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