FastQC Error Problem

FastQC Error Problem

3

I would really like to use FastQC for my project but am getting the following error message when I try to run it on my Ubuntu server 15.04

bio@ubuntu:~$ fastqc &

[1] 716
rafay@ubuntu:~$ Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
        at java.awt.Window.<init>(Window.java:535)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:174)
        at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:71)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:324)

 

Whereas java is already installed

bio@ubuntu:~$ java -version

java version "1.7.0_79"
OpenJDK Runtime Environment (IcedTea 2.5.6) (7u79-2.5.6-0ubuntu1.15.04.1)
OpenJDK Client VM (build 24.79-b02, mixed mode, sharing)

 

 


FastQC


error


Ubuntu


server

• 12k views

It is complaining X11 is not set (maybe not even installed?). When you call fastqc without arguments, it opens the graphical interface. Try:

fastqc *.fastq &

Another thing to consider is whether you’re ssh-ing into the server, and by default X11 forwarding isn’t enabled. If that’s the case, add a -X flag into your command and then try and open fastqc as standard (or firefox or any graphical program).

i.e.:

ssh -X bio@ubuntu.co.uk

$ fastqc &

updated 2.0 years ago by

35k

written 6.1 years ago by

&utrif;

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