Set classpath in Java for fastqc

Question

[Wet&DryImmunology]

Hi, I was trying to use fastqc to check the sequencing quality of my sample. When I tried to use: "fastqc" I got error like:

Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/bbsrc/babraham/FastQC/FastQCApplication
Caused by: java.lang.ClassNotFoundException: uk.ac.bbsrc.babraham.FastQC.FastQCApplication
    at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:268)

Could not find the main class: uk.ac.bbsrc.babraham.FastQC.FastQCApplication. Program will exit.

I searched, some one suggested that in similar case, I need to set the class path to the directory which contains FastQC installation:

and depending on having a standard class path or non-standard classpath on my machine, I need to append existing classpath like:

java -Xmx250m -classpath /usr/local/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication

or

java -Xmx250m -classpath /usr/local/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication

Since my directory which contains the FastQC is /u32/myusername/Tool/FastQC

so I tried both:

java -Xmx250m -classpath /u32/myusername/Tool/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication

and

java -Xmx250m -classpath /u32/myusername/Tool/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication

but none of them seemed to work.

Did I mess something up? I am not sure about what "-Xmx250m" means, with or without it, the path setting did not work. Any idea or suggestion appreciated.

[WouterDeCoster]

The Xmx part tells Java the amount of heap space it can use (memory).

Are you using a recent version of FastQC and java?

[Wet&DryImmunology]

Hi, WouterDeCoster, thanks for your response. For Xmx, I see. then i guess it should not be the problem.

Here is the version information of FastQC and java runtime environment: java version "1.6.0_39" OpenJDK Runtime Environment (IcedTea6 1.13.11) (rhel-1.13.11.0.el5_11-x86_64) OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode) the java version seems to meet the minimal requirement of fastqc.

RELEASE NOTES FOR FastQC v0.11.5 the FastQC is the most recent release, I believe. Kindly let me know if you have any thought.

[WouterDeCoster]

Well can't see anything wrong with that, while waiting for other replies you could try updating java :p That won't hurt.

[Wet&DryImmunology]

@WouterDeCoster, It seemed to me that to update the java, I need to use "su" or "sudo" command (http://openjdk.java.net/install/index.html) which I could not to use. if that is not the case, please kindly let me know. Tsk.

[WouterDeCoster]

Should be possible, if you google for install java without sudo there are some stackoverflow hits.