diff --git a/ariaec/__init__.pyc b/ariaec/__init__.pyc
index 42b779115f1d982b021de34a3c088eee58d048d0..8beec7da806c597f90cc1923e67032e7aa62f134 100644
Binary files a/ariaec/__init__.pyc and b/ariaec/__init__.pyc differ
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index f4a63e0bc26248ccb20121c00f6978ce683ea0ab..d6f1402e1fc0c50fce3f807e87cb99c13241e5d5 100644
Binary files a/ariaec/base.pyc and b/ariaec/base.pyc differ
diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index 0986351f81727604baf3a0aa6c042b6851c464f2..e58e41ac9f3a8f238b0b9abc9e6e13b9066d6d5a 100644
Binary files a/ariaec/commands.pyc and b/ariaec/commands.pyc differ
diff --git a/ariaec/conf/aria_ec.ini b/ariaec/conf/aria_ec.ini
index d47d9cf3470ad2653ff0e813f3319df6c04f0204..a36fcfabbdaa7006a17da7ad1a0502bae387996f 100644
--- a/ariaec/conf/aria_ec.ini
+++ b/ariaec/conf/aria_ec.ini
@@ -73,7 +73,6 @@ nd_control:                                 0
 runid:                                      1
 cpus:                                       100
 host_command:                               sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
-working_directory:                          data/examples/out/setup
 temp_root:                                  data/examples/out/setup
 parameter_definition:                       automatic
 ss_dist_format:                             tbl
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index ea6211843985c309edbf4a9e22b8e0200a957ccf..e9b76686f55ee774ba37e8f1d66f18ac2972f0e7 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -712,6 +712,15 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
     def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files,
                           desc=""):
+        """
+        Generate ariaproject.xml file
+        :param aria_template: ariaproject.xml template path
+        :param seqfile:
+        :param dist_files:
+        :param tbl_files:
+        :param desc:
+        :return:
+        """
         if aria_template:
             template = os.path.abspath(aria_template)
 
@@ -737,26 +746,24 @@ class AriaEcXMLConverter(AriaXMLConverter):
                      'the ratio %.2f:%.2f' % (steps_1, steps_2))
 
         aria_project_dict.update(self.settings.setup.config)
-        work_dir = os.path.abspath(aria_project_dict['working_directory'])
+        work_dir = os.path.abspath(self.settings.outdir)
         temp_root = os.path.abspath(aria_project_dict['temp_root'])
 
         if not os.path.exists(work_dir) or not os.path.exists(temp_root):
-            logger.info("Working dir %s and temp directory %s doesn't exist." % (
-                work_dir, temp_root))
+            logger.info("Working dir %s doesn't exist." % work_dir)
             logger.info("Create new directory %s" % work_dir)
             os.makedirs(work_dir)
+
+        if not os.path.exists(temp_root):
+            logger.info("Temp directory %s doesn't exist." % temp_root)
             logger.info("Create new directory %s" % temp_root)
             os.makedirs(temp_root)
 
-        for direct in (work_dir, temp_root):
-
-            if not os.path.exists(os.path.join(direct, self.outprefix)):
-                os.makedirs(os.path.join(direct, self.outprefix))
-
-            if not os.path.exists(os.path.join(direct, self.outprefix, desc)):
-                os.makedirs(os.path.join(direct, self.outprefix, desc))
+        if not os.path.exists(os.path.join(temp_root, self.outprefix)):
+            os.makedirs(os.path.join(temp_root, self.outprefix))
+        if not os.path.exists(os.path.join(temp_root, self.outprefix, desc)):
+            os.makedirs(os.path.join(temp_root, self.outprefix, desc))
 
-        work_dir = os.path.join(work_dir, self.outprefix, desc)
         temp_root = os.path.join(temp_root, self.outprefix, desc)
 
         aria_project_dict['working_directory'] = work_dir
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 1e89d37d3a6835f86c91c4bcacca99b2cd3c8bbe..b86dacd13ed269c6f95c4e984d70cd0ade0610d3 100644
Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 209f3ab6b90d317fbeb8c04d9881955e3da2623d..14a6ab0431a6f0549d2010cb1be33f34717c8df2 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index a21fef1bed62dd942c979bb3f41cec9c39e17d56..f774d93fd4dbee644841d77ba4619ebb527daa0e 100644
Binary files a/ariaec/maplot.pyc and b/ariaec/maplot.pyc differ
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 284b67088a7c769f0534a12991a39d4cbd2b4cf9..9384a753ca62347a0205225fbddc43a197d46c95 100644
Binary files a/ariaec/protein.pyc and b/ariaec/protein.pyc differ
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index f99062db6e3547d723a669c9252b023a9f829c85..4f99b29d49eeb0eaf9a7665a9a708f3355841745 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index fada925ea836ec7c758856a3e4ef48a20448ebc7..32c3329cf97c194f6d91309a7ffd312a215a9608 100644
Binary files a/ariaec/reader.pyc and b/ariaec/reader.pyc differ
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index 4f16a2b361a1c02638a25850235bf1943cb5f8fb..9acd618838fbdac5ab9e9b455d1417883426c65d 100644
Binary files a/ariaec/setup.pyc and b/ariaec/setup.pyc differ
diff --git a/version.py b/version.py
index 70bb33137bbb9bab28eb1bf82564e7980edaa20f..282defff11555733eda4731f253d20d680bfeec7 100644
--- a/version.py
+++ b/version.py
@@ -1,2 +1,2 @@
 # Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev1
\ No newline at end of file
+__version__=v0.1.11-dev2
\ No newline at end of file