HiSeq Temp run folders are not automatically deleted. If temp folders are not removed, hard drive space can become limited, which can impact data processing. Regularly deleting run folders or performing a quick format is recommended.

As an alternative to manually deleting files from your D:\ and E:\ drives on the HiSeq 1000/1500/2000/2500, clear all the data on the data drives by doing a quick format which provides a quick way to clear the drives, providing space for new run data.

Important note before starting

The D: drive contains files that need to be saved. Copy the following folders (found in D:\ or E:\) to the desktop before formatting this drive and copy them back to the drive afterwards:

• Illumina Maintenance Logs (always present)

The following might not be present, but need to be retained or reviewed if present:

• Test Images
• Diagnostic Images
  • Contains diagnostic images from problematic runs, keep these files if you have runs that need attention or review by Technical Support
• ASLscripts

Transfer any run data or additional files you still need to your server and shut down the instrument control software before formatting the drives.

Important: Format only D:\ and E:\ drives. The C:\ and DONOTEJECT drives are critical to the functioning of the system. Reformatting these drives results in system failure.

How to quick format

1. Open the computer File Explorer window
2. Right-click the D: or E: drive and select Format…
3. Select Quick Format and do not change the other options
4. Select Start and accept the warning to erase all data from the drive

After the Quick Format is finished, make sure that the drive letter assigned to the disk is still correct (D: or E: depending on which drive was formatted). If it is not:

1. Open the disk management utility by right-clicking Computer from the Windows Start Menu, and select Manage
2. Go to Disk Management in the right-hand pane of the window - the drives are in the bottom middle pane
3. Right-click on the drive you wish to reassign and select Change Drive Letter and Paths
4. Select Change and assign the correct drive letter from the drop-down list
5. Select OK