Re: [Samtools-help] Error in CollectGcBiasMetrics (Picard)

[Kathleen T. <kti...@br...>]

Sorry! The R scripts were inadvertently left behind when moving these  
tools to the public Picard repository.  I'm working on moving and  
testing them now, and will send a note to the list when that is done.

Kathleen Tibbetts

On Jun 21, 2010, at 5:33 PM, Tadigotla, Vasisht wrote:

> Hi,
>
> I'm trying to run CollectGcBiasMetrics and I'm getting the error  
> below with picard release 1.23. Are there any other files that I  
> need apart from the zip archive on sourceforge to get this to work.
>
> Thanks,
> Vasisht
>
> [Mon Jun 21 16:56:43 EDT 2010]  
> net.sf.picard.analysis.CollectGcBiasMetrics done.
> Runtime.totalMemory()=1530593280
> Exception in thread "main" java.lang.IllegalArgumentException:  
> Script [edu/mit/broad/picard/sam/gcBias.R] not found in classpath
>        at  
> net.sf.picard.util.RExecutor.writeScriptFile(RExecutor.java:85)
>        at  
> net.sf.picard.util.RExecutor.executeFromClasspath(RExecutor.java:54)
>        at  
> net 
> .sf 
> .picard 
> .analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:212)
>        at  
> net 
> .sf 
> .picard 
> .cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
>        at  
> net 
> .sf 
> .picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java: 
> 91)
>
>
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