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How to Troubleshoot No Intensity or 0% Passing Filter at Inlet and Outlet Tiles on NovaSeq X/X Plus

Background
Issues with sequencing runs presenting No Intensity or 0% Clusters Passing Filter for tiles at both the flow cell inlet and outlet are typically caused by skewed flow cell registration. The root cause for this can be either a transient flow cell seating issue, or issues with the flow cell clamping assembly.
Figure 1: 0% Intensity in Inlet and Outlet of Flow Cell Chart in Sequencing Analysis Viewer (SAV)
Figure 2. 0% Cluster Passing Filters in Inlet and Outlet of Flow Cell Chart in Sequencing Analysis Viewer (SAV)
Troubleshooting Actions
If a NovaSeq X/X Plus sequencing run shows No Intensity or 0% Clusters Passing Filters in tiles at the flow cell inlet and outlet across all lanes, collect the following files from the instrument.
  • Inspect the flow cell and flow cell stage for debris using lint-free Contec Polynit Heatseal wipes as detailed in the NovaSeq X Plus Product Documentation
  • From within:/usr/local/illumina/mnt/runs/[RunID]
    • RunInfo.xml
    • InterOp folder
    • Logs.zip
    • Cycle 1 thumbnails for 1-2 affected lanes (../Thumbnail_Images/L00#/C1.1 directory where # is the Lane number)
  • From within:/usr/local/illumina/runs/[RunID]/Logs/Logs.zip
    • AutoCenterLineScan folder
Once these files have been collected, zip/compress them into a single file and then contact Illumina Technical Support for next steps.
For any feedback or questions regarding this article (Illumina Knowledge Article #7994), contact Illumina Technical Support [email protected].
Last modified 2mo ago
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