Question: FastQC Error Problem
3
gravatar for Abdul Rafay Khan
3.5 years ago by
Karachi, PK
Abdul Rafay Khan940 wrote:

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 • 6.6k views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 3.5 years ago by Abdul Rafay Khan940
7
gravatar for h.mon
3.5 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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 &
ADD COMMENTlink written 3.5 years ago by h.mon24k

Thanks its work!!

 

ADD REPLYlink written 3.5 years ago by Abdul Rafay Khan940
1
gravatar for Daniel
3.5 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

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 &
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Daniel3.7k

X still needs to be installed on the server, and X-forwarding needs to be enabled on sshd. A trick to sped up X11-forwarded sessions is to use blowfish, which is faster according than the default 3des:

ssh -X -c blowfish user@server.dot

And if your internet is slow, compressing data may help too:

ssh -X -C -c blowfish user@server.dot
ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by h.mon24k
1
gravatar for egf25
3.5 years ago by
egf2510
United Kingdom
egf2510 wrote:

Unfortunately there's a bug in Ubuntu 15.04 for SSH X11 Forwarding.

https://bugs.launchpad.net/ubuntu/+bug/1463263

"ssh-based X11 forwarding not working in 15.04 following upgrade from 14.10 "

 

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by egf2510
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