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 [email protected].

Last updated

Was this helpful?