Hi,

Any chances someone could give me hint on this issue?

Thanks in advance,
Carlos

On Tue, Nov 29, 2011 at 2:02 PM, Carlos Borroto
<carlos.borr...@gmail.com> wrote:
> Hi,
>
> I'm testing the GATK pipeline and I ran into a problem with "Variant
> Recalibrator" tool. It seems I don't have correctly configure R and
> GATK on my instance, as this tool is failing with this error:
> mv: 
> /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf:
> No such file or directory
>
> I see this PDF is builded with R and I also see this in the log file:
> INFO  17:11:44,260 VariantRecalibrator - Executing: Rscript
> /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat
> WARN  17:11:48,407 RScriptExecutor - RScript exited with 1. Run with
> -l DEBUG for more info.
>
> In the testing server this tool does work:
> http://test.g2.bx.psu.edu/u/cjav/h/variant-recalibrator---tutorial
>
> At least after making sure the input VCF file has matching annotations
> string to the one you want to select in Galaxy.
>
> Any help on what need to be done to get this configuration right. BTW
> I already have R and Rpy correctly configured and I can run tools like
> "Statistics/Summary Statistics".
>
> Thanks!
> Carlos

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