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How to troubleshoot clustering failures on the NovaSeq X/X Plus

Issues with clogs in the fluidics lines for the NovaSeq X/X Plus 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. 1.
    Collect the run metrics files from /usr/local/illumina/mnt/runs/[RunID]
    1. 1.
    2. 2.
      InterOp folder
  2. 2.
    Collect the Fluidics Low Level Diagnostics (LLD) files:
    1. 1.
      Navigate to /usr/local/illumina/runs/[RunID]/Logs
    2. 2.
      Right-click on the file, then select Extract Here.
    3. 3.
      Navigate to ../Logs/LowLevelDiagnostics and collect the four Fluidics LLD files only:
      1. 1.
        [Serial]_[Time Stamp]_LLD_Fluidics.LLD_FLU
For any feedback or questions regarding this article (Illumina Knowledge Article #8328), contact Illumina Technical Support [email protected].
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