Troubleshooting Stalled or Frozen Sequencing Runs on the MiSeq i100 Series

Background

The MiSeq i100 Series uses two onboard computers to handle the user interface and process sequencing run data separately. If the computer handling data processing becomes unresponsive during a sequencing run, it can lead to the sequencing run appearing to stall or freeze without completing. If this is observed, see the following Troubleshooting Actions and contact Illumina Tech Support.

Troubleshooting Actions

1. If instrument is configured to copy data to a local network or Cloud storage, monitor output folder from a separate computer for new files to rule out a potential Control Software display issue.

   1. Illumina recommends checking the /[Output_Dir]/[RunID]/Data/Intensities/BaseCalls/L001/ directory for new Cx.1 directories, where x is the cycle number.

   2. Ensure that the sequencing run is not performing Cluster Generation, Read Preparation, or Paired-end Turnaround when checking for new files.

   3. See Knowledge Article Run time estimates for each sequencing step on Illumina sequencing platforms for additional details.

2. If no new files are observed over several hours, toggle the power switch on the back of the instrument to power down the instrument.

3. Leave instrument powered down for 2 minutes, then toggle power switch to ON and press the power button on the front bottom-right corner to boot the instrument.

4. If the instrument successfully initializes, collect the Export Logs - Medium and contact Illumina Tech Support for a secure upload link.

   1. See Illumina Knowledge Article How to Export Logs on the MiSeq i100 Series for additional details.

For any feedback or questions regarding this article (Illumina Knowledge Article #9606), contact Illumina Technical Support [e-mail].