Java not found

Modified on Mon, 19 Sep 2022 at 03:21 AM

Q: "java: command not found"

When submitting jobs to your on-prem HPC (regardless of whether using SSH or Tower-Agent authentication), the following error may appear in your Nextflow logs even though you have Java on your $PATH environment variable:

java: command not found
Nextflow is trying to use the Java VM defined for the following environment variables:
  JAVA_CMD: java
  NXF_OPTS:

Possible reasons for this error:

The queue where the Nextflow head job runs is in a different environment/node than your login node userspace.
If your HPC cluster uses modules, the Java module may not be loaded by default.

To troubleshoot:

Open an interactive session with the head job queue.
Launch the Nextflow job from the interactive session.
If you cluster uses modules:
1. Add module load <your_java_module> in the Advanced Features > Pre-run script field when creating your HPC compute environment within Nextflow Tower.
If your cluster does not use modules:
1. Source an environment with java and Nextflow using the Advanced Features > Pre-run script field when creating your HPC compute environment in Nextflow Tower.