--- est_prepro.pm.ori	2011-02-21 11:37:20.000000000 +0100
+++ est_prepro.pm	2011-02-22 00:46:57.000000000 +0100
@@ -478,7 +478,7 @@
 					}
 					else {
 						print localtime()." There is a problem with the length in sequence ".$temp_seq->id."\n";
-						print localtime()." from file: $seq_file\n. Quality and sequence length don't match.\n";
+						print localtime()." from file: $seq_file. Quality $temp_qual->length and sequence $temp_seq->length length don't match.\n";
 						#print $temp_seq->desc."\n";
 						return 0;
 					}
@@ -973,7 +973,7 @@
 	#check that $assignments_file exist
 	if (not(-r $assi_file)){
 		print localtime().": ######################################################################\n";
-		print localtime().": WARNING: Assignment file for lucy is not found or not defined\n";
+		print localtime().": WARNING: Assignment file $assi_file for lucy is not found or not defined\n";
 		print localtime().": Lucy will not be used in the preprocessing\n";
 		print localtime().": ######################################################################\n";
 	}else{
@@ -1062,7 +1062,7 @@
 	my $tag=read_config($config,'assignment_tag','');
 	$command="echo $tag".$library.">> $temp_log";
 	chdir ($temp_dir);	#we change the directory becouse lucy write some stuff in the working directory
-	system($command);
+	system($command) or die print localtime().": $command failed: $!\n";
 	chdir ($actual_dir);
 	# Options used:
 		# $in_seq		fasta sequences generated by phred
@@ -1086,9 +1086,9 @@
 	
 	# lucy log is moved to the results directory
 	$command="cat $temp_log >> $log";
-	system($command);
+	system($command) or die print localtime().": failed to append $temp_log contents to $log\n";
 	$command="rm $temp_log";
-	system($command);
+	system($command) or die print localtime().": failed to delete $temp_log\n";
 	
 	if ($success)
 	{
@@ -1112,8 +1112,8 @@
 	print localtime().": Parsing the lucy output\n";
 	# now we check that the input file is in place
 	unless (check_file($lucy_log_file,"lucy log file")){
-		print localtime().": WARNING there is no lucy log file\n";
-		print localtime().": Maybe lucy has not been used by any library\n";
+		print localtime().": WARNING there is no lucy log file $lucy_log_file\n";
+		print localtime().": Maybe lucy has not been used by any library?\n";
 		return 1;
 	}
 	
@@ -1490,7 +1490,7 @@
 sub run_seqclean($$$$$$$$$$$$)
 {
 	my $config=shift;
-	my $library=shift;		# informational porpouse only
+	my $library=shift;		# informational purpose only
 	my $trimmed_fasta_file=shift;	# name for the trimmed sequences file
 	my $trimmed_qual_file=shift;	# name for the trimmed quality file
 	my $seqclean_report_file=shift;	# report file with the masked area
@@ -1518,7 +1518,13 @@
 	#The file with the vector (univec recommended)
 	my $vec_file=read_config($config,'seqclean_vec_dat','');
 	unless (check_file($vec_file,"vector database")){return 0};
-	
+	if (! -r $vec_file.".nin") {
+		print localtime().": Formatting database with formatdb -p F -i $vec_file\n";
+		system("cd `dirname $vec_file` && formatdb -p F -i $vec_file");
+		if (! -r $vec_file.".nin") {
+			die "Failed to formatdb $vec_file: $!\n";
+		}
+	}
 	my $seqclean_success=1;	# control variable
 	my $command;
 	my $temp;
@@ -1749,7 +1755,7 @@
 sub seqclean_masking_assignments ($$$$$$)
 {
 	my $config=shift;
-	print localtime().": Masking the sequences following seqclean's recomendations\n";
+	print localtime().": Masking the sequences following seqclean's recommendations\n";
 	my @libraries=split(',',read_config($config,'libraries',''));	# libraries names
 	my $report=read_config($config,'seqclean_report','');	# base name for the report generated by seqclean, this is the file with the instruccions for masking the sequences
 	my $in_seq=shift;		# base name for the trimmed sequences file generated by lucy