diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index 7d344382ebf15097af0f8c23f343b17779aee755..d07d9eb2e101ec8727d043f892f93ba46582ea8b 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #PBS -l walltime=48:00:00
 #PBS -l ncpus=16,mem=8gb
-#PBS -q uv2000
+#PBS -q sgp
 #PBS -N trio_whole_exome_bcbio
 #PBS -j oe
 
diff --git a/submit_trio_wes_checksums.sh b/submit_trio_wes_checksums.sh
index 20acb0d723905014289b6d4f0d34162f64129cb0..d91b877097483fbb2b72f9bbd5cafae598e15889 100755
--- a/submit_trio_wes_checksums.sh
+++ b/submit_trio_wes_checksums.sh
@@ -18,6 +18,7 @@ fi
 
 # Expects environment variables to be set
 # PROJECT_ID - e.g. 12345_LastnameFirstname
+# VERSION - e.g. v1, v2
 # CONFIG_SH - absolute path to configuration script setting environment variables
 
 source $CONFIG_SH
@@ -26,7 +27,7 @@ FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tai
 
 # This assumes that ${PROJECT_ID}_${FAMILY_ID} is unique, and it should be - if there was
 # a re-run of a family, it should have a new project id.
-cd $OUTPUT_DIR/*${PROJECT_ID}_${FAMILY_ID}*
+cd $OUTPUT_DIR/*${VERSION}_${PROJECT_ID}_${FAMILY_ID}*
 
 rm md5sum.txt 2> /dev/null
 
diff --git a/submit_trio_wes_cram_compression.sh b/submit_trio_wes_cram_compression.sh
index 48917bf8def2371b96726142e024accfcc10491e..467bcff276bcf6685c85301595ba98c85bbb0016 100755
--- a/submit_trio_wes_cram_compression.sh
+++ b/submit_trio_wes_cram_compression.sh
@@ -18,6 +18,7 @@ fi
 
 # Expects environment variables to be set
 # PROJECT_ID - e.g. 12345_LastnameFirstname
+# VERSION - e.g. v1, v2
 # CONFIG_SH - absolute path to configuration script setting environment variables
 
 source $CONFIG_SH
@@ -26,7 +27,7 @@ FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tai
 
 # This assumes that ${PROJECT_ID}_${FAMILY_ID} is unique, and it should be - if there was
 # a re-run of a family, it should have a new project id.
-cd $OUTPUT_DIR/*${PROJECT_ID}_${FAMILY_ID}*
+cd $OUTPUT_DIR/*${VERSION}_${PROJECT_ID}_${FAMILY_ID}*
 
 for BAM in */*.bam
 do
diff --git a/trio_whole_exome_parse_peddy_ped_csv.pl b/trio_whole_exome_parse_peddy_ped_csv.pl
index 9e973f660a6b6a5496f8e961ed6ccc9b6b44ade9..7f964789ecfabfb906ebcf53e2b14ce38595c461 100644
--- a/trio_whole_exome_parse_peddy_ped_csv.pl
+++ b/trio_whole_exome_parse_peddy_ped_csv.pl
@@ -70,7 +70,7 @@ while (my $line = <$in_fh>)
 
 $in_fh->close();
 
-my $out_file = "$out_dir/qc/$version.$project_id.ped_check.txt";
+my $out_file = sprintf("$out_dir/qc/%s_%s.ped_check.txt", $version, $project_id);
 my $out_fh = new IO::File;
 $out_fh->open($out_file, "w") or die "Could not open $out_file\n$!";