--- pipe_db.pm.ori	2011-02-22 18:08:58.000000000 +0100
+++ pipe_db.pm	2011-02-22 14:48:03.000000000 +0100
@@ -90,29 +90,29 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 
 	#the location statistics
 	my $st="INSERT INTO pssr_location_view SELECT CASE ((ssr_end<orf_begin)*1+(ssr_begin>orf_end)*2+(ssr_begin>orf_begin && ssr_end<orf_end)*3) WHEN 0 THEN 'other' WHEN 1 THEN '5_utr' WHEN 2 THEN '3_utr' WHEN 3 THEN 'in_orf' END AS location,count(*) AS count FROM ESTScan_orf,sputnik_ssr WHERE sputnik_ssr.seq_name=ESTScan_orf.seq_name  GROUP BY (ssr_end<orf_begin)*1+(ssr_begin>orf_end)*2+(ssr_begin>orf_begin && ssr_end<orf_end)*3";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	#the unit kind statistics
 	$st="INSERT INTO pssr_kind_view SELECT unit,count(*) AS count FROM sputnik_ssr GROUP BY unit";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -128,18 +128,18 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 
 	#we calculate the min, max and average unigene length
 	my $st="SELECT MIN(length) AS min_seq_len, MAX(length) AS max_seq_len, AVG(length) AS avg_seq_len FROM sequence WHERE object_type='contig' OR object_type='singleton'";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my $min;my $max;my $avg;
@@ -154,11 +154,11 @@
 	}
 	$st="INSERT unigene_structure_annotation_view (min_seq_len,max_seq_len,avg_seq_len) VALUES ($min,$max,$avg)";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -173,20 +173,20 @@
 	#we calculate the min, max and average num ESTs per unigene
 	$st='CREATE TEMPORARY TABLE est_per_unigene SELECT count(*) AS num_est,unigene FROM est WHERE unigene IS NOT NULL GROUP BY unigene';
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my $st='SELECT MAX(num_est) AS max_num_est, AVG(num_est) AS avg_num_est FROM est_per_unigene';
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	while (my @record=$sth->fetchrow_array){
@@ -196,11 +196,11 @@
 	close_st($sth);
 	$st="UPDATE  unigene_structure_annotation_view SET max_est=$max,avg_est=$avg";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -213,11 +213,11 @@
 	#now the annotated unigenes
 	my $st="SELECT COUNT(*) FROM sequence WHERE annotation IS NOT NULL AND (object_type='contig' OR object_type='singleton')";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my @record=$sth->fetchrow_array;
@@ -225,22 +225,22 @@
 	close_st($sth);
 	$st="UPDATE unigene_structure_annotation_view SET n_uni_with_annot=$n_annot";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	#now the full len
 	my $st="SELECT COUNT(*) FROM sequence WHERE full_length IS NOT NULL AND (object_type='contig' OR object_type='singleton')";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	@record=$sth->fetchrow_array;
@@ -248,11 +248,11 @@
 	close_st($sth);
 	$st="UPDATE unigene_structure_annotation_view SET n_uni_with_full_len=$n_annot";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	); 
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -263,14 +263,14 @@
 	my $dbh=shift;
 	my $values=shift;
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	my $i=1;
 	foreach my $value (@$values){
 		$sth->bind_param($i,$value);
 		execute_st($sth) or (
-			print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+			print localtime().": There was a problem executing the statement $st" and
 			return 0
 		);
 		$i++;
@@ -282,7 +282,7 @@
 	my $dbh=shift;
 	my $intervals=shift;
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	my $bottom;
@@ -293,7 +293,7 @@
 			$sth->bind_param(1,$bottom);
 			$sth->bind_param(2,$top);
 			execute_st($sth) or (
-				print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+				print localtime().": There was a problem executing the statement $st" and
 				return 0
 			);
 			my @record=$sth->fetchrow_array;
@@ -329,16 +329,16 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="INSERT psnp_accessions_view (accession) SELECT DISTINCT accession FROM putative_snp_seq";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -354,26 +354,26 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="CREATE TEMPORARY TABLE psnp_mutations_temp (nucleotides CHAR(10),is_snp BOOL,INDEX(nucleotides,is_snp)) SELECT GROUP_CONCAT(DISTINCT(putative_snp_seq.nucleotide) ORDER BY putative_snp_seq.nucleotide) AS nucleotides,putative_snp.is_snp FROM putative_snp_seq,putative_snp WHERE putative_snp_seq.psnp_id=putative_snp.psnp_id AND putative_snp_seq.nucleotide!='*' AND putative_snp.is_indel=0 GROUP BY putative_snp_seq.psnp_id";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="INSERT INTO psnp_mutations_view (mutations,is_snp,count) SELECT nucleotides,is_snp,COUNT(*) AS count FROM psnp_mutations_temp WHERE LENGTH(nucleotides)=3 GROUP BY nucleotides,is_snp";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -389,16 +389,16 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="INSERT reciprocal_species_view (species,type) SELECT species,type FROM reciprocal_similar_sequences GROUP BY species";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -416,46 +416,46 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="INSERT INTO go_uni_aspect_view (db,aspect,num_unigenes,word) SELECT go.db,go.aspect,count(DISTINCT go.seq_id) AS num_unigenes, CONCAT(go.aspect,go.db) AS word FROM clone,go,est WHERE est.clone=clone.name AND go.seq_id=est.unigene AND go.is_slim=1 GROUP BY word";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="INSERT INTO go_uni_aspect_library_view (db,aspect,library,num_unigenes,word) SELECT go.db,go.aspect,clone.library,count(DISTINCT go.seq_id) AS num_unigenes, CONCAT(go.aspect,go.db,clone.library) AS word  FROM clone,go,est WHERE est.clone=clone.name AND go.seq_id=est.unigene AND go.is_slim=1 GROUP BY word";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="INSERT INTO go_term_aspect_view (db,aspect,go_id,definition,num_go,word) SELECT db,go.aspect,go.go_id,definition,count(DISTINCT go.seq_id) AS num_go, CONCAT(go.go_id,go.aspect,db) AS word FROM go,go_def WHERE is_slim=1 AND go_def.go_id=go.go_id GROUP BY word";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="INSERT INTO go_term_aspect_library_view (db,aspect,go_id,definition,library,num_go,word) SELECT db,go.aspect,go.go_id,definition,clone.library,count(DISTINCT go.seq_id) AS num_go, CONCAT(go.go_id,go.aspect,db,clone.library) AS word FROM go,go_def,est,clone WHERE is_slim=1 AND go_def.go_id=go.go_id AND go.seq_id=est.unigene AND est.clone=clone.name GROUP BY word";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -473,27 +473,27 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="CREATE TEMPORARY TABLE super_count (INDEX(type)) SELECT superunigene,count(*)>1 AS type FROM superunigene GROUP BY superunigene";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	
 	$st="INSERT INTO superunigene_view (type,num_superunigenes) SELECT type,count(*) AS num_superunigenes FROM super_count GROUP BY type";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -510,17 +510,17 @@
 
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	
 	my $st="INSERT INTO unigene_view (type,num_unigenes) SELECT object_type,count(*) AS num_unigenes FROM sequence WHERE object_type='contig' OR object_type='singleton' GROUP BY object_type";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
@@ -539,7 +539,7 @@
 	clean_tables($config,@table) or return 0;
 	my $db=read_config($config,'db_path','');		#database in the form dbi:$dbi_driver:$db_name:$host
 	my $dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	
@@ -547,11 +547,11 @@
 	#clones per library
 	my $st="SELECT clone.library,COUNT(distinct clone.name) AS num_clones FROM clone GROUP BY clone.library";
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %clones;
@@ -563,11 +563,11 @@
 	#raw_est per library
 	$st="SELECT clone.library,COUNT(*) AS num_raw_est FROM est,clone WHERE est.clone=clone.name AND raw_seq IS NOT NULL GROUP BY clone.library";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %raw_est;
@@ -579,11 +579,11 @@
 	#clean_est per library
 	$st='SELECT clone.library,COUNT(*) AS num_clean_est,AVG(sequence.length) AS mean_length,STD(sequence.length) AS std_dev FROM est,sequence,clone WHERE est.processed_seq=sequence.name AND est.clone=clone.name GROUP BY clone.library;';
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %clean_est;
@@ -599,11 +599,11 @@
 	#singletons per library
 	$st="SELECT clone.library,COUNT(distinct sequence.name) AS num_singletons FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='singleton' GROUP BY clone.library";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %singletons;
@@ -615,11 +615,11 @@
 	#contigs per library
 	$st="SELECT clone.library,COUNT(distinct sequence.name) AS num_contigs FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='contig' GROUP BY clone.library";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %contigs;
@@ -631,11 +631,11 @@
 	#unigenes per library
 	$st="SELECT clone.library,COUNT(distinct unigene) AS num_unigenes FROM est,clone WHERE est.clone=clone.name GROUP BY clone.library";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %unigenes;
@@ -647,11 +647,11 @@
 	#full length per library
 	$st="SELECT clone.library,COUNT(distinct sequence.name) AS num_full_len FROM clone,sequence,est WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.full_length IS NOT NULL GROUP BY clone.library";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %full_len;
@@ -663,21 +663,21 @@
 	#spec unigenes length per library
 	$st="CREATE TEMPORARY TABLE uni_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib,  clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name  GROUP BY sequence.name";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="SELECT lib_concat as library,COUNT(*) AS num_unigenes_ex FROM uni_library_count WHERE num_lib=1 GROUP BY lib_concat";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %spec_unigenes;
@@ -689,21 +689,21 @@
 	#spec contigs per library
 	$st="CREATE TEMPORARY TABLE contig_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib, clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='contig' GROUP BY sequence.name";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="SELECT lib_concat as library,COUNT(*) AS num_contigs_ex FROM contig_library_count WHERE num_lib=1 GROUP BY lib_concat";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %spec_contigs;
@@ -715,21 +715,21 @@
 	#spec singletons per library
 	$st="CREATE TEMPORARY TABLE singleton_library_count (PRIMARY KEY(name), INDEX (num_lib))SELECT sequence.name, COUNT(DISTINCT clone.library) AS num_lib, clone.library AS lib_concat FROM sequence,est,clone WHERE sequence.name=est.unigene AND est.clone=clone.name AND sequence.object_type='singleton' GROUP BY sequence.name";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	close_st($sth);
 	$st="SELECT lib_concat as library,COUNT(*) AS num_singletons_ex FROM singleton_library_count WHERE num_lib=1 GROUP BY lib_concat";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	execute_st($sth) or (
-		print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem executing the statement $st" and
 		return 0
 	);
 	my %spec_singletons;
@@ -742,7 +742,7 @@
 	#now we have all the data and we should store it in the view
 	$st="INSERT INTO library_view (library, num_clones, num_raw_est, num_clean_est, num_singletons, num_contigs, num_unigenes, num_full_len, num_spec_singletons, num_spec_contigs, num_spec_unigenes,avg_est_len,std_est_len) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)";
 	$sth=prepare_st($dbh,$st) or (
-		print localtime().": There was a problem preparing the statement $st: $DBI::errstr\n" and
+		print localtime().": There was a problem preparing the statement $st" and
 		return 0
 	);
 	foreach my $lib (keys(%libraries)){
@@ -760,7 +760,7 @@
 		$sth->bind_param(12,$avg_est_len{$lib});
 		$sth->bind_param(13,$std_est_len{$lib});
 		execute_st($sth) or (
-			print localtime().": There was a problem executing the statement $st: $DBI::errstr\n" and
+			print localtime().": There was a problem executing the statement $st" and
 			return 0
 		);
 	}
@@ -776,12 +776,12 @@
 	my $config=shift;
 	my $dir = $$config{'chromat_dir'};
 	opendir DIR,$dir or (
-		print localtime().": It was not possible to open the chromat directory $dir: $!\n" and
+		print localtime().": It was not possible to open the chromat directory: $dir\n" and
 		return 0
 	);
 	my @libraries = grep {/^[^\.]/} readdir(DIR);
 	if (!$libraries[0]){
-		print localtime().": No libraries found in the libraries directory $dir: $!\n";
+		print localtime().": No libraries found in the libraries directory: $dir\n";
 		return 0;
 	}
 	close DIR;
@@ -791,18 +791,18 @@
 	my $db=read_config($config,'db_path','');
 	my $dbh=open_db($db);
 	unless ($dbh) {
-		print localtime().": Database $dbh is not reachable: $DBI::errstr\n";
+		print localtime().": Database $dbh is not reachable\n";
 		return 0;
 	}
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": Unable to prepare statement: $st: $DBI::errstr\n" and
+		print localtime().": Unable to prepare statement: $st\n" and
 		return 0
 	);
 	foreach my $lib (@libraries){
 		$sth->bind_param(1,$lib);
 		$sth->execute() or (
 			print localtime().": There was a problem executing the statement:\n" and
-			print localtime().": $st: : $DBI::errstr\n" and
+			print localtime().": $st:\n" and
 			print localtime().": with the library $lib:\n" and
 			return 0
 		);
@@ -818,7 +818,7 @@
 	my $db=read_config($config,'db_path','');
 	my $dbh; my $sth;	#database and statements handlers
 	$dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	my $st="SELECT UNCOMPRESS(COMPRESS('holacaracola'))='holacaracola'";
@@ -841,7 +841,7 @@
 	if ($version){return $version}
 	my $dbh; my $sth;	#database and statements handlers
 	$dbh=open_db($db) or (
-		print localtime().": There was a problem opening the database $db: $DBI::errstr\n" and
+		print localtime().": There was a problem opening the database $db\n" and
 		return 0
 	);	#we open the database
 	$version=$dbh->get_info(18);
@@ -924,11 +924,11 @@
 		if (!$only_clean){	#nothing more to do because we just should clean 
 			if (-r $file){
 				put_csv_into_db($config,$file,$table) or (
-					print localtime().": There was a problem populating the table $table with file $file\n" and
+					print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 					return 0
 				);
 			}else{
-				print localtime().": WARNING no database file found, it should be $file\n";
+				print localtime().": WARNING no database file found, it should be $file: $!\n";
 				return 0;
 			}
 		}
@@ -945,11 +945,11 @@
 		if (!$only_clean){	#nothing more to do because we just should clean 
 			if (-r $file){
 				put_csv_into_db($config,$file,$table) or (
-					print localtime().": There was a problem populating the table $table with file $file\n" and
+					print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 					return 0
 				);
 			}else{
-				print localtime().": WARNING no working on file found, it should be $file\n";
+				print localtime().": WARNING no working_on_dat file found, it should be $file: $!\n";
 				return 0;
 			}
 		}
@@ -966,11 +966,11 @@
 		if (!$only_clean){	#nothing more to do because we just should clean 
 			if (-r $file){
 				put_csv_into_db($config,$file,$table) or (
-					print localtime().": There was a problem populating the table $table with file $file\n" and
+					print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 					return 0
 				);
 			}else{
-				print localtime().": WARNING no researcher file found, it should be $file\n";
+				print localtime().": WARNING no researcher file found, it should be $file: $!\n";
 				return 0;
 			}
 		}
@@ -987,11 +987,11 @@
 		if (!$only_clean){	#nothing more to do because we just should clean 
 			if (-r $file){
 				put_csv_into_db($config,$file,$table) or (
-					print localtime().": There was a problem populating the table $table with file $file\n" and
+					print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 					return 0
 				);
 			}else{
-				print localtime().": WARNING no marker-EST file found, it should be $file\n";
+				print localtime().": WARNING no marker-EST file found, it should be $file: $!\n";
 				return 0;
 			}
 		}
@@ -1026,11 +1026,11 @@
 	my $table = 'microarray_extract';
 	if (-r $file){
 		put_csv_into_db($config,$file,$table) or (
-			print localtime().": There was a problem populating the table $table with file $file\n" and
+			print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 			return 0
 		);
 	}else{
-		print localtime().": WARNING no extracts file found, it should be $file\n";
+		print localtime().": WARNING no extracts file found, it should be $file: $!\n";
 		return 0;
 	}
 	#loading extract mixes
@@ -1038,11 +1038,11 @@
 	my $table = 'microarray_extract_mix';
 	if (-r $file){
 		put_csv_into_db($config,$file,$table) or (
-			print localtime().": There was a problem populating the table $table with file $file\n" and
+			print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 			return 0
 		);
 	}else{
-		print localtime().": WARNING no extract mixes file found, it should be $file\n";
+		print localtime().": WARNING no extract mixes file found, it should be $file: $!\n";
 		return 0;
 	}
 	#loading the hybridizations
@@ -1050,18 +1050,18 @@
 	my $table = 'microarray_hybridization';
 	if (-r $file){
 		put_csv_into_db($config,$file,$table) or (
-			print localtime().": There was a problem populating the table $table with file $file\n" and
+			print localtime().": There was a problem populating the table $table with file $file: $!\n" and
 			return 0
 		);
 	}else{
-		print localtime().": WARNING no hybridizations file found, it should be $file\n";
+		print localtime().": WARNING no hybridizations file found, it should be $file: $!\n";
 		return 0;
 	}
 	my $file = read_config($config,'microarray_normalized_dat','');
 	my $table = 'microarray_normalized_expression';
 	if (-r $file){
 		open IN,"<$file" or (
-			print localtime().": Imposible to open file: $file\n" and
+			print localtime().": Imposible to open file: $file: $!\n" and
 			return 0
 		);
 	
@@ -1099,15 +1099,15 @@
 				$sth->bind_param(4,$cv);
 				$i_hyb++;
 				$sth->execute or (
-					print localtime().": Unable to execute stament: $st: $DBI::errstr\n" and
-					print localtime().": With line: $line\n" and
+					print localtime().": Unable to execute stament: $st\n" and
+					print localtime().": With line: $line: $DBI::errstr\n" and
 					return 0
 				);
 			}
 		}
 		close IN;
 	}else{
-		print localtime().": WARNING no normalized expression file found, it should be $file\n";
+		print localtime().": WARNING no normalized expression file found, it should be $file: $!\n";
 		return 0;
 	}
 
@@ -1179,7 +1179,7 @@
 			#print $contents{$table},"\n";
 			create_table($db,$table,$contents{$table}) or $ok=0;
 			unless ($ok){
-				print localtime().": Annotation table: $table from $db can't be created\n";
+				print localtime().": Annotation table: $table from $db can't be created: $DBI::errstr\n";
 			}
 		}
 	}
@@ -1200,7 +1200,7 @@
 			#if the table exist is removed
 		        if (check_table($db,$table)) {drop_table($db,$table) or $ok=0}
 			unless ($ok){
-				print localtime().": Annotation table: $table from $db can't be dropped\n";
+				print localtime().": Annotation table: $table from $db can't be dropped: $DBI::errstr\n";
 			}
 		}
 	}
@@ -1220,7 +1220,7 @@
 	my $db=read_config($config,'db_path','');
 	
 	open IN,"<$file" or (
-		print localtime().": Imposible to open file $file: $!\n" and
+		print localtime().": Imposible to open file: $file: $!\n" and
 		return 0
 	);
 	
@@ -1235,10 +1235,13 @@
 		return 0;
 	}
 	my $sth=prepare_st($dbh,$st) or (
-		print localtime().": Unable to prepare statement $st: $DBI::errstr\n" and
+		print localtime().": Unable to prepare statement: $st: $DBI::errstr\n" and
 		return 0
 	);
 	while ($line = <IN>){
+		if ($line =~ /^#/) {
+			next;
+		}
 		chomp ($line);
 		$line =~ s/"//g;
 		my @fields=split (',',$line);
@@ -1248,8 +1251,8 @@
 			$i++;
 		}
 		$sth->execute or (
-			print localtime().": Unable to execute stament $st: $DBI::errstr\n" and
-			print localtime().": With line: $line\n" and
+			print localtime().": Unable to execute stament: $st\n" and
+			print localtime().": With line: $line: $DBI::errstr\n" and
 			return 0
 		);
 	}
@@ -1312,7 +1315,7 @@
 	#here we read all the db structure, the table fields and contigs
 	my %db_structure=read_db_structure ($db_structure_file,$config);
 	unless (%db_structure) {
-		print localtime().": There was a problem reading the database definition from file $db_structure_file: $!\n";
+		print localtime().": There was a problem reading the database definition from file: $db_structure_file";
 		return 0;
 	}
 	#the table is regenerated
@@ -1351,12 +1354,14 @@
 		#Here we check that the database is reachable and has all the necesary tables
 		$ok=check_db_structure($db_path,%db_structure);
 	}
-	#print_db_structure(%db_structure);
+	if (!$ok) {
+		print_db_structure(%db_structure);
+	}
 	return $ok;
 }
 
 #Here we check that the database is reachable and has all the necesary tables
-#this is not enough becouse fields should be checked too, so TODO 
+#this is not enough because fields should be checked too, so TODO 
 #(although not a very important thing anyway)
 sub check_db_structure($\%) {
 	my $db=shift;
@@ -1375,6 +1380,8 @@
 				}
 			}
 		}
+	} else {
+		$ok=0;
 	}
 	if ($ok) {
 		print localtime().": Database structure seems ok\n";
@@ -1422,7 +1429,7 @@
 		print localtime().": Connection to the database server $db_path_no_name has failed: $DBI::errstr\n";
 		return 0;
 	}
-	#Now we check if db exists and if does is dropped
+	#Now we check if db exists and if it does it is dropped
 	if(db_ok($db_path)){
 		#database exits, we should remove it
 		if(drop_db($db_path,$db_name)) {
@@ -1458,13 +1465,23 @@
 sub populate_db ($\%) {
 	my $db=shift;
 	my $tables=shift;
+	my %t = %$tables;
 	my $ok=1;
 
+	print "populate_db called with db=$db, tables=$tables\n";
+	#foreach my $table(keys(%t)) {
+	#	print "table=$table, $t{$table}\n";
+	#}
+
 	my $table;
 	foreach $table(keys %$tables) {
 		if ($ok) {
-			$ok=create_table($db,$table,${%{$tables}}{$table});
+			$ok=create_table($db,$table,$t{$table}); # avoid Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1477.
+			if ($ok) {
 			print localtime().": Table $table created\n";
+			} else {
+				print localtime().": Table $table could not be created under dsn=$db: $DBI::errstr\n";
+			}
 		}
 	}
 	return $ok;
@@ -1476,7 +1493,7 @@
 	my $db=shift;
 	my $table_name=shift;
 	my $table_content=shift;	#table content in sql format
-	#first we check that the database is avaliable
+	#first we check that the database is available
 	my $ok=1;
 	unless (db_ok($db)) {
 		print localtime().": Something went wrong checking database: $db\n";
@@ -1488,9 +1505,13 @@
 	my $st="CREATE TABLE $table_name ($table_content);";
 	if($ok) {
 		$sth=prepare_st($dbh,$st) or $ok=0;
+	} else {
+		print localtime().": There was a problem preparing a statement: $DBI::errstr\n";
 	}
 	if ($ok) {
 		execute_st($sth) or $ok=0;
+	} else {
+		print localtime().": There was a problem executing a statement: $DBI::errstr\n";
 	}
 	#print $table;
 	$sth->finish();
@@ -1533,17 +1554,13 @@
 #needs a db handler
 sub close_db ($) {
 	my $dbh=shift;
-	if ($dbh){
-		$dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n";
-	}
+	if ($dbh){$dbh->disconnect();}
 }
 
 #needs a statement handler
 sub close_st ($) {
 	my $sth=shift;
-	if ($sth){
-		$sth->finish() or print localtime().": Cannot finish execution over database: $DBI::errstr\n";
-	}
+	if ($sth){$sth->finish();}
 }
 
 
@@ -1563,9 +1580,7 @@
 		}
 	}
 	
-	if ($dbh){
-		$dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n";
-	}
+	if ($dbh){$dbh->disconnect();}
 	return $ok;
 }
 
@@ -1581,9 +1596,7 @@
 	else {
 		$ok=0;
 	}
-	if ($dbh){
-		$dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n";
-	}
+	if ($dbh){$dbh->disconnect();}
 	return $ok;
 }
 
@@ -1594,7 +1607,7 @@
 	my $ok=1;
 	#is the database to remove ok?
 	unless (db_ok($db)) {
-		print localtime().": Something went wrong checking database $db: $DBI::errstr\n";
+		print localtime().": Something went wrong checking database: $db: $DBI::errstr\n";
 		$ok=0;
 	}
 	#we should open it
@@ -1619,7 +1632,7 @@
 		}
 	}
 	if ($ok) {$sth->finish();}
-	if ($dbh){$dbh->disconnect() or print localtime().": Cannot disconnect from database: $DBI::errstr\n";}
+	if ($dbh){$dbh->disconnect();}
 	return $ok;
 }