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Old 10-12-2011, 02:28 PM   #1
shuang
Senior Member
 
Location: IL

Join Date: Jul 2011
Posts: 100
Default error from VarScan

I was trying to run VarScan for variants calling. However, when I typed this command below,

$java net.sf.varscan.VarScan pileup2snp t01.pileup > outfile.snp


I received this error message below. What should I do?
PS. I've installed gcj-4.4-jre-headless on my computer.



Exception in thread "main" java.lang.NoClassDefFoundError: java
Caused by: java.lang.ClassNotFoundException: java
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: java. Program will exit.
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Old 10-13-2011, 07:35 AM   #2
dkoboldt
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Location: St. Louis

Join Date: Mar 2009
Posts: 62
Default

Hello,

It looks like you need to point Java to the VarScan Jar file, e.g.:

java -jar VarScan.jar pileup2snp t01.pileup > outfile.snp
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