How to Troubleshoot No Intensity or 0% Passing Filter at Inlet and Outlet Tiles on NovaSeq X Series
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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 techsupport@illumina.com.
