# 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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-450710c579d17dcdc88eb954b429ab059d32c31f%2Fimage1.png?alt=media\&token=565a258b-8122-4e34-a008-953391c9b243)

**Figure 1**: 0% Intensity in Inlet and Outlet of Flow Cell Chart in Sequencing Analysis Viewer (SAV)

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-572a6cf5ba70f9a074e485381ff106668e02c3aa%2Fimage2.png?alt=media\&token=1b86f413-2e76-44a9-90e8-608001b32780)

**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](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/Consumables.htm?Highlight=polynit)
* 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](https://www.illumina.com/company/contact-us.html) for next steps.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7994), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007994%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |