errors when running copyseq

[young...@gmail.com]

Hi,

   I am just starting to learn the execution aspects of CopySeq, and I am already having issues.  I installed the software, along with other dependency programs on CentOS5, and just tried to execute the following command:

 java -jar copyseq-1.7.1.jar -b /projects/seqdev/ysong_CNV_test/CNV_test_normal.sorted.bam -t /home/ysong/copyseq_test/hg18.2bit -n data/gcm/hg18/gcm_30Mb_10kb.svf -r data/vlibs/hg18/example_cnv_library.svf -v data/vm/hg18/ -M data/mmap/hg18/ -f example_cnv_library_cs -o /projects/seqdev/ysong_CNV_test/CopySeq_test/

 and I am getting the following error messages:

Exception in thread "main" java.lang.NoClassDefFoundError: de.hswt.copyseq.cs.CS
   at java.lang.Class.initializeClass(libgcj.so.7rh)
   at de.hswt.copyseq.main.Main.main(Main.java:120)
Caused by: java.lang.ClassFormatError: net.sf.samtools.util.CloseableIterator (unrecognized class file version)
   at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
   at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
   at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
   at java.net.URLClassLoader.findClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at java.lang.Class.forName(libgcj.so.7rh)
   at java.lang.Class.initializeClass(libgcj.so.7rh)
   ...1 more

 
   I am not sure exactly where these messages are coming from.  If you could help me out with this, I'd be much appreciated.  Thank you in advance.

 Young