diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e95a0e6c1..ddd75e232 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -275,13 +275,16 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed public void onTraversalDone(Long result) { logger.info("Calculating quantized quality scores..."); quantizeQualityScores(); + + logger.info("Writing recalibration report..."); + generateReport(); + logger.info("...done!"); + if (!RAC.NO_PLOTS) { logger.info("Generating recalibration plots..."); generatePlots(); } - logger.info("Writing recalibration report..."); - generateReport(); - logger.info("...done!"); + logger.info("Processed: " + result + " sites"); }