--- a/siRNA.pl	Wed Oct 29 05:03:38 2014 -0400
+++ b/siRNA.pl	Thu Oct 30 21:31:55 2014 -0400
@@ -143,6 +143,8 @@
 for (my $i=0;$i<@mark ;$i++) {
 	$id{$mark[$i]}=$i+4;
 }
+
+
 group_and_filter();   #collapse reads to tags
 
 rfam();
@@ -423,16 +425,20 @@
 }
 
 sub dec_pel{
-	print "start:\n";
+	print "\n******************\nstart:\n";
 	Time();
 	my $sample=shift(@_);
 	my @each=split/\s+/,$sample;
 	print "$each[0]\t$each[1]\n";
 	my $deg_sample_dir=$deg_dir."$each[0]_VS_$each[1]\/";
 	mkdir ("$deg_sample_dir");
+	print "read: $read\n";
+	print "deg_sample_dir: $deg_sample_dir\n";
+	print "$id{$each[0]}\t$each[0]\n";
+	print "$id{$each[1]}\t$each[1]\n";
 	my $deg=`perl $path\/DEGseq_2.pl -i $read -outdir $deg_sample_dir -column1 $id{$each[0]} -mark1 $each[0] -column2 $id{$each[1]} -mark2 $each[1]`; #-depth1 -depth2
 	my $time2=time();
-	print "end:\n";
+	print "end:\n*************************\n";
 	Time();
 	sleep 1;
 }