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

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 Series 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 and clean using lint-free Contec Polynit Heatseal wipes as detailed in the NovaSeq X Plus Product Documentation
• From the /usr/local/illumina/mnt/runs/[RunID] directory, collect:

  • RunInfo.xml

  • InterOp directory

  • Cycle 1 thumbnails for 1-2 affected lanes (../Thumbnail_Images/L00#/C1.1 directory where # is the Lane number)

• From the /usr/local/illumina/runs/[RunID]/Logs/Logs.zip directory, collect:

  • AutoCenterLineScan directory

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 [e-mail].