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.