diff --git a/non-regression-tests/run_HK97.sh b/non-regression-tests/run_HK97.sh
index d9a33c0738cb0a666a406c54f1a3284d807da292..2c1bc07884d0540ea4b3a16b2e950780287d3ee7 100755
--- a/non-regression-tests/run_HK97.sh
+++ b/non-regression-tests/run_HK97.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on HK97 genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/HK97_assembly.fasta || exit 1
diff --git a/non-regression-tests/run_HK97_long.sh b/non-regression-tests/run_HK97_long.sh
index 88b482eb62960ea39710c2e09fdbeb09b9987378..f73a421d50b34c06a2b654dd3efd4c1a124c9131 100755
--- a/non-regression-tests/run_HK97_long.sh
+++ b/non-regression-tests/run_HK97_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 
 echo "running PhageTerm on HK97 genome and a dataset with a minimum 50x coverage"
diff --git a/non-regression-tests/run_HK97_long_multiproc.sh b/non-regression-tests/run_HK97_long_multiproc.sh
index 3998511e1d1f686cb02bc8c2f30ec72d29134530..97cdd3f3fb8335bd2279d015002d92ca0f7c708c 100755
--- a/non-regression-tests/run_HK97_long_multiproc.sh
+++ b/non-regression-tests/run_HK97_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on HK97 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/HK97_assembly.fasta --nrt
diff --git a/non-regression-tests/run_Lamda_long.sh b/non-regression-tests/run_Lamda_long.sh
index e73b552614506c7690ae7443f8bbeed2eca3b636..deec09aa9a5dfeb6c95ae78200a7d482fd6ff201 100755
--- a/non-regression-tests/run_Lamda_long.sh
+++ b/non-regression-tests/run_Lamda_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on Lamda genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Lambda_assembly.fasta --nrt || exit 1
diff --git a/non-regression-tests/run_Lamda_long_multiproc.sh b/non-regression-tests/run_Lamda_long_multiproc.sh
index cf5d6f1ce994d7229f8cfc5cea80133ab22c57ce..aba82b2eb8d40f1ef496048d754318859fda5ad0 100755
--- a/non-regression-tests/run_Lamda_long_multiproc.sh
+++ b/non-regression-tests/run_Lamda_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on Lamda genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Lambda_assembly.fasta --nrt
diff --git a/non-regression-tests/run_N1.sh b/non-regression-tests/run_N1.sh
index 949eb94affd4b0b942ac9a0de5e82b567f177114..b3b92783b2d60ae118896cd3f1038894e8f0fdc0 100755
--- a/non-regression-tests/run_N1.sh
+++ b/non-regression-tests/run_N1.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on StaphN1 genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta ||exit 1
diff --git a/non-regression-tests/run_P1.sh b/non-regression-tests/run_P1.sh
index e6edcfb13e65261fa840a861bddd2d52ea027f47..f263748bb17ff8748e34cee66b3efbe862f8d541 100755
--- a/non-regression-tests/run_P1.sh
+++ b/non-regression-tests/run_P1.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on P1 genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/P1_assembly.fasta || exit 1
diff --git a/non-regression-tests/run_P1_long.sh b/non-regression-tests/run_P1_long.sh
index a11885042d81d26e5ac5264784dc44df86cc1a86..6d003e46d187500fbe2fd7d57d1a66e8aa0c77ab 100755
--- a/non-regression-tests/run_P1_long.sh
+++ b/non-regression-tests/run_P1_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on P1 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/P1_assembly.fasta --nrt || exit 1
diff --git a/non-regression-tests/run_P1_long_multiproc.sh b/non-regression-tests/run_P1_long_multiproc.sh
index a1faf53bbdeb2d9eb73ea3f2685109512cbd18e5..041de796b1aee4b3854230a270b929914c27752d 100755
--- a/non-regression-tests/run_P1_long_multiproc.sh
+++ b/non-regression-tests/run_P1_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on P1 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/P1_assembly.fasta --nrt
diff --git a/non-regression-tests/run_StaphN1_long.sh b/non-regression-tests/run_StaphN1_long.sh
index 44823634f5fd5bb40d44e8d587d21ba6bef65365..bf09d49e08a1b785d7a272a301fc1c2759375500 100755
--- a/non-regression-tests/run_StaphN1_long.sh
+++ b/non-regression-tests/run_StaphN1_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on Staph1N genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py --nrt -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Staph1N_assembly.fasta || exit 1
diff --git a/non-regression-tests/run_StaphN1_long_multiproc.sh b/non-regression-tests/run_StaphN1_long_multiproc.sh
index 792ca822784caa9f7510645d0522f94dd02076ce..c19f98124a4f807ee15f090a352b191a79e6c950 100755
--- a/non-regression-tests/run_StaphN1_long_multiproc.sh
+++ b/non-regression-tests/run_StaphN1_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on Staph1N genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 --nrt -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Staph1N_assembly.fasta
diff --git a/non-regression-tests/run_T4.sh b/non-regression-tests/run_T4.sh
index 07aafdeb049121cdeedc8a178033e32db4b5af62..5b4dd137aa39e45f9aef52403cda5508377198c3 100755
--- a/non-regression-tests/run_T4.sh
+++ b/non-regression-tests/run_T4.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T4 genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T4_assembly.fasta || exit 1
diff --git a/non-regression-tests/run_T4_long.sh b/non-regression-tests/run_T4_long.sh
index f135e35231b20cc64e301356046f609cd34ffcd5..e9d2adae8a88c42110aa80fcb3ac75237f3f7818 100755
--- a/non-regression-tests/run_T4_long.sh
+++ b/non-regression-tests/run_T4_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T4 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T4_assembly.fasta --nrt || exit 1
diff --git a/non-regression-tests/run_T4_long_multiproc.sh b/non-regression-tests/run_T4_long_multiproc.sh
index c89c37d930a7d0b65d8281d4f9f1643a8c2e46b6..957251901505d445b49c30e4c37f675e6d62dd3d 100755
--- a/non-regression-tests/run_T4_long_multiproc.sh
+++ b/non-regression-tests/run_T4_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T4 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T4_assembly.fasta --nrt
diff --git a/non-regression-tests/run_T7.sh b/non-regression-tests/run_T7.sh
index a9ea89499786abe05c1c582f2221978e376c884c..2990beb112c002f9f6224a2e4446e1a838cc148e 100755
--- a/non-regression-tests/run_T7.sh
+++ b/non-regression-tests/run_T7.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T7 genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T7_assembly.fasta || exit 1
diff --git a/non-regression-tests/run_T7_long.sh b/non-regression-tests/run_T7_long.sh
index 3aeeb83d61695ebc1d8da42bfd14beb1dcb01d85..4b302d712c9df7f372c44d515a9f82eab4d749af 100755
--- a/non-regression-tests/run_T7_long.sh
+++ b/non-regression-tests/run_T7_long.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T7 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T7_assembly.fasta --nrt || exit 1
diff --git a/non-regression-tests/run_T7_long_multiproc.sh b/non-regression-tests/run_T7_long_multiproc.sh
index 5e06af353b504c887518f686ac15fce45174f95a..a359b98ea611ac08d0133e52c6e0fd5ea9c21b4a 100755
--- a/non-regression-tests/run_T7_long_multiproc.sh
+++ b/non-regression-tests/run_T7_long_multiproc.sh
@@ -1,6 +1,6 @@
 #/bin/bash
 DATA_PATH=./data
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on T7 genome and a dataset with a minimum 50x coverage"
 python $SCRIPT_PATH/PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T7_assembly.fasta --nrt
diff --git a/non-regression-tests/run_lamda.sh b/non-regression-tests/run_lamda.sh
index 7a89197784f1d28b53b88a733421566bcd88f09f..685931c1d27c4857f99942f35c0f3e6b1ee17dba 100755
--- a/non-regression-tests/run_lamda.sh
+++ b/non-regression-tests/run_lamda.sh
@@ -1,7 +1,7 @@
 #/bin/bash
 DATA_PATH=./data
 REF_RES_PATH=./reference_results
-SCRIPT_PATH=../_modules
+SCRIPT_PATH=../phagetermvirome
 
 echo "running PhageTerm on lamda genome"
 python $SCRIPT_PATH/PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Lambda_assembly.fasta || exit 1