How to requeue analysis of a run with MiSeq Reporter

MiSeq Reporter performs secondary analysis of data generated on the MiSeq instrument. The run data can be re-analyzed multiple times locally by requeueing analysis with MiSeq Reporter. Some common reasons for requeueing analysis include changing the analysis workflow or correcting index sequences, sample IDs, or samples names in the sample sheet. The instructions to edit the sample sheet correctly and requeue analysis with MiSeq Reporter, either using the web interface or from the run folder, are provided below. Always make sure that a sequencing run is not in progress when requeuing analysis with MiSeq Reporter. How to edit the sample sheet

1. Navigate to the MiSeq Analysis run folder on the D drive. For example:

   1. D:\Illumina\MiSeq Analysis\141007_M001_0016_000000000-AB8A8

2. To edit the SampleSheet.csv file, open in it a text editor such as Notepad. If you use a spreadsheet editor, make sure to save the sample sheet as a comma separated value (.csv) file. Make sure to maintain the format of the sample sheet.

3. If you create a new sample sheet, keep a copy of the original sample sheet by renaming the SampleSheet.csv file to SampleSheet_original.csv. Place the new sample sheet in the MiSeq Analysis run folder and name it SampleSheet.csv.

Requeue analysis of a run using the MiSeq Reporter web interface

1. To launch the MiSeq Reporter web interface, open the Internet Explorer web browser and type http://localhost:8042 in the address bar.

2. From the MiSeq Reporter web interface, select the Analyses tab on the top left.

3. Locate the run from the list of available runs in the Analyses tab, click on the checkbox next to the run name, then select Requeue.

During analysis, a status bar with elapsed time appears on the Analyses Info tab. If analysis needs to be stopped prior to completion, select the Stop analysis icon next to the status bar on the Analysis Info tab.

Requeue without using the MiSeq Reporter web interface

1. If the run was sent to BaseSpace Sequence Hub, but has not been analyzed locally, the run will not be listed in the Analyses section of the MiSeq Reporter web interface. In these situations, the analysis must be requeued from the run folder. Once the analysis is requeued, the run will appear in the MiSeq Reporter web interface. The following steps outline how to requeue analysis from the run folder.

2. Navigate to the MiSeq Analysis run folder on the D drive. For example:

   1. D:\Illumina\MiSeq Analysis\141007_M001_0016_000000000-AB8A8

3. Delete the file called queuedforanalysis.txt (or QueuedForAnalysis.txt) in the run folder. Deleting this file from the run folder triggers MiSeq Reporter to start analysis. This file will reappear (as QueuedForAnalysis.txt) with current date and time stamp, indicating that MiSeq Reporter has started analyzing the run.

Files for troubleshooting

MiSeq Reporter Error.txt and MiSeq Reporter Log.txt are found in D:\Illumina\MiSeqAnalysis

To view the status of the analysis, open the Internet Explorer web browser and type http://localhost:8042 in the address bar to launch the MiSeq Reporter web interface. Select the Analyses tab on the top left. The run that was just requeued will be at the bottom of the list. Select the run to see the status bar for the analysis.

For any feedback or questions regarding this article (Illumina Knowledge Article #1782), contact Illumina Technical Support [e-mail].