Hi Carlos,

Are you using a version of GATK that is 1.3? 

Another possibility is that you are missing an R library (e.g. 'ggplot2'), that 
is used by the VariantRecalibrator for building the plots. Start up an 
interactive R session and type: "library('ggplot2')"

If you are missing the library, then you will have to install it (it is 
available in CRAN).  If you have the library, then that is not the problem, but 
you can get the actual reason for the Rscript failure by running the Rscript 
directly, in this case:
"Rscript 
/Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat"


Please let us know what you find out and if we can provide additional 
assistance.


Thanks for using Galaxy,

Dan



dan$ R

R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('ggplot2')
Loading required package: reshape
Loading required package: plyr

Attaching package: 'reshape'

The following object(s) are masked from 'package:plyr':

    rename, round_any

Loading required package: grid
Loading required package: proto
> 






On Dec 1, 2011, at 10:37 AM, Carlos Borroto wrote:

> 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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