Troubleshooting

For technical questions, visit the NovaSeq 6000Dx Instrument page on the Illumina support site. The support site provides access to documentation, downloads, and frequently asked questions. For access to support bulletins, sign into your MyIllumina account.

For run quality or performance problems, contact Illumina Technical Support.

Ending a run on the NovaSeq 6000Dx system is final. The software cannot resume the run or save sequencing data, and consumables cannot be reused.

1. Select End, and then select Yes to confirm the command.

If the run was ended after Read 1, the software initiates the automatic post-run wash.

2. If prompted, select from the following wash options:
• End Run Without Wash—End the run and initiate a maintenance wash.
• End Run and Wash—End the run and perform an automatic post-run wash.
• Cancel—Continue with the current run.

If the run is ended between clustering completion and Read 1 completion, the software displays the wash options. Otherwise, the software initiates the automatic post-run wash.

3. If you selected End Run Without Wash, follow the software prompts to set up a maintenance wash.

A leak tray is built into the base of the instrument to collect leaked reagents or coolant and collect overflow from the used reagent bottles. Under normal conditions, the leak tray is dry. Leakage indicates a problem with the instrument, and overflow occurs when the used reagent bottles are not regularly emptied.

During the pre-run check, sensors detect whether the leak tray contains any liquids:

• If the leak tray contains liquid but is not full, the run can proceed but you must contact Illumina Technical Support.
• If the leak tray is full, the run cannot proceed and you must contact Illumina Technical Support.

CAUTION

Empty the used reagent bottles with every run. Runs are stopped if either of the used reagent bottles is full. Overflow from either of the used reagent bottles damages the instrument, requires a site visit from an Illumina representative, and poses a safety risk.

The following table provides troubleshooting options for the N/A icon on the Process Management screen. The location of the icon depends on the run configuration.

• N/A icon displays in the BaseSpace Sequence Hub column when the run is configured to upload to BaseSpace Sequence Hub.
• N/A icon displays in the Network column when the run is configured to upload an output folder on the network.

Run Status

Troubleshooting Action

A run is in progress

Close the Process Management screen, wait approximately 5 minutes, and then reopen the screen.

A run is not in progress

Shut down and restart the instrument, and then reopen the Process Management screen.

If the N/A icon still displays after the troubleshooting action is complete, contact Illumina Technical Support.

If an error occurs during the pre-run checks, use the following actions to resolve the error. If you are setting up a dual flow cell run and one side fails, you can cancel the failed side and proceed with the side that passed.

When a pre-run check fails, the RFIDs for the flow cell, reagents, and buffers are not locked so you can use the consumables for a subsequent run. When the run is started, the sippers pierce the foil seals on the reagent cartridges and all RFIDs are locked.

System Check

Reason for Failure

Recommended Action

Sensors

A compartment door is open, a consumable is not properly loaded, or at least one sensor is not functional.

Select Retry and follow the onscreen prompts to resolve the error.

Disk Space

Disk space is insufficient because the specified location of the output folder is full.

Use the Process Management screen to clear disk space from the specified output folder location.

System Connectivity

The connection to RTA3, the fluidics system, or other connection has been interrupted.

Select Retry and follow the onscreen prompts to resolve the error.

Alignment

The position of the flow cell prevents imaging.

Follow the onscreen prompts to reload the flow cell.

The NovaSeq 6000Dx can only be rebooted, shut down, or power cycled when the instrument is idle. If sequencing or analysis is in progress, a warning is displayed and there is no option to proceed.

• Reboot—Reboot restarts the instrument without fully shutting down.
– To reboot the instrument, select Reboot from the Settings menu on the instrument.
• Shut Down—Shutting down the instrument safely shuts down all software and turns off instrument power. The status bar fades from green to white, indicating that the shutdown is in progress. Under normal circumstances, shutting down the instrument is unnecessary.
– To shut down the instrument, select Shut Down from the Settings menu on the instrument or through a browser.
• Power Cycle—Power cycle fully shuts down and restarts the instrument. A power cycle should be performed any time a software crash event occurs.
– To power cycle the instrument, select Power Cycle from the Settings menu on the instrument.

If no changes to run settings are made, a new run is created from the original run and reanalysis is started.

1. From the run results page, select Requeue Analysis.

The Requeue Analysis window opens.

2. Select the option to requeue with no changes and provide a reason for requeue in the Reason field.
3. The new run appears on the Active Runs tab.
1. From the run results page, select Requeue Analysis.
2. On the Requeue Analysis window, select the option to edit run settings and requeue analysis. Provide a reason for requeue in the Reason field.
3. Edit the run description and select Next.
4. Edit samples or import a new sample sheet and select Next.
5. Edit analysis settings as desired and select Requeue.

The run results for the original run are updated with a link to the requeued run.

If the software fails the run before clustering starts, you can save the reagent cartridges and library tube (including sample) for a new run. If reused immediately, you can also save the flow cell. When clustering starts, sippers pierce the foil seals and reagents are transferred to the library tube and flow cell, so the consumables and libraries cannot be used for another run.

You can use one of the following options for setting up a new run using the reagent cartridges, library tube, and flow cell saved from the failed run:

• Set up a new run immediately—Set up the new run within 4 hours of the failed run. The reagent cartridges, library tube, and flow cell remain loaded.
• Set up a new run later—Set up the new run within three weeks of the failed run. The reagent cartridges are unloaded from the instrument and stored. The saved consumables should be labeled with the date and stored under the original conditions. The flow cell cannot be reused and must be discarded.
1. When the run fails and the other side of the instrument is idle, reboot the instrument. Otherwise, select Home.
2. Set up a new run.
3. Leave the current flow cell in place.
4. Open and close the reagent chiller door and the buffer drawer to prompt the NVOS to reread the reagent cartridge RFIDs.

The cartridges, library tube, and flow cell can remain in the instrument for up to 4 hours after the failed run.

5. Empty the used reagent bottles, if needed, and return them to the instrument.
6. Proceed with run setup.

File

Folder

Description

Run information file (RunInfo.xml)

Root folder

Contains the following run information:

• Number of cycles in the run
• Number of reads in the run
• Whether the read is indexed
• Number of swaths and tiles on the flow cell

Run parameters file (RunParameters.xml)

Root folder

Contains the run name and information about run parameters and run components, including the following RFID information: serial numbers, lot numbers, expiration dates, and catalog numbers.

InterOp files (*.bin)

InterOp

InterOp files are updated throughout the run.

Log files
Log files

Logs

Log files describe each step performed by the instrument for each cycle, including which reagent is used, and list software and firmware versions used with the run. The file named [InstrumentName]_CurrentHardware.csv lists the serial numbers of instrument components.