iScan Reader Issues

Cause

Resolution

Cable between iScan Reader and PC might be unplugged.

Inspect the cable between the iScan Reader and the instrument control computer to confirm that the cable is securely connected at both ends.

Initialization failure error when starting the iCS.

Remove any external hard drive or other USB device. Power on the iScan Reader and its computer, allowing the override.cfg file to be loaded on the internal drive H.

Cause

Resolution

iScan Reader does not initialize correctly.

Reinitialize the iScan Reader and iCS. For more information, refer to Start the iScan System.

iScan Reader does not initialize correctly after cycling instrument power and restarting iCS.

Reinitialize the iScan Reader and iCS, and perform a power cycle on the computer. If the scanner still fails to initialize correctly, contact Illumina Technical Support.

Cause

Resolution

An environmental electrostatic discharge is affecting the status lights.

If the status lights turn on or off spontaneously during a run, and no error message appears in the iCS, continue the run through completion. Then, reinitialize the iScan Reader. For more information, refer to Start the iScan System. If the problem persists, contact Illumina Technical Support.

Cause

Resolution

BeadChip not properly seated in the carrier.

Eject the tray, lift out the carrier, and remove the BeadChips. Reload the BeadChips following the directions in Load BeadChips. Make sure the BeadChips are securely seated. Replace the loaded carrier in the tray.

Carrier tray not properly seated in iScan Reader tray.

Eject the tray. Remove the carrier from the tray and then replace it. Match the notches on the carrier with the posts on the tray to ensure proper seating. For more instructions, refer to Load BeadChips.

Cause

Resolution

iScan Reader requires reinitialization.

From the menu in the upper left corner of the iCS screen, select Scanner, and then select Initialize.

Cause

Resolution

Problems with emission filter slide, excitation filter wheel, tilt motor, tray switch, and/or laser safety switch.

Take a screen capture of the error and save it. Close the iCS and power cycle the scanner to clear the FPGA. Restart the iCS. If the error occurs again, contact Illumina Technical Support and schedule a field service call.

Cause

Resolution

If the iScan Reader detects a possible mechanical error, it immediately disables all motors for safety. User error can also cause a mechanical error.

Visually inspect the iScan Reader internally and around the carrier tray where the BeadChips are loaded. If there is an obvious physical problem, call Illumina Technical Support to guide you through safely freeing the BeadChip.

If there is no apparent physical problem, either reinitialize or shut down and power cycle the iScan Reader. To reinitialize the iScan Reader, select the menu in the upper left corner of the iCS screen, select Scanner, and then select Initialize.

Cause

Resolution

A motor error occurred in an x-, y-, or z-stage motor. Sometimes an error occurs for one motor because of an initial error in another motor.

Take a screen capture of the error and save it. If the error caused the scan to stop, close the iCS and power cycle the scanner to rehome the motors. Restart the iCS. If the error occurs again, contact Illumina Technical Support and schedule a field service call.

BeadChip does not lie flat or is improperly seated within a carrier.

Eject the BeadChip carrier and examine how the carrier is seated in the iScan Reader adapter tray. Reset the BeadChips within the carrier and restart the scan.

Cause

Resolution

Barcode quality is poor.

Eject the BeadChip carrier. Examine the barcodes to make sure that they are present and of good print quality. Reload the carrier and rescan. If the internal barcode scanner still fails to read the barcode, try entering the barcode number manually into the correct position using the iCS.