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How to troubleshoot MiSeq runs taking longer than usual or expected

Expected run times on the MiSeq vary between 5.6-62.3 hours. Run time is dependent on the run length, kit type used, and whether the run is single-end or paired-end. A full list of run time estimates can be found in the Illumina Knowledge Article Run time estimates for each sequencing step on Illumina sequencing platforms. However, users may experience runs taking longer than expected. This may occur for a variety of reasons. In order to troubleshoot longer than expected run time, review the following settings on the instrument:
On Instrument Root Causes
  • Determine the amount of free disk space on the C:\ and D:\ drives. Files in the Recycle Bin are still included in space calculation. The Recycle Bin needs to be emptied to fully allocate free space. Lower amounts of free disk space on the C:\ and D:\ drives may lead to reduced run speed.
  • If saving runs locally, consider moving off-instrument to long-term storage. It is recommended to move old run folders from the MiSeqAnalysis and MiSeqOutput folders to long-term storage regularly to maintain free disk space on the instrument.
  • Extended run times may occur if the instrument is not power cycled regularly.
To troubleshoot, power cycle prior to sequencing run, clear the hard disk drive (HDD) and monitor the run time of subsequent runs. Information on steps to Power Cycle the MiSeq can be found in the Illumina Knowledge Article How to shut down or power cycle the MiSeq.
Off Instrument Root Causes* Transient internet or network issues may also contribute to run time slowness. When Illumina Proactive is enabled, delays at the end of runs may occur if internet or network issues occurred during the run.
  • Changes to the network environment, group policy objects (GPOs), or antivirus (AV) updates occurred during the time that run slowness was observed.
If review of the above does not resolve the extended run times and the issue is persistent, contact Illumina Technical Support for continued troubleshooting.
For any feedback or questions regarding this article (Illumina Knowledge Article #6023), contact Illumina Technical Support [email protected].
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