diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index f69ed47e1a91629a1ca6b3a4c43a3ec9303cddd3..dfddf5cbf7dcee20262dfdc391ffa6c18f7a2a84 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
@@ -102,8 +102,20 @@ sub submit_exonerate {
   my $queryfile = basename($query);
   my $targetfile = basename($target);
 
+  my $disk_space_needed = (stat($query))[7]+(stat($target))[7];
+
+  $disk_space_needed /= 1024000; # convert to MB
+  $disk_space_needed = int($disk_space_needed);
+  $disk_space_needed += 1;
+#  print "disk space needed = ".$disk_space_needed."\n";
+
   my $num_jobs = calculate_num_jobs($query);
 
+  # array features barf if just one job 
+  if($num_jobs == 1){
+    $num_jobs++;
+  }
+
   $self->jobcount($self->jobcount()+$num_jobs);
 
   my $options_str = join(" ", @options);
@@ -117,9 +129,11 @@ sub submit_exonerate {
 
   my $output = $self->get_class_name() . "_" . $ensembl_type . "_" . "\$LSB_JOBINDEX.map";
 
-  my @main_bsub = ( 'bsub', '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
+  my @main_bsub = ( 'bsub', '-R' .'rusage[tmp='.$disk_space_needed.']',  '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
+
+#  my @main_bsub = ( 'bsub', '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
 
-  #print "bsub command: " . join(" ", @main_bsub) . "\n\n";
+#  print "bsub command: " . join(" ", @main_bsub) . "\n\n";
 
   # Create actual execute script to be executed with LSF, and write to pipe
   my $main_job = <<EOF;
@@ -129,12 +143,12 @@ cd /tmp
 
 rm -f /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile /tmp/$output
 
-lsrcp $target /tmp/\$LSB_JOBINDEX.$targetfile
-lsrcp $query  /tmp/\$LSB_JOBINDEX.$queryfile
+lsrcp ecs2c:$target /tmp/\$LSB_JOBINDEX.$targetfile
+lsrcp ecs2c:$query  /tmp/\$LSB_JOBINDEX.$queryfile
 
 $exonerate_path /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > /tmp/$output
 
-lsrcp /tmp/$output $root_dir/$output
+lsrcp /tmp/$output ecs2c:$root_dir/$output
 
 rm -f /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile /tmp/$output
 EOF