We are having trouble running FastQC on our production server.

The original stacktrace looked like this;

Fastq failed.
Error executing FastQC. Unknown option: djava.awt.headless
Exception in thread "main" java.lang.NoClassDefFoundError:
Caused by: java.lang.ClassNotFoundException:
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class:
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.  Program will exit.

Then I tried to update java to the most current version. The current
version is

java -version
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

This changed the error message we got when we ran FastQC. The new trace
looks like this;

Fastq failed.
Error executing FastQC. Unknown option: djava.awt.headless
Error: Could not find or load main class

The strange thing is that the tools works on our test server, which is
almost an exact copy of the production server.



Sure enough, this fixed the problem. I just installed the latest Sun JRE
and it is working now. Thanks for the suggestion! I would have never


On Mon, Jun 25, 2012 at 11:34 AM, simon andrews <[hidden
> wrote:
Yes, that's the broken version of gcj.  I don't have a Centos machine here
at the moment, but I think if you install OpenJDK and use the alternatives
system to select that as the default JRE then that should fix things.


 On 25 Jun 2012, at 17:19, Josh Nielsen wrote:

 Hi Simon,

I recently installed Java with the yum package manager on our compute
nodes, and our cluster is a Centos 6 environment. Here is what the results
of "java -version" returned on the compute nodes:

"*bash# java -version*
*java version "1.5.0"*
*gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)*
*Copyright (C) 2007 Free Software Foundation, Inc.*
*This is free software; see the source for copying conditions.  There is NO*

 Is this version of Java too old? Perhaps I need to install the JRE


On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews <[hidden

> Are you by any chance running an older version of gcj as your java version?  
> There is a known bug in some of these where they don't correctly configure 
> the headless environment, even if the correct parameters are passed.  This 
> causes exactly the kind of errors you're seeing.
> If this is the case you'll need to install a more recent JRE (or update your 
> path to point to one which is already present).
> Simon.
> On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen <[hidden 
> email]<http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=node&node=4655462&i=2>>
> wrote:
> > Hello,
> >
> > I am having an issue with getting the FastQC tool to work with Galaxy on
> our
> > server. I downloaded the FastQC files (version 0.8.0) and changed the
> > directory that the wrapper script looks for the 'fastqc' executable in,
> but
> > when we run a job with it we have been getting the following output:
> >
> > "Started analysis of Clip
> >
> > Approx 5% complete for Clip
> > Approx 10% complete for Clip
> > ...
> > ...
> > Approx 95% complete for Clip
> > Approx 100% complete for Clip
> >
> > Analysis complete for Clip
> >
> > (.:9754): Gtk-WARNING **: cannot open display: "
> >
> > And then the job shows as failed in Galaxy. The output .dat file just has
> > that same output/error message in it (though it seems to indicate it got
> to
> > 100%). Also when I try to execute the fastqc file directly (albeit with
> no
> > arguments) I get this:
> >
> > "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:173)
> > at java.awt.Window.<init>(Window.java:437)
> > at java.awt.Frame.<init>(Frame.java:419)
> > at java.awt.Frame.<init>(Frame.java:384)
> > at javax.swing.JFrame.<init>(JFrame.java:174)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)"
> >
> > Both errors seem to have something to do with the graphical GUI
> component of
> > FastQC (which I have seen some screenshots for on the FastQC webpage). If
> > this application is GUI-driven how did the online PSU Galaxy get it to
> work
> > with their wrapper script when the tools are run in a command-line
> > environment with no X11 or Gtk? Essentially I'm just wondering what steps
> > I'm missing here to getting this to work with our Galaxy mirror, other
> than
> > just dropping the executable in place? Any suggestions?
> >
> > Thanks,
> > Josh
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >  http://lists.bx.psu.edu/
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: <a
> href="tel:%2B61%20385321444" value="+61385321444" target="_blank"> +61
> 385321444;

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