How to troubleshoot The process cannot access the file error on MiSeq

"The process cannot access..." errors can occur when a file is being scanned by anti-virus software during the run, or when a communication issue occurs between the hardware and software.

• The run will often stop at the start of the next read. For example, if a virus scan is performed during Read 1, the run will stop at the start of Index Read 1.

Error message:

"The process cannot access the file 'D:\Illumina\MiSeqTemp[RUNFOLDER]\Recipe\RunState.xml' because it is being used by another process."

Troubleshooting steps:

1. Determine if the run stopped or is paused.

• For MiSeq Control Software (MCS) v4.0.0 and above this notification can show up during cluster generation steps and will not stop the run. Acknowledge the notification and the run will proceed.

1. If the run stopped:

• Perform a Post-run wash.

• Power cycle MiSeq (Note: if a run is in progress, it will not be able to be resumed). See instructions for How to Power Cycle the MiSeq.

• If the instrument initializes without error and no virus scan or Group Policy Objects (GPO) activity is enabled then proceed to setup the next run.

• If a virus scan or GPO activity occurred, update the settings before the next run following the guidance provided below, or request that the settings be updated by the institutional internal IT department before setting up the next run.

  • Illumina Control Computer Security Guide.

  • MiSeq System Site Prep Guide (see Networking).

• If the error persists during the next run, contact Illumina Technical Support for further assistance.

For any feedback or questions regarding this article (Illumina Knowledge Article #1910), contact Illumina Technical Support [e-mail].