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:
Please let us know what you find out and if we can provide additional assistance.
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Loading required package: reshape
Loading required package: plyr
Attaching package: 'reshape'
The following object(s) are masked from 'package:plyr':
Loading required package: grid
Loading required package: proto
On Dec 1, 2011, at 10:37 AM, Carlos Borroto wrote:
> Any chances someone could give me hint on this issue?
> Thanks in advance,
> On Tue, Nov 29, 2011 at 2:02 PM, Carlos Borroto
> <carlos.borroto(a)gmail.com> wrote:
>> 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:
>> 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
>> 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:
>> At least after making sure the input VCF file has
>> 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".
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