Troubleshooting spent reagent cartridge is full on the NextSeq 500/550

Background The NextSeq 500/550 instruments divert used reagents to the spent reagents cartridge for storage until the user empties it after sequencing runs complete. When the spent reagents cartridge sensor detects that the cartridge is full, it will notify the user and the cartridge must be emptied prior to resuming normal instrument operation. Importantly, there are two different sensors for the spent reagent cartridge on the NextSeq 500/550. This "Spent Reagent Cartridge is full..." error indicates the waste container is full. The error can also be related to a communication issue, a dirty sensor, a broken sensor, or a broken sensor flag for the container. If this occurs during a run, this will pause the run until the waste container has been emptied. If receiving an “unable to detect spent reagent cartridge” related error, please see article: Troubleshooting spent reagent cartridge not detected on NextSeq 500/550.

Troubleshooting Actions

1. Empty the waste container and attempt to continue with the run.

2. If the error persists, clean the waste container sensor with lens paper or a Kim Wipe. The sensor is a small black circle located at the back of the instrument, above the waste container, as shown in the image below.

1. If the error persists after cleaning the sensor, check the waste cartridge itself.

   1. In some instances, the waste cartridge mechanism gets clogged up and does not click open when inserted.

   2. This can lead to waste pooling in the top part of the waste cartridge as shown below.

   3. If observed, empty the pooled spent reagents.

   4. Once the pooled liquid is cleared, add 70% ethanol solution and manually rotate the lever that controls the port opening several time, confirm if the port opens and the ethanol then drains.

   5. Discard the ethanol solution according to location Environmental Health & Safety (EH&S) guidelines.

1. If cleaning does not help and there is still pooled liquid visible:

   1. If another NextSeq 500/550 spent reagent container is available, swap out the container to attempt to resolve the error and allow the run to complete, OR

   2. If a second spent reagents container is not available, contact Illumina Technical Support for additional assistance.

2. After the run, power cycle the instrument to reset all communications.

   1. For further information, search for Knowledge Base articleHow to Perform a NextSeq 500/550 Power Cycle.

If the error message continues to appear, an Illumina Field Service Engineer (FSE) may be required to clean the waste sensor, replace the waste sensor flag, or replace the waste cartridge. In this case, contact Illumina Technical Support for additional assistance.