I was trying to use a tool a tool written in java called "fastqc" (for people who are interested in what is fastqc. when I tried typing the command :" fastqc" I got the error:

Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication
Caused by: java.lang.ClassNotFoundException: uk.ac.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)

when someone had similar previously,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


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


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. Sorry for my ignorance. Any idea or suggestion appreciated.


1.well the easy step to do is go to install folder 2.copy the address of bin folder 3.open my computer properties -> advanced system setting -> environment variables 4.click on new and past that address and name it as path if the address is in the bin and put ; 5.again new past the address remove bin and insert lib and names it as classpath 6.put ; after end 7.restart cmd 8.open cmd check by typing javac thats it

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