PromethION 2 Solo user manual
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PromethION: Protocol
PromethION 2 Solo user manual V P2S_9172_v1_revR_14Oct2022
This guide will help you install, check and configure your PromethION 2 Solo.
Our PromethION 2 Solo 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 (with GridION)
- 4. Installing and powering on the device (with workstation/laptop)
- 5. Network settings and connection
- 6. Hardware check
Pre-sequencing checks and sequencing run
After completing a sequencing run
Updating the software
Troubleshooting
Overview
This guide will help you install, check and configure your PromethION 2 Solo.
Our PromethION 2 Solo FAQs are located here.
For Research Use Only.
1. Device information
The PromethION 2 Solo
The PromethION 2 Solo is a small benchtop device designed to run up to two flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or individually. The PromethION 2 Solo plugs into a GridION Mk1 or user compute for real-time data streaming and analysis.
Technical specification
Component | Specification |
---|---|
Size and weight | 152 x 110 x 87 mm, 1.5 kg |
Mains supply voltage | 100-240 VAC (50/60 Hz) |
Peak power consumption | 60 W |
Installation ports | 1x USB Type-C (3.0 at 5 Gps) 1x 12 VDC barrel power connector |
Compute specification | N/A |
Environmental conditions | Designed to sequence at +18ºC to +25ºC* |
*Functional range of electronics +5ºC to +40ºC
FAQs
Our PromethION 2 Solo FAQs are located here.
2. What's in the box
For more information about setting up your P2 Solo, refer to our Nanopore Learning video:
P2 Solo: First-time setup and hardware check
Our P2 Solo FAQs are located here.
PromethION 2 Solo packaging
What's in the box - PromethION 2 Solo
- PromethION 2 Solo device
- 2x Configuration Test Cells (CTC)
- 60 W power adapter
- USB Type-C cable
LED lights There are two sets of LED lights on the device, five for each flow cell position. They display the following patterns:
- All five LEDs are solid white: Device ready, no flow cells inserted.
- All five LEDs are solid blue: Flow cells inserted.
- All five LEDs scroll green from left to right: Data acquisition in progress (this includes the hardware check and flow cell check).
- All five LEDs flash yellow: Temperature warning. If you observe this, check that your flow cell/CTC has a heat pad (black pad on the underside of the flow cell), and that the device is within ambient temperature range (+18°C to +23°C) with 30 cm clearance all around the instrument and away from direct sunlight. Then re-insert your flow cell and perform a flow cell check to check the temperature control. Contact Support if you continue to see this pattern.
- All five LEDs flash red: MinKNOW script error. Flashing alert that indicates that the script running has encountered and error and stopped. Contact Support if you continue to see this pattern.
- All five LEDs flash blue: Data transfer too slow between P2 solo and attached computer. If you see this, ensure that you are using the included USB-C cable (‘labelled P2’) and that you have inserted your cable into a super speed compatible port (USB 3.0 or greater). Additionally, ensure that no unnecessary USB devices are plugged into your computer.
- All five LEDs are solid green: Script ended successfully.
3. Installing and powering on the device (with GridION)
For more information about setting up your P2 Solo, refer to our Nanopore Learning video:
P2 Solo: First-time setup and hardware check
Our P2 Solo FAQs are located here.
Recommended laboratory location
- Place the P2 Solo and GridION devices on a strong, clean laboratory bench
- Ensure power 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 lid closed prior to sequencing beginning
- Allow 30 cm clearance to rear and sides of the device
- Do not cover any ventilation grills
- WARNING - The rear of the device will heat up during operation
Check that your GridION™ serial number is greater than GXB002xxx.
The serial number can be found on the sticker on the back of the GridION. Ensure your GridION is powered on and check your GridION is updated to the latest MinKNOW™ version that is compatible with the P2 Solo (see the Software Downloads page on the Nanopore Community). Please read the IT requirements document for full details. Launch MinKNOW by clicking on the Nanopore Wheel icon on your desktop.
Unpack the PromethION 2 Solo device and place it on the bench where it is to be run.
Download the PromethION 2 Solo software.
For Windows and Mac computers, navigate to the Software Downloads page of the Nanopore Community. For Linux, see the instructions in this section for how to install the software via the Terminal.
Ensure there are no flow cells or CTCs inserted into the P2 Solo.
Plug the P2 Solo AC power adapter into a wall socket and the plug the power cable into the P2 Solo.
Plug one end of the USB Type-C to Type-C cable into the USB Type-C port on the GridION (see diagram) and the other end into P2 Solo USB Type-C port. Make sure you can feel and hear the USB-C connection click in on the P2 Solo and GridION. You may need to pull down the metal tabs on either side of the USB-C connector on the GridION to fully insert. Toggle the power switch to turn on the device. Wait up to 60 seconds for the devices to be initialised in MinKNOW. The front LEDs will light up once complete.
For more information about how to correctly connect your PromethION 2 Solo to the GridION via the USB Type-C cable, refer to this FAQ: I'm unable to connect my P2 Solo to MinKNOW
We recommend users to log into the MinKNOW software using their Community credentials.
To log in, you must be connected to the internet.
From here, you can also change the language in the user interface in the bottom right corner.
You will be prompted to enter your email address and Nanopore password:
If you experience login issues, please visit the Community Support channel (https://community.nanoporetech.com/support) and use Continue as guest for temporary use.
Select the sequencing device in the Connection Manager to connect to the computer.
You will be taken to the sequencing overview page.
4. Installing and powering on the device (with workstation/laptop)
For more information about setting up your P2 Solo, refer to our Nanopore Learning video:
P2 Solo: First-time setup and hardware check
Our P2 Solo FAQs are located here.
Recommended laboratory location
- Place the P2 Solo device on a clean laboratory bench
- Ensure power 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 lid closed prior to sequencing beginning
- Allow 30 cm clearance to rear and sides of the device
- Do not cover any ventilation grills
- WARNING - The rear of the device will heat up during operation
Make sure the compute meets the IT requirements set out in the P2 Solo IT Requirements document.
Downloading and installing MinKNOW
The MinKNOW software for the PromethION 2 Solo is available to download from the Software Downloads page on the Community.
All Oxford Nanopore devices use MinKNOW™ as the primary software. The MinKNOW software carries out several core tasks: data acquisition, real-time analysis and feedback, basecalling, data streaming, controlling the device, and ensuring that the platform chemistry is performing correctly to run the samples. MinKNOW takes the raw data and converts it into reads by recognition of the distinctive change in current that occurs when a DNA strand enters and leaves the pore. MinKNOW then basecalls the reads, and writes out the data into POD5 or FASTQ files.
Please follow the MinKNOW protocol for information on how to install the software.
Unpack the PromethION 2 Solo device and place it on the bench where it is to be run.
Download the PromethION 2 Solo software.
For Windows and Mac computers, navigate to the Software Downloads page of the Nanopore Community. For Linux, see the instructions in this section for how to install the software via the Terminal.
Ensure there are no flow cells or CTCs inserted into the P2 Solo.
Plug the P2 Solo AC power adapter into a wall socket and the plug the power cable into the P2 Solo.
Plug one end of the USB Type-C to Type-C cable into the USB Type-C port on the laptop and the other end into P2 Solo USB Type-C port. Make sure you can feel and hear the USB-C connection click in on the P2 Solo and your workstation. Toggle the power switch to turn on the device. Wait up to 60 seconds for the devices to be initialised in MinKNOW. The front LEDs will light up once complete.
Double-click the MinKNOW icon located on the desktop to open the MinKNOW UI.
We recommend users to log into the MinKNOW software using their Community credentials.
To log in, you must be connected to the internet.
From here, you can also change the language in the user interface in the bottom right corner.
You will be prompted to enter your email address and Nanopore password:
If you experience login issues, please visit the Community Support channel (https://community.nanoporetech.com/support) and use Continue as guest for temporary use.
Select the sequencing devices in the Connection Manager to connect to the computer.
You will be taken to the sequencing overview page.
5. Network settings and connection
CAUTION
Changing your network configuration
WARNING! Changing the network parameters on your PromethION 2 Solo may leave your device non-functional.
The network parameters for your PromethION 2 Solo must be suited to your local network.
If you are uncertain about which parameters to use to configure your PromethION 2 Solo network settings, please contact your IT department.
Networking requirements
The PromethION 2 Solo has no networking functionality. If using your own computer, please ensure it has internet connection (wired or wireless). The GridION uses a uses a 1x1 Gbps Copper interface for connecting to your local infrastructure. This has a single port with the IP address configured to DHCP by default (however static IPs are configurable). 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 2 Solo 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.
Configuring your network
For instructions on configuring your network, see the Network settings and connection section of the GridION user manual.
Check your IP address
To validate that the IP address has been set correctly using a static or DHCP address, you can use the command: ifconfig
The returned information will contain the IP address (highlighted in bold) for the Ethernet link, as below:
prom@PRO00001:~$ ifconfig enp0s31f6 Link encap:Ethernet HWaddr 70:85:c2:4b:30:f5
inet addr:
10.160.24.40
Bcast:10.160.24.255 Mask:255.255.255.0
6. Hardware check
For more information about setting up your P2 Solo, refer to our Nanopore Learning video:
P2 Solo: First-time setup and hardware check
Our P2 Solo FAQs are located here.
IMPORTANT
Hardware check
A hardware check must be performed on all new devices or when software has been upgraded.
Load all the CTCs that came with the device into the flow cell positions.
The MinKNOW UI will recognise the CTCs as they are loaded. If your software version is greater than 22.08, the LEDs adjacent to the flow cell will turn white.
Close the device lid once the CTCs are loaded.
IMPORTANT
Correct insertion of PromethION CTCs
Place the CTC flat on the metal plate.
Firmly slide the CTC into the docking port until the gold pins or green board cannot be seen and you hear a click.
Navigate to the start homepage and click 'Hardware check'.
Select all the CTCs in the GUI and select 'Start' for the check to begin.
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the checks.
END OF STEP
The hardware check will complete after approximately one minute.
Hardware check pass is indicated by a green check icon.
A fail is indicated by an orange check icon.
If the hardware check fails, remove and reinsert the CTC, and run a hardware check again. If the check fails for a second time, please contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.
IMPORTANT
Do not leave the CTCs in the flow cell positions when the device is not in use.
Do not leave the CTCs in the PromethION flow cell positions once the device is powered down, and do not insert them into the device until the device is powered on and you are about to begin a Hardware check.
Store the CTCs in dry conditions at room temperature.
7. Flow cell check
Consumables
- PromethION Flow Cell
Equipment
- PromethION 2 Solo
Flow cell check
We strongly recommend performing a flow cell check before loading a DNA or RNA library to assess the number of pores available.
Oxford Nanopore Technologies will replace any flow cell that falls below the warranty number of active pores within 12 weeks of purchase, provided that you report the results within two days of performing the flow cell check and you have followed the storage recommendations.
Flow cell | Minimum number of active pores covered by warranty |
---|---|
Flongle Flow Cell (FLO-FLG001) | 50 |
MinION/GridION Flow Cell | 800 |
PromethION Flow Cell | 5000 |
IMPORTANT
After taking flow cells out of the fridge, wait 20 minutes before inserting the flow cell into the PromethION for the flow cell to come to room temperature. Condensation can form on the flow cell in humid environments. Inspect the gold connector pins on the top and underside of the flow cell for condensation and wipe off with a lint-free wipe if any is observed. Ensure the heat pad (black pad) is present on the underside of the flow cell.
Load the flow cells to be run into the docking ports of the PromethION.
IMPORTANT
Correct insertion of PromethION flow cells
Firmly slide the two PromethION Flow Cells into the device, taking care to ensure the dark grey heat pad on the underside of the flow cell is not torn or deformed. Press the flow cell firmly into the loader until a click is heard.
Navigate to the start homepage and click 'Flow cell check'.
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.
Flow cell health indicators
The quality of the flow cell will be shown as one of the three outcomes:
Yellow exclamation mark (Flongle flow cell): The number of sequencing pores is below warranty. Take the flow cell out of the device, re-insert it and run a flow cell check again. If the flow cell is still below warranty, contact support@nanoporetech.com
Green tick (MinION flow cell): The number of sequencing pores is above warranty.
Question mark (PromethION flow cell): A flow cell check has not been run on the flow cell during this MinKNOW session.
Note: The indicator of quality will only remain visible during a MinKNOW session. Once the MinKNOW session has ended, the status of the flow cell will be erased.
8. Sequencing and monitoring the experiment
For instructions on how to set up a sequencing experiment and how to monitor the progress of the experiment, refer to the MinKNOW protocol in the Nanopore Community.
9. Data management
Data transfer and long-term storage - all devices (GridION, Linux/Mac/Windows workstations)
It is essential that data is streamed from the device in real-time to prevent runs from terminating due to lack of storage space (this is common for high specification laptops). For this, a customer site must ensure that connectivity to the local infrastructure/external SSD is of sufficient bandwidth to prevent data backing up. We recommend using a remote server or network-attached storage (NAS). These typically offer a choice of NFS, SMB, or CIFS shares. If the workstation attached to the P2 Solo uses a Linux-based operating system, we recommend using NFS mounts due to the supported Linux user and group permissions. For Windows workstations, use SMB and for Mac OS use either SMB or NFS. To stream data to storage in real-time, SSD is required due to its high write speed compared to HDD. After initial writing to networked SSD drives, data can be moved to storage with a slower write speed for long-term storage.
The form and volume of data to be stored will depend on your requirements and whether you wish to basecall your sequencing data in the future when more advanced basecalling algorithms are available:
- Storing .POD5 files with raw read data in will permit re-basecalling of data when new algorithms are released by Oxford Nanopore Technologies. In such cases, new releases of basecallers have enabled significant improvements in basecalling accuracy of existing datasets through re-basecalling. Further, selected Oxford Nanopore and third-party tools use the raw signal information contained within the POD5 to extract additional information from the raw signal, e.g. calling modified bases, reference-guided SNP calling, or polishing of data.
- Retaining only FASTQ files will allow use of standard downstream analysis tools using the DNA/RNA sequence, but no further sequence data can be generated when improvements in basecalling become available.
Oxford Nanopore is unable to provide exact recommendations for storage, as these will be site-specific.
For more information about offloading data, refer to our Nanopore Learning video:
GridION: Data offload to remote storage
Our device FAQs are located here.
GridION data transfer
If you are using a P2 Solo in combination with a GridION and require additional SSD storage, ensure you are using the correct USB port/Ethernet on the rear of the device. Do NOT use either the USB port with a white, rectangular centre or those at the front of the device (if your GridION has front-facing USB ports).
Instead, use the blue USB Type-A ports on the rear of the GridION (see the image below for reference). Alternatively if using Ethernet, ensure that you are using a cable capable of at least 1 Gbps (CAT5e) and the minimum length for reduced latency.
From MinKNOW version 21.02 onwards, we have added new functionality to enable smoother data transfer off the box during a sequencing run. The instructions below are an example method to mount an external NFS and transfer data. Please consult your local IT department before implementing any code to ensure it is compatible with the local infrastructure and the correct permissions are in place.
Run the following command:
sudo sed -i 's/prom/grid/g' /lib/systemd/system/ont-platform-data-offload.service
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:
grid@GXB02000:~$ sudo su -
grid@GXB02000:~$ apt install autofs
grid@GXB02000:~$ echo -en “+auto.master\n/nfs /etc/auto.ont\n” > /etc/auto.master
grid@GXB02000:~$ echo -en "NETWORKSTORAGE -nfsvers=3,rw,bg,async,actimeo=300,soft,intr,noatime,tcp,nolock IPADDRESS:/PATH/TO/SHARE" > /etc/auto.ont
grid@GXB02000:~$ ln -s /nfs/NETWORKSTORAGE /media/NETWORKSTORAGE
grid@GXB02000:~$ ls -al /media/NETWORKSTORAGE/*
Install the latest version of the MinKNOW software:
grid@GXB02000:~$ sudo apt update
grid@GXB02000:~$ sudo apt install ont-gridion-release
Make a source directory that your experiments will be saved to in /data/ , for example:
grid@GXB02000:~$ mkdir /data/data-offload
Make a destination directory on your networked storage. This also tests that the ‘grid’ user can write to the networked storage:
grid@GXB02000:~$ 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.
grid@GXB02000:~$ sudo vi /etc/systemd/ont-platform-data-offload.conf
A log of the actions taken by the script will be written to /data/data-offload.log
Start your sequencing in the MinKNOW UI, setting the output location to SOURCE_DIR set above.
We currently recommend manually controlling the service, as the data offload activity could affect active runs.
To start the offload service as root:
sudo systemctl start ont-platform-data-offload
To stop the offload service as root:
sudo systemctl stop ont-platform-data-offload
To check that the service is running, run the following command:
sudo systemctl status ont-platform-data-offload
IMPORTANT
Data transfer speeds will depend on local network infrastructure. Oxford Nanopore recommends a 10 Gbps (PromethION) connection is used to maximise transfer speeds.
IMPORTANT
Initially, write the data directly to the internal SSD drives. Writing to a networked drive is not currently supported.
10. Shutting down
Stop your sequencing run through the MinKNOW UI and wait for the sequencing to terminate.
Disconnect the USB Type-C cable from the P2 Solo.
Toggle the power switch on the rear of the device to the "Off" position. The internal (front/rear-facing) green LED should turn off.
11. Updating the software via the UI
IMPORTANT
Updating the software
Oxford Nanopore Technologies will post a release note when new software or updates go out via the Nanopore Community.
We urge you to update as soon as reasonably possible after the release has been made available.
Please note, you will not be able to update your device if connected remotely or if a sequencing run is in progress.
Open the MinKNOW UI via the desktop icon and the auto-updater will automatically check for updates when connected to the device.
A dialogue box will open when a new update is available.
Select Get Update to update the device software automatically.
Updates may be skipped. However, we recommend to update the device as soon as updates are available. Some updates will be mandatory to use the device and are unable to be skipped.
Note: For MinION Mk1B, clicking Get Update will open the Software Downloads page on the connected computer for you to download the updated MinION software.
You can also update the device from the Software page of the Host settings.
Navigate to Software in the Host settings and click Get Update to open the installer window.
An update button will only appear when a new version of the software is available to download.
Note: For MinION Mk1B devices, clicking Get Update will open the Software Downloads page on the connected computer for you to select and download the updated MinION software.
Click Install Update in the installer window to download the new update.
A change log for the update is available in this dialogue box.
Wait for the software to update; this may take several minutes.
The installer window will notify you when the update is complete.
After the update has completed successfully, complete a full power cycle to reboot the device.
IMPORTANT
Re-installing MinKNOW
In some cases (e.g. if there is a problem with the version of MinKNOW that you are using), it may be necessary to re-install the software. To do this, first do a full uninstall of the current version by following the instructions in the Support article: How to uninstall MinION Software for Mk1B and P2 Solo
12. (Advanced) Updating the software via the Terminal
To update MinKNOW from 23.04.6 onwards:
Please refer to the GridION user manual or MinKNOW protocol update sections.
If you are currently on MinKNOW 22.07.9 or earlier for P2 Solo, use the following commands to update to the latest version of MinKNOW:
For GridION:
sudo rm /etc/apt/sources.list.d/p2-testing.list /etc/apt/preferences.d/p2-testing
sudo apt update
sudo apt install ont-gridion-release
sudo poweroff
For standalone Linux computers For the new automatic GPU release (recommended):
sudo rm /etc/apt/sources.list.d/p2-testing.list /etc/apt/preferences.d/p2-testing
sudo apt update
sudo apt install ont-standalone-minknow-gpu-release
sudo poweroff
For the release without the automatic GPU configuration:
sudo rm /etc/apt/sources.list.d/p2-testing.list /etc/apt/preferences.d/p2-testing
sudo apt update
sudo apt install ont-standalone-minknow-release
sudo poweroff
13. Troubleshooting
FAQs
Our PromethION 2 Solo FAQs are located here.
To export logs:
For the PromethION 24/48, PromethION 2i, GridION and PromethION 2 Solo connected to a GridION:
- Click Export in the Export Logs section.
When you have successfully exported the logs, you will be notified of where they are located below the button. The logs will be downloaded as a TGZ file in the logs directory.
You can change the location of the logs by using the file manager, where you can easily retrieve them without needing SSH:
- Click on the file next to Logs exported to: in the Export Logs panel. This will open where the logs are located in the File Manager of MinKNOW.
- Use the control panel in the lower right corner of the File Manager to move the log files.
If the PromethION 2 Solo is connected to a stand-alone computer
Log files for each sequencing experiment can be found in:
Windows C:\data\logs
Mac OS X /private/var/log/MinKNOW
Linux /var/log/minknow
To remove logs and temporary data:
In the "Help" page, click Clean up in the Clean Up Files section and confirm in the in the pop-up.
Note: Run data will not be deleted. Logs and temporary data will be removed.
To repair device issues:
Click Run repair in the troubleshooting section of the Help page and confirm in the pop-up. MinKNOW will attempt to repair the following issues:
- Ensure required directories under "/data" exist and have the correct ownership and permissions
- Ensure required files under "/data" have the correct ownership and permissions
- Ensure the GPU is working at maximum performance
- Ensure that Bluetooth is disabled