diff --git a/pype/plugins/global/publish/collect_rendered_files.py b/pype/plugins/global/publish/collect_rendered_files.py
index 552fd49f6d..35d875dc02 100644
--- a/pype/plugins/global/publish/collect_rendered_files.py
+++ b/pype/plugins/global/publish/collect_rendered_files.py
@@ -4,7 +4,7 @@ import json
 import pyblish.api
 from avalon import api
 
-from pypeapp import PypeLauncher
+from pypeapp import PypeLauncher, Roots
 
 
 class CollectRenderedFiles(pyblish.api.ContextPlugin):
@@ -82,8 +82,23 @@ class CollectRenderedFiles(pyblish.api.ContextPlugin):
             "Missing `PYPE_PUBLISH_DATA`")
         paths = os.environ["PYPE_PUBLISH_DATA"].split(os.pathsep)
 
+        project_name = os.environ.get("AVALON_PROJECT")
+        if project_name is None:
+            root = None
+            self.log.warning(
+                "Environment `AVLAON_PROJECT` was not found."
+                "Could not set `root` which may cause issues."
+            )
+        else:
+            self.log.info("Getting root setting for project \"{}\"".format(
+                project_name
+            ))
+            root = {"root": Roots(project_name)}
+
         session_set = False
         for path in paths:
+            if root:
+                path = path.format(**root)
             data = self._load_json(path)
             if not session_set:
                 self.log.info("Setting session using data from file")
diff --git a/pype/plugins/global/publish/submit_publish_job.py b/pype/plugins/global/publish/submit_publish_job.py
index 8b43bec544..82bd0c5a78 100644
--- a/pype/plugins/global/publish/submit_publish_job.py
+++ b/pype/plugins/global/publish/submit_publish_job.py
@@ -185,15 +185,26 @@ class ProcessSubmittedJobOnFarm(pyblish.api.InstancePlugin):
             batch=job["Props"]["Name"], subset=subset
         )
 
-        metadata_filename = "{}_metadata.json".format(subset)
         output_dir = instance.data["outputDir"]
-        metadata_path = os.path.join(output_dir, metadata_filename)
-
-        metadata_path = os.path.normpath(metadata_path)
-        mount_root = os.path.normpath(os.environ["PYPE_STUDIO_PROJECTS_MOUNT"])
-        network_root = os.environ["PYPE_STUDIO_PROJECTS_PATH"]
-        metadata_path = metadata_path.replace(mount_root, network_root)
-        metadata_path = os.path.normpath(metadata_path)
+        # Convert output dir to `{root}/rest/of/path/...` with Anatomy
+        anatomy_obj = instance.context.data["anatomy"]
+        root_name = anatomy_obj.templates["work"].get("root_name")
+        success, rootless_path = (
+            anatomy_obj.roots.find_root_template_from_path(
+                output_dir, root_name
+            )
+        )
+        if not success:
+            # `rootless_path` is not set to `output_dir` if none of roots match
+            self.log.warning((
+                "Could not find root path for remapping \"{}\"."
+                " This may cause issues on farm."
+            ).format(output_dirt))
+            rootless_path = output_dir
+        else:
+            # If root was found then use `mount` root for `output_dir`
+            anatomy_obj.roots._root_key = "mount"
+            output_dir = rootless_path.format(**{"root": anatomy_obj.roots})
 
         # Generate the payload for Deadline submission
         payload = {
@@ -221,8 +232,14 @@ class ProcessSubmittedJobOnFarm(pyblish.api.InstancePlugin):
         # Transfer the environment from the original job to this dependent
         # job so they use the same environment
 
+        metadata_filename = "{}_metadata.json".format(subset)
+        metadata_path = os.path.join(rootless_path, metadata_filename)
+        "TODO metadata_path replace root with {root[root_name]}
+
         environment = job["Props"].get("Env", {})
         environment["PYPE_METADATA_FILE"] = metadata_path
+        environment["AVALON_PROJECT"] = pyblish.api.Session["AVALON_PROJECT"]
+
         i = 0
         for index, key in enumerate(environment):
             if key.upper() in self.enviro_filter:
diff --git a/pype/scripts/publish_filesequence.py b/pype/scripts/publish_filesequence.py
index fe795564a5..8e14b62306 100644
--- a/pype/scripts/publish_filesequence.py
+++ b/pype/scripts/publish_filesequence.py
@@ -89,13 +89,6 @@ def __main__():
     print("Paths: {}".format(kwargs.paths or [os.getcwd()]))
 
     paths = kwargs.paths or [os.environ.get("PYPE_METADATA_FILE")] or [os.getcwd()]  # noqa
-
-    for path in paths:
-        data = _load_json(path)
-        log.info("Setting session using data from file")
-        os.environ["AVALON_PROJECT"] = data["session"]["AVALON_PROJECT"]
-        break
-
     args = [
         os.path.join(pype_root, pype_command),
         "publish",