Question: FastQC Error Problem
gravatar for Abdul Rafay Khan
4.5 years ago by
Karachi, PK
Abdul Rafay Khan1.1k 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(
        at java.awt.Window.<init>(
        at java.awt.Frame.<init>(
        at java.awt.Frame.<init>(
        at javax.swing.JFrame.<init>(


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 • 8.6k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 4.5 years ago by Abdul Rafay Khan1.1k
gravatar for h.mon
4.5 years ago by
h.mon29k 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 4.5 years ago by h.mon29k

Thanks its work!!


ADD REPLYlink written 4.5 years ago by Abdul Rafay Khan1.1k
gravatar for Daniel
4.5 years ago by
Cardiff University
Daniel3.8k 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).


ssh -X

$ fastqc &
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Daniel3.8k

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

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

ssh -X -C -c blowfish
ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by h.mon29k
gravatar for egf25
4.4 years ago by
United Kingdom
egf2510 wrote:

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

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

ADD COMMENTlink modified 4 months ago by RamRS26k • written 4.4 years ago by egf2510
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