MinION Mk1C user manual
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MinION: Protocol
MinION Mk1C user manual V MKC_2005_v1_revAG_27Nov2019
This user manual will enable the user of the MinION Mk1C to:
- Power up and down the device
- Learn the shortcuts enabled by touchscreen in the MinION Mk1C Graphical User Interface (GUI)
- Use the Host Settings for system software configuration
- Access the device remotely for control of MinKNOW and to transfer data on Windows, macOS and Linux computers
- Access the device through SecureShell/the Terminal for data transfer and device configuration
Our device FAQs are located here.
For Research Use Only
FOR RESEARCH USE ONLY
Contents
Overview
Installation
- 2. What's in the box
- 3. Powering the device
- 4. Onboarding process
- 5. General connection information
- 6. Changing the default password and hostname
- 7. Network settings and connection
- 8. Mount network drive
- 9. (Advanced) Connecting by the command-line
- 10. (Advanced) Network configuration - static vs dynamic IP
- 11. Hardware check
Pre-sequencing checks and sequencing run
After completing a sequencing run
Updating the software
- 17. Updating the software via the UI
- 18. (Advanced) Updating the software via SSH
- 19. OS update/device recovery using microSD cards
- 20. Updating the signing key to update MinKNOW (IMPORTANT)
Troubleshooting
概览
This user manual will enable the user of the MinION Mk1C to:
- Power up and down the device
- Learn the shortcuts enabled by touchscreen in the MinION Mk1C Graphical User Interface (GUI)
- Use the Host Settings for system software configuration
- Access the device remotely for control of MinKNOW and to transfer data on Windows, macOS and Linux computers
- Access the device through SecureShell/the Terminal for data transfer and device configuration
Our device FAQs are located here.
For Research Use Only
1. Device information
The MinION Mk1C
The MinION Mk1C combines the real-time, rapid, portable sequencing of a MinION Mk1B with a Graphical Processing Unit (GPU) and a high-resolution screen. The device applies the technology of the MinION Mk1B with the basecalling power of the MinIT and the additional features of smartphone, such as a cellular modem and touch screen.
The hardware
Component | Specification |
---|---|
Model Number | MIN-101C |
Size and weight | H 32 mm x L 142 mm x W 118 mm; 440 g |
Power | • Supplied with a 6.3-19.6 VDC power supply • Max rated current 10 A • Max rated power 60 W |
Compute spec | 1 TB SSD Storage, 8 GB RAM, GPU embedded analysis accelerator (ARM processor 6 cores, 256 core GPU) |
Connections | • 1x USB 2.0 • 1x eSATA (currently non-functional) • 1x microSD card • 1x 1 GB Ethernet • Wi-Fi connectivity |
Pre-loaded software | Linux OS, MinKNOW and Dorado |
Security | Kensington Nano Security Slot |
Environmental conditions | • Designed to sequence at +10°C to +30°C* • Do not cover vents on the sides of the device • Indoor use • Altitude up to 2,000 metres • Maximum relative humidity 80% for temperatures up to 31°C, decreasing linearly to 50% relative humidity at 40°C • Applicable pollution degree 2 in the intended environment |
* Functional range of electronics +5°C to +40°C
MinION Mk1C information
FAQs
Our MinION Mk1C FAQs are located here.
2. What's in the box
What's in the box
The MinION Mk1C is shipped with:
- Configuration Test Cell (CTC)
- Power adapter
- Plugs compatible with UK, US, EU and Australian sockets
- Quick Start Guide
The components of the MinION Mk1C are shown below.
Touch screen The touch screen allows the user to interact with the MinION Mk1C software directly on the device. LED lights There are five LED lights to the right of the touch screen. All five LEDs illuminate white when the device starts up and then cycle as the system software loads. The cycling indicates that the device is working. When a USB is inserted into the MinION Mk1C, all LEDs illuminate and flash three times before the normal cyclical pattern resumes. Lid The lid can be flipped open to access the flow cell housing. Clip The clip holds the flow cell or Configuration Test Cell securely in place. Configuration Test Cell (CTC) The CTC is used during the hardware check to ensure that the communication between the device and the flow cell is working correctly.
The connections and ports available on the MinION Mk1C are shown below.
3. Powering the device
The AC/DC adapter power specification
The power requirements for the MinION Mk1C using the AC/DC adapter supplied with the device are detailed below.
Power supply | Power input | Power output |
---|---|---|
AC/DC adapter | Standard Mains input: 100-240 VAC 50/60 Hz 1.5 A | Output: 6.3-19.6 VDC Max rated current 10 A Max rated power 60 W Estimated power dissipation: 20-25 W at room temperature |
The MinION Mk1C is compatible with portable DC power supplies.
Oxford Nanopore Technologies does not supply a portable power supply for this purpose and as such it is not officially supported. If you wish to make use of a portable power supply, then it must be compatible with the below specification.
DC power pack requirements
Power supply | Power input | Power output |
---|---|---|
DC power pack | Standard Mains input for charging: 100-240 VAC 50/60 Hz | Estimated power dissipation: 20-25 W at room temperature |
Fit the appropriate pin-plug into the base unit of the AC/DC adapter.
Insert the barrel pin into the MinION Mk1C power port.
Switch on the AC Mains.
Press the power button on the device to switch it on.
Once the MinION Mk1C is powered on, the power button will illuminate blue and the device fans will sound.
On switching on the device for the first time, users will be taken through the onboarding flow for setting up the device. Once the MinION Mk1C is set up, users will need to log into their MinKNOW accounts when switching on their device if the onboarding flow has already been completed.
If you experience login issues, contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.
To log in, you must be connected to the internet.
For more information see the Onboarding process section in this document.
4. Onboarding process
Onboarding process for new devices
The onboarding process is available when a MinION Mk1C is first switched on to guide users through setting up a network connection, logging into MinKNOW, enabling remote access and running a hardware check.
Update to the latest version of MinKNOW for the MinION Mk1C, which supports the latest chemistry, bug fixes and performance enhancements.
Please visit our Oxford Nanopore FAQ and Help Centre if you are having difficulties updating MinKNOW on the MinION Mk1C.
Select the language for the device.
Choose the network connection to connect to the internet.
We strongly recommend users to connect their device to the internet to allow them to log into their MinKNOW account.
There are two options:
Connect using WiFi: click WiFi and select the network to join and enter password, if prompted.
Connect using Ethernet: plug-in the Ethernet cable and click Ethernet.
Note: If your network configuration requires you to use a static IP address, click Offline and configure the network through the main Network Settings page.
Log into your MinKNOW account using your Nanopore account credentials.
Configure remote access from the options displayed.
These settings can be altered again using the Host settings after the onboarding flow has ended.
Complete a hardware check to ensure the device is working correctly for sequencing experiments.
A hardware check only needs to be completed once. However, it can be skipped for users who will not be using their device for sequencing.
Navigate to the Device Settings to verify that the date and time are correct. Having the correct time is important to successfully establishing a connection to a network.
5. General connection information
Connection
There are several options to connect to your MinION Mk1C. These are:
General Options
- If you would like to use the sequencing software (MinKNOW) directly on the MinION Mk1C device: Log into MinKNOW using the device GUI and select the MinION Mk1C device on the Connection Manager.
- If you would like to connect to the MinION Mk1C remotely using a computer: Download MinKNOW software and select the MinKNOW icon shortcut and log into MinKNOW. Select the MinION Mk1C device on the Connection Manager to remotely connect.
Advanced users
- Secure Shell access - see the (Advanced) Connecting by the command-line section of the user manual.
MinKNOW and data access with your MinION Mk1C
MinION Mk1C sequences and basecalls data via the integrated sequencing device and Oxford Nanopore Technologies basecaller - Dorado - in MinKNOW. POD5, FASTQ and BAM files are output and stored locally on the MinION Mk1C in the Data folder.
This folder and the output files can be accessed through File Manager in MinKNOW. For more information, please see the Data management section of this document.
6. Changing the default password and hostname
Navigate to the host settings to open 'Device settings'.
Click 'Reset password' in the System box.
In the 'Change password' dialogue box, enter your current password, followed by the new password.
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
7. Network settings and connection
Network settings display internet connectivity information. The MinION Mk1C can be connected via Ethernet or Wi-Fi.
Both options are supported, however if Ethernet is available, we recommend using Ethernet because the connection will likely be quicker and more reliable.
Ethernet
To connect using Ethernet:
- Connect a Ethernet cable to the device
- Navigate to network settings in host settings to confirm connection. IP configuration information will appear when connected.
Wi-Fi
To connect using Wi-Fi, navigate to network settings and toggle Wi-Fi on. Select a network from the Available Networks panel to connect to the internet.
Select Advanced to open Advanced Wi-Fi Configurations. From here, all available networks can be viewed, connected or removed.
重要
Please note that Wi-Fi connections with captive portals (a web page that the user is required to view and enter login details before access is granted) cannot be used with the MinION Mk1C.
Configuring static IP address
The static IP address can be configured through MinKNOW UI for both WiFI and Ethernet. Below is an example for Ethernet.
- Click Edit in "IP configuration" to open "Edit the IP address configuration" dialogue box.
- Select either DHCP or Static tab and click Confirm to save.
- Once the IP address configuration has changed successfully, click Finish to close the dialogue box.
Hotspot can be activated to allow users to connect to a larger screen.
This can be used to connect to the MinION Mk1C in places where there is no network infrastructure, e.g. in the field. To enable hotspot, select the toggle to ON. When active, the device hotspot name will be displayed.
Hotspot configs can be edited to select a channel if required for congested networks where there may be competition for channels.
- Navigate to the network settings
- For hotspot, select the toggle to ON
- Click 'Configure hotspot'
- Select channel using the dropdown menu
- Enter new password
- Click 'Confirm'
The hotspot should be confirmed as specified in the hotspot configs.
To connect the MinION Mk1C Wi-Fi router to a Windows device:
- Locate the MinION Mk1C ID on the underside label of the device:
- Click on the MinION Mk1C ID under the Wi-Fi Connections Panel in the Control Panel or the options in the right side of the Task Bar
Login with the Security Key: WarmButterflyWings98
- Access the MinION Mk1C by the File Explorer: Go to \\mc-XXXXXX (XXXXXX is the MinION Mk1C ID) in the Address Bar. You will be prompted for the network credentials on connecting to the MinION Mk1C through File Explorer.
To connect the MinION Mk1C router to a macOS device:
- Locate the MinION Mk1C ID on the underside label of the device:
- Click on the Wi-Fi icon on the right of Menu bar at the top of the screen:
Identify the MC-XXXXXX ID in the Network Name under Network Panel (the final option under the Wi-Fi icon), which is show in the window below (left)‡. Selecting the MinION Mk1C ID and clicking Apply will present the Wi-Fi login pop-up. Use the password credentials shown below.
Login with the Password: WarmButterflyWings98
- Access the MinION Mk1C by the Network browser: Search for Network using Finder. Click on Server in the tab to lower left of the Search bar.
MC-XXXXXX (XXXXXX is the MinION Mk1C ID) will be displayed as a server option. Click the MC-XXXXXX icon, click Connect as under the Search bar and enter the network credentials.
‡ When connecting to your device by SSH, it can be addressed in three different ways:
- Using DNS
- Using mDNS
- Using its IP address directly
In most organisations, central DNS servers are used. If your device is using a 'static' IP configuration, your IT department will have to create a DNS entry for it manually. If your device is using a dynamic (DHCP) IP configuration, the DNS entry will often be created automatically. To SSH into your device using DNS, set the hostname in your client to the device's hostname, e.g. MC-112345.
If DNS is not provided by your organisation or your broadband router, try using mDNS. When your device is connected to a network, it announces its presence to all other nearby devices such as your laptop or PC. If your laptop or PC is configured to recognise these announcements, you can SSH into your device using mDNS by setting the hostname in your client to the device's hostname followed by ".local", e.g. MC-112345.local.
If the above methods are not successful, use the devices IP address directly. The MinKNOW UI shows the IP addresses for each interface in the Settings - Network page. If your device has LAN and Wi-Fi interfaces, each will have a different IP address. To SSH into your device using its IP address, set the hostname in your client to the IP address, e.g. 10.20.30.41.
To connect the MinION Mk1C router to a Linux device:
- Locate the MinION Mk1C ID on the underside label of the device:
- Click on the Wi-Fi icon on the right of Menu bar at the top of the screen.
Identify and click on the MC-XXXXXX ID under the Wi-Fi network options icon (shown above). Enter the Wi-Fi password (shown below) in the pop-up Wi-Fi Network Authentication window:
Login with the Password: WarmButterflyWings98
The following window will be presented when you have connected to the MinION Mk1C Wi-Fi router.
- Access the MinION Mk1C using the Linux File Browser and enter the server address.
Open the File Browser (this can be found using the Search tool). Select Connect to server on the bottom of the list in the left panel. You will need to enter:
smb://mc-110013
8. Mount network drive
Mount drives
The MinION Mk1C contains 1 TB SSD storage, which provides an average capacity of roughly 50 Gbases, stored in .POD5, .fast5 and/or FASTQ format. Once the SSD fills up, you will need to move your sequencing data off the device to a networked storage location. Network drives for data storage can be mounted from either the Device Settings or the File Manager in the Network tab:
Device Settings:
File manager:
Click "Add network drive".
A modal will open. Click either SMB (Samba) or NFS (Network File System) shares.
Use SMB for connecting to a shared drive on a Windows server, and NFS for Linux. If your shared drive is on a macOS machine or NAS (Network-Attached Storage), you can use either SMB or NFS.
SMB:
NFS:
To mount SMB shares:
- Enter the host name or IP address of the SMB share. This is acquired from your network admin.
- Enter the drive on the network host that the user wants to share. Take note to start with a '/'. E.g.
/data
. - The 'Mount Point' field will auto-populate with the host name and path to the network share. However, you can customise this. In the file manager, it will appear as:
/data/network/mt-111111-data
for example. - Add a username.
- (Optional) Enter a password.
- (Optional) Enter a domain name.
- Click Mount.
Providing the settings were correct, the mounted drive will be added to the 'Disk Management' overview. The user will be able to:
- View the space information for the drive
- Unmount the network drive
- A link to jump to the mount point inside the file manager
To mount NFS shares:
- Enter the host name or IP address of the NFS share. Obtain this from your network admin.
- Enter the drive on the network host that the user wants to share. Take note to start with a '/'. E.g.
/data
. - The 'Mount Point' field will auto-populate with the host name and path to the network share. However, you can customise this. In the file manager, it will appear as:
/data/network/mt-111111-data
for example. - Click Mount.
Providing the settings were correct, the mounted drive will be added to the 'Disk Management' overview. You will be able to:
- View the space information for the drive
- Unmount the network drive
- A link to jump to the mount point inside the file manager
Click "Add network drive".
9. (Advanced) Connecting by the command-line
重要
If you are uncertain about changing any network parameters on your device, you will need to contact your IT department.
Network configuration - connection to your MinION Mk1C
The MinION Mk1C has two interfaces that we support for data transfer. These are:
- Ethernet port - direct to interface or LAN
- Wi-Fi - direct to interface
Networking with MinION Mk1C. Blue lines indicate a connection via the internet. The black line indicates a wired connection. The computer on the LAN (B.) can be used to configure the device using parameters that are not available through the Admin interface. You can also configure the MinION Mk1C using the Wi-Fi connected device (A.), however network compatibility issues may inhibit the update.
Internet connection:
This configuration requires an ethernet connection to the Local Area Network (LAN) from the MinION Mk1C. The LAN is connected to the internet, which enables updating of MinKNOW on the device.
Interface connection:
An interface, such as a laptop/mobile device/computer, can be wirelessly connected to the MinION Mk1C. Alternatively, the MinION Mk1C may be accessed and controlled by a computer on the LAN.
Other configurations are also possible, however they are not supported by Oxford Nanopore Technologies:
- Ethernet-desktop/laptop computer to control the MinION Mk1C - no internet
- MinION Mk1C Wi-Fi (Client) to a router and desktop/laptop Wi-Fi to a router, which is itself connected to the internet
- It is possible to adapt other data connections through the USB 2.0 port, however, Oxford Nanopore Technologies cannot advise or support this use.
Connecting by SSH/the terminal provides options to configure and access your MinION Mk1C computer and network.
Connecting by the command line via SSH or the terminal enables several options:
- Access and transfer data on to a mounted USB-hard drive - for instructions, see the Data transfer via SFTP section of this user manual.
- Change the output directory from
/data
- Change between static and DHCP (dynamic) IP address of the ports on the MinION Mk1C
- Access to the logs
Windows
Option 1
If SSH is enabled in your Windows build, you can use the built-in Windows Command Prompt (CMD). Open a CMD prompt, then enter ssh minit@hostname
(e.g. ssh minit@mc-111414
):
If it is your first time connecting, you will be asked to confirm the authenticity of the host. Enter yes
to continue:
Enter the password to establish an SSH connection. The default password is minit
. Please note that characters will not appear on-screen as you type in the password.
If the SSH connection is successfully established, the shell prompt will now read minit@hostname:~$
Option 2
A third-party SSH client such as Bitvise (example images shown below) or Putty may be used. The following default options can be entered:
Host – device ID or IP address (e.g. MC-111414) Port – 22 Username – minit Initial method – password Password – minit
If a connection is successfully established, Bitvise will automatically open a terminal window and an SFTP browser. Alternatively, you can click on New terminal console or New SFTP window on the left-hand side:
Linux/macOS
On both Linux and macOS operating systems, you can use the built-in Terminal program.
Open a Terminal, then type ssh minit@hostname
(e.g. ssh minit@mc-111414
):
If it is your first time connecting, you will be asked to confirm the authenticity of the host. Enter yes
to continue:
Enter the password to establish an SSH connection. The default password is minit
. Please note that characters will not appear on-screen as you type in the password.
If the SSH connection is successfully established, the shell prompt will now read minit@hostname:~$
10. (Advanced) Network configuration - static vs dynamic IP
重要
If you are uncertain about changing any network parameters on your device, you will need to contact your IT department.
Network configuration - Static vs dynamic IP
The LAN interface on the MinION Mk1C can operate in either DHCP (dynamic) mode or static mode. When in DHCP mode, the settings are acquired from the network’s DHCP server. Some networks do not have a DHCP server or you may wish to override the settings it provides. In such circumstances, the static mode can be used.
The static mode comes pre-configured with the following settings:
IP Address/Subnet Mask: 192.168.0.1/24
Default Gateway: 192.168.0.1
DNS Servers: 9.9.9.9, 8.8.8.8
To configure static IP addressing on the Ethernet port:
Here is an example of possible static settings that may be provided by your IT department:
IP Address: 10.20.30.40
Subnet Mask: 255.255.255.128
Default Gateway: 10.20.30.1
DNS Servers: 10.0.0.53, 10.0.1.53
To change the static profile to match these settings:
- Log in to your MinION Mk1C using SSH via the WiFi connection.
- If you are given the subnet mask in the form
xxx.xxx.xxx.xxx
, convert this to CIDR format, which is a number between 1 and 32 (common values are 16, 24 and 25). You can use the following website to convert fromxxx.xxx.xxx.xxx
to a CIDR value: https://docs.netgate.com/pfsense/en/latest/network/cidr.html - Look up the
xxx.xxx.xxx.xxx
value in the first column and find the corresponding CIDR value in the second column. In the example above,255.255.255.128
corresponds to a CIDR value of/25
. - Once you have this value, open a terminal window and enter the following commands:
sudo nmcli con down dhcp
sudo nmcli con down static
sudo nmcli con mod static ipv4.method manual ipv4.address 10.20.30.40/25 ipv4.gateway 10.20.30.1 ipv4.dns 10.0.0.53,10.0.1.53 ipv4.routes "" connection.autoconnect yes
sudo nmcli con up static
In some instances, these commands may give an error message, however this is not a problem and the error should be ignored. The addresses specified in the third command line are the values that need to be changed to match particular settings. Note that there is no space between the DNS server addresses.
Use the following command to verify that your settings are correctly applied:
sudo nmcli dev show eth0
To configure dynamic IP addressing on the Ethernet port:
Open a terminal window and enter the following commands:
sudo nmcli con down static
sudo nmcli con up dhcp
11. Hardware check
重要
硬件检测
请务必在新设备或更新软件后使用配置测试芯片(CTC)进行硬件检测。CTC已预先插入测序设备的测序芯片卡槽内。
注意: 如您使用 Flongle 测序芯片,请定期将 空 适配器插入GridION并进行硬件检测,以确保 Flongle 适配器的正常运行。如需检查设备或测序芯片卡槽,请使用 MinION CTC,此方法同样适用于使用 Flongle 测序芯片时。
Navigate to the Start homepage and select the 'Hardware Check' option.
The hardware check page will open.
Select 'Start' on the Hardware Check page to start check.
Note: To check the Flongle adapter, insert the EMPTY adapter. To check device or position, insert only a MinION CTC.
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the check.
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__。
- Flongle 通过硬件检测
- MinION 通过硬件检测
- Flongle 未通过硬件检测
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)联系我们的客服。
12. Flow cell check
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12周之内进行。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。
Navigate to the Start page and select 'Flow Cell Check' to open the flow cell check page.
When you see the flow cell type and flow cell IDs recognised, click 'Start' to begin.
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the check.
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!(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√(图中MinION 测序芯片): 活性测序孔数量在质保范围之上。
?(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。
13. 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。
14. Data management
文件管理器(File Manager)
用户可通过测序设备设置(Host Settings)下的文件管理器页面管理和传输数据。
浏览选项卡,查看储存的数据:
- Internal (内置存储)标签页:数据存储于MinKNOW所连接的测序仪中(MinIONMk1C、GridION、PromethION)
- Removable (可移动存储)标签页:数据存储于MinKNOW所连接的可移动存储设备中,如USB移动硬盘
- Network (网络存储)标签页:数据存储于MinKNOW所连接的预挂载的网络驱动器上。
将设备作为共享/网络硬盘远程访问:
导航至“Device settings”(仪器设置),将“Share”(共享)切换至开。
请在弹出的新窗口填写您为此创建的安全密码。
点击“Set Password”(设置密码)。几秒钟后,共享切换按钮即被激活。
用户即可在不同的网络上访问并共享数据。
请注意 上图是在GridION上共享数据的示例。如在MinION或PromethION测序仪上共享数据,则按钮上的文本会相应替换为“Min”或“Prom”。
提示
如需取消共享,请将共享按钮切换至关。
请注意: 如再次打开共享,用户之前所设密码会被删除,须要重置。
如需在内置存储、可移动存储和网络存储选项间移动数据:
将页面底部的“Select”(选择)选项切换至“On”(开启),即可使用右下角的“Copy”(复制)、“Move”(移动)、“Delete”(删除)和“Rename”(重命名)选项。
选择一个文件或文件夹,然后使用右下角的选项。
提示
请先选定待移动或删除的文件,再点击 “Move”(移动)或“Delete”(删除)。
点击“Copy”(复制)或“Move”(移动),以打开新的对话框,其中列出了设备可访问的全部硬盘。
请注意:插入的USB硬盘或SD卡会显示在“Device”(设备)文件夹下。
点击要打开的硬盘,浏览文件目录以选择目标路径。然后点击“Copy”(复制)或“Move”(移动)以确认操作。
点击界面上的“New Directory”(新的目录)图标即可创建新目录。
如下图所示,点击标签页右下方红框内的图标,打开“Create New Directory”(新建目录)对话框并键入目录名称。然后点击 Create (创建)。
Disk management
Navigate to Device settings to view availabe disk space on the device.
Any peripherals plugged in, including USB, can be ejected using the Eject option.
A network drive can also be connected to the device by selecting Mount Network Drive and filing in the required credentials for connecting using a Samba (SMB) server or a Network File System (NFS).
Compatible disk formats: SD and USB on MinION Mk1C supports DOS FAT, Windows 95 FAT, exFAT, and Linux ext(2|3|4).
Please refer to the 'Mount Network Drive' section of this protocol for more information.
15. Data transfer via SFTP
To transfer data using this method, you will first need to connect to your MinION Mk1C using SSH or via the Terminal.
For instructions, see the (Advanced) connecting by the command-line section of this user manual.
Filezilla - A multi-operating system (OS) compatible software for data transfer
You can use software like Filezilla, which enables data transfer for mounted hard drives on Linux, Windows, and macOS. It may also transfer using the SFTP protocol which is available whenever an SSH connection can be established.
Filezilla can be downloaded for various OS to enable data transfer from your MinION Mk1C.
The following default options can be entered: Host – device ID or IP address (e.g. MC-111414) Username – minit Password – minit Port – 22
If it is your first time connecting, you will be asked to confirm the authenticity of the host. Check the box to Always trust this host, add this key to the cache and click OK to continue:
If the SFTP connection is successfully established, you will see the Mk1C file directory shown on the right-hand side of the UI. Please note that Filezilla defaults to the home directory (/home/minit
):
You can navigate to the /data directory by entering /data
into the Remote site field and clicking Enter:
16. Rebooting and shutting down
Either press the power button or navigate to the 'Device settings' in the Host settings and click either 'Shutdown' or 'Reboot'.
Wait for the dialogue box to open and click either 'Shut down' or 'Reboot'.
提示
The reboot will disconnect the MinION Mk1C from any device that is remotely connecting via Wi-Fi or SSH.
You will need to reconnect the MinION Mk1C to any device that was connected before the reboot using the procedure described in the Network settings and connection section of this document.
步骤结束
The powering down sequence:
You will initially see some scrolling code. After ~10 seconds, the screen will go blank and the lights at the side of the screen will power down. It is safe to remove the power cable from the MinION Mk1C at this point, if shutting down.
17. Updating the software via the UI
概述
MinKNOW是专供纳米孔测序设备使用的软件。有关该软件的更多详情,请参阅MinKNOW 技术文档。 有关如何使用MinKNOW软件的说明,请参考 MinKNOW 实验指南。
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: 请于本节查看软件须访问的IP地址及范围,据此设置防火墙。
如果设备通过远程连接或正在运行实验,将无法进行设备更新。
Oxford Nanopore Technologies设备的防火墙设置
Oxford Nanopore Technologies软件将需要访问列于此处的AWS IP范围:
http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html
以及以下两个IP地址:
178.79.175.200
96.126.99.215
请将宽带网线插入宽带网接口并连接至网络。
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 (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。
选择”Get update'“(获取更新)
在安装窗口点击“Install Update”(安装更新)以下载更新。
对话框中将显示版本变更信息。
等待软件更新;需要几分钟的时间。
在“Current version”(当前版本)查看软件版本。
18. (Advanced) Updating the software via SSH
Although MinION Mk1C software can be updated via the user interface, there are occasions where software updates have to be executed manually. This can also be done if the user prefers to update via the command line, since the UI does not give feedback during updates.
Always refer to the release notes for any version-specific commands that may be supplied.
Connect to the MinION Mk1C using SSH.
Open a terminal window, and update the list of available software using the following commands:
sudo apt clean
sudo apt update
sudo apt install ont-mk1c-release
These commands should complete successfully, without any errors or warnings. If you do see an error or warning message, check your MinION Mk1C is able to connect to the Internet. Run the following command to diagnose network connection problems:
sudo /opt/ont/mooneye/bin/ont-mooneye-check-network --verbose --diagnose
Once the commands have completed successfully without errors, please reboot the device using the command:
sudo reboot
To update all software (operating system and the MinKNOW software), enter the following command:
export DEBIAN_FRONTEND=noninteractive
sudo apt upgrade
可选操作
Alternatively, to update just the MinKNOW software, enter the following command:
export DEBIAN_FRONTEND=noninteractive
sudo apt install ont-mk1c-release
If you are prompted to continue, type ‘y’ and press Enter.
Restart your MinION Mk1C following the update for all processes to complete successfully (this will not be prompted for).
19. OS update/device recovery using microSD cards
From March 2022, we are delivering microSD cards to customers to update their OS so that they can use future versions of MinKNOW (22.03 onwards) with the latest features.
If you meet the requirements below, you can update your device before the microSD card arrives.
Note: there is no guarantee this process will work, as not all vendors of microSD cards have been tested internally at Oxford Nanopore.
重要
Requirements
- Blank 16 GB+ microSD SDXC card
- Computer with a microSD port/USB SD card adapter
- Balena Etcher for Windows or Mac (https://www.balena.io/etcher/)
Find out the current version of Ubuntu on your MinION Mk1C.
If your MinION Mk1C serial number is greater than MC-112454, your device shipped with Ubuntu 18.04 (Bionic).
Alternatively, on the user interface navigate to Settings and then Software. Click on the ‘I’ icon next to the MinKNOW version: you should see either ubuntu-bionic
or ubuntu-xenial
.
Download the correct SD card image.
If your Mk1C is currently on Ubuntu Xenial, download the following image (with MinKNOW 21.11 included): https://nanoporetech.box.com/s/bsuzar12lvjp15qawz421t9zghk59jw0
Please visit our Help website for information on how to update MinKNOW on the MinION Mk1C after upgrading to Bionic (https://help.nanoporetech.com).
The recovery SD card for devices on Bionic is available here (latest image has MinKNOW 22.12.5 preinstalled): https://nanoporetech.box.com/s/yftsu9fr9ukqilairdjx8xadtr1u5ygl
If your MinION Mk1C is already on Bionic, you will need to update to the more stable version if you are unable to update to MinKNOW 22.03.
Complete the factory restore.
Power down the Mk1C. Insert the microSD card and power on your Mk1C. After 30 seconds you should see a System Recovery pop-up screen:
Select Factory Reset to re-image the device with the software on the microSD card.
Follow the on-screen instructions to complete the OS update.
If no screen is observed, it is likely you have downloaded the wrong microSD card OS image, so check your OS version again. Alternatively, your device needs to perform some pre-requisite actions, see the Troubleshooting section ("If your Mk1C does not boot from microSD card") for more information. If you have issues, contact support@nanoporetech.com.
Update to the latest version of MinKNOW for the MinION Mk1C, which supports the latest chemistry, bug fixes and performance enhancements.
Please visit our Oxford Nanopore FAQ and Help Centre if you are having difficulties updating MinKNOW on the MinION Mk1C.
Completing your OS update
All sequencing data stored in the /data folder is retained after the OS upgrade. However, please note that you may need to configure some device settings after the update.
If you use a mounted external storage to the Mk1C, you will need to remount the external storage. Follow the instructions in the Mount network drive section in this user manual.
If you cannot connect to the internet (you may see the error "Unknown connection 'static'"), follow the instructions in the (Advanced) Network configuration - static vs dynamic IP section in this user manual.
20. Updating the signing key to update MinKNOW (IMPORTANT)
重要
The MinION Mk1C device has a signing key installed, which is a piece of software used to authenticate MinKNOW updates. On the 16th June 2022 the current signing key has expired, which means you will not be able to update the Mk1C software unless you are either on MinKNOW version 22.05.8, or if you add a new signing key to your device. Below are the instructions for adding the new key to your trusted list via the command line.
To add recognition of the signing key to a MinION Mk1C by command line without also updating the software, connect to the device via SSH.
For details on how to connect via Secure Shell for various operating systems, see the (Advanced) Connecting by the command-line section of this user manual.
Once connected, run the command:
wget -O- https://cdn.oxfordnanoportal.com/apt/ont-repo.pub.2022 | sudo apt-key add -
This command can also be used for MinKNOW for MinION Mk1B Linux installations.
Confirm that you can update MinKNOW via the MinION Mk1C UI after following the steps above.
If you are unable to update MinKNOW or check for updates, repeat the steps above again. If the issue is not resolved, contact Customer Support at support@nanoporetech.com.
21. Export logs
Navigate to the Help section of the Host settings.
In the 'Export Logs' panel, select 'Export'.
When the logs are successfully exported, the user will be notified of where they are located.
The logs will be downloaded as a TGZ file in the logs directory.
22. If your Mk1C does not boot from microSD card
Some Mk1C devices with serial numbers MC-110999 or lower may not be able to recognise the microSD card with OS updates. Follow the steps below to change your device so that boot from SD card works.
Copy the file from the link below to your Mk1C.
https://nanoporetech.box.com/s/2vsqb3d6n5mbbtyrbpu1kyai2p3ohknj
Use the following command at your PC/Mac command line/terminal, respectively, to copy the attached file to your Mk1C:
scp ./u-boot.img minit@<your-device>:/home/minit
Note: if you encounter issues, make sure that your PC/Mac is connected via Ethernet to the same network as your MinION Mk1C.
Connect to your device using SSH:
ssh minit@<your-device>
Overwrite the kernel and kernel_b partitions with the image:
sudo dd if=~/u-boot.img of=/dev/disk/by-partlabel/kernel
then run:
sudo dd if=~/u-boot.img of=/dev/disk/by-partlabel/kernel_b
Reboot the device:
sudo reboot now
Leave the device to boot to completion, and do not turn it off mid-reboot.