Adding in program assertion as sometimes this is quite a large reason for things going wrong

modules/Bio/EnsEMBL/Pipeline/Base.pm

@@ -213,4 +213,22 @@ sub unlink_all_files {
   return;
 }
 
+sub assert_executable {
+  my ($self, $exe) = @_;
+  if(! -x $exe) {
+    my $output = `which $exe 2>&1`;
+    chomp $output;
+    my $rc = $? >> 8;
+    if($rc != 0) {
+      my $possible_location = `locate -l 1 $exe 2>&1`;
+      my $loc_rc = $? >> 8;
+      if($loc_rc != 0) {
+        my $msg = 'Cannot find the executable "%s" after trying "which" and "locate -l 1". Please ensure it is on your PATH or use an absolute location and try again';
+        $self->throw(sprintf($msg, $exe));
+      }
+    }
+  }
+  return 1;
+}
+
 1;

modules/Bio/EnsEMBL/Pipeline/FASTA/BlatIndexer.pm

@@ -80,6 +80,14 @@ sub param_defaults {
   };
 }
 
+sub fetch_input {
+  my ($self) = @_;
+  $self->assert_executable($self->param('program'));
+  $self->assert_executable('zcat');
+  $self->assert_executable('gunzip');
+  return;
+}
+
 sub run {
   my ($self) = @_;
   if($self->run_indexing()) {

modules/Bio/EnsEMBL/Pipeline/FASTA/EmailSummary.pm

@@ -7,6 +7,9 @@ use Bio::EnsEMBL::Hive::Utils qw/destringify/;
 
 sub fetch_input {
   my ($self) = @_;
+  
+  $self->assert_executable('sendmail');
+  
   my $dump_dna = $self->jobs('DumpDNA');
   my $copy_dna = $self->jobs('CopyDNA');
   my $dump_genes = $self->jobs('DumpGenes');

modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm

@@ -77,6 +77,8 @@ sub fetch_input {
   if($type ne 'genomic' && $type ne 'genes') {
     throw "param 'type' must be set to 'genomic' or 'genes'";
   }
+  $self->assert_executable($self->param('program'));
+  $self->assert_executable('gunzip');
 }
 
 sub write_output {