How to troubleshoot clustering failures on the NovaSeq X Series

Background

Issues with clogs in the fluidics lines for the NovaSeq X Series instrument can impact clustering and sequencing fidelity. This can lead to severely reduced clusters passing filter (%PF), low quality scores, and increased PhiX error rates across all lanes of the flow cell.

If a clustering issue is suspected, collect the following files and contact Illumina Technical Support for next steps.

1. Collect the run metrics files from /usr/local/illumina/mnt/runs/[RunID]

   1. RunInfo.xml

   2. InterOp folder

   3. Thumbnails Folder

2. Collect the Fluidics Low Level Diagnostics (LLD) files:

   1. Navigate to/usr/local/illumina/runs/[RunID]/Logs

   2. Right-click on the Logs.zip file, then select Extract Here.

   3. Navigate to ../Logs/LowLevelDiagnostics and collect the four Fluidics LLD files only:

      1. [Serial]_[Time Stamp]_LLD_Fluidics.LLD_FLU

3. Collect the InstrumentAnalyticsLogs folder:

   1. /usr/local/illumina/runs[RunID]/InstrumentAnalyticsLogs

4. Confirm if the Lyo Vials used for run are full or empty after post run wash.

5. Confirm if the Library Tube volume is even across all 8 individual lanes.

For any feedback or questions regarding this article (Illumina Knowledge Article #8328), contact Illumina Technical Support [e-mail].