PromethION 24/48 user manual
Protocol
PromethION 24/48 user manual VPIC_1013_v1_revZ_12Nov2019
This guide will help you install, check and configure your PromethION 24, PromethION 48 or PromethION 24/48 A-Series.
Our PromethION 24/48 FAQs are located here.
For Research Use Only.
FOR RESEARCH USE ONLY
Contents
Overview
Installation
- 2. What's in the box
- 3. Installing and powering on the device
- 4. Network settings and connection
- 5. Changing the default password and hostname
- 6. (Advanced) Updating the timezone and setting a local NTP server
- 7. Hardware check
Pre-sequencing checks and sequencing run
After completing a sequencing run
Updating the software
Operating system update on PromethION
- 14. Downloading the ISO image and burning it to a USB drive
- 15. Preparing the PromethION for UEFI boot
- 16. How to boot from USB
- 17. Completing the restore
- 18. If problems are encountered
常见问题解答
概览
This guide will help you install, check and configure your PromethION 24, PromethION 48 or PromethION 24/48 A-Series.
Our PromethION 24/48 FAQs are located here.
For Research Use Only.
1. Device information
The PromethION 24 and 48
The PromethION is a benchtop device designed to run up to 24 (for PromethION 24 and PromethION 24 Combined) or 48 (for PromethION 48) flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or individually. Integrated compute in the PromethION enables real-time data streaming and analysis.
Technical specification
| Component | Specification |
|---|---|
| Size and weight | PromethION 24 Sequencing Unit: H190 x W590 x D430 mm Weight 23 kg PromethION 48 Sequencing Unit: H190 x W590 x D430 mm Weight 30 kg Data Acquisition Unit: H470 x W178 x D440 mm Weight 26 kg |
| Power | 2x for Data Acquisition Unit C13 cables included with device Mains supply voltage: 200-240 VAC (50/60 Hz) Peak power consumption: 2,450 W 1x for Sequencing Unit C13 cable included with device Mains supply voltage: 100-240 VAC (50/60 Hz) Peak power consumption: 1,200 W |
| Compute specification | PromethION P24: 30 TB SSD Storage, 384 GB RAM PromethION P48: 60 TB SSD Storage, 384 GB RAM PromethION 24/48 A100: 60 TB SSD Storage, 512 GB RAM, 4x Ampere-Series GPUs Common features: Intel CPU for Ubuntu OS and basecalling orchestration PromethION Accelerator |
| Pre-loaded software | Ubuntu OS, PromethION OS, MinKNOW |
| Environmental conditions | Designed to sequence at +18ºC to +22ºC* |
*Functional range of electronics +5ºC to +40ºC
FAQs
Our PromethION 24/48 FAQs are located here.
2. What's in the box
PromethION 24/PromethION 48 packaging
PromethION 24/48 A-Series
This device ships to most countries worldwide. The device is shipped in two separate boxes: one for the Data Acquisition unit and one for the Sequencing Unit. The devices are stored and shipped at ambient temperature (15–25°C).
PromethION 24 Combined
This device ships to selected countries worldwide. The Data Acquisition Unit and Sequencing Unit that make up The PromethION 24 Combined are shipped in one box. The device is stored and shipped at ambient temperature (15–25°C). The PromethION 24 Combined must only be unpacked and installed by an Oxford Nanopore Technologies Field Service Engineer.
What's in the box - PromethION 24
- PromethION 24 Sequencing Unit
- PromethION 24 Data Acquisition Unit
- 3x Country-specific C13 cables
- 24x Configuration Test Cells (CTCs)
- 2x PCIe cables
- 2x USB-A/Mini USB cable
- 1x USB-A/USB B cable
- 1x MiniDP/Display port cable
- 1x USB-A stick (ISO reset image)
- 1x USB-C/USB-A adapter
What's in the box - PromethION 48
What’s in the box: 1. PromethION 48 Sequencing Unit 2. PromethION 48 Data Acquisition Unit 3. 3x Country-specific C13 cables 4. 48x Configuration Test Cells (CTCs) 5. 3x PCIe cables 6. 3x USB-A/Mini-USB cable 7. 1x USB-A/USB-B cable 8. 1x MiniDP/Display port cable 9. 1x USB-A stick (ISO reset image) 10. 1x USB-C/USB-A adapter
3. Installing and powering on the device
Preparing for installation
The following should be available before installing the device: - SFP+ modules and cabling for 2x 10 Gbps fibre OR cabling for 2x 10 Gbps Copper (Ethernet - Cat6a or above) - A single Copper cable for hardware check
- Fibre OR Copper ports providing: - IP address through DHCP - Outbound-only access to the internet over ports 80 and 443
- 1x VGA-capable monitor (for original PromethION 24/48 Data Acquisition Unit)
- 1x VGA-capable/DisplayPort-capable monitor (for new PromethION A-Series Data Acquisition Unit)
- 1x VGA cable
- 1x USB connected keyboard
- 1x USB connected mouse
- 3x Power supplies/wall sockets for the PromethION Data Acquisition Unit and Sequencing Unit - 1x Power supply/wall socket for a monitor
- Optional: UPS solution with C14 cables
Recommended laboratory location
- Place the device on a strong, clean laboratory bench. If you are using a PromethION 24 Combined, the device needs to be installed with the Sequencing and Data Acquisition units next to each other. The bench space required for a PromethION installation is 167 cm x 75 cm
- Ensure power, Ethernet and/or Fibre connectors are in close proximity
- Ensure power socket is easily accessible should a disconnection be required in case of emergency
- Sequencing should be carried out at a room temperature of +18°C to +22°C with device doors closed prior to sequencing beginning
- Allow 30 cm clearance to rear and sides of the device to ensure correct airflow
- Do not cover any ventilation grills
- WARNING - The rear of the device will heat up during operation
Unpack the device and place it on the bench where it is to be run.
Place the Sequencing Unit on the bench where it is to be run and the Data Acquisition Unit within two meters of the Sequencing Unit.
If you are using the PromethION 24 Combined, the device must only be unpacked and installed by an Oxford Nanopore Technologies Field Service Engineer. Once your device has been correctly installed, proceed from step 9.
PromethION 24 Sequencing and Data Acquisition Units
PromethION 48 Sequencing and Data Acquisition Units
可选操作
Optional: insert the SFP+ modules into the ports shown below.
If the fibre optic cables are to be used, then you must insert your chosen SFP+ modules into the ports on the rear of the Data Acquisition Unit.
Connect the data cabling into the appropriate port shown below.
For the hardware check, a single copper cable should be used and connected to a port with a DHCP service running.
Download the latest software, then complete full network configuration after the hardware check.
See the Network configuration section in this document to set up single vs dual connectivity and copper vs fibre connections.
This is the first step of the inter-unit connections. Connect the PCIe cables between your Sequencing Unit and Data Acquisition Unit.
PromethION 24 Connect the PCIe cables to the rear of the Sequencing Unit and the rear of the Data Acquisition Unit.
Note There is a port-to-cable colour requirement on both units.
PromethION 48 Connect the PCIe cables to the rear of the Sequencing Unit and the rear of the Data Acquisition Unit.
Note There is a port-to-cable colour requirement on both units.
This is the second step of the inter-unit connections. Connect the USB cables between the Data Acquisition Unit and Sequencing Unit.
PromethION 24 Connect:
- 2x USB A – Mini USB
- 1x USB A to USB B
from the Data Acquisition Unit to the Sequencing Unit (see the diagram below):
PromethION 48 Connect:
- 3x USB A – Mini USB
- 1x USB A to USB B
from the Data Acquisition Unit to the Sequencing Unit (see the diagram below):
Connect peripheral devices to the appropriate ports.
Plug in the following:
1a. Monitor VGA cable (if using original PromethION 24/48 Data Acquisition Unit) 1b. Monitor VGA/miniDP cable* (if using the PromethION A-Series Data Acquisition Unit) 2. USB keyboard 3. USB mouse into the remaining USB A port.
* Use either the miniDP output or the VGA output. It is not possible to use both outputs simultaneously.
Two C13 power cables will plug into the Data Acquisition Unit and one C13 power cable will plug into the Sequencing Unit.
Insert two of the supplied C13 cables into the top of the Data Acquisition Unit, and the third into the Sequencing Unit. Connect all to a mains power supply.
Note: You will be provided with at least three C13 cables with plugs for your country of use.
Turn on the power at the mains supply. Then turn on the PromethION units in the order below:
- Turn on the Sequencing Unit
- Wait for 3 minutes
- Turn on the Data Acquisition Unit
双击桌面上的MinKNOW图标，打开MinKNOW图形用户界面。
我们建议您使用纳米孔社区的账户信息登录MinKNOW软件。
您须连接到互联网方可登录。
用户可在此页面的右下角选择界面语言。
界面将提示您输入电邮地址和纳米孔密码：
如您在登录时遇到问题，请通过我们的纳米孔微信公众号（NanoporeSupport）或社区支持通道(https://community.nanoporetech.com/support) 联系我们的客服。与此同时，您可点击 Continue as guest ，以访客身份暂时使用MinKNOW。
Select the sequencing device in the Connection Manager to connect to the computer.
You will be taken to the Sequencing Overview, displaying the connected flow cells.
4. Network settings and connection
注意
Changing your network configuration
The network parameters for your PromethION 24 or PromethION 48 must be suited to your local network.
WARNING! Changing the network parameters on your PromethION may leave your device non-functional.
If you are uncertain about which parameters to use to configure your PromethION network settings, please contact your IT department.
Networking requirements
Your PromethION can use copper or fibre interfaces for connecting to your local infrastructure. The type of port is labelled on the diagram of the back of the PromethION below:
This connection will be used for:
- Sending telemetry* information to Oxford Nanopore Technologies
- Receiving software and firmware updates to the device
- Streaming biological sequence data to your local storage infrastructure
To implement the PromethION into the local infrastructure, *all appropriate cabling must be provided by the customer.
* Telemetry contains metadata about the settings and conditions of a sequencing run. Nothing specific about the genomic content of individual reads is included - only generic information is logged, such as sequence length and q-score.
Copper or fibre data transfer connections can be used - but not both.
You can run with copper or fibre connections for your data transfer. We do not recommend one over the other, however, it is down to your local network environment for which connectivity you may prefer to use.
Note: Please only attach copper or fibre cables. Using both is not supported and will cause networking issues.
A summary of the connectivity options is shown in the diagram below. Please consult the instructions below to ensure the PromethION network connections are set up correctly.
Instructions for setting up a copper connection
Single copper port on DHCP service
- Open a Terminal window and enter the following command:
ont-network-settings --dhcp --interfaces eno2 --overwrite
2. Power cycle the PromethION.
Connections: Use only the lower RJ45 port for this configuration. 
Dual copper ports on DHCP service
- Open a Terminal window and enter the following command:
ont-network-settings --dhcp --interfaces copper --bond failover --overwrite
2. Power cycle the PromethION.
Note: If using LACP/Cisco/802.3ad, then enter:
--bond lacp
Connections: Use both RJ45 ports for this configuration. 
Dual copper ports with a static IP address
- Open a Terminal window and enter the following command:
ont-network-settings --address 1.1.1.1 --subnet 255.255.255.0 --gateway 1.1.1.254 --dns 1.1.1.2,1.1.1.3 --search mycompany.local --bond failover --interfaces copper --overwrite
2. Power cycle the PromethION.
Note: You must change the IP addresses above according to your site's network configuration.
Connections: Use both RJ45 ports for this configuration; however, the configuration will also function with only the bottom port occupied. 
Instructions for setting up a fibre connection
Single fibre port on DHCP service
- Open a Terminal window and enter the following command:
ont-network-settings --dhcp --interfaces enp129s0f1 --overwrite
2. Power cycle the PromethION.
Connections: Use the right fibre port for this configuration:
Dual fibre ports on DHCP service
- Open a Terminal window and enter the following command:
ont-network-settings --dhcp --interfaces fibre --bond failover --overwrite
2. Power cycle the PromethION.
Note: If using LACP/Cisco/802.3ad, then enter:
--bond lacp
Connections: Use both fibre ports for this configuration. 
Dual fibre ports with a static IP address
- Open a Terminal window and enter the following command:
ont-network-settings --address 1.1.1.1 --subnet 255.255.255.0 --gateway 1.1.1.254 --dns 1.1.1.2,1.1.1.3 --search mycompany.local --bond failover --interfaces fibre --overwrite
2. Power cycle the PromethION.
Note: You must change the IP addresses above according to your site's network configuration.
Connections: Use both fibre ports for this configuration; however, the configuration will also function with only the right port port occupied. 
Validate the IP address
You can use the command: ifconfig to validate that the IP address has been set correctly using a static or DHCP address.
The returned information will contain the IP address for the Ethernet link, as below:
prom@PRO00001:~$ ifconfig
docker0: flags=4099<UP,BROADCAST,MULTICAST> mtu 1500
inet 172.17.0.1 netmask 255.255.0.0 broadcast 172.17.255.255
ether 02:42:35:39:60:40 txqueuelen 0 (Ethernet)
RX packets 0 bytes 0 (0.0 B)
RX errors 0 dropped 0 overruns 0 frame 0
TX packets 0 bytes 0 (0.0 B)
TX errors 0 dropped 0 overruns 0 carrier 0 collisions 0
eno1: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500
inet 10.150.60.13 netmask 255.255.255.0 broadcast 10.150.60.255
inet6 fe80::78cf:8a5c:26ec:4611 prefixlen 64 scopeid 0x20<link>
ether 3c:7c:3f:be:02:81 txqueuelen 1000 (Ethernet)
5. Changing the default password and hostname
导航至“Host Settings”（测序设备设置）下的“Device Settings”（仪器设置）板块。
点击“System”（系统）框内的“Reset password”（重置密码）。
在“Change Password”（更改密码）对话框中，输入您当前使用的密码，然后输入新密码。
点击“Reset Password”（重置密码），确认密码变更。
（进阶）变更默认的主机名
- 如您需要更新设备的主机名，请运行以下命令并将“
”部分替换为您所需的主机名（请省略尖括号“<>”）：
sudo -S hostnamectl set-hostname <new_hostname>
- 使用以下命令关闭设备，然后按下设备上的电源按钮重新启动设备：
sudo shutdown -h now
6. (Advanced) Updating the timezone and setting a local NTP server
更新时区：
首先键入以下命令，找到正确的时区名称：
sudo timedatectl list-timezones
使用以下命令更改时区：
sudo su -
Timezone="Europe/London"
timedatectl set-timezone $Timezone
systemctl restart systemd-timesyncd
设置本地NTP服务器：
请注意： 如使用外部时间服务器，则需访问NTP/123端口。
键入如下命令：
NTPserver="ntp.ubuntu.com" timedatectl set-ntp false cat << EOF > /etc/systemd/timesyncd.conf # See timesyncd.conf(5) for details.[Time] NTP=$NTPserver EOF systemctl stop ntp ntpdate $NTPserver systemctl disable ntp timedatectl set-ntp true hwclock --systohc timedatectl set-local-rtc 0
请忽略运行上述命令时可能出现的报错。
如需确认命令是否成功运行，请键入：
timedatectl status
__请注意：__ 与 NTP 服务器同步可能需要几分钟。
7. Hardware check
重要
硬件检测
如您使用的是新设备或刚刚更新过软件，请务必进行硬件检测。
Load all the CTCs that came with the device into the flow cell positions.
All the strips should be loaded with CTCs.
Note:
- A PromethION 24 has three strips that contain a total of 24 flow cell positions.
- A PromethION 48 has six strips that contain a total of 48 flow cell positions.
The MinKNOW UI recognises the CTCs as they are loaded, and the LED adjacent to the flow cell will first show blue (initialising), followed by green (ready).
Close all of the doors on the top of the Sequencing Unit once the CTCs are loaded.
重要
Correct insertion of PromethION CTCs
Note that regular flow cells are shown in the images, however the recommendations apply equally to CTCs.
Line up the CTC with the connector (horizontally and vertically) and smoothly insert it into position.
Press the CTC down firmly into the loader, and ensure that the latch engages.
Insertion of the CTC at the wrong angle can damage the pins on the PromethION:
Once the flow cells are correctly loaded into the PromethION, the flow cells undergo an automatic hardware check:
- Green tick: flow cell has passed
- Red tick: flow cell needs to be re-inserted
打开主页（Start），选择“Hardware Check”（硬件检测）。
Select all the CTCs in the UI and click Start for the check to begin.
随即进入“Sequencing Overview”（测序概览）页面。
测序芯片下方将有进度栏显示检测进度。
下图以Flongle配置测试芯片（CTC）为例（红框内为进度栏）。
步骤结束
硬件检测历时约1分钟。
如检测 通过 ， __指示框呈绿色__。
如检测 未通过 ，则 __指示框为橙色__。
如硬件未通过检测，请卸下并重新插入CTC，再次运行硬件检测。如果仍未通过检测，请通过电子邮件（support@nanoporetech.com）或纳米孔社区的LiveChat联系我们的客服。
重要
Do not store the CTCs in the flow cell positions when the platform/position is not in use.
Do not leave the CTCs in the Sequencing Unit flow cell positions once the unit is powered down, and do not insert the CTCs until the Sequencing Unit is powered on and the position is required for a Hardware check.
Store the CTCs in dry conditions at room temperature.
8. Flow cell check
耗材
- PromethION 测序芯片
仪器
- PromethION测序设备
测序芯片质检
在DNA/RNA文库上样前，请务必对测序芯片的活性纳米孔数进行质检。质检需在您收到测序芯片三个月之内进行。Oxford Nanopore Technologies会对活性孔数量少于以下标准的芯片进行替换** ：
| 测序芯片 | 芯片上的活性孔数确保不少于 |
|---|---|
| Flongle 测序芯片 (FLO-FLG001) | 50 |
| MinION/GridION 测序芯片 | 800 |
| PromethION 测序芯片 | 5000 |
** 请注意：自收到之日起，芯片须一直贮存于Oxford Nanopore Technologies推荐的条件下。且质检结果须在质检后的两天内递交给我们。
重要
将芯片从冰箱中取出后，请将其置于室温环境孵育20分钟再插入PromethION测序仪。潮湿环境下的测序芯片上可能会形成冷凝水。因此，请检查测序芯片顶部和底部的金色连接器引脚处是否有水凝结。如有，请使用无纤维布擦干。请确保测序芯片底部有热垫（黑色）覆盖。
Load the flow cells to be run into the docking ports of the PromethION.
Insert the chip connector fully into the docking port. Take note to ensure the latch to hold the chip in place clicks in.
重要
Correct insertion of PromethION flow cells into a PromethION 24/48 device
Line up the flow cell with the connector (horizontally and vertically) and smoothly insert it into position.
Press the flow cell down firmly into the loader, and ensure that the latch engages.
Insertion of the flow cell at the wrong angle can damage the pins on the PromethION and affect your sequencing results. If you find the pins on a PromethION position damaged, please contact support@nanoporetech.com for assistance.
Once the flow cells are correctly loaded into the PromethION, the flow cells undergo an automatic hardware check:
- Green tick: flow cell has passed
- Red tick: flow cell needs to be re-inserted
导航至“Start”（开始）页面，点击“Flow Cell Check”，打开测序芯片质检页面。
When you see the flow cell type and flow cell IDs recognised, click Start to begin.
随即进入“Sequencing Overview”（测序概览）页面。
测序芯片下方将有进度栏显示检测进度。
下图以Flongle配置测试芯片（CTC）为例（红框内为进度栏）。
测序芯片健康状况指示框
测序概览（Sequencing Overview）页面会显示测序芯片的质量。质量分为三个等级：
黄色感叹号（图中Flongle测序芯片）: 活性测序孔数量低于质保范围。将芯片从测序设备中取出后重新插入，并运行测序芯片质检。如果测序芯片活性孔数仍然低于质保范围，请您发邮件至support@nanoporetech.com。
绿色对勾（图中MinION 测序芯片）： 活性测序孔数量在质保范围之上。
问号（图中PromethION 测序芯片）： 测序芯片在本次MinKNOW使用期间还未经过质检。
请注意： 芯片质量指示框仅在当次MinKNOW使用期间可见。一旦该次使用结束，测序芯片的状态将被清除。
9. 测序并监测实验
请参阅纳米孔社区中的MinKNOW实验指南，查看如何设置测序实验及监测实验进度。
10. Data management
自MinKNOW21.02版起，我们向MinKNOW中添加了新功能，以实现测序期间更顺畅的数据传输。 以下示例方法向您展示了如何挂载外部NFS及传输数据：在执行任何代码之前，请您咨询当地的IT部门，确保代码与本地基础架构兼容且具有正确权限。
Mount your local NFS file system on the device (note that Linux mounts a remote filesystem into a directory locally). Below is an example setup through the terminal:
prom@PCT0001:~$ sudo su - prom@PCT0001:~$ apt install autofs prom@PCT0001:~$ echo -en “+auto.master\n/nfs /etc/auto.ont\n” > /etc/auto.master prom@PCT0001:~$ echo -en "NETWORKSTORAGE -nfsvers=3,rw,bg,async,actimeo=300,soft,intr,noatime,tcp,nolock IPADDRESS:/PATH/TO/SHARE" > /etc/auto.ont prom@PCT0001:~$ ln -s /nfs/NETWORKSTORAGE /media/NETWORKSTORAGE prom@PCT0001:~$ ls -al /media/NETWORKSTORAGE/*
Install the latest version of the MinKNOW software:
prom@PCT0001:~$ sudo apt update prom@PCT0001:~$ sudo apt install ont-promethion-release
Make a source directory that your experiments will be saved to in /data/ , for example:
prom@PCT0001:~$ mkdir /data/data-offload
Make a destination directory on your networked storage. This also tests that the ‘prom’ user can write to the networked storage:
prom@PCT0001:~$ mkdir /media/mounted_drive/destination_directory/
As root, edit /etc/systemd/ont-platform-data-offload.conf to set the SOURCE_DIR and DESTINATION_DIR variables. SOURCE_DIR is the directory the PromethION software writes to, and DESTINATION_DIR is on your networked storage.
prom@PCT0001:~$ sudo vi /etc/systemd/ont-platform-data-offload.conf
脚本所执行操作会被写入/data/data-offload.log日志文件
在MinKNOW用户界面上开启测序，将输出路径设为上述SOURCE_DIR。
我们当前建议您手动控制服务，因数据卸载可能影响正在运行的实验。
以 root用户身份启动卸载服务：
sudo systemctl start ont-platform-data-offload
以 root用户身份停止卸载服务：
sudo systemctl stop ont-platform-data-offload
如需检查服务是否在运行中，请运行以下命令：
sudo systemctl status ont-platform-data-offload
重要
数据传输速度取决于本地网络基础设施。Oxford Nanopore 建议使用 10 Gbps (PromethION) 带宽以最大化传输速度。
重要
数据首先需直接写入内置固态硬盘。当前不支持写入网络硬盘。
11. Shutting down
Shutting down your PromethION 24/48
The PromethION Data Acquisition Unit requires a stepwise, processed shut down, otherwise you may face problems e.g. when recognising flow cells.
Follow the instructions in this section to ensure you do not face errors with your PromethION from incorrectly shutting down your device.
Remove all flow cells from the device.
Navigate to Device Settings in the admin interface.
Select Shutdown.
Click Shut Down in the pop-up to confirm.
提示
Do not click on Reboot, as this will lead to errors in recognising the flow cells when starting an experiment.
Switch off the Sequencing Unit using the switch on the back of the device.
Turn off the device at the mains supply, if you are using mains power.
12. 通过用户界面更新软件
重要
更新软件
当有新软件或更新时，Oxford Nanopore Technologies 会通过社区发布公告。
我们强烈建议用户在新版本发布后尽快更新。
请注意：用户将无法更新远程连接或正在运行的设备。
通过桌面图标打开MinKNOW图形用户界面，连接测序设备后，软件的自动更新程序将自动检查更新。
当有新更新可用时，将弹出一个对话框。
选择 Get Update （获取更新）以自动更新软件。
您可以跳过更新，但是我们建议您在 有可用更新时尽快更新软件。 有些更新为仪器使用必需，因此无法跳过。
请注意： 对MinION Mk1B，单击 Get Update （获取更新）将在测序仪所连计算机上打开 软件下载 页面。用户可于该页面下载更新后的 MinION 软件。
用户可以通过“Host settings”（测序设备设置）下的“Software”（软件）板块更新仪器。
导航至“Host Settings”（测序设备设置）下的“Software”（软件）板块。点击“Get Update”（获取更新）以打开安装窗口。
当软件有可下载的新版本时，界面会出现“Update”（更新）按钮。
请注意： 对MinION Mk1B，单击 Get Update Update”（获取更新）将在测序仪所连计算机上打开软件下载页面。用户可于该页面下载更新后的 MinION 软件。
在安装窗口点击“Install Update”（安装更新）以下载更新。
对话框中将显示变更日志。
等待软件更新；需要几分钟的时间。
更新完成后，您将收到安装窗口的通知。
更新完成后，请关闭设备，然后重新启动。
重要
重装MinKNOW
一些情况下，您可能需要重装软件（比如如果您目前使用的MinKNOW版本存在问题）。为此，您需要首先彻底卸载当前版本。请按照“Support ”（支持）文章中的说明进行卸载：如何卸载适用于Mk1B及P2 Solo的MinION 软件
13. (Advanced) Updating the software via the Terminal
Obtain the latest updates
After successfully checking the hardware, you should update to the latest software release. To do this, enter the following commands into the terminal:
sudo apt clean
sudo apt update
sudo apt install ont-promethion-release
The default sudo password is __prom__; change this to ensure the security of your device. Once these commands have completed successfully with no errors, turn off the device using the following command. ``` sudo poweroff ```
Then turn the device on again to complete a full power cycle.
后续的测序设备更新
当有GridION相关的新软件或更新时，Oxford Nanopore Technologies 会在社区发布公告。
我们强烈建议用户在新版本发布后尽快更新。
请遵循本地IT部门的建议，及时对设备的Linux系统进行安全更新。
请注意： 请务必配置防火墙，允许使用443端口进行出站访问，以便顺利更新。
14. Downloading the ISO image and burning it to a USB drive
概览
您可参考下文说明，制作用于测序设备操作系统重建的USB启动盘。
如果您尚未收到带有ISO镜像的USB硬盘，请继续阅读以下步骤。 如果您已经收到USB硬盘，请直接跳至下一步骤：“如何从USB启动”。
重要
即使您已选择保留数据，我们仍强烈建议您将数据传输到备份存储。这是因为在操作系统重建的过程中可能会发生意外情况，比如USB断开、断电等，导致数据损坏。
使用以下链接下载 ISO 镜像：
刻录IOS镜像至USB硬盘
适用于刻录ISO镜像的软件：
- Windows： Rufus
请注意： 另一款ISO刻录工具balenaEtcher不适用于我们的ISO镜像 。您需使用运行 Windows系统的计算机，并可能需要管理员权限来安装Rufus软件。
请使用下述配置刻录 ISO 镜像（须 使用EFI/GPT引导）：
- 分区方案：GPT
- 目标系统：UEFI
USB硬盘须具备如下规格：
- 容量须在32BG及以上
- 推荐使用USB 3.0接口
- 须使用 UEFI 引导选项
请注意： 我们建议使用两个来自不同制造商的USB硬盘进行闪存备份。普通的USB硬盘在重建操作系统时可能会无缘故地出现故障。
15. Preparing the PromethION for UEFI boot
The PromethION must be configured for UEFI Hard disk boot before you begin the rebuild process.
Power down the Data Acquisition Unit if it is switched on.
Insert the bootable USB into the USB port with the blue interior on the back of the device.
Note: If using an A-series/A100 Data Acquisition Unit, you may need to remove one of the USB firmware update cables connected to the sequencer.
Power on the Data Acquisition Unit, then when the below screen appears, press Delete to enter setup.
On A100/A-series Data Acquisition Units, ensure you are using the VGA output.
Once in setup, press the Right cursor key until Boot is highlighted.
Within Boot, configure the following settings:
- Boot mode select: UEFI
- Boot Option #1: UEFI Hard Disk
- Boot option #2: UEFI USB Hard Disk
Use the cursor keys to navigate to Save & Exit, then select Save Changes and Reset.
16. How to boot from USB
Power off the Data Acquisition Unit.
Power on the Data Acquisition Unit.
When the below screen appears, press F11 to enter the Boot Menu.
Choose the UEFI USB boot option using the cursor keys.
In the below example the USB drive is called SanDisk. If the system has not been prepared to boot from UEFI, this will not work. See the section Preparing the PromethION for UEFI boot for how to configure this.
Press Enter once the UEFI option is chosen, then highlight Customer Factory Reset, and press Enter. This option will detect your installation and try to keep network configurations, hostname and /data partition. We recommend backing up data prior to proceeding with this step wherever possible.
Make sure to connect your device to the network if configured to run online.
| Option | What it does | When to use option |
|---|---|---|
| Customer Factory Reset | - Keeps network configuration - Keeps hostname (i.e. PCA1XXX) - Keeps data - Does not clear the metadata or format all the disks | - To reset the device to a MinKNOW version reflected on the image name (e.g. 22.10 ISO = MinKNOW 22.10) - To reset the device to a known state whilst attempting to keep existing data |
| Reset Install and keep /data | - Keeps network configuration - Keeps hostname (i.e. PCA1XXX) - Keeps data - Does not clear the metadata or format all the disks | Functionally identical to the Customer Factory Reset option |
| Format Disks and lose /data | - Does not keep network configuration - Does not keep hostname (i.e. PCA1XXX) - Does not keep data - Clears the metadata and formats all the disks | - Issue with data storage or a new unformatted drive (e.g. faulty drive or drive replaced) - If the keep /data option does not resolve the issue |
| SECURE WIPE - can take hours | - Does not keep network configuration - Does not keep hostname (i.e. PCA1XXX) - Does not keep data | Use only if requested by a member of Technical Services - this option completely wipes the disks by writing all data to 0 |
You will see the screen below. Select Standard Installation. A confirmation prompt will appear; click Okay.
Note: The blue desktop may fill the entire screen. You can press Esc to view the menu in the default browser.
The following screen will appear and the progress will be shown on the progress bar. The entire process may take ~1 hour to complete.
Note: It is normal for the system to restart multiple times. Do not turn off the Data Acquisition Unit while installation is in progress. It is also expected behaviour for the progress bars to stay temporarily stuck at specific stages.
Once the rebuild process has completed, the standard login screen will be displayed. After logging in, you will see the MinKNOW icon on the desktop. If the MinKNOW icon is not present, carry out one final power cycle of the Data Acquisition Unit.
Any previous changes to the device password will have defaulted back to prom. If you need to update the default password, follow the instructions here
Once the MinKNOW icon is displayed on the desktop, power down the Data Acquisition Unit. To use the PromethION for sequencing, now power on the Sequencing Unit followed by the Data Acquisition Unit and check all flow cell positions are detected.
17. Completing the restore
打开文件资源管理器，通过点击USB 启动盘一旁的弹出图标来移除USB 启动盘。
设备在首次启动时可能需要几分钟才能识别键盘和鼠标。
按下“Ctrl+Alt+T”，以打开终端窗口。
If your hostname has not been maintained through the restore process (it should be visible on the command line), type:
ont-promethion-serial set NAME_OF_DEVICE
where NAME_OF_DEVICE is the serial ID as included on the label on the side of your Data Acquisition Unit. For example:
ont-promethion-serial set PC24A0012
按回车键。
键入“bash”，然后按回车键，确认已设定主机名。
配置您的网络：
以下脚本可帮助您配置网络。 打开终端窗口，输入以下命令：
ont-network-settings
脚本选项包括：
--dhcp（非必需）-使用DCHP，并仅保留接口、绑定和覆盖这三项属性
--address ip_address（必需）-此GridION的IP地址
--subnet subnet_mask（必需）-此GridION的子网掩码
--gateway gateway_address（必需）-此GridION的默认网关
--dns DNS_server1,DNS_server2（必需）-此GridION的DNS服务器
--search your_domain（必需）-您的域名后缀 （例如，公司名.地域）
--overwrite（非必需）
--help -详细说明上述选项
如需重置设置，请在上述命令选项前使用--overwrite 标志，再关闭设备后重启。
Open MinKNOW and check for software updates, or check for updates in the terminal:
sudo apt update
sudo apt install ont-promethion-release
ont-system-test (not available on some ISO images)
ont-validate-install
You should see the following message if the installation was successful:
This should be complete, please retry any apt commands that failed to work previously
eg: sudo apt install
All Packages installed and nvidia is happy, so resetting ont-restore-apt
If the installation was unsuccessful, run the following commands:
sudo apt update
sudo apt dist-upgrade
sudo ont-validate-install
sudo reboot
If the issue has not been resolved after a reboot, contact Technical Support at support@nanoporetech.com.
18. If problems are encountered
Boot to the "Platform Rescue and Recovery" screen.
Click the "Format disks and lose /data" option.
Once returned to the following screen, click the top "Customer Factory Reset im" option.
Note: this step may happen automatically and proceed immediately to step 4 without user input.
If the system takes more than 20 minutes between Step 2 and returning to the following screen, click "Standard Installation".
Allow the factory reset to continue.
Note: It is normal behaviour for the system to restart multiple times. Do not turn off the PromethION Data Acquisition Unit/GridION while the reset is in progress.
It is also expected behaviour for the progress bars to stay temporarily stuck at specific stages.
Once the reset is complete, you will be prompted to login.
19. 常见问题解答
如果您的测序设备出现问题或在测序过程中遇到困难，请联系我们的技术服务团队。
如需查看常见问题解答，请参阅MinKNOW支持板块 。
通常，需要排除故障时，我们建议您导出日志并发送给技术服务团队。
Help feature and support link from MinKNOW.
The Nanopore support hub can also be accessed directly from your MinKNOW UI.
In the top right of MinKNOW you will see the "Help" option:
Clicking this option will bring you to a page with a link and a QR code:
On larger devices such as the GridION and PromethION 24/48, and devices such as the MinION Mk1b and P2 Solo, clicking the link will directly bring you to the Nanopore support page.
On devices such as the P2 Integrated and MinION Mk1C, you will be able to scan the QR code with another device, or type in the shortened URL on another device to quickly reach the support hub.
导出日志：
对GridION、PromethION 24/48、PromethION 2i、及与GridION连接的PromethION 2 Solo:
- 在“Export Logs”（导出日志）栏目下选择 Export（导出）。
日志成功导出后，“Export”按钮下方将显示导出路径。日志将以.tgz压缩文件格式下载至“logs”（日志）目录中。
您可于“Host Settings ”（测序设备设置）下的“File Manager”（文件管理器）中按需设定日志导出路径：
- 在“Export Logs”（导出日志）栏目下，点击 **Logs exported to:**（日志导出至：）对话框右侧的文件，在MinKNOW的文件管理器中打开日志所在路径。
- 使用文件管理器右下角的控制面板移动日志文件。
如 PromethION 2 Solo 与独立计算机连接
您可于下述路径获取各测序实验的日志：
Windows C:\data\logs
Mac OS X /private/var/log/MinKNOW
Linux /var/log/minknow
清除日志和临时数据：
在“帮助”（Help）页面的“清除文件”（Clean up files）部分选择清除（Clean up），并在弹出的对话框内确认。
请注意： 将清除日志及临时数据，实验数据不会被删除。
修复仪器故障：
在“帮助”（Help）页面的“Troubleshooting”（故障排查）部分点击 Run repair（修复问题），并在弹出的对话框内确认。MinKNOW将尝试修复以下问题：
- 确保“/data”下所需路径存在，且具有正确的所有权和权限。
- 确保“/data”下所需文件的所有权和权限正确。
- 确保GPU正以最高性能运行
- 确保已禁用蓝牙
