diff --git a/test/integration/test_intrahost.py b/test/integration/test_intrahost.py
index 481cac256..c98d36ba9 100644
--- a/test/integration/test_intrahost.py
+++ b/test/integration/test_intrahost.py
@@ -100,7 +100,7 @@ class TestSnpEff(TestCaseWithTmp):
     def capsys(self, capsys):
         self.capsys = capsys
 
-    @unittest.skipIf(True, "test is marked to be skipped")
+    #@unittest.skipIf(True, "test is marked to be skipped")
     def test_snpeff(self):
         temp_dir = tempfile.gettempdir()
         input_dir = util.file.get_test_input_path(self)
diff --git a/tools/snpeff.py b/tools/snpeff.py
index 186f297ff..da14dff65 100644
--- a/tools/snpeff.py
+++ b/tools/snpeff.py
@@ -43,7 +43,7 @@ def __init__(self, install_methods=None, extra_genomes=None):
     def version(self):
         return "4.1"
 
-    def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None):    # pylint: disable=W0221
+    def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None, stderr=None):    # pylint: disable=W0221
         if not JVMmemory:
             JVMmemory = self.jvmMemDefault
 
@@ -59,7 +59,7 @@ def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None):    #
             ] + args
 
         _log.debug(' '.join(tool_cmd))
-        return util.misc.run_and_print(tool_cmd, stdin=stdin, buffered=True, silent=("databases" in command), check=True)
+        return util.misc.run_and_print(tool_cmd, stdin=stdin, stderr=stderr, buffered=True, silent=("databases" in command), check=True)
 
     def has_genome(self, genome):
         if not self.known_dbs:
@@ -109,7 +109,9 @@ def create_db(self, accessions, emailAddress=None, JVMmemory=None):
             self.execute('build', args, JVMmemory=JVMmemory)
 
     def available_databases(self):
-        command_ps = self.execute("databases", args=[])
+        # do not capture stderr, since snpEff writes 'Picked up _JAVA_OPTIONS'
+        # which is not helpful for reading the stdout of the databases command
+        command_ps = self.execute("databases", args=[], stderr=subprocess.DEVNULL)
 
         split_points = []
         keys = ['Genome', 'Organism', 'Status', 'Bundle', 'Database']
diff --git a/util/misc.py b/util/misc.py
index 0716879af..eb20a6813 100644
--- a/util/misc.py
+++ b/util/misc.py
@@ -229,6 +229,9 @@ def run_and_print(args, stdout=None, stderr=None,
     This is useful for nose, which has difficulty capturing stdout of
     subprocess invocations.
     '''
+
+    stderr = stderr or subprocess.STDOUT
+
     if loglevel:
         silent = False
     if not buffered:
@@ -238,7 +241,7 @@ def run_and_print(args, stdout=None, stderr=None,
                     args,
                     stdin=stdin,
                     stdout=subprocess.PIPE,
-                    stderr=subprocess.STDOUT,
+                    stderr=stderr,
                     env=env,
                     cwd=cwd,
                     timeout=timeout,
@@ -268,7 +271,7 @@ def run_and_print(args, stdout=None, stderr=None,
                 raise(e)
         else:
             result = run(args, stdin=stdin, stdout=subprocess.PIPE,
-                         stderr=subprocess.STDOUT, env=env, cwd=cwd,
+                         stderr=stderr, env=env, cwd=cwd,
                          timeout=timeout, check=check)
             if not silent and not loglevel:
                 print(result.stdout.decode('utf-8'))
@@ -281,7 +284,7 @@ def run_and_print(args, stdout=None, stderr=None,
         'CompletedProcess', ['args', 'returncode', 'stdout', 'stderr'])
 
         process = subprocess.Popen(args, stdin=stdin, stdout=subprocess.PIPE,
-                                    stderr=subprocess.STDOUT, env=env,
+                                    stderr=stderr, env=env,
                                     cwd=cwd)
         output = []
         while process.poll() is None: