Resolving issues with Process Management on NextSeq 1000/2000

Background

The NextSeq 1000/2000 Control Software manages run uploads and analyses through Process Management and manages the temporary run folder through Disk Management. For more information, search for Knowledge Base article What is the difference between process management and disk management on the NextSeq 1000/2000.

Run progress and transfers are tracked through a combination of contract files for Instrument Orchestrator and Universal Copy Service (UCS), respectively. If a temporary run folder is manually set to save outside of Disk Management, this can create a disconnect between Process Management, Disk Management, and Instrument Orchestrator.

Key features of this phenotype:

• Runs listed in Process Management that are not listed in Disk Management.

• No run folders in the temporary runs directory /usr/local/Illumina/runs/[runfolder].

This can manifest in a few ways, including:

• NextSeq 1000/2000 Control Software initialization issues.

• Process Management stalling when attempting to load.

• Errors that stop runs due to the Control Software suspecting a run is in progress.

• Inability to requeue analysis of a previously completed run.

  • For more information, search for Knowledge Base article Troubleshooting “Failed to execute connectivity check input parameters …” on the NextSeq 1000/2000.

Troubleshooting steps:

1. Close the Control Software.

2. Open a terminal from the instrument desktop by right-clicking the Desktop and selecting Open Terminal.

   1. If in 'ilmnuser' account, run the su ilmnadmin command and enter the ilmnadmin password.

3. Stop the Universal Copy Service and Instrument Orchestrator processes by running the following commands.

   1. sudo systemctl stop universal-copy-service.service

   2. sudo systemctl stop instrument-orchestrator.service

4. Open the Files application and navigate to /usr/local/illumina/persistence directory.

5. Under the 'instrument-orchestrator' directory:

   1. Create a new directory labeled Archive.

   2. Move the .rdf files associated with the affected run(s) to the Archive directory

6. Under the universal-copy-service directory:

   1. Create a new directory labeled Archive.

   2. Move the .log and .json files associated with the affected run(s) to the Archive directory.

7. Start the Universal Copy Service and Instrument Orchestrator processes by running the following commands.

   1. sudo systemctl start universal-copy-service.service

   2. sudo systemctl start instrument-orchestrator.service

8. Launch the Control Software and verify successful initialization.

9. Check Disk Management and Process Management to confirm that affected runs have been removed.

For any feedback or questions regarding this article (Illumina Knowledge Article #6526), contact Illumina Technical Support [e-mail].