Troubleshooting

• Troubleshooting Flow Check Failure
• Troubleshooting Run Problems
• Recovering a Run

Troubleshooting Flow Check Failure

Note

The software allows three attempts to successfully pass the flow check before allowing you to bypass the flow check. Bypassing the flow check can result in some lanes not clustering successfully.

First Attempt

• If all eight lanes failed, the flow cell is probably loaded improperly. Remove the manifold and confirm that the flow cell holes are facing upward, and the flow cell orientation is correct for the flow cell you are using.
• If only some lanes failed, the flow cell might not be properly seated. Remove the manifold, reseat the flow cell, and then reinstall the manifold.

Second Attempt

• If all eight lanes failed again, you probably have a faulty manifold. Remove the manifold and replace it with a new manifold.
• If different lanes failed, you do not have a faulty manifold. Visually inspect the volumes of HT1 in row 1 to make sure that the tubes contain equal volumes.

Third Attempt

After replacing the manifold—If the flow check failed a third time after replacing the manifold, you might have a clog in the hardware. Do the following to correct the problem:

1. Visually inspect the volumes of HT1 in row 1 to make sure the tubes contain equal volumes. A hardware clog is indicated by higher volumes in the tubes that correspond to the lanes that repeatedly failed the flow check. This further confirms a hardware clog.
2. Unload the run components and perform a maintenance wash.
3. After the wash, turn off the instrument using the power switch. After a few seconds, turn the power switch on, and then press the start button to restart the software. You have to power cycle the instrument in this way to reset the allowable number of pre-run check attempts.
4. Follow the software prompts to reload run components and set up your run.

After using the same manifold—If the flow check failed a third time and you have confirmed that you do not have a faulty manifold, you can now safely use the option to bypass the flow check. After the run, check reagent delivery from all tubes.

Troubleshooting Run Problems

Problem	Possible Cause	Action
Temperature out of range	Potential Peltier or Peltier control board failure.	EmailIlluminaTechnical Support to schedule service.
Coolant is flowing and coolant level is low	Coolant has slowly evaporated to a low level.	AddIllumina-supplied coolant (part # 1003709) to the coolant reservoir.
Coolant is not flowing and coolant level is low	Coolant level may be too low to generate flow.	AddIllumina-supplied coolant (part # 1003709) to the coolant reservoir.
Coolant is not flowing and coolant level is not low	Potential coolant pump failure.	EmailIlluminaTechnical Support to schedule service.
System is in a locked state	Potential software error.	EmailIlluminaTechnical Support to schedule service.

Recovering a Run

1. Restart the instrument. Upon restart, the following message appears on the start screen: “A recoverable run exists. Select Start to recover the run.”
2. TouchStart. The cBot Recover Run dialog box appears.
3. TouchOK. The software opens to the pre-run check screen. Upon successful completion of the pre-run check, the run restarts from the point where it stopped.
4. Alternatively, touchCancelto completely cancel the partial run.