--- a/run-multi_join_serial.pl	Wed Apr 15 14:43:04 2015 -0400
+++ b/run-multi_join_serial.pl	Wed Apr 15 16:31:04 2015 -0400
@@ -11,7 +11,6 @@
 #require '/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/GetOptWC.pm';
 
 GetOptions(
-    "log=s"                     => \$log,
     "join_file=s"             => \$data_in,
     "join_col=s"	     => \$coljoin,
     "time"                   => \$mTime,
@@ -36,8 +35,6 @@
 
 # #
 use IO::Handle;
-open OUTPUT, '>>',$log or die "cant open this file for OUTPUT: $log. Computer says: $!\n";;
-open ERROR,  '>>', $log  or die "cant open this file for ERROR: $log. Computer says: $!\n";
 STDOUT->fdopen( \*OUTPUT, 'a' ) or die "cant open file $!\n";   #cms changing mode from 'w' to 'a' for multiple files in one run
 STDERR->fdopen( \*ERROR,  'a' ) or die "cant open file $!\n";   #cms changing mode from 'w' to 'a' for multiple files in one run
 # # #
@@ -55,7 +52,6 @@
         ## At the end of the last iteration
 	close($Filenames);
         
-	print "\nLAST ITERATION COMPLETED and at least two input files provided.\n";
 
 	##Read in file temp_filenames.txt
 	open(my $tmpfile, "<", "temp_filenames.txt") or die "Cannot open temp file: $!";
@@ -69,11 +65,6 @@
 	##Also need to send yes/no for keeping header:
 	push @fileArray, $header_yes;
 
-	##Debug:
-	print "\nFirst file fileArray[0] is $fileArray[0].";
-	print "\nOutput file is next-to-last val in fileArray, $fileArray[-2].";
-	print "\nUse header? is last val in fileArray, $fileArray[-1].";
-	print "\nSecond file now is fileArray[2], $fileArray[2].";
 
 	##@fileArray has one file per line,output,header_yes, so $N+1 rows
 	my $f=0;
@@ -82,7 +73,6 @@
 	do {
 
 		@first = split('\t',$fileArray[$f]);  ##was filename\tJoinCol
-		print "\njoin column from first line is $first[1].";
 
 		##CMS DEALING WITH HEADER OR NOT:
                 if ($header_yes eq "no") {
@@ -90,7 +80,6 @@
                 	$fh1 = IO::File->new("<$first[0]");
 			my $line1file1 = $fh1->getline();
 			$line1file1 =~ s/\s+$//;
-			#print "\nline1file1 is $line1file1\n"; ##DEBUG
 			@cols = split "\t",$line1file1;
 			my $numcols1 = @cols;
 			my $head1;
@@ -99,7 +88,6 @@
 			}
 			$head1.="C$numcols1\n";
 			open(my $fh_sub, '>', './header1.txt') or die "OOPIES: $!\n";
-			print "\nheader first file $first[0] on next line:\n$head1"; ##DEBUG
 			print $fh_sub $head1;
 			close $fh_sub;
 			system("cat $first[0] >> ./header1.txt");  ##put header in front of file
@@ -123,18 +111,14 @@
                                 $head2.="C$i\t";
                         }
                         $head2.="C$numcols2\n";
-                        open(my $fh_sub, '>', './header2.txt') or die "OOPIES: $!\n";
-                        print "\nheader from $second[0] on next line:\n$head2";  ##DEBUG
+                        open(my $fh_sub, '>', './header2.txt') or die "ERROR: $!\n";
 			print $fh_sub $head2;
                         close $fh_sub;
 			system("cat $second[0] >> ./header2.txt");
 			$second[0]="./header2.txt";
                 }
 
-		print "\ncommand following:\n";
-		print "/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl -File1=$first[0] -File2=$second[0] -cola1=$first[1] -cola2=$second[1] -colb1=$first[1] -colb2=$second[1]";
 		system("/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl", "-File1=$first[0]", "-File2=$second[0]", "-cola1=$first[1]", "-cola2=$second[1]", "-colb1=$first[1]", "-colb2=$second[1]");
-		print "\nOut from system call on next line:\n$!";
 		$f+=2;
 		system("mv file1_file2.txt joined.txt");
 		if ($header_yes eq "no") {
@@ -145,7 +129,6 @@
 	
 	for ($f; $f<$N; $f++) {
                 my @current = split('\t',$fileArray[$f]);  ##was filename\tJoinCol
-                print "\njoin column from first line is $first[1].";
 
 		if ($header_yes eq "no") {
                         my $fh;
@@ -160,17 +143,13 @@
                         }
                         $head.="C$numcols\n";
                         open(my $fh_sub, '>', './header.txt') or die "OOPIES: $!\n";
-			print "\nheader from file $current[0] on next line:\n$head";  ##DEBUG
                         print $fh_sub $head;
                         close $fh_sub;
                         system("cat $current[0] >> ./header.txt");
                         $current[0]="./header.txt";
                 }
 
-		print "\ncommand following:\n";
-		print "/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl -File1=joined.txt -File2=$current[0] -cola1=$first[1] -cola2=$current[1] -colb1=$first[1] -colb2=$current[1]";
                 system("/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/addColumnsFromFile2ToFile1.pl","-File1=joined.txt", "-File2=$current[0]", "-cola1=$first[1]", "-cola2=$current[1]", "-colb1=$first[1]", "-colb2=$current[1]");
-                print "\nOut from system call on next line:\n$!";
 		system("mv file1_file2.txt joined.txt");
 		if ($header_yes eq "no") {
 			system("rm ./header.txt");
@@ -188,9 +167,7 @@
 
 }
 elsif ($N<2) {
-	print "\n<br /><i>Only one file; not running join.</i>\n";
 }
 
 
 
-#print "LOG $mv\n";