[svtoolkit-help] FW: problem encountered, can you please help?

[Szatkiewicz, J. P <jin...@me...>]

To whom it may concern, 

I am a new user to GenomeStrip. I am creating the genome mask file as the first step. 

However, using the command below, I got the following error message. Can anyone have an idea how to fix it? Many thanks!!

Best,

Jin

COMMAND:
+++++++++++++++++++++
export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}

java -Xmx2g -cp SVToolkit.jar:GenomeAnalysisTK.jar \
    org.broadinstitute.sv.apps.ComputeGenomeMask \
     -R hg19pfs.fasta \
     -O hg19pfs.mask100.chr1.fasta \
     -readLength 100 \
     -sequence chr1
+++++++++++++++++++++++

ERROR:
++++++++++++++++++++++++++++
Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sv/apps/ComputeGenomeMask
Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sv.apps.ComputeGenomeMask
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: org.broadinstitute.sv.apps.ComputeGenomeMask.  Program will exit.