Troubleshooting file is not properly formatted warning on the MiSeq

The following warning messages can occur if the Control Software is reading the files in the output location and is not recognizing the formatting of these files.

This warning may result from a communication error on the MiSeq. Potential communication-related causes include corrupted formatting or old files generated by outdated control software versions at the output location. In some cases, this is a temporary situation that requires no action.

Warning: The RunParameters.xml file located at ['file path'] is not properly formatted.

Troubleshooting steps:

1. Check if the mentioned file (following the file path) is corrupt.

a. If it is corrupt, remove the file from the folder to avoid future communication errors with the control software.

1. If the is not corrupt, back up these files to an external hard drive or another location as there may be some momentary incompatibility between these files and the checks made by the control software.

2. Power cycle the MiSeq (Note: If a run is in progress, let the run finish before taking any kind of action.)

a. If there are no warnings with re-initialization, the machine is clear to use.

Note:This warning does not impact run performance neither prevent users to start a new run. The instrument can continue to be used, even if this warning is displayed.

For further information, see the following Knowledge Base articles:

• How to shut down or power cycle the MiSeq

• How To Power Cycle the MiSeq Video

For any feedback or questions regarding this article (Illumina Knowledge Article #9180), contact Illumina Technical Support [e-mail].