The current GATK version is 3.3-0

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# (howto) Debug AnalyzeCovariates Error in R

edited June 18

When you are running AnalyzeCovariates to analyze your BQSR outputs, you may run into an error starting with this:

org.broadinstitute.sting.utils.R.RScriptExecutorException: RScript exited with 1. Run with -l DEBUG for more info.


The main reason why this error often occurs is simple, and so is the solution. The script depends on some external R libraries, so if you don’t have them installed, the script fails. To find out what libraries are necessary and how to install them, you can refer to this FAQ article.

One other common issue is that the version of ggplot2 you have installed is very recent and is not compatible with the BQSR script. If so, download this file and use it to generate the plots manually according to the instructions below.

If you have already checked that you have all the necessary libraries installed, you’ll need to run the script manually in order to find out what is wrong. To new users, this can seem complicated, but it only takes these 3 simple steps to do it!

### 1. Re-run AnalyzeCovariates with these additional parameters:

• -l DEBUG (that's a lowercase L, not an uppercase i, to be clear) and
• -csv my-report.csv (where you can call the .csv file anything; this is so the intermediate csv file will be saved).

### 2. Identify the lines in the log output that says what parameters the RScript is given.

The snippet below shows you the components of the R script command line that AnalyzeCovariates uses.

INFO  18:04:55,355 AnalyzeCovariates - Generating plots file 'RTest.pdf'
DEBUG 18:04:55,672 RecalUtils - R command line: Rscript (resource)org/broadinstitute/gatk/utils/recalibration/BQSR.R /Users/schandra/BQSR_Testing/RTest.csv /Users/schandra/BQSR_Testing/RTest.recal /Users/schandra/BQSR_Testing/RTest.pdf
DEBUG 18:04:55,687 RScriptExecutor - Executing:
DEBUG 18:04:55,688 RScriptExecutor -   Rscript
DEBUG 18:04:55,688 RScriptExecutor -   -e
DEBUG 18:04:55,688 RScriptExecutor -   tempLibDir = '/var/folders/j9/5qgr3mvj0590pd2yb9hwc15454pxz0/T/Rlib.2085451458391709180';source('/var/folders/j9/5qgr3mvj0590pd2yb9hwc15454pxz0/T/BQSR.761775214345441497.R');
DEBUG 18:04:55,689 RScriptExecutor -   /Users/schandra/BQSR_Testing/RTest.csv
DEBUG 18:04:55,689 RScriptExecutor -   /Users/schandra/BQSR_Testing/RTest.recal
DEBUG 18:04:55,689 RScriptExecutor -   /Users/schandra/BQSR_Testing/RTest.pdf


So, your full command line will be:

RScript BQSR.R RTest.csv RTest.recal RTest.pdf


• BQSR.R is the name of the script you want to run. It can be found here
• RTest.csv is the name of the original csv file output from AnalyzeCovariates.
• RTest.recal is your original recalibration file.
• RTest.pdf is the output pdf file; you can name it whatever you want.

### 3. Run the script manually with the above arguments.

For new users, the easiest way to do this is to do it from within an IDE program like RStudio. Or, you can start up R at the command line and run it that way, whatever you are comfortable with.

Post edited by Geraldine_VdAuwera on
Tagged:

• IndianaPosts: 5Member

Hi GATK! Would it be possible for you to post an updated link to the BQSR.R script? The link above is no longer working. I spent awhile poking around GitHub looking for it, but seemed to just be going in circles. Best wishes!

• IndianaPosts: 5Member

Nevermind, link at the top of the page DOES work, I'll try with this script...