diff --git a/non-regression-tests/mimic_multi_machine/run_virome_mm.sh b/non-regression-tests/mimic_multi_machine/run_virome_mm.sh
index cf79ac1376b7830949eca4860120dfde81217a9d..ab75c9de2c943ef52eec5775b66772317afc5678 100755
--- a/non-regression-tests/mimic_multi_machine/run_virome_mm.sh
+++ b/non-regression-tests/mimic_multi_machine/run_virome_mm.sh
@@ -4,7 +4,7 @@ DATA_PATH=../data
 mkdir tmp
 for i in 0 1 2 3 4
 do
-	python ../../PhageTerm.py --mm --dir_cov_mm tmp -c 5 --core_id $i -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4"  -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 1$i
+	python ../../phagetermvirome/PhageTerm.py --mm --dir_cov_mm tmp -c 5 --core_id $i -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4"  -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 1$i
 done
 
 mkdir tmp2
@@ -12,8 +12,8 @@ mkdir DR
 
 for i in 0 1 2 3 4 5
 do
-python ../../PhageTerm.py --mm --dir_cov_mm=tmp --dir_seq_mm=tmp2 --DR_path=DR --seq_id=$i --nb_pieces=5 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 2$i
+python ../../phagetermvirome/PhageTerm.py --mm --dir_cov_mm=tmp --dir_seq_mm=tmp2 --DR_path=DR --seq_id=$i --nb_pieces=5 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 2$i
 done
 
-python ../../PhageTerm.py --mm -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" --DR_path=DR --dir_seq_mm=tmp2 ||exit 3
+python ../../phagetermvirome/PhageTerm.py --mm -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" --DR_path=DR --dir_seq_mm=tmp2 ||exit 3
 python check_virome_res.py
diff --git a/phagetermvirome/PhageTerm.py b/phagetermvirome/PhageTerm.py
index 7aaa7648bf126320534acf96753a37ed63bc25ef..4894d27b4e8a36e5e6647bea2dfcac821db73362 100755
--- a/phagetermvirome/PhageTerm.py
+++ b/phagetermvirome/PhageTerm.py
@@ -120,12 +120,12 @@ def main():
                 f.close()
             exit() # Consider that if we put results in files, it is because we are processing large datasets on a cluster.
         if tParms.dir_cov_mm!=None and tParms.seq_id!=None and tParms.dir_seq_mm!=None and tParms.DR_path!=None:
-            from _modules.seq_processing import sum_readsCoverage_for_seq
+            from seq_processing import sum_readsCoverage_for_seq
             # in that case, we are processing all the results of readCoverage sequence by sequence in an embarrassingly parallel way on a cluster.
             sum_readsCoverage_for_seq(tParms.dir_cov_mm, tParms.seq_id, tParms.nb_pieces, inDArgs, fParms, inRawDArgs, tParms.dir_seq_mm,tParms.DR_path)
             exit()
         if tParms.dir_seq_mm!=None and tParms.dir_cov_mm==None and tParms.seq_id==None and tParms.DR_path!=None: # report generation
-            from _modules.generate_report import loadDR,genReport
+            from generate_report import loadDR,genReport
             loadDR(tParms.DR_path, DR)
             genReport(fParms, inDArgs, inRawDArgs, no_match, DR)
             exit()
diff --git a/phagetermvirome/generate_report.py b/phagetermvirome/generate_report.py
index abd73fa1f3ae631fc39b9d2b0803c562f1cc7a28..c11c92c96d45e7ecdbb55f232b1343f89966c023 100644
--- a/phagetermvirome/generate_report.py
+++ b/phagetermvirome/generate_report.py
@@ -3,7 +3,7 @@ import os
 import pickle
 from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Image, Table, TableStyle, PageBreak
 from reportlab.lib.pagesizes import letter, landscape
-from _modules.functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport
+from functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport
 
 
 def loadDR(DR_path,DR):
diff --git a/phagetermvirome/seq_processing.py b/phagetermvirome/seq_processing.py
index f3c66b2e474be2c34fbf5c09b8c264c65d93bc13..d188f4a3d394b73d284bb2706e710a10aebcf622 100755
--- a/phagetermvirome/seq_processing.py
+++ b/phagetermvirome/seq_processing.py
@@ -7,9 +7,9 @@ from __future__ import print_function
 from time import gmtime, strftime
 import os
 import numpy as np
-from _modules.utilities import checkReportTitle
-from _modules.readsCoverage_res import loadRCRes
-from _modules.common_readsCoverage_processing import processCovValuesForSeq
+from utilities import checkReportTitle
+from readsCoverage_res import loadRCRes
+from common_readsCoverage_processing import processCovValuesForSeq
 #from SeqStats import SeqStats
 def sum_readsCoverage_for_seq(dir_cov_res,idx_refseq,nb_pieces,inDArgs,fParms,inRawDArgs,dir_seq_res,DR_path):
     if os.path.exists(DR_path):