diff --git a/recipes/ispyb/em-spa-refine-wrapper.json b/recipes/ispyb/em-spa-refine-wrapper.json
index c5ae8b3b..f5751b0f 100644
--- a/recipes/ispyb/em-spa-refine-wrapper.json
+++ b/recipes/ispyb/em-spa-refine-wrapper.json
@@ -10,7 +10,8 @@
       "original_pixel_size": "{pixel_size}",
       "refine_class_nr": "{class_number}",
       "refine_job_dir": "{refine_job_dir}",
-      "relion_options": {}
+      "relion_options": {},
+      "submit_to_slurm": "True"
     },
     "queue": "extract_class",
     "service": "ExtractClass"
diff --git a/src/cryoemservices/services/class2d.py b/src/cryoemservices/services/class2d.py
index 8b7a659c..8557f4d3 100644
--- a/src/cryoemservices/services/class2d.py
+++ b/src/cryoemservices/services/class2d.py
@@ -19,7 +19,7 @@ class Class2D(CommonService):
     def initializing(self):
         """Subscribe to a queue. Received messages must be acknowledged."""
         self.log.info("Class2D service starting")
-        wrap_subscribe(
+        self.subscription_id = wrap_subscribe(
             self._transport,
             self._environment["queue"] or "class2d",
             self.class2d,
@@ -34,7 +34,7 @@ def class2d(self, rw, header: dict, message: dict):
             if not isinstance(message, dict):
                 self.log.error("Rejected invalid simple message")
                 self._transport.nack(header)
-                return
+                return False
 
             # Create a wrapper-like object that can be passed to functions
             # as if a recipe wrapper was present.
@@ -58,7 +58,7 @@ def class2d(self, rw, header: dict, message: dict):
                 f"with exception: {e}"
             )
             rw.transport.nack(header)
-            return
+            return False
 
         # In this setup we cannot nack messages on failure, so instead check here
         if message.get("requeue", 0) >= 5:
@@ -71,6 +71,8 @@ def class2d(self, rw, header: dict, message: dict):
             f"Running disconnected Class2D job for {class2d_params.particles_file}"
         )
         rw.transport.ack(header)
+        rw.transport.unsubscribe(self.subscription_id)
+        rw.transport.drop_callback_reference(self.subscription_id)
 
         # Run the class2d job
         try:
@@ -88,3 +90,7 @@ def class2d(self, rw, header: dict, message: dict):
             # Send back to the queue but mark a failure in the message
             message["requeue"] = message.get("requeue", 0) + 1
             rw.send_to("class2d", message)
+
+        # Reconnect to rabbitmq
+        self.initializing()
+        return True
diff --git a/src/cryoemservices/services/class3d.py b/src/cryoemservices/services/class3d.py
index 5f43b6ab..0c5892ee 100644
--- a/src/cryoemservices/services/class3d.py
+++ b/src/cryoemservices/services/class3d.py
@@ -19,7 +19,7 @@ class Class3D(CommonService):
     def initializing(self):
         """Subscribe to a queue. Received messages must be acknowledged."""
         self.log.info("Class3D service starting")
-        wrap_subscribe(
+        self.subscription_id = wrap_subscribe(
             self._transport,
             self._environment["queue"] or "class3d",
             self.class3d,
@@ -34,7 +34,7 @@ def class3d(self, rw, header: dict, message: dict):
             if not isinstance(message, dict):
                 self.log.error("Rejected invalid simple message")
                 self._transport.nack(header)
-                return
+                return False
 
             # Create a wrapper-like object that can be passed to functions
             # as if a recipe wrapper was present.
@@ -58,7 +58,7 @@ def class3d(self, rw, header: dict, message: dict):
                 f"with exception: {e}"
             )
             rw.transport.nack(header)
-            return
+            return False
 
         # In this setup we cannot nack messages on failure, so instead check here
         if message.get("requeue", 0) >= 5:
@@ -71,6 +71,8 @@ def class3d(self, rw, header: dict, message: dict):
             f"Running disconnected Class3D job for {class3d_params.particles_file}"
         )
         rw.transport.ack(header)
+        rw.transport.unsubscribe(self.subscription_id)
+        rw.transport.drop_callback_reference(self.subscription_id)
 
         # Run the class3d job
         try:
@@ -88,3 +90,7 @@ def class3d(self, rw, header: dict, message: dict):
             # Send back to the queue but mark a failure in the message
             message["requeue"] = message.get("requeue", 0) + 1
             rw.send_to("class3d", message)
+
+        # Reconnect to rabbitmq
+        self.initializing()
+        return True
diff --git a/src/cryoemservices/services/common_service.py b/src/cryoemservices/services/common_service.py
index 85e91182..ed57b293 100644
--- a/src/cryoemservices/services/common_service.py
+++ b/src/cryoemservices/services/common_service.py
@@ -31,6 +31,7 @@ def __init__(
         self.log = logging.getLogger(self._logger_name)
         self.log.setLevel(logging.INFO)
         self.single_message_mode: bool = single_message_mode
+        self.subscription_id: int = 0
 
     def _transport_interceptor(self, callback):
         """Takes a callback function and adds headers and messages"""
diff --git a/src/cryoemservices/services/cryolo.py b/src/cryoemservices/services/cryolo.py
index b265b827..57f8263c 100644
--- a/src/cryoemservices/services/cryolo.py
+++ b/src/cryoemservices/services/cryolo.py
@@ -346,6 +346,18 @@ def cryolo(self, rw, header: dict, message: dict):
             rw.transport.ack(header)
             return
 
+        # Rename any flattened files
+        if scaled_input_path != cryolo_params.input_path:
+            (job_dir / f"CBOX/{Path(cryolo_params.output_path).stem}_flat.cbox").rename(
+                job_dir / f"CBOX/{Path(cryolo_params.output_path).stem}.cbox"
+            )
+            (job_dir / f"STAR/{Path(cryolo_params.output_path).stem}_flat.star").rename(
+                job_dir / f"STAR/{Path(cryolo_params.output_path).stem}.star"
+            )
+            (job_dir / f"EMAN/{Path(cryolo_params.output_path).stem}_flat.box").rename(
+                job_dir / f"EMAN/{Path(cryolo_params.output_path).stem}.box"
+            )
+
         # Read in the cbox file for particle selection and finding sizes
         try:
             cbox_file = cif.read_file(
diff --git a/src/cryoemservices/services/extract_class.py b/src/cryoemservices/services/extract_class.py
index ef0d789a..a59da6c0 100644
--- a/src/cryoemservices/services/extract_class.py
+++ b/src/cryoemservices/services/extract_class.py
@@ -3,6 +3,7 @@
 import math
 import os
 import re
+import subprocess
 from pathlib import Path
 
 from pydantic import BaseModel, Field, ValidationError
@@ -30,6 +31,7 @@ class ExtractClassParameters(BaseModel):
     downscale: bool = True
     normalise: bool = True
     invert_contrast: bool = True
+    submit_to_slurm: bool = False
     relion_options: RelionServiceOptions
 
 
@@ -254,19 +256,22 @@ def extract_class(self, rw, header: dict, message: dict):
         if extract_params.downscale:
             command.append("--downscale")
 
-        result = slurm_submission_for_services(
-            log=self.log,
-            service_config_file=self._environment["config"],
-            slurm_cluster=self._environment["slurm_cluster"],
-            job_name="ReExtract",
-            command=command,
-            project_dir=extract_job_dir,
-            output_file=extract_job_dir / "slurm_run",
-            cpus=40,
-            use_gpu=False,
-            use_singularity=False,
-            script_extras="module load EM/cryoem-services",
-        )
+        if extract_params.submit_to_slurm:
+            result = slurm_submission_for_services(
+                log=self.log,
+                service_config_file=self._environment["config"],
+                slurm_cluster=self._environment["slurm_cluster"],
+                job_name="ReExtract",
+                command=command,
+                project_dir=extract_job_dir,
+                output_file=extract_job_dir / "slurm_run",
+                cpus=40,
+                use_gpu=False,
+                use_singularity=False,
+                script_extras="module load EM/cryoem-services",
+            )
+        else:
+            result = subprocess.run(command, capture_output=True)
 
         # Register the Re-extraction job with the node creator
         self.log.info(f"Sending {self.extract_job_type} to node creator")
diff --git a/src/cryoemservices/services/motioncorr.py b/src/cryoemservices/services/motioncorr.py
index 2a9daba5..14ea6b34 100644
--- a/src/cryoemservices/services/motioncorr.py
+++ b/src/cryoemservices/services/motioncorr.py
@@ -579,7 +579,7 @@ def motion_correction(self, rw, header: dict, message: dict):
             )
             if mc_params.do_icebreaker_jobs and not icebreaker_output.is_file():
                 # Three IceBreaker jobs: CtfFind job is MC+4
-                ctf_job_number = 6
+                ctf_job_number = job_number + 4
 
                 # Both IceBreaker micrographs and flattening inherit from motioncorr
                 self.log.info(
@@ -624,10 +624,10 @@ def motion_correction(self, rw, header: dict, message: dict):
                 ctf_job_number = job_number + 4
             else:
                 # No IceBreaker jobs: CtfFind job is MC+1
-                ctf_job_number = 3
+                ctf_job_number = job_number + 1
         else:
             # Tomography: CtfFind job is MC+1
-            ctf_job_number = 3
+            ctf_job_number = job_number + 1
 
         # Forward results to ctffind (in both SPA and tomography)
         self.log.info(f"Sending to ctf: {mc_params.mrc_out}")
diff --git a/src/cryoemservices/services/refine3d.py b/src/cryoemservices/services/refine3d.py
index 45864436..ca8334a8 100644
--- a/src/cryoemservices/services/refine3d.py
+++ b/src/cryoemservices/services/refine3d.py
@@ -19,7 +19,7 @@ class Refine3D(CommonService):
     def initializing(self):
         """Subscribe to a queue. Received messages must be acknowledged."""
         self.log.info("Refine3D service starting")
-        wrap_subscribe(
+        self.subscription_id = wrap_subscribe(
             self._transport,
             self._environment["queue"] or "refine3d",
             self.refine3d,
@@ -34,7 +34,7 @@ def refine3d(self, rw, header: dict, message: dict):
             if not isinstance(message, dict):
                 self.log.error("Rejected invalid simple message")
                 self._transport.nack(header)
-                return
+                return False
 
             # Create a wrapper-like object that can be passed to functions
             # as if a recipe wrapper was present.
@@ -58,7 +58,7 @@ def refine3d(self, rw, header: dict, message: dict):
                 f"with exception: {e}"
             )
             rw.transport.nack(header)
-            return
+            return False
 
         # In this setup we cannot nack messages on failure, so instead check here
         if message.get("requeue", 0) >= 5:
@@ -71,6 +71,8 @@ def refine3d(self, rw, header: dict, message: dict):
             f"Running disconnected Refine3D job for {refine_params.particles_file}"
         )
         rw.transport.ack(header)
+        rw.transport.unsubscribe(self.subscription_id)
+        rw.transport.drop_callback_reference(self.subscription_id)
 
         # Run the refinement job
         try:
@@ -90,3 +92,7 @@ def refine3d(self, rw, header: dict, message: dict):
             # Send back to the queue but mark a failure in the message
             message["requeue"] = message.get("requeue", 0) + 1
             rw.send_to("refine3d", message)
+
+        # Reconnect to rabbitmq
+        self.initializing()
+        return True
diff --git a/src/cryoemservices/util/ispyb_commands.py b/src/cryoemservices/util/ispyb_commands.py
index 48478c9f..d8127429 100644
--- a/src/cryoemservices/util/ispyb_commands.py
+++ b/src/cryoemservices/util/ispyb_commands.py
@@ -7,7 +7,7 @@
 
 import ispyb.sqlalchemy as models
 import sqlalchemy.exc
-import sqlalchemy.orm
+from sqlalchemy.orm import Session
 
 from cryoemservices.util import ispyb_buffer
 
@@ -36,27 +36,35 @@ def parameters_with_replacement(param: str, message: dict, all_parameters: Calla
     return value_to_return
 
 
-def multipart_message(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def multipart_message(message: dict, parameters: Callable, session: Session):
     """
     The multipart_message command allows the recipe or client to specify a
     list of API calls to run.
     Each API call may have a return value that can be stored and passed on.
     """
     commands = parameters("ispyb_command_list")
-    step = message.get("checkpoint", 0) + 1
     if not commands or not isinstance(commands, list):
         logger.error("Received multipart message containing no command list")
         return False
 
     current_command = commands[0]
-    command = globals().get(current_command.get("ispyb_command"))
+    command: Callable | None = globals().get(current_command.get("ispyb_command"))
     if not command:
         logger.error(
             f"Multipart command {current_command} does not have a valid ispyb_command"
         )
         return False
+    return run_multipart_command(message, parameters, session, command)
+
+
+def run_multipart_command(
+    message: dict, parameters: Callable, session: Session, command: Callable
+):
+    """Run specific commands from a multipart message"""
+    # Get the commands and steps again
+    commands = parameters("ispyb_command_list")
+    step = message.get("checkpoint", 0) + 1
+    current_command = commands[0]
     logger.info(
         f"Processing step {step} of multipart message ({current_command}) "
         f"with {len(commands) - 1} further steps",
@@ -102,7 +110,7 @@ def step_parameters(parameter):
     }
 
 
-def buffer(message: dict, parameters: Callable, session: sqlalchemy.orm.Session):
+def buffer(message: dict, parameters: Callable, session: Session):
     """
     The buffer command supports running buffer lookups before running
     a command, and storing the result in a buffer after running the command.
@@ -171,7 +179,7 @@ def buffer(message: dict, parameters: Callable, session: sqlalchemy.orm.Session)
     return result
 
 
-def insert_movie(message: dict, parameters: Callable, session: sqlalchemy.orm.Session):
+def insert_movie(message: dict, parameters: Callable, session: Session):
     try:
         foil_hole_id = (
             parameters("foil_hole_id") if parameters("foil_hole_id") != "None" else None
@@ -205,9 +213,7 @@ def insert_movie(message: dict, parameters: Callable, session: sqlalchemy.orm.Se
         return False
 
 
-def insert_motion_correction(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_motion_correction(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -265,7 +271,7 @@ def movie_parameters(p):
 
 
 def insert_relative_ice_thickness(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
+    message: dict, parameters: Callable, session: Session
 ):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
@@ -292,7 +298,7 @@ def full_parameters(param):
         return False
 
 
-def insert_ctf(message: dict, parameters: Callable, session: sqlalchemy.orm.Session):
+def insert_ctf(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -330,9 +336,7 @@ def full_parameters(param):
         return False
 
 
-def insert_particle_picker(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_particle_picker(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -359,7 +363,7 @@ def full_parameters(param):
 
 
 def insert_particle_classification(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
+    message: dict, parameters: Callable, session: Session
 ):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
@@ -421,7 +425,7 @@ def full_parameters(param):
 
 
 def insert_particle_classification_group(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
+    message: dict, parameters: Callable, session: Session
 ):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
@@ -479,9 +483,7 @@ def full_parameters(param):
         return False
 
 
-def insert_cryoem_initial_model(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_cryoem_initial_model(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -513,9 +515,7 @@ def full_parameters(param):
         return False
 
 
-def insert_bfactor_fit(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_bfactor_fit(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -558,9 +558,7 @@ def full_parameters(param):
         return False
 
 
-def insert_tomogram(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_tomogram(message: dict, parameters: Callable, session: Session):
     if not message:
         message = {}
 
@@ -624,9 +622,7 @@ def full_parameters(param):
         return False
 
 
-def insert_processed_tomogram(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_processed_tomogram(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -651,9 +647,7 @@ def full_parameters(param):
         return False
 
 
-def insert_tilt_image_alignment(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def insert_tilt_image_alignment(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -706,9 +700,7 @@ def full_parameters(param):
         return False
 
 
-def update_processing_status(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def update_processing_status(message: dict, parameters: Callable, session: Session):
     def full_parameters(param):
         return parameters_with_replacement(param, message, parameters)
 
@@ -755,9 +747,7 @@ def full_parameters(param):
 
 
 # These are needed for the old relion-zocalo wrapper
-def add_program_attachment(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def add_program_attachment(message: dict, parameters: Callable, session: Session):
     file_name = parameters("file_name")
     file_path = parameters("file_path")
     logger.error(
@@ -767,9 +757,7 @@ def add_program_attachment(
     return {"success": True, "return_value": 0}
 
 
-def register_processing(
-    message: dict, parameters: Callable, session: sqlalchemy.orm.Session
-):
+def register_processing(message: dict, parameters: Callable, session: Session):
     program = parameters("program")
     cmdline = parameters("cmdline")
     environment = parameters("environment") or ""
diff --git a/src/cryoemservices/util/murfey_db_commands.py b/src/cryoemservices/util/murfey_db_commands.py
index f6f09ac2..1f58fb42 100644
--- a/src/cryoemservices/util/murfey_db_commands.py
+++ b/src/cryoemservices/util/murfey_db_commands.py
@@ -14,6 +14,29 @@
 logger.setLevel(logging.INFO)
 
 
+def multipart_message(message: dict, parameters: Callable, session: Session):
+    """
+    Override of the multipart message command,
+    which uses commands from this file rather than ispyb commands
+    """
+    commands = parameters("ispyb_command_list")
+    if not commands or not isinstance(commands, list):
+        logger.error("Received multipart message containing no command list")
+        return False
+
+    current_command = commands[0]
+    ispyb_command = current_command.get("ispyb_command")
+    command: Callable | None = globals().get(ispyb_command) or getattr(
+        ispyb_commands, ispyb_command, None
+    )
+    if not command:
+        logger.error(
+            f"Multipart command {current_command} does not have a valid ispyb_command"
+        )
+        return False
+    return ispyb_commands.run_multipart_command(message, parameters, session, command)
+
+
 def buffer(message: dict, parameters: Callable, session: Session):
     """
     Override of the buffer command,