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.

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

Our PromethION 24/48 FAQs are located here

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.

1. PromethION 24 Sequencing Unit
2. PromethION 24 Data Acquisition Unit
3. 3x Country-specific C13 cables
4. 24x Configuration Test Cells (CTCs)
5. 2x PCIe cables
6. 2x 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

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

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

• 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

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.

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.

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)

• If you need to update the hostname of the device, run the following command and replace the <new_hostname> portion with your desired hostname (omitting the angle bracket characters <>):

sudo -S hostnamectl set-hostname <new_hostname>

• Power cycle the device by shutting down with the following command, then press the physical power button to turn the device back on:

sudo shutdown -h now

First find the correct timezone name by typing the command:

sudo timedatectl list-timezones

Then change the timezone using the following commands:

sudo su -
Timezone="Europe/London"
timedatectl set-timezone $Timezone
systemctl restart systemd-timesyncd

Note: this requires NTP/port 123 access if using an external internet time server.

Enter the following commands:

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

Some error messages may appear, however these can be ignored. You can check that the process has worked by typing:

timedatectl status

Note: it may take several minutes to sync with the NTP server.

A loading bar appears under the flow cell during the checks.

This example is a Flongle CTC (loading bar highlighted in red).

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

A loading bar appears under the flow cell during the checks.

This example is a Flongle CTC (loading bar highlighted in red).

The quality of the flow cell will be shown as one of the three outcomes:

1. 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

2. Green tick (MinION flow cell): The number of sequencing pores is above warranty.

3. 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.

To run a sequencing experiment, you will need your DNA or RNA sample purified and a sequencing library prepared. For more information about sample preparation, refer to the Prepare section of our Documentation.

You can access the MinKNOW protocol by following this link.

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.

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.

Oxford Nanopore Technologies will post a release note in the Nanopore Community when new software or updates to the device go out.

We urge users to update as soon as reasonably possible after the release has been made available.

Keep the device up-to-date with Linux security updates, in line with advice from your local IT department.

Note: It is specifically required that you make outbound-only access to the internet over port 443 to enable updates through your network Firewall.

The below instructions can be used to create a bootable USB drive that can be used to rebuild the OS on your device.

These instructions are for users who did not receive a USB drive with the ISO image. If you have received a USB drive, proceed to the next step: "How to boot from USB".

https://nanoporetech.box.com/s/i7c2itn6sro0mhumi3lxefpp0yddh3y6

Appropriate software for burning the ISO image is:

• Rufus on Windows

Note: The alternate ISO burning tool balenaEtcher does not work for our ISO image. You will need access to a computer running Windows and may need Administrator rights to install the Rufus software.

When burning the ISO image, use the below settings (it must use an EFI/GPT boot):

• Partition scheme: GPT
• Target system: UEFI

The USB drive should have the below specification:

• Must be 32 GB or larger
• USB 3.0 recommended
• UEFI boot option must be used

Note: We recommend flashing two USB drives with a different vendor as a backup. Common USB drives can fail to reimage devices with no obvious root cause.

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.

To find our most common FAQs, please see the support section for MinKNOW here.

In most cases where troubleshooting is required, we recommend exporting your logs and sending them to Technical Services.

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/Mk1D 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.

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

• macOS: /private/var/log/MinKNOW

• Linux: /var/log/minknow

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.

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