diff --git a/test/test_functional/test_align.py b/test/test_functional/test_align.py
index 5cad330d48f2062d60c6e2fd23ee9cdddb896170..cd9eb9bbe40bc7b8b425b474e623b86aa8bf5d5e 100755
--- a/test/test_functional/test_align.py
+++ b/test/test_functional/test_align.py
@@ -111,98 +111,98 @@ def setup_teardown_module():
 #     assert "END" in " ".join(log_content)
 
 
-def test_main_exist_ok():
-    """
-    Test main all files exist and are ok, no force -> end without error, with warnings on re-use
-    """
-    corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
-    list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
-    dname = "TEST4exists"
-    dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
-    outdir = os.path.join(GENEPATH, "test_main_exist_ok")
-    threads = 1
-    force = False
-    cmd = "cmd test_main_exist_ok"
-    # Create output directories and files
-    aldir = os.path.join(outdir, "Align-" + dname)
-    listdir = os.path.join(outdir, "List-" + dname)
-    treedir = os.path.join(outdir, "Phylo-" + dname)
-    os.makedirs(aldir)
-    os.makedirs(listdir)
-    os.makedirs(treedir)
-    # Create content of listdir
-    ex_listdir = os.path.join(EXPPATH, "exp_listdir-pers")
-    genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
-    for gen in genomes:
-        outgen = os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt")
-        refgen = os.path.join(ex_listdir, f"getEntry_gen_{gen}")
-        shutil.copyfile(refgen, outgen)
-        outprt = os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt")
-        refprt = os.path.join(ex_listdir, f"getEntry_prt_{gen}")
-        shutil.copyfile(refprt, outprt)
-    # Create content of aldir
-    ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers")
-    fams = [1, 4, 6, 8, 10, 11, 13, 14]
-    for fam in fams:
-        outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen')
-        refgen = os.path.join(ex_aldir, f"current.{fam}.gen")
-        shutil.copyfile(refgen, outgen)
-        outprt = os.path.join(aldir, f'{dname}-current.{fam}.prt')
-        refprt = os.path.join(ex_aldir, f"current.{fam}.prt")
-        shutil.copyfile(refprt, outprt)
-        outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')
-        refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst")
-        shutil.copyfile(refmiss, outmiss)
-        outaln = os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln')
-        refaln = os.path.join(ex_aldir, f"mafft-align.{fam}.aln")
-        shutil.copyfile(refaln, outaln)
-        outbtr = os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln')
-        refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln")
-        shutil.copyfile(refbtr, outbtr)
-    outcat = os.path.join(aldir, dname + "-complete.cat.aln")
-    refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
-    shutil.copyfile(refcat, outcat)
-    # Create content of treedir
-    outgrp = os.path.join(treedir, dname + ".grp.aln")
-    refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
-    shutil.copyfile(refgrp, outgrp)
-    # Run align module
-    al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
-    # Check logs
-    logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details")
-    with open(logfile, "r") as lc:
-        log_content = lc.readlines()
-    assert ("Reading PersGenome and constructing lists of missing genomes in "
-            "each family") in " ".join(log_content)
-    for gen in genomes:
-        assert (f"For genome {gen}, test/data/align/generated_by_func_tests/test_main_exist_ok/"
-                f"List-TEST4exists/TEST4exists-getEntry_prt_{gen}.txt and test/data/align/"
-                "generated_by_func_tests/test_main_exist_ok/List-TEST4exists/"
-                f"TEST4exists-getEntry_gen_{gen}.txt already exist. The program "
-                "will use them to extract proteins and genes. If you prefer to rewrite "
-                "them, use option -F ") in " ".join(log_content)
-    assert ("Starting alignment of all families: protein alignment, back-translation to "
-            "nucleotides, and add missing genomes in the family") in " ".join(log_content)
-    for fam in fams:
-        assert "Checking extractions for family {}".format(fam) in " ".join(log_content)
-        assert ("Alignment already done for family {}. The program will use it for next "
-                "steps").format(fam) in " ".join(log_content)
-    assert ("All extraction files already existing (see detailed log for more "
-            "information)") in " ".join(log_content)
-    assert ("All prt and gene files for all families already exist. The program will use them "
-            "for the next step. If you want to re-extract a given family, remove its prt and "
-            "gen extraction files. If you want to re-extract all families, use option -F "
-            "(or --force).") in " ".join(log_content)
-    assert ("Alignments already concatenated in "
-            "test/data/align/generated_by_func_tests/test_main_exist_ok/Align-TEST4exists/"
-            "TEST4exists-complete.cat.aln. Program will "
-            "use it for next steps. If you want to redo it, remove it before "
-            "running.") in " ".join(log_content)
-    assert ("Alignments already grouped by genome in "
-            "test/data/align/generated_by_func_tests/test_main_exist_ok/Phylo-TEST4exists/"
-            "TEST4exists.grp.aln. Program will "
-            "end.") in " ".join(log_content)
-    assert "END" in " ".join(log_content)
+# def test_main_exist_ok():
+#     """
+#     Test main all files exist and are ok, no force -> end without error, with warnings on re-use
+#     """
+#     corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
+#     list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
+#     dname = "TEST4exists"
+#     dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
+#     outdir = os.path.join(GENEPATH, "test_main_exist_ok")
+#     threads = 1
+#     force = False
+#     cmd = "cmd test_main_exist_ok"
+#     # Create output directories and files
+#     aldir = os.path.join(outdir, "Align-" + dname)
+#     listdir = os.path.join(outdir, "List-" + dname)
+#     treedir = os.path.join(outdir, "Phylo-" + dname)
+#     os.makedirs(aldir)
+#     os.makedirs(listdir)
+#     os.makedirs(treedir)
+#     # Create content of listdir
+#     ex_listdir = os.path.join(EXPPATH, "exp_listdir-pers")
+#     genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
+#     for gen in genomes:
+#         outgen = os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt")
+#         refgen = os.path.join(ex_listdir, f"getEntry_gen_{gen}")
+#         shutil.copyfile(refgen, outgen)
+#         outprt = os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt")
+#         refprt = os.path.join(ex_listdir, f"getEntry_prt_{gen}")
+#         shutil.copyfile(refprt, outprt)
+#     # Create content of aldir
+#     ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers")
+#     fams = [1, 4, 6, 8, 10, 11, 13, 14]
+#     for fam in fams:
+#         outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen')
+#         refgen = os.path.join(ex_aldir, f"current.{fam}.gen")
+#         shutil.copyfile(refgen, outgen)
+#         outprt = os.path.join(aldir, f'{dname}-current.{fam}.prt')
+#         refprt = os.path.join(ex_aldir, f"current.{fam}.prt")
+#         shutil.copyfile(refprt, outprt)
+#         outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')
+#         refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst")
+#         shutil.copyfile(refmiss, outmiss)
+#         outaln = os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln')
+#         refaln = os.path.join(ex_aldir, f"mafft-align.{fam}.aln")
+#         shutil.copyfile(refaln, outaln)
+#         outbtr = os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln')
+#         refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln")
+#         shutil.copyfile(refbtr, outbtr)
+#     outcat = os.path.join(aldir, dname + "-complete.cat.aln")
+#     refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
+#     shutil.copyfile(refcat, outcat)
+#     # Create content of treedir
+#     outgrp = os.path.join(treedir, dname + ".grp.aln")
+#     refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
+#     shutil.copyfile(refgrp, outgrp)
+#     # Run align module
+#     al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
+#     # Check logs
+#     logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details")
+#     with open(logfile, "r") as lc:
+#         log_content = lc.readlines()
+#     assert ("Reading PersGenome and constructing lists of missing genomes in "
+#             "each family") in " ".join(log_content)
+#     for gen in genomes:
+#         assert (f"For genome {gen}, test/data/align/generated_by_func_tests/test_main_exist_ok/"
+#                 f"List-TEST4exists/TEST4exists-getEntry_prt_{gen}.txt and test/data/align/"
+#                 "generated_by_func_tests/test_main_exist_ok/List-TEST4exists/"
+#                 f"TEST4exists-getEntry_gen_{gen}.txt already exist. The program "
+#                 "will use them to extract proteins and genes. If you prefer to rewrite "
+#                 "them, use option -F ") in " ".join(log_content)
+#     assert ("Starting alignment of all families: protein alignment, back-translation to "
+#             "nucleotides, and add missing genomes in the family") in " ".join(log_content)
+#     for fam in fams:
+#         assert "Checking extractions for family {}".format(fam) in " ".join(log_content)
+#         assert ("Alignment already done for family {}. The program will use it for next "
+#                 "steps").format(fam) in " ".join(log_content)
+#     assert ("All extraction files already existing (see detailed log for more "
+#             "information)") in " ".join(log_content)
+#     assert ("All prt and gene files for all families already exist. The program will use them "
+#             "for the next step. If you want to re-extract a given family, remove its prt and "
+#             "gen extraction files. If you want to re-extract all families, use option -F "
+#             "(or --force).") in " ".join(log_content)
+#     assert ("Alignments already concatenated in "
+#             "test/data/align/generated_by_func_tests/test_main_exist_ok/Align-TEST4exists/"
+#             "TEST4exists-complete.cat.aln. Program will "
+#             "use it for next steps. If you want to redo it, remove it before "
+#             "running.") in " ".join(log_content)
+#     assert ("Alignments already grouped by genome in "
+#             "test/data/align/generated_by_func_tests/test_main_exist_ok/Phylo-TEST4exists/"
+#             "TEST4exists.grp.aln. Program will "
+#             "end.") in " ".join(log_content)
+#     assert "END" in " ".join(log_content)
 
 
 def test_main_exist_emptygrp(capsys):