Troubleshooting SIPDOWN Errors on the MiSeq

Background

The MiSeq Control Software (MCS) shows a SIPDOWN error if the reagent sippers are not functioning or cannot be lowered to pierce the foil on the reagent cartridge at the start of a Sequencing Run.

• This can be caused by physical obstruction (if the reagent cartridge is not fully inserted or is damaged), a hardware problem with the sipper assembly, or a communication error.

• When present, this error occurs before the run starts when the sippers first lower, typically shortly after selecting the Start button.

• This error can present in older versions of MCS as an Object Reference error.

  

Troubleshooting Actions

If a SIPDOWN error is observed, see the following Troubleshooting Actions or review the Troubleshooting Sipdown Errors on the MiSeq video.

1. Remove and inspect the reagent cartridge:

2. • Following a SIPDOWN error, the sippers should be in the raised position. Open the reagent compartment door and verify the reagent cartridge is fully inserted all the way to the back of the instrument chiller compartment.

   • Remove the reagent cartridge and verify no damage to the exterior of the cartridge.

   • Confirm if reagent foils are pierced.

   • Confirm the reagents are fully thawed. See Knowledge Article Reagent Stability and Thawing Guidelines for MiSeq Sequencing Kits for details.

   • Store the reagent cartridge, PR2 buffer, and the current flow cell in the buffer in the fridge (4°C).

3. Power cycle instrument to reset communications.

   1. See Knowledge Article How to Power Cycle the MiSeq for details.

4. After MCS initialization, select Wash and then select Post-Run Wash.

5. Perform the post-run wash with a previously used flow cell, the MiSeq wash cartridge and wash bottle.

   • See Knowledge Article Wash best practices for the MiSeq for details.

   • Often, the run can be re-started with the same consumables. However, if those consumables are used to complete the post-run wash prior to reloading, the run will fail.

   • The post-run wash MUST be completed with previously used consumables and/or wash specific consumables.

6. If there is no indication of damage to the reagent cartridge and the post-run wash completes successfully, restart the run with the same consumables.

   1. If the reagent cartridge looks damaged, contact Illumina Technical Support and provide the reagent serial number (SN), cartridge lot number, and cartridge expiration date.

For any feedback or questions regarding this article (Illumina Knowledge Article #1456), contact Illumina Technical Support [e-mail].