfunctionality. Hard drive retention is intended to comply with
customer information security or data retention policies and standards.
6 Uninstall server from the rack.
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Return the Original Server
Package the Server
1 Clear adequate space in the lab for the server and packaging.
2 Place the protective foam cover over the server.
3 Place the foam pad at the bottom of the box.
4 Place the original server into the box so that the top of the server faces up.
5 Place the foam cover on top of the server.
6 If necessary, place the accessories box into the center of the foam cover.
7[Optional] Place the Ethernet cable and power cord anywhere in the box.
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8 Make sure that the foam is flush with the top of the box.
9 Close the top of the box.
Ship the Server
1 Secure the box with shipping tape.
2 Remove the original shipping label and attach the provided return label to the box. Alternatively, place
the return shipping label over the original shipping label.
3 If shipping international, affix the commercial invoice to the shipping box.
4 Ship the instrument to Illumina via UPS.
uIf your facility has daily deliveries scheduled with UPS, give the labeled shipping box to the driver.
uIf your facility does not have daily deliveries with UPS, notify Illumina Customer Service so that they
can schedule the return shipment for you.
NOTE
Lift the box by the handles. A two-person lift is recommended.
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Revision History
Document Date Description of Change
Document #
1000000075000 v01
September
2019
Added Advanced Exchange instructions.
Added shutdown instructions.
Added DNS configuration information.
Added BMC configuration information.
Added information about changing system time settings.
Added network card information.
Document #
1000000075000 v00
January 2019 Initial release.
Document # 1000000075000 v01
For Research Use Only. Not for use in diagnostic procedures.
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Document # 1000000075000 v01
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