Does anyone know what is meant by the following message?
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
This message occurs when I put my data through the FastQC tool, the SortSam tool and the Add or Replace Read Groups tool. I load my data (pair-ended), then I put it through FastQ Groomer before FastQC and FastQ Quality Trimmer. FastQC completes successfully however the above message displays in the history pane of my Galaxy instance. Then after I have run a mapping step and used the sort tool and applied reading tags to the data, I get this message again despite the sorting tool and add or replace read groups tool running successfully.
I'd just like to know if this message implies some underlying issue with my processing pipeline.