How to Troubleshoot a "no base calls are available for its lane(s)" error in Local Run Manager
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Error context and text:
GenerateFASTQ Analysis in Local Run Manager (LRM) fails with the error "Analysis terminated with error: System.Exception: Error in FASTQ generation: For sample ID #, no base calls are available for its lane(s). Please check the sample sheet definition, and remove or recover any lanes that don't exist on disk".
Cause of error:
Basecall (bcl) files are missing from the file path D:\Illumina\MiSeqAnalysis[RunFolderName]\Data\Intensities\BaseCalls
Troubleshooting steps:
Navigate to the file path D:\Illumina\MiSeqAnalysis[RunFolderName]\Data\Intensities\BaseCalls and confirm if bcl files are present for all cycles of the run
If bcl files are absent, navigate to D:\Illumina\MiSeqOutput[RunFolderName]\Data\Intensities\BaseCalls and copy all bcl files
Note: A copy of the bcl files can also be found in the designated output location of the run folder. Navigate to the MiSeq Control Software Menu and select System Settings, then select the tab for Folders. See the file path entered for Output Folder to confirm the output location of the saved run.
Paste the copied bcl files into the file path D:\Illumina\MiSeqAnalysis[RunFolderName]\Data\Intensities\BaseCalls
Requeue the analysis from the LRM dashboard
Additional Resource:
How to request an import run data for reanalysis with Local Run Manager
For any feedback or questions regarding this article (Illumina Knowledge Article #9398), contact Illumina Technical Support .