diff --git a/scripts/pipeline.py b/scripts/pipeline.py
index aa91419..b3b74cd 100644
--- a/scripts/pipeline.py
+++ b/scripts/pipeline.py
@@ -28,11 +28,11 @@ OBELIKS_RAW_FILE_NAME = TMP_DIRECTORY + '/obeliks_raw.conllu'
 OBELIKS_TWEAKED_FILE_NAME = TMP_DIRECTORY + '/obeliks_tweaked.conllu'
 CLASSLA_FILE_NAME = TMP_DIRECTORY + '/classla.conllu'
 TEI_INIT_FILE_NAME = TMP_DIRECTORY + '/tei_initial.xml'
-TEI_STRUCTURE_FILE_NAME = TMP_DIRECTORY + '/tei_with_structure_ids.xml'
+TEI_STRUCTURE_1_FILE_NAME = TMP_DIRECTORY + '/tei_with_structure_ids1.xml'
+TEI_STRUCTURE_2_FILE_NAME = TMP_DIRECTORY + '/tei_with_structure_ids2.xml'
 MWE_CSV_1_FILE_NAME = TMP_DIRECTORY + '/mwes1.csv'
 MWE_CSV_2_FILE_NAME = TMP_DIRECTORY + '/mwes2.csv'
 STRUCTURE_NEW_FILE_NAME = TMP_DIRECTORY + '/structures_new.xml'
-TEI_STRUCTURE_FILE_NAME = TMP_DIRECTORY + '/tei_with_structure_ids.xml'
 
 NLP_CONFIG_MAP = {
     'treebank': 'sl_ssj_jos',
@@ -52,12 +52,12 @@ def run_pipeline(input_file_name, output_file_name):
     run_classla(OBELIKS_TWEAKED_FILE_NAME, CLASSLA_FILE_NAME)
     convert_to_tei(CLASSLA_FILE_NAME, TEI_INIT_FILE_NAME)
     run_mwe_extraction(STRUCTURE_CURRENT_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_1_FILE_NAME)
-    run_structure_assignment(STRING_LIST_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_1_FILE_NAME, TEI_STRUCTURE_FILE_NAME)
-    run_structure_creation(STRUCTURE_CURRENT_FILE_NAME, TEI_STRUCTURE_FILE_NAME, STRUCTURE_NEW_FILE_NAME)
+    run_structure_assignment(STRING_LIST_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_1_FILE_NAME, TEI_STRUCTURE_1_FILE_NAME)
+    run_structure_creation(STRUCTURE_CURRENT_FILE_NAME, TEI_STRUCTURE_1_FILE_NAME, STRUCTURE_NEW_FILE_NAME)
     run_mwe_extraction(STRUCTURE_NEW_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_2_FILE_NAME)
-    run_structure_assignment(STRING_LIST_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_2_FILE_NAME, TEI_STRUCTURE_FILE_NAME)
+    run_structure_assignment(STRING_LIST_FILE_NAME, TEI_INIT_FILE_NAME, MWE_CSV_2_FILE_NAME, TEI_STRUCTURE_2_FILE_NAME)
     # run_format_lexicon() # TODO: implement
-    shutil.copyfile(TEI_STRUCTURE_FILE_NAME, output_file_name)
+    shutil.copyfile(TEI_STRUCTURE_2_FILE_NAME, output_file_name)
 
 def run_obeliks4J(obeliks_file_name, classla_file_name):
     print('Running obeliks ...')