Cloud Analysis Errors using Sample Sheet Workflow on the MiSeq i100 Series

Background

The MiSeq i100 Series instruments allow users to setup sequencing runs using Sample Sheets through either Run Planning or importing the sample sheet under the Manual Mode option. Only Local Analysis using onboard DRAGEN is available when setting up runs using a Sample Sheet; Cloud Analysis is not available for this setup workflow.

If a Sample Sheet that is configured for Cloud Analysis is used to setup a sequencing run through either Run Planning or importing the sample sheet in Manual Mode, the following errors will present:

Run Planning

Cannot import SampleSheet.csv: Fix the following 2 issues in the sample sheet file and try importing again.

Manual Mode

This sample sheet is configured for cloud analysis. Select a sample sheet without a cloud configuration.

Resolution Actions

The Sample Sheet workflow is only compatible with on-instrument DRAGEN Local Analysis. If the Sample Sheet is configured for Cloud Analysis in BaseSpace, see the following options to correct the Sample Sheet and configure the Cloud Settings if needed.

Correcting the Sample Sheet

1. Option 1: Edit the Sample Sheet to remove [Cloud_Settings] the section ONLY, leave the [Cloud_Data] section in place.

   1. Open file in a simple text editor such as Notepad or Text Editor.

   2. Do NOT use Excel or other spreadsheet editor as these can modify the comma-separated values.

   3. 
2. Option 2: Create a new Sample Sheet in BaseSpace and select Local under Secondary Analysis on the Run Settings user interface.

   1. 
   2. Complete the Run Settings and Configuration workflows, then select Export to create a new SampleSheet.csv file.

Uploading Analysis Files to Cloud Storage

While the Analysis must be performed locally when using the Sample Sheet workflow, the resulting FASTQ, BAM, or CRAM analysis files can be uploaded to BaseSpace for storage or sharing. See the following steps if this is required:

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

2. Open the Settings menu and select Cloud Settings.

3. Select the checkbox for Cloud Storage.

4. Select the checkboxes to upload FASTQ and BAM/CRAM files as appropriate.

5. Select Save.

6. During run setup, login as BaseSpace user and then setup sequencing run using Manual - Sample Sheet workflow.

7. On Run Review page, confirm Cloud run settings shows Run Monitoring and Storage.

For any feedback or questions regarding this article (Illumina Knowledge Article #9549), contact Illumina Technical Support [e-mail].