diff --git a/scripts/run_definite_error_checking_sql.pl b/scripts/run_definite_error_checking_sql.pl
new file mode 100755
index 0000000..86ac53c
--- /dev/null
+++ b/scripts/run_definite_error_checking_sql.pl
@@ -0,0 +1,136 @@
+#!/usr/bin/perl -w
+use DBI;
+use Getopt::Long; 
+use Data::Dumper;
+use strict;
+use warnings;
+
+# E = ERROR    : These are cases in which data appears to break the rules outlined by the CS schema.  These suggest a likely problem with the load or fix. 
+#                New things that show up here need to be addressed before the data can be released.  Potentially a Jira ticket made.  Example: Genomes without contigs. 
+
+my $db_name = undef; 
+my $db_user = undef; 
+my $db_pwd = undef; 
+ 
+my $usage = "This command requires the db_name, db_user, db_pwd\n". 
+    "The DB parameters need to be in single quotes.  \n". 
+    "Example Call : \n". 
+    "perl run_error_checking_sql.pl -db_name='kbase_sapling_v4:db4.chicago.kbase.us' -db_user='YOUR_DB_USER' -db_pwd='YOUR_DB_PWD'\n"; 
+(GetOptions('db_name=s' => \$db_name, 
+            'db_user=s' => \$db_user, 
+            'db_pwd=s' => \$db_pwd 
+) 
+ && @ARGV == 0) || die $usage; 
+die $usage if ((!defined $db_user) || (!defined $db_pwd) || (!defined $db_name)); 
+ 
+my $full_db_name = 'DBI:mysql:'.$db_name; 
+my $dbh = DBI->connect($full_db_name,$db_user, $db_pwd, { RaiseError => 1, ShowErrorStatement => 1 } ); 
+
+my ($db,$dummy) = split(':',$db_name);
+
+my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); 
+$year += 1900; 
+$mon = $mon + 1;
+
+my $out = "./definite_errors_".$db_name."_".$year."_".$mon."_".$mday.".txt"; 
+open (OUT,">$out") || die "Did not create $out"; 
+
+
+my @sql_queries = (
+"select 'Genomes_without_contigs_count' query_name, current_date(), database() as db, count(*) 
+from (select g.id, count(c.id) as cnt 
+from Genome g left outer join IsComposedOf i on i.from_link = g.id 
+left outer join Contig c on c.id = i.to_link 
+group by g.id 
+having cnt = 0) no_contigs"
+,
+"select 'Genomes_with_inconsistent_contigs_count' query_name, current_date(), database() as db, count(*) 
+from (select g.id, g.contigs, count(c.id) as cnt 
+from Genome g left outer join IsComposedOf i on i.from_link = g.id 
+left outer join Contig c on c.id = i.to_link 
+group by g.id, g.contigs) as subq 
+where subq.contigs != subq.cnt"
+,
+"select 'Genomes_without_CDS_count' query_name, current_date(), database() as db, count(*) from 
+(select g.id, su.from_link 
+from Genome g inner join Submitted su on g.id = su.to_link inner join Source s on s.id = su.from_link 
+where g.id not in (select distinct g1.id 
+from Genome g1 inner join IsOwnerOf i1 on g1.id = i1.from_link 
+inner join Feature f1 on f1.id = i1.to_link 
+where f1.feature_type = 'CDS')) subq"
+,
+"select 'Genomes_with_inconsistent_peg_and_cds_count' query_name, current_date(), database() as db, count(*) 
+from ( 
+select g.id, g.pegs, count(*) cnt 
+from Genome g inner join IsOwnerOf io on io.from_link = g.id 
+inner join Feature f on f.id = io.to_link 
+where f.feature_type = 'CDS' 
+group by g.id, g.pegs 
+having g.pegs != cnt) subq"
+,
+"select 'CDS_Features_length_inconsistent_with_IsLocatedIn_length_sum_count' query_name, current_date(), database() as db, count(*) 
+from 
+(select f.id, f.sequence_length, sum.sum_length 
+from 
+(select sum(len) as sum_length, from_link from IsLocatedIn group by from_link) sum 
+inner join Feature f on f.id = sum.from_link 
+where f.sequence_length != sum.sum_length 
+and f.feature_type = 'CDS') subq"
+,
+"select 'Pairings_without_component_features_count' query_name, current_date(), database() as db, count(*) 
+from (select p.* from Pairing p where id not in (select to_link from IsInPair)) subq"
+,
+"select 'Missing_source_count' query_name, current_date(), database() as db, count(*) from ( 
+select distinct r.from_link as ID 
+  from HasCompoundAliasFrom r where r.from_link not in 
+  (select id from Source) 
+union select distinct r.to_link 
+  from HasReactionAliasFrom r where r.to_link not in 
+  (select id from Source) 
+union select distinct r.from_link 
+  from AssertsFunctionFor r where r.from_link not in 
+  (select id from Source) 
+union select distinct r.from_link 
+  from Aligned r where r.from_link not in 
+  (select id from Source) 
+union select distinct r.from_link 
+  from Treed r where r.from_link not in 
+    (select id from Source)) m"
+,
+"select 'Select_plasma_genomes_with_wrong_genetic_code_count' query_name, current_date(), database() as db, count(*) from ( 
+select scientific_name, domain, genetic_code from Genome 
+where (scientific_name like 'Acholeplasma%' or scientific_name like 'Mesoplasma%' or scientific_name like 'Mycoplasma%' 
+or scientific_name like 'Spiroplasma%' or scientific_name like 'Ureaplasma%') 
+and domain = 'Bacteria' and genetic_code != 4 order by scientific_name) m"
+,
+"select 'Eukaryotic_genomes_with_wrong_genetic_code_count' query_name, current_date(), database() as db, count(*) from ( 
+select scientific_name, genetic_code, domain from Genome where domain like 'Eukaryota%' and genetic_code != 1) m"
+, 
+"select 'Genomes_without_domains_count' query_name, current_date(), database() as db, count(*) from Genome where domain = ''"
+,
+"select 'Feature_with_duplicated_ordinals_count' query_name, current_date(), database() as db, count(*) 
+from ( 
+select count(*) as cnt, from_link, ordinal from IsLocatedIn group by from_link, ordinal having cnt > 1) subq"
+, 
+"select 'Features_without_location_information_count' query_name, current_date(), database() as db, count(*) 
+from (select id from Feature where id not in (select from_link from IsLocatedIn where ordinal = 0)) subq"
+, 
+"select 'Features_where_ordinal_count_does_not_correspond_to_number_of_location_count' query_name, current_date(), database() as db, count(*) 
+from (select count(*) as cnt, max(ordinal) as maxOrd, from_link from IsLocatedIn group by from_link having cnt != (maxOrd + 1)) subq" 
+);
+
+#print headers
+print OUT "Query_Name\tDate\tDB\tCount\n";
+foreach my $sql_query (@sql_queries)
+{
+    my $sth = $dbh->prepare($sql_query) or die "Unable to prepare query : $sql_query :".$dbh->errstr(); 
+    $sth->execute or die "SQL Error: for query $sql_query : $DBI::errstr\n"; 
+    my (@results) = $sth->fetchrow_array();
+    print "Completed $results[0] ". localtime(time)."\n";
+    if ($results[3] > 0)
+    {
+	print OUT join("\t",@results). "\n";
+    }
+}
+
+close OUT;
diff --git a/scripts/run_monitor_situation_checking_sql.pl b/scripts/run_monitor_situation_checking_sql.pl
new file mode 100755
index 0000000..c4be969
--- /dev/null
+++ b/scripts/run_monitor_situation_checking_sql.pl
@@ -0,0 +1,137 @@
+#!/usr/bin/perl -w
+use DBI;
+use Getopt::Long; 
+use Data::Dumper;
+use strict;
+use warnings;
+
+
+# M = Monitor  : These are situations where increases in numbers are probably problematic data, but could theoretically be explained by rare biology occurrences. 
+#                If the number of increases are larger than expected rarity of the biological occurrence, these should be investigated further. 
+
+
+my $db_name = undef; 
+my $db_user = undef; 
+my $db_pwd = undef; 
+ 
+my $usage = "This command requires the db_name, db_user, db_pwd\n". 
+    "The DB parameters need to be in single quotes.  \n". 
+    "Example Call : \n". 
+    "perl run_probable_error_checking_sql.pl -db_name='kbase_sapling_v4:db4.chicago.kbase.us' -db_user='YOUR_DB_USER' -db_pwd='YOUR_DB_PWD'\n"; 
+(GetOptions('db_name=s' => \$db_name, 
+            'db_user=s' => \$db_user, 
+            'db_pwd=s' => \$db_pwd 
+) 
+ && @ARGV == 0) || die $usage; 
+die $usage if ((!defined $db_user) || (!defined $db_pwd) || (!defined $db_name)); 
+
+
+ 
+my $full_db_name = 'DBI:mysql:'.$db_name; 
+my $dbh = DBI->connect($full_db_name,$db_user, $db_pwd, { RaiseError => 1, ShowErrorStatement => 1 } ); 
+
+my ($db,$dummy) = split(':',$db_name);
+
+my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); 
+$year += 1900; 
+$mon = $mon + 1;
+
+my $out = "./monitor_situations_".$db_name."_".$year."_".$mon."_".$mday.".txt"; 
+open (OUT,">$out") || die "Did not create $out"; 
+
+
+my @sql_queries = (
+"select 'CDS_length_too_small_count' query_name, current_date(), database() as db, count(*) 
+from (select f.id, f.sequence_length from Feature f where sequence_length < 10 and feature_type = 'CDS') subq"
+,
+"select 'CDS_length_too_large_count' query_name, current_date(), database() as db, count(*)
+from (select f.id, f.sequence_length from Feature f where feature_type = 'CDS' and sequence_length > 100000) subq"
+, 
+"select 'Genomes_with_a_CDS_length_too_large_count' query_name, current_date(), database() as db, count(*)
+from ( 
+select g.id, g.scientific_name, g.domain, g.prokaryotic, s.id as source, count(*) as cnt
+from Feature f inner join IsOwnerOf i on f.id = i.to_link inner join Genome g on g.id = i.from_link
+inner join Submitted su on g.id = su.to_link inner join Source s on s.id = su.from_link 
+where feature_type = 'CDS' and sequence_length > 100000 group by g.id, g.scientific_name, g.domain, g.prokaryotic, s.id
+having cnt > 0 
+order by count(*) desc) subq"
+, 
+"select 'Genomes_with_non_methionine_starting_methione_ending_proteins_count' query_name, current_date(), database() as db, count(*)
+from ( 
+select g.id, g.scientific_name, count(*) as cnt 
+from Genome g inner join IsOwnerOf io on g.id = io.from_link 
+inner join IsProteinFor ip on ip.to_link = io.to_link 
+inner join ProteinSequence ps on ip.from_link = ps.id 
+where ps.sequence not like 'M%' 
+and ps.sequence like '%M' 
+group by g.id, g.scientific_name 
+having cnt > 0 
+order by cnt ) subq"
+,
+"select 'CDS_with_non_methionine_starting_methione_ending_proteins_count' query_name, current_date(), database() as db, sum(cnt) 
+from ( 
+select g.id, g.scientific_name, count(*) as cnt 
+from Genome g inner join IsOwnerOf io on g.id = io.from_link 
+inner join IsProteinFor ip on ip.to_link = io.to_link 
+inner join ProteinSequence ps on ip.from_link = ps.id 
+where ps.sequence not like 'M%' 
+and ps.sequence like '%M' 
+group by g.id, g.scientific_name 
+having cnt > 0 
+order by cnt ) subq"
+,
+"select 'CDS_length_inconsistent_with_protein_length_count' query_name, current_date(),  database() as db, sum(cnt) 
+from ( 
+select substring_index(f.id,'.',2), count(*) cnt 
+from Feature f 
+inner join IsProteinFor i on f.id = i.to_link 
+inner join ProteinSequence p on p.id = i.from_link 
+where f.feature_type = 'CDS' 
+and f.sequence_length/3 != (length(p.sequence) + 1) 
+and f.sequence_length/3 != length(p.sequence) 
+group by substring_index(f.id,'.',2)) subq"
+,
+"select 'CDS_Features_not_modulo3_count' query_name, current_date(), database() as db, count(*) 
+from (select f.id, f.sequence_length from Feature f inner join IsOwnerOf i on f.id = i.to_link 
+where feature_type = 'CDS' and f.sequence_length%3 != 0 order by f.id) subq"
+,
+"select 'Genomes_with_CDS_Features_not_modulo3_count' query_name, current_date(), database() as db, count(*) 
+from ( 
+select g.id genome_id, g.scientific_name, g.domain, g.prokaryotic, s.id, count(*) as cnt
+from Feature f inner join IsOwnerOf i on f.id = i.to_link inner join Genome g on g.id = i.from_link 
+inner join Submitted su on g.id = su.to_link inner join Source s on s.id = su.from_link
+where feature_type = 'CDS' and f.sequence_length%3 != 0 group by g.id, g.scientific_name, g.domain, g.prokaryotic, s.id
+having cnt > 0 
+order by count(*) desc) subq"
+,
+"select 'Genomes_with_at_least_1%_of_CDS_Features_not_modulo3_count' query_name, current_date(), database() as db, count(*) 
+from ( 
+select r1.genome_id, ((r1.not_modulo3_count/r2.total_cds_count) * 100) percent_not_modulo3, r1.not_modulo3_count, r2.total_cds_count 
+from (select g1.id genome_id, count(f1.id) as not_modulo3_count 
+from Feature f1 inner join IsOwnerOf i1 on f1.id = i1.to_link inner join Genome g1 on g1.id = i1.from_link 
+where f1.feature_type = 'CDS' and f1.sequence_length%3 != 0 
+group by g1.id) r1 inner join 
+(select g2.id genome_id, count(f2.id) as total_cds_count 
+from Feature f2 inner join IsOwnerOf i2 on f2.id = i2.to_link inner join Genome g2 on g2.id = i2.from_link 
+where f2.feature_type = 'CDS' 
+group by g2.id) r2 on r1.genome_id = r2.genome_id 
+where ((r1.not_modulo3_count/r2.total_cds_count) * 100) > 1 
+order by ((r1.not_modulo3_count/r2.total_cds_count) * 100) desc) subq"
+,
+"select 'CDS_Features_without_functions_count' query_name, current_date(), database() as db, count(f.id)
+from Feature f
+where f.feature_type = 'CDS' and f.function = ''"
+);
+
+#print headers
+print OUT "Query_Name\tDate\tDB\tCount\n";
+foreach my $sql_query (@sql_queries)
+{
+    my $sth = $dbh->prepare($sql_query) or die "Unable to prepare query : $sql_query :".$dbh->errstr(); 
+    $sth->execute or die "SQL Error: for query $sql_query : $DBI::errstr\n"; 
+    my (@results) = $sth->fetchrow_array();
+    print "Completed $results[0] ". localtime(time)."\n";
+    print OUT join("\t",@results). "\n";
+}
+
+close OUT;
diff --git a/scripts/run_probable_error_checking_sql.pl b/scripts/run_probable_error_checking_sql.pl
new file mode 100755
index 0000000..fdc9a70
--- /dev/null
+++ b/scripts/run_probable_error_checking_sql.pl
@@ -0,0 +1,164 @@
+#!/usr/bin/perl -w
+use DBI;
+use Getopt::Long; 
+use Data::Dumper;
+use strict;
+use warnings;
+
+# P = Probable Error :  These are situations where the data is almost definitely wrong, but we already have data of this type.
+#                       These are likely to be as a result of bad quality data or errors in the load scripts.  These need to be investigated further. 
+
+
+my $db_name = undef; 
+my $db_user = undef; 
+my $db_pwd = undef; 
+ 
+my $usage = "This command requires the db_name, db_user, db_pwd\n". 
+    "The DB parameters need to be in single quotes.  \n". 
+    "Example Call : \n". 
+    "perl run_probable_error_checking_sql.pl -db_name='kbase_sapling_v4:db4.chicago.kbase.us' -db_user='YOUR_DB_USER' -db_pwd='YOUR_DB_PWD'\n"; 
+(GetOptions('db_name=s' => \$db_name, 
+            'db_user=s' => \$db_user, 
+            'db_pwd=s' => \$db_pwd 
+) 
+ && @ARGV == 0) || die $usage; 
+die $usage if ((!defined $db_user) || (!defined $db_pwd) || (!defined $db_name)); 
+
+
+ 
+my $full_db_name = 'DBI:mysql:'.$db_name; 
+my $dbh = DBI->connect($full_db_name,$db_user, $db_pwd, { RaiseError => 1, ShowErrorStatement => 1 } ); 
+
+my ($db,$dummy) = split(':',$db_name);
+
+my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); 
+$year += 1900; 
+$mon = $mon + 1;
+
+my $out = "./probable_errors_".$db_name."_".$year."_".$mon."_".$mday.".txt"; 
+open (OUT,">$out") || die "Did not create $out"; 
+
+
+my @sql_queries = (
+"select 'Genomes_with_a_CDS_length_too_large_and_big_for_protein_count' query_name, current_date(), database() as db, 'Way too large CDS', count(*)
+from (
+select g.id, g.scientific_name, g.domain, g.prokaryotic, s.id as source, count(*) as cnt
+from Feature f inner join IsOwnerOf i on f.id = i.to_link inner join Genome g on g.id = i.from_link 
+inner join Submitted su on g.id = su.to_link inner join Source s on s.id = su.from_link 
+inner join IsProteinFor ip on f.id = ip.to_link
+inner join ProteinSequence p on p.id = ip.from_link
+where feature_type = 'CDS' and sequence_length > 100000 
+and sequence_length/3 > ((length(p.sequence) + 1)* 1.10)
+group by g.id, g.scientific_name, g.domain, g.prokaryotic, s.id
+having cnt > 0 
+order by count(*) desc) subq"
+,
+"select 'Protein_sequences_that_look_like_DNA_count' query_name, current_date(), database() as db, 'Protein sequences that are DNA only',count(*)
+from (select p.id, p.sequence from ProteinSequence p where p.sequence RLIKE '^[AGTC]+\$') subq"
+,
+"select 'CDS_length_definitely_wrong_with_protein_length_count' query_name, current_date(),  database() as db,
+'Query is geared to allow for stop codon being included or not. This would allow for up to 3 frameshifts (in same direction - deletion or insertion), which would be extremely unlikely   ', sum(cnt)
+from ( 
+select substring_index(f.id,'.',2), count(*) cnt
+from Feature f
+inner join IsProteinFor i on f.id = i.to_link
+inner join ProteinSequence p on p.id = i.from_link 
+where f.feature_type = 'CDS'
+and FLOOR(f.sequence_length/3) != (length(p.sequence) + 1)
+and CEIL(f.sequence_length/3) != (length(p.sequence) + 1) 
+and FLOOR(f.sequence_length/3) != length(p.sequence) 
+group by substring_index(f.id,'.',2)) subq"
+,
+"select 'Genomes_with_5percent_or_more_obviously_inconistent_proteins' query_name, current_date(), database() as db, 
+'Genomes with 5% of CDS features having this case.  Red flag. Query is geared to allow for stop codon being included or not. This would allow for up to 3 frameshifts (in same direction - deletion or insertion), which would be extremely unlikely', 
+count(*)
+from ( 
+select g.id, g.scientific_name, subq1.cnt, subq2.cds_cnt, (subq1.cnt/subq2.cds_cnt) 
+from Genome g inner join
+(select substring_index(f.id,'.',2) as genome_id, count(*) cnt
+from Feature f 
+inner join IsProteinFor i on f.id = i.to_link
+inner join ProteinSequence p on p.id = i.from_link
+where f.feature_type = 'CDS'
+and FLOOR(f.sequence_length/3) != (length(p.sequence) + 1) 
+and CEIL(f.sequence_length/3) != (length(p.sequence) + 1) 
+and FLOOR(f.sequence_length/3) != length(p.sequence) 
+group by substring_index(f.id,'.',2)) subq1 
+on subq1.genome_id =g.id 
+inner join (select substring_index(f1.id,'.',2) as genome_id, count(*) as cds_cnt from Feature f1 
+where f1.feature_type = 'CDS' group by substring_index(f1.id,'.',2)) subq2 
+on g.id = subq2.genome_id 
+where (subq1.cnt/subq2.cds_cnt) > .05) fullsub"
+,
+"select 'CDS_Features_without_protein_sequences_count' query_name, current_date(), database() as db, 'CDS FEATURES SHOULD HAVE AN ASSOCIATED PROTEIN SEQUENCE', count(*) 
+from (select f.id from
+Feature f where feature_type = 'CDS' and id not in (select to_link from IsProteinFor)) subq"
+,
+"select 'CDS_length_equal_to_protein_length_count' query_name, current_date(), database() as db, 'CDS length equal to protein length', count(*) 
+from (select f.id, f.sequence_length 
+from Feature f 
+inner join IsProteinFor i on f.id = i.to_link 
+inner join ProteinSequence p on p.id = i.from_link 
+where f.feature_type = 'CDS' 
+and f.sequence_length = (length(p.sequence))) subq"
+,
+"select 'Genomes_without_IsTaxonomyOf_relationship_count' query_name, current_date(), database() as db, 
+'The following are false positives (g.23746, g.26015, g.26860, g.2876, g.484, g.626, g.96) - This count should not be more than 7',
+count(*) 
+from Genome g 
+where id not in (select to_link from IsTaxonomyOf)"
+,
+"select 'Genomes_with_suspicious_reversed_ordinals_count' query_name, current_date(), database() as db, 'Ordinals reversed', count(*) 
+from ( 
+select substring_index(s.feature,'.',2), g.scientific_name, g.domain, u.from_link, g.pegs, count(*) as cnt 
+from
+(select distinct i1.from_link as feature 
+from IsLocatedIn i1 inner join IsLocatedIn i2 on i1.from_link = i2.from_link and i1.to_link = i2.to_link 
+where i1.dir = '-' 
+and i1.begin > i2.begin 
+and i1.ordinal > i2.ordinal) s 
+inner join Genome g on g.id = substring_index(s.feature,'.',2) 
+inner join Submitted u on u.to_link = g.id 
+group by substring_index(s.feature,'.',2), g.scientific_name, g.domain, u.from_link, g.pegs) subq"
+,
+"select 'Protein_sequences_that_may_be_reversed_that_have_corresponding_features_count' query_name, current_date(), database() as db, 
+'Ends in Methinonine and does not start with Methionine',count(*) 
+from ( 
+select distinct ps.id 
+from ProteinSequence ps 
+inner join IsProteinFor ip on ip.from_link = ps.id 
+inner join Feature f on ip.to_link = f.id 
+where sequence not like 'M%' 
+and sequence like '%M') subq"
+, 
+"select 'Genomes_that_may_have_reversed_Protein_sequences_count' query_name, current_date(), database() as db, 
+'Genomes with reversed proteins - Ends in Methinonine and does not start with Methionine',count(*) 
+from ( 
+select g.id, g.scientific_name, count(*) as cnt 
+from Genome g inner join IsOwnerOf io on g.id = io.from_link 
+inner join IsProteinFor ip on ip.to_link = io.to_link 
+inner join ProteinSequence ps on ip.from_link = ps.id 
+where ps.sequence not like 'M%' 
+and ps.sequence like '%M' 
+group by g.id, g.scientific_name 
+having cnt > 0 
+order by cnt) subq "
+, 
+"select 'Multiple_location_features_on_both_strands_count' query_name, current_date(), database() as db, 'Genes located on both strands', count(*) 
+from (select distinct i1.from_link 
+from IsLocatedIn i1 inner join IsLocatedIn i2 on i1.from_link = i2.from_link and i1.to_link = i2.to_link 
+where i1.dir = '-' and i2.dir = '+') subq"
+);
+
+#print headers
+print OUT "Query_Name\tDate\tDB\tComments\tCount\n";
+foreach my $sql_query (@sql_queries)
+{
+    my $sth = $dbh->prepare($sql_query) or die "Unable to prepare query : $sql_query :".$dbh->errstr(); 
+    $sth->execute or die "SQL Error: for query $sql_query : $DBI::errstr\n"; 
+    my (@results) = $sth->fetchrow_array();
+    print "Completed $results[0] ". localtime(time)."\n";
+    print OUT join("\t",@results). "\n";
+}
+
+close OUT;