Troubleshooting FPGA Timeout Errors on the MiSeq

Field-Programmable Gate Array (FPGA) is the circuit board that translates the commands from the instrument control software into action by an instrument component.

In simpler terms, the FPGA mediates communications between the subsystems of the MiSeq

If the FPGA loses communication with a subsystem, the MiSeq Control Software (MCS) will show a software message mentioning the FPGA timeout.

• For example, if there is a command from the control software to aspirate a certain volume of reagent, the FPGA board translates that command into actual aspiration.

• Once the aspiration occurs, the board receives feedback that the component was responsive, which enables the next command to proceed.

These communication issues can be transient or can point to problems with instrument hardware.

Example of Error Messages:

• The FPGA reported an error while executing the command "YHOME"; error message: "ERROR: Home sensor never tripped error."

• WRN: FPGA: FPGA: Expected no response from FPGA: command = EXLED1ON; Response =

• ERR: Timeout of 60.000 seconds exceeded while waiting for FPGA command

• WRN: Y Motor: Y Motor: UpdatePositionAndLimits failed: FPGA: Unable to write 'YRDPOS\n': Exception = 'The write timed out.'

• WRN: Y Motor: Y Motor: MoveAbsScaled failed: Y Motor: UpdatePositionAndLimits failed: FPGA: Unable to write 'YRDPOS\n': Exception = 'The write timed out.'

  

  

Troubleshooting steps:

1. E-mail Illumina Technical Support at [e-mail] with the information from the section below titled Information to Provide to Tech Support.

2. Complete the post-run wash.

3. Power cycle the MiSeq (note that if a run is in progress, it will not be able to be resumed).

   1. Close MiSeq Control Software shut down Windows, and turn off the instrument using the power switch on the back panel.

   2. Leave the instrument off for 5 minutes to allow all parts to completely power down.

   3. Turn on the instrument using the power switch on the back panel. The control software will initialize on its own once Windows fully loads.

4. If the control software fails to initialize, contact Illumina Technical Support.

5. If the instrument initializes without error, proceed with the next run.

Information to provide to Tech Support:

1. System uptime: This can be seen from Task Manager - Performance tab.

2. Software uptime: Available on the 'MiSeq Control Software' About screen (the time restarts when software is launched).

3. MiSeq Control Software (MCS) version: Available on the 'MiSeq Control Software' About screen.

4. FPGA version: Available on the 'MiSeq Control Software' About screen.

5. MiSeq Control Software logs: D:\Illumina\MiSeq Control Software\Logs

6. Run cycle logs, if applicable: D:\Illumina\MiSeqAnalysis<run folder>\Logs folder

• Also available in D:\Illumina\MiSeqTemp<run folder>\Logs folder

7. Instrument usage rate: On average, how many runs were performed in the last month?

8. Run type, if applicable, when the error happened: Chemistry version and length of the run.

• example: v2 500 cycle kit, 251 x 8 x 8 x 251

For any feedback or questions regarding this article (Illumina Knowledge Article #1444), contact Illumina Technical Support [e-mail].