Question: What is meant by: Picked up _JAVA_OPTIONS:
gravatar for hamaisa
3.2 years ago by
hamaisa20 wrote:


Does anyone know what is meant by the following message?

Picked up _JAVA_OPTIONS:


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.


Thank you!



job galaxy • 3.5k views
ADD COMMENTlink modified 3.1 years ago by joshmillerenterprises0 • written 3.2 years ago by hamaisa20
gravatar for Bjoern Gruening
3.2 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

This just means that Galaxy tells Java where to store temporary files.

Hope this helps,


ADD COMMENTlink written 3.2 years ago by Bjoern Gruening5.1k
gravatar for joshmillerenterprises
3.1 years ago by
United Kingdom
joshmillerenterprises0 wrote:

You can remove this _JAVA_OPTIONS message by following this tutorial:

ADD COMMENTlink written 3.1 years ago by joshmillerenterprises0
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