Troubleshooting Stalled Secondary Analyses Onboard the MiSeq i100 Series.

Background

The MiSeq i100 Series instrument allows onboard DRAGEN Analysis of sequencing run data. If this process stalls or is not able to complete, the Run Details page shows the Secondary Analysis as 'In progress' and the File transfer status as 'Not started'. See the following mitigations below if this issue is identified.

Too many external storage configurations

Cause: On the MiSeq i100 Series instruments, it is possible to configure more external storage mounts than are supported. The maximum supported number of external configurations is two.

If three or more external storage configurations are in place, it is possible the Secondary Analysis will appear to stall, and never start Secondary Analysis Data Transfer. The image below is an example of what the status of the run may look like in this scenario.

Resolution: If the system is configured with three or more external storage mounts, follow the steps below to resolve the issue.

1. Cancel the ongoing analysis:

   1. From the Control Software Home screen, select the dropdown menu in the top-left corner, then select Runs.

   2. Within the Runs user interface (UI), select the Active tab.

   3. Under the Run Name column, select the sequencing run to open the Run Details UI.

   4. From within the Run Details user interface (UI), select scroll down to the Secondary Analysis header.

   5. Select Cancel Analysis.

2. From the Control Software Home screen, select the dropdown menu in the top-left corner, then select Settings, then External Storage.

3. Remove one External Storage location to leave a maximum of two configurations in place.

   1. See MiSeq i100 Product Documentation - External Storage for additional details.

4. Requeue Secondary Analysis:

   1. From the Control Software Home screen, select the dropdown menu in the top-left corner, then select Runs.

   2. Within the Runs user interface (UI), select the Completed tab.

   3. Under the Run Name column, select the sequencing run to open the Run Details UI.

   4. Scroll down to the Secondary Analysis header, then select Requeue Analysis.

   5. Follow the prompts to requeue the analysis using the Run Planning tool or from a sample sheet.

   6. Use the dropdown menu under Output folder location to select the intended output folder on the configured External Storage location.

   7. Input the Reanalysis Reason.

   8. Select Requeue Analysis.

For any feedback or questions regarding this article (Illumina Knowledge Article #9386), contact Illumina Technical Support [e-mail].