diff --git a/quast_libs/ca_utils/align_contigs.py b/quast_libs/ca_utils/align_contigs.py
index dad4b7f75a..87ddeff50b 100644
--- a/quast_libs/ca_utils/align_contigs.py
+++ b/quast_libs/ca_utils/align_contigs.py
@@ -13,7 +13,8 @@
 
 from quast_libs import options_parser
 from quast_libs import qconfig, qutils
-from quast_libs.ca_utils.misc import bin_fpath, is_emem_aligner, compile_aligner, e_mem_failed_compilation_flag
+from quast_libs.ca_utils.misc import bin_fpath, is_emem_aligner, compile_aligner, e_mem_failed_compilation_flag, \
+    create_nucmer_output_dir, clean_tmp_files
 
 from quast_libs.log import get_logger
 from quast_libs.qutils import is_python_2
@@ -52,11 +53,14 @@ def check_emem_functionality(logger):
     if not is_emem_aligner():
         return True
     logger.debug('Checking correctness of E-MEM compilation...')
-    return_code = run_nucmer(qconfig.output_dirpath, options_parser.test_reference, options_parser.test_contigs_fpaths[0],
+    nucmer_output_dirpath = create_nucmer_output_dir(qconfig.output_dirpath)
+    nucmer_fpath = join(nucmer_output_dirpath, 'test')
+    return_code = run_nucmer(nucmer_fpath, options_parser.test_contigs_fpaths[0], options_parser.test_contigs_fpaths[1],
                              '/dev/null', '/dev/null', 0, emem_threads=1)
     if return_code != 0:
         logger.main_info('E-MEM does not work properly. QUAST will try to recompile contig aligner software.')
         open(e_mem_failed_compilation_flag, 'w').close()
+    clean_tmp_files(nucmer_fpath)
     return compile_aligner(logger)
 
 
diff --git a/quast_libs/ca_utils/misc.py b/quast_libs/ca_utils/misc.py
index 7a3ee22c9c..aac68bd840 100644
--- a/quast_libs/ca_utils/misc.py
+++ b/quast_libs/ca_utils/misc.py
@@ -34,19 +34,20 @@ def is_emem_aligner():
     return contig_aligner == 'E-MEM'
 
 
-def compile_aligner(logger, only_clean=False):
+def compile_aligner(logger, only_clean=False, compile_all_aligners=False):
     global contig_aligner
     global contig_aligner_dirpath
 
-    if contig_aligner_dirpath is not None and not check_prev_compilation_failed(contig_aligner, join(contig_aligner_dirpath, 'make.failed'),
-                                                                                just_notice=True, logger=logger):
-        return True
+    if not compile_all_aligners:
+        if contig_aligner_dirpath is not None and not \
+                check_prev_compilation_failed(contig_aligner, join(contig_aligner_dirpath, 'make.failed'), just_notice=True, logger=logger):
+            return True
 
-    if not contig_aligner_dirpath and qconfig.platform_name == 'macosx' and not \
-            check_prev_compilation_failed('E-MEM', e_mem_failed_compilation_flag, just_notice=True, logger=logger):
-        contig_aligner = 'E-MEM'
-        contig_aligner_dirpath = join(qconfig.LIBS_LOCATION, 'E-MEM-osx')
-        return True
+        if not contig_aligner_dirpath and qconfig.platform_name == 'macosx' and not \
+                check_prev_compilation_failed('E-MEM', e_mem_failed_compilation_flag, just_notice=True, logger=logger):
+            contig_aligner = 'E-MEM'
+            contig_aligner_dirpath = join(qconfig.LIBS_LOCATION, 'E-MEM-osx')
+            return True
 
     default_requirements = ['nucmer', 'delta-filter', 'show-coords', 'show-snps', 'mummer', 'mgaps']
 
@@ -65,6 +66,10 @@ def compile_aligner(logger, only_clean=False):
             continue
         contig_aligner = name
         contig_aligner_dirpath = dirpath  # successfully compiled
+        if not compile_all_aligners:
+            return True
+
+    if compile_all_aligners and contig_aligner and contig_aligner_dirpath:
         return True
     logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
     return False
diff --git a/setup.py b/setup.py
index bd8f9491b3..984d0b70fc 100755
--- a/setup.py
+++ b/setup.py
@@ -142,8 +142,7 @@ def find_package_files(dirpath, package=quast_package):
 
 if cmd_in(['install', 'develop', 'build', 'build_ext']):
     logger.info('* Compiling aligner *')
-    compile_aligner(logger)
-    check_emem_functionality(logger)
+    compile_aligner(logger, compile_all_aligners=True)
     logger.info('* Compiling Glimmer *')
     compile_glimmer()
     logger.info('* Compiling GAGE *')