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Troubleshooting "Upload mode has been set to None" Errors on the MiSeq i100 Series

Background

The MiSeq i100 Series instruments can be configured to upload Sequencing Run data to BaseSpace Sequencing Hub (BSSH) for run monitoring or storage.

If there are issues with connecting to BaseSpace, the MiSeq i100 Series Control Software can present an error indicating Upload mode has been set to None when the following conditions are met:

  1. The Sequencing Run is configured to upload to BaseSpace only with no additional External Storage option configured

  2. Universal Copy Service (UCS) encounters an issue with connecting to BaseSpace at the start of the Run upload

If this error message is observed, allow the Sequencing Run to complete as normal then login to BaseSpace and confirm if the Run upload shows as Complete. If the upload recovered, no additional troubleshooting is required and the user can proceed with a normal workflow.

If the Sequencing Run upload did not recover or is incomplete, see the following Actions.

Troubleshooting Actions

  1. Configure a new output location using a USB storage device or local network storage using the External Storage user interface (UI).

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

  2. Follow the Restart File Transfer workflow to copy the Sequencing Run data to the configured External Storage.

    1. See Knowledge Article How to Restart File Transfer on the MiSeq i100 Series for additional details.

    2. If using a USB storage device, navigate to the External Storage UI and select Eject to safely remove the device once the data copy is complete.

  3. Use the BaseSpace Command Line Interface (CLI) tool to upload the Sequencing Run data from the new output location to BaseSpace.

    1. This step must be performed from a separate computer that has access to the internet and cannot be performed in the MiSeq i100 Series instrument.

    2. See Knowledge ArticleHow to upload a run to BaseSpace using BaseSpace Command Line Interface (CLI) for additional details.

For further assistance with troubleshooting uploading Sequencing Run data to BaseSpace, contact Illumina Tech Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #9936), contact Illumina Technical Support [email protected].

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