--- a/wrapper.sh	Wed Jun 22 10:07:28 2016 -0400
+++ b/wrapper.sh	Thu Jun 23 03:58:03 2016 -0400
@@ -146,11 +146,23 @@
 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
 
 echo "---------------- aa_histogram.r ----------------"
-echo "---------------- aa_histogram.r ----------------<br />" >> $output
+echo "---------------- aa_histogram.r ----------------<br />" >> $log
 
 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png "" 2>&1
+
+echo "---------------- aa_histogram.r ca ----------------"
+echo "---------------- aa_histogram.r ca ----------------<br />" >> $log
+
 Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1
+
+echo "---------------- aa_histogram.r cg ----------------"
+echo "---------------- aa_histogram.r cg ----------------<br />" >> $log
+
 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1
+
+echo "---------------- aa_histogram.r cm ----------------"
+echo "---------------- aa_histogram.r cm ----------------<br />" >> $log
+
 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1
 
 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
@@ -367,10 +379,10 @@
 
 echo "</table>" >> $outdir/base_overview.html
 
+mv $log $outdir/log.html
+
+cp $outdir/index.html $log
+
 echo "---------------- Done! ----------------"
 echo "---------------- Done! ----------------<br />" >> $log
 
-mv $log $outdir/log.html
-
-mv $outdir/index.html $log
-