Troubleshooting Waste Bottle is Full notification on the MiSeq

A run may pause and give a "Waste bottle is full" error. This occurs when the waste bottle is full, the waste sensor is dirty, or if there is a communication issue on the instrument.

Troubleshooting steps:

Full Waste bottle:

1. Empty the waste bottle.

2. Replace the waste bottle in the instrument.

3. Resume the run.

Dirty Waste Sensor:

1. Clean the waste bottle sensor with ethanol and a lint-free wipe. Note: The sensor is the black bulb that can be seen at the top of the sipper into the waste bottle. To see it clearly, lift the sipper from the waste bottle and remove the bottle to view the sensor.

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2. Wipe down the sensor and resume the run.

Communication Error:

If the error persists after emptying the waste bottle and cleaning the waste sensor, the root cause may be a communication error.

1. Power cycle the instrument, following the guidance in How to Power Cycle the MiSeq.

2. If the error persists after the power cycle, contact Illumina Technical Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #1429), contact Illumina Technical Support [e-mail].