Troubleshooting low disk space issues in the /var/log/ volume on NextSeq 1000/2000 and NovaSeq X/X Plus

Background

Linux Operating System (OS) file systems record system events and logs in the messages log file, located in the /var/log/ directory. Over time, these logs can accumulate and cause the messages file size to reach several gigabytes. As a result, this can cause the /dev/mapper/--log-log partition to completely fill up. This does not typically affect run performance, though it can present warnings and errors in the Linux OS if it is not addressed.

Figure 1: Low Disk Space on "log". The volume "log" has only 266.1 MB disk space remaining.

Important Note: The NextSeq 1000/2000 Control Coftware v1.5 implements a pre-run disk space check to ensure local Linux OS partition has sufficient space. This pre-run check will present a warning if any OS partition is over 70% full, though sequencing runs can proceed after this warning is acknowledged. If any partition reaches over 90% full, the pre-run check will prevent sequencing runs from starting and space must be cleared.

Troubleshooting Actions

If a warning presents that a partition is over the limit for the pre-run check, see the following instructions to identify the affected partition:

1. Minimize the Control Software and open a terminal in the Linux OS by selecting Applications > System Tools > Terminal.

2. Run the df -Th command in the terminal to check the available capacity on the available partitions.

For assistance with checking the Linux OS partitions and clearing out excess files, contact Illumina Technical Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #6273), contact Illumina Technical Support [email protected].