diff --git a/prepare_bcbio_config.sh b/prepare_bcbio_config.sh
index 85cc75757ca5e0503ab435912ec14f88a28dd043..e81baac99f6144d41a50a0f97df902e9050bf92e 100755
--- a/prepare_bcbio_config.sh
+++ b/prepare_bcbio_config.sh
@@ -44,6 +44,9 @@ cd $PARAMS_DIR
 # remove DOS newline characters if necessary
 perl -pi -e 's/\r//' $PROJECT_ID.ped
 
+# create reads directory for project
+mkdir -p $READS_DIR/$PROJECT_ID
+
 cat $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/file_list.tsv | \
   perl $SCRIPTS/trio_whole_exome_create_parameter_files.pl \
     --prefix ./$PROJECT_ID \
@@ -68,13 +71,13 @@ do
 
   done
 
-  bcbio_prepare_samples.py --out $READS_DIR --csv ${PROJECT_ID}_${FAMILY_ID}.csv
+  bcbio_prepare_samples.py --out $READS_DIR/$PROJECT_ID --csv ${PROJECT_ID}_${FAMILY_ID}.csv
 
   mv ${PROJECT_ID}_${FAMILY_ID}-merged.csv ${PROJECT_ID}_${FAMILY_ID}.csv
 
   BARE_FAMILY_ID=`echo $FAMILY_ID | cut -d '_' -f 2`
 
-  bcbio_nextgen.py -w template $BCBIO_TEMPLATE ${PROJECT_ID}_${FAMILY_ID}.csv $READS_DIR/*_${BARE_FAMILY_ID}_R[12].fastq.gz
+  bcbio_nextgen.py -w template $BCBIO_TEMPLATE ${PROJECT_ID}_${FAMILY_ID}.csv $READS_DIR/$PROJECT_ID/*_${BARE_FAMILY_ID}_R[12].fastq.gz
 
   mv ${PROJECT_ID}_${FAMILY_ID}/config/${PROJECT_ID}_${FAMILY_ID}.yaml $CONFIG_DIR/