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Question: What is meant by: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch?
0
gravatar for hamaisa
3.2 years ago by
hamaisa • 20
hamaisa • 20 wrote:

Hi,

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.

 

Thank you!

 

 
job galaxy • 3.5k views
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modified 3.1 years ago by joshmillerenterprises • 0 • written 3.2 years ago by hamaisa • 20
2
gravatar for Bjoern Gruening
3.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

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

Hope this helps,

Bjoern
ADD COMMENT • link written 3.2 years ago by Bjoern Gruening ♦ 5.1k
0
gravatar for joshmillerenterprises
3.1 years ago by
joshmillerenterprises • 0
United Kingdom
joshmillerenterprises • 0 wrote:

You can remove this _JAVA_OPTIONS message by following this tutorial: https://youtube.com/watch?v=JF_o8WNt3hs
ADD COMMENT • link written 3.1 years ago by joshmillerenterprises • 0
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