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

[Bob H. <han...@br...>]

Hi, Jin,
Forgive me if this is too obvious, but is SVToolkit.jar in the current 
directory?
The -cp argument must list the paths to SVToolkit.jar and 
GenomeAnalysisTK.jar.
If this isn't the problem, can you check the version with "java -jar 
SVToolkit.jar"?
-Bob

On 10/24/11 11:55 AM, Szatkiewicz, Jin P wrote:
> 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.
>
>
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