diff --git a/R/plot_GATK_performance_log.R b/R/plot_GATK_performance_log.R
index 39b2b3c70..e435e871d 100644
--- a/R/plot_GATK_performance_log.R
+++ b/R/plot_GATK_performance_log.R
@@ -4,16 +4,16 @@ RUNME = T
 onCMDLine = ! is.na(args[1])
 DATA_FILE = args[1]
 DESCRIPTION = args[2]
-OUTPUT_PDF = paste(DATA_FILE, ".pdf", sep="")
+#OUTPUT_PDF = paste(DATA_FILE, ".pdf", sep="")
 
-MAX_POINTS = 1000
+MAX_POINTS = 100000
 
 if ( onCMDLine ) { 
    print(paste("Reading data from", DATA_FILE))
    d = read.table(DATA_FILE, header=T)
 } 
 
-if ( onCMDLine ) pdf(OUTPUT_PDF)
+#if ( onCMDLine ) pdf(OUTPUT_PDF)
 
 vec.margin <- function(x) {
     l = length(x)
@@ -43,24 +43,27 @@ generateOneReport <- function(d) {
     qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99))
 
     # unit processing time
+    if ( onCMDLine ) png(paste(DATA_FILE, ".speed.png", sep=""), width=1080, height=1080)
     dpoints = everyNth(d, MAX_POINTS)
     plot(dpoints$elapsed.time, dpoints$processing.speed, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Processing speed (seconds per 1M units)", ylim=c(qs[1], qs[3]), type="b", col="cornflowerblue", lwd=2)
     abline(h=qs[2], lty=2)
+    if ( onCMDLine ) dev.off()
 
     # instantaneous processing speed
+    if ( onCMDLine ) png(paste(DATA_FILE, ".marginal.png", sep=""), width=1080, height=1080)
     running_median_window = 101
     rm = runmed(d$units.processed.margin, running_median_window)
     POINT_COL = "#0000AA33"
     plot(dpoints$elapsed.time, dpoints$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL)
     lines(d$elapsed.time, rm, lwd=3, col="red")
     legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
+    if ( onCMDLine ) dev.off()
 }
 
 if ( RUNME ) {
     generateOneReport(d)
 }
 
-if ( onCMDLine ) dev.off()