# 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](https://www.illumina.com/company/contact-us.html) 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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-fcaa098ff1eaa0c3e8aa9c8e9abbd1b023d601b3%2Fimage1.png?alt=media)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #8328), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008328%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |