--- a/quantify.pl	Tue Oct 28 01:35:32 2014 -0400
+++ b/quantify.pl	Thu Oct 30 21:29:19 2014 -0400
@@ -422,16 +422,16 @@
 sub mapping{
     my $err;
 ## build bowtie index
-    print STDERR "building bowtie index\n";
+    #print STDERR "building bowtie index\n";
     $err = `bowtie-build $pre_file_name miRNA_precursor`;
 
 ## map mature sequences against precursors
-    print STDERR "mapping mature sequences against index\n";
-	$err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature mature_mapped.bwt`;
+    #print STDERR "mapping mature sequences against index\n";
+	$err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature > mature_mapped.bwt 2> run.log`;
 
 ## map reads against precursors
-    print STDERR "mapping read sequences against index\n";
-    $err=`bowtie -p $threads -f -v $mismatch -a --best --strata --norc miRNA_precursor $read --al mirbase_mapped.fa --un mirbase_not_mapped.fa read_mapped.bwt `;
+    #print STDERR "mapping read sequences against index\n";
+    $err=`bowtie -p $threads -f -v $mismatch -a --best --strata --norc miRNA_precursor $read --al mirbase_mapped.fa --un mirbase_not_mapped.fa > read_mapped.bwt 2> run.log`;
 
 }