diff --git a/.vscode/launch.json b/.vscode/launch.json
index 15932eb4..6b116a90 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -56,10 +56,16 @@
             //     "--type_session", "multi-ses",
             //     "--type_system", "sge"
             // ]
+            // "args": [
+            //     "--project-root",
+            //     "/home/faird/zhaoc/data/test_babs_multi-ses_toybidsapp",
+            //     "--container-config-yaml-file",
+            //     "/home/faird/zhaoc/babs_tests/notebooks/bidsapp-toybidsapp-0-0-7_task-rawBIDS_system-slurm_cluster-MSI_egConfig.yaml",
+            //     "--job-account"
+            // ]
             "args": [
                 "--project-root",
-                "/home/faird/zhaoc/data/test_babs_multi-ses_toybidsapp""--container-config-yaml-file",
-                "/home/faird/zhaoc/babs_tests/notebooks/bidsapp-toybidsapp-0-0-7_task-rawBIDS_system-slurm_cluster-MSI_egConfig.yaml",
+                "/home/faird/zhaoc/data/test_babs_single-ses_PNC_fmriprep_sloppy",
                 "--job-account"
             ]
             // "args": [
diff --git a/babs/babs.py b/babs/babs.py
index 1a25b894..0180d75e 100644
--- a/babs/babs.py
+++ b/babs/babs.py
@@ -1179,6 +1179,8 @@ def babs_status(self, flags_resubmit,
         # `create_job_status_csv(self)` has been called in `babs_status()`
         #   in `cli.py`
 
+        from .constants import MSG_NO_ALERT_IN_LOGS
+
         # Load the csv file
         lock_path = self.job_status_path_abs + ".lock"
         lock = FileLock(lock_path)
@@ -1256,7 +1258,7 @@ def babs_status(self, flags_resubmit,
                     # NOTE: in theory can skip failed jobs in previous round,
                     #       but making assigning variables hard; so not to skip
                     #       if df_job.at[i_job, "is_failed"] is not True:    # np.nan or False
-                    alert_message_in_log_files, if_no_alert_in_log = \
+                    alert_message_in_log_files, if_no_alert_in_log, if_found_log_files = \
                         get_alert_message_in_log_files(config_msg_alert, log_fn)
                     # ^^ the function will handle even if `config_msg_alert=None`
                     df_job_updated.at[i_job, "alert_message"] = \
@@ -1436,6 +1438,15 @@ def babs_status(self, flags_resubmit,
                             df_job_updated.at[i_job, "job_state_code"] = np.nan
                             df_job_updated.at[i_job, "duration"] = np.nan
                             # ROADMAP: ^^ get duration via `qacct`
+                            if if_found_log_files == False:   # bool or np.nan
+                                # If there is no log files, the alert message would be 'np.nan';
+                                # however this is a failed job, so it should have log files,
+                                #   unless it was killed by the user when pending.
+                                # change the 'alert_message' to no alert in logs,
+                                #   so that when reporting job status,
+                                #   info from job accounting will be reported
+                                df_job_updated.at[i_job, "alert_message"] = \
+                                    MSG_NO_ALERT_IN_LOGS
 
                             # check the log file:
                             # TODO ^^
@@ -1575,7 +1586,7 @@ def babs_status(self, flags_resubmit,
                             get_last_line(o_fn)
                         # Check if any alert message in log files for this job:
                         #   this is to update `alert_message` in case user changes configs in yaml
-                        alert_message_in_log_files, if_no_alert_in_log = \
+                        alert_message_in_log_files, if_no_alert_in_log, _ = \
                             get_alert_message_in_log_files(config_msg_alert, log_fn)
                         # ^^ the function will handle even if `config_msg_alert=None`
                         df_job_updated.at[i_job, "alert_message"] = \
@@ -2542,7 +2553,9 @@ def generate_bash_participant_job(self, bash_path, input_ds, type_session,
         # Write into the bash file:
         bash_file = open(bash_path, "a")   # open in append mode
 
-        bash_file.write("#!/bin/bash\n")
+        # NOTE: not to automatically generate the interpreting shell;
+        #   instead, let users specify it in the container config yaml file
+        #   using `interpreting_shell`
 
         # Cluster resources requesting:
         cmd_bashhead_resources = generate_bashhead_resources(system, self.config)
@@ -2745,7 +2758,9 @@ def generate_bash_test_job(self, folder_check_setup,
         # Write into the bash file:
         bash_file = open(fn_call_test_job, "a")   # open in append mode
 
-        bash_file.write("#!/bin/bash\n")
+        # NOTE: not to automatically generate the interpreting shell;
+        #   instead, let users specify it in the container config yaml file
+        #   using `interpreting_shell`
 
         # Cluster resources requesting:
         cmd_bashhead_resources = generate_bashhead_resources(system, self.config)
diff --git a/babs/cli.py b/babs/cli.py
index 0f3e9f0b..faa5947d 100644
--- a/babs/cli.py
+++ b/babs/cli.py
@@ -493,8 +493,10 @@ def babs_status_cli():
         action='store_true',
         # ^^ if `--job-account` is specified, args.job_account = True; otherwise, False
         help="Whether to account failed jobs, which may take some time."
-             " If `--resubmit failed` or `--resubmit-job` for this failed job is also requested,"
-             " this `--job-account` will be skipped.")
+             " When using ``--job-account``, please also add ``--container_config_yaml_file``."
+             " If ``--resubmit failed`` or ``--resubmit-job`` (for some failed jobs)"
+             " is also requested,"
+             " this ``--job-account`` will be skipped.")
 
     return parser
 
diff --git a/babs/dict_cluster_systems.yaml b/babs/dict_cluster_systems.yaml
index 29392207..3027a717 100644
--- a/babs/dict_cluster_systems.yaml
+++ b/babs/dict_cluster_systems.yaml
@@ -3,18 +3,22 @@
 
 # format: <name in UI>: "<cluster-understandable format>"
 # placeholder "$VALUE" will be replaced by the real value provided by the user.
+# For 'interpreting_shell': nothing else will be added by BABS
+# For other keys: cluster-type-specific prefix will be added
+#   e.g., '#$ ' for SGE clusters
+#   e.g., '#SBATCH ' for Slurm clusters
 
 sge:
-  interpreting_shell: "-S $VALUE"   # "-S /bin/bash" on cubic
+  interpreting_shell: "#!$VALUE"   # "#!/bin/bash" on cubic
   hard_memory_limit: "-l h_vmem=$VALUE"   # "-l h_vmem=25G" on cubic
   soft_memory_limit: "-l s_vmem=$VALUE"   # "-l s_vmem=23.5G" on cubic
   temporary_disk_space: "-l tmpfree=$VALUE"   # "-l tmpfree=200G" on cubic
   number_of_cpus: "-pe threaded $VALUE"   # "-pe threaded N" or a range: "-pe threaded N-M", N<M on cubic
   hard_runtime_limit: "-l h_rt=$VALUE"    # "-l h_rt=24:00:00" on cubic
 slurm:
-  interpreting_shell: ""
+  interpreting_shell: "#!$VALUE"  #    e.g., "#!/bin/bash -l" on MSI
   hard_memory_limit: "--mem=$VALUE"
   soft_memory_limit: ""
-  temporary_disk_space: "--tmp=$VALUE"   # "--tmp=20g" on MSI
+  temporary_disk_space: "--tmp=$VALUE"   # "#SBATCH --tmp=20g" on MSI
   number_of_cpus: "--cpus-per-task=$VALUE"
   hard_runtime_limit: "--time=$VALUE"
\ No newline at end of file
diff --git a/babs/utils.py b/babs/utils.py
index ff5ad49c..1d324616 100644
--- a/babs/utils.py
+++ b/babs/utils.py
@@ -653,12 +653,19 @@ def generate_one_bashhead_resources(system, key, value):
         This does not include "\n" at the end.
         e.g., "#$ -S /bin/bash".
 
+    Notes:
+    ---------
+    For interpreting shell, regardless of system type,
+    it will be '#!' + the value user provided.
     """
-    cmd = "#"
-    if system.type == "sge":
-        cmd += "$ "    # e.g., `#$ -l h_vmem=xxx`
-    elif system.type == "slurm":
-        cmd += "SBATCH "   # e.g., `#SBATCH --xxx=yyy`
+    if key == "interpreting_shell":
+        cmd = ""   # directly use the format provided in the dict
+    else:
+        cmd = "#"
+        if system.type == "sge":
+            cmd += "$ "    # e.g., `#$ -l h_vmem=xxx`
+        elif system.type == "slurm":
+            cmd += "SBATCH "   # e.g., `#SBATCH --xxx=yyy`
 
     # find the key in the `system.dict`:
     if key not in system.dict:
@@ -675,8 +682,8 @@ def generate_one_bashhead_resources(system, key, value):
 
 def generate_bashhead_resources(system, config):
     """
-    This is to generate the head of the bash file
-    for requesting cluster resources.
+    This is to generate the directives ("head of the bash file")
+    for requesting cluster resources, specifying interpreting shell, etc.
 
     Parameters:
     ------------
@@ -700,10 +707,25 @@ def generate_bashhead_resources(system, config):
         raise Exception("There is no section `cluster_resources`"
                         + " in `container_config_yaml_file`!")
 
-    # loop: for each key, call `generate_one_bashhead_resources()`:
+    # generate the command for interpreting shell first:
+    if "interpreting_shell" not in config["cluster_resources"]:
+        warnings.warn("The interpreting shell was not specified for 'participant_job.sh'."
+                      + " This should be specified using 'interpreting_shell'"
+                      + " under section 'cluster_resources' in container's"
+                      + " configuration YAML file.")
+    else:
+        key = "interpreting_shell"
+        value = config["cluster_resources"][key]
+        one_cmd = generate_one_bashhead_resources(system, key, value)
+        cmd += one_cmd + "\n"
+
+    # loop for other keys:
+    #   for each key, call `generate_one_bashhead_resources()`:
     for key, value in config["cluster_resources"].items():
         if key == "customized_text":
             pass   # handle this below
+        elif key == "interpreting_shell":
+            pass   # has been handled - see above
         else:
             one_cmd = generate_one_bashhead_resources(system, key, value)
             cmd += one_cmd + "\n"
@@ -1926,6 +1948,9 @@ def get_alert_message_in_log_files(config_msg_alert, log_fn):
         When `alert_message` is `msg_no_alert`,
         or is `np.nan` (`if_valid_alert_msg=False`), this is True;
         Otherwise, any other message, this is False
+    if_found_log_files: bool or np.nan
+        np.nan if `config_msg_alert` is None, as it's unknown whether log files exist or not
+        Otherwise, True or False based on if any log files were found
 
     Notes:
     -----------------
@@ -1938,15 +1963,18 @@ def get_alert_message_in_log_files(config_msg_alert, log_fn):
     msg_no_alert = MSG_NO_ALERT_IN_LOGS
     if_valid_alert_msg = True    # by default, `alert_message` is valid (i.e., not np.nan)
     # this is to avoid check `np.isnan(alert_message)`, as `np.isnan(str)` causes error.
+    if_found_log_files = np.nan
 
     if config_msg_alert is None:
         alert_message = np.nan
         if_valid_alert_msg = False
+        if_found_log_files = np.nan   # unknown if log files exist or not
     else:
         o_fn = log_fn.replace("*", 'o')
         e_fn = log_fn.replace("*", 'e')
 
         if op.exists(o_fn) or op.exists(e_fn):   # either exists:
+            if_found_log_files = True
             found_message = False
             alert_message = msg_no_alert
 
@@ -1977,6 +2005,7 @@ def get_alert_message_in_log_files(config_msg_alert, log_fn):
                     break   # no need to go to next log file
 
         else:    # neither o_fn nor e_fn exists yet:
+            if_found_log_files = False
             alert_message = np.nan
             if_valid_alert_msg = False
 
@@ -1986,7 +2015,7 @@ def get_alert_message_in_log_files(config_msg_alert, log_fn):
     else:   # `alert_message`: np.nan or any other message:
         if_no_alert_in_log = False
 
-    return alert_message, if_no_alert_in_log
+    return alert_message, if_no_alert_in_log, if_found_log_files
 
 def get_username():
     """
@@ -2073,18 +2102,24 @@ def _check_job_account_slurm(job_id_str, job_name, username_lowercase):
         stdout=subprocess.PIPE
     )
     # ref: https://slurm.schedmd.com/sacct.html
+    # also based on ref: https://github.com/ComputeCanada/slurm_utils/blob/master/sacct-all.py
 
     proc_sacct.check_returncode()
     # even if the job does not exist, there will still be printed msg from sacct,
     #   at least a header. So `check_returncode()` should always succeed.
-    msg_l = proc_sacct.stdout.decode('utf-8').split("\n")
+    msg_l = proc_sacct.stdout.decode('utf-8').split("\n")   # all lines from `sacct`
+    # 1st line: column names
+    # 2nd and forward lines: job information
+    #   ^^ if using `--parsable2` and `--delimiter`, there is no 2nd line of "----" dashes
+    #   Usually there are more than one job lines;
+    #   However if the job was manually killed when pending, then there will only be one job line.
     msg_head = msg_l[0].split(the_delimiter)   # list of column names
 
     # Check if there is any problem when calling `sacct` for this job:
     if "State" not in msg_head or "JobID" not in msg_head or "JobName" not in msg_head:
         if_no_sacct = True
-    if len(msg_l) <= 2 or msg_l[2] == '':
-        # if there is only header (len <= 2 or the 3rd element is empty):
+    if len(msg_l) <= 1 or msg_l[1] == '':
+        # if there is only header (len <= 1 or the 2nd element is empty):
         if_no_sacct = True
 
     if if_no_sacct:   # there is no information about this job in sacct:
@@ -2189,6 +2224,9 @@ def _check_job_account_sge(job_id_str, job_name, username_lowercase):
         print("Hint: check if the job is still in the queue, e.g., in state of qw, r, etc")
         print("Hint: check if the username used for submitting this job"
               + " was not current username '" + username_lowercase + "'")
+        print("Hint: check if the job was killed during pending state")
+        # ^^ for SGE cluster: job manually killed during pending: `qacct` will fail:
+        #   "error: job id xxx not found"
         msg_toreturn = msg_failed_to_call_qacct
 
     return msg_toreturn
diff --git a/docs/source/babs-status.rst b/docs/source/babs-status.rst
index 57a1dd82..6c0d8ae1 100644
--- a/docs/source/babs-status.rst
+++ b/docs/source/babs-status.rst
@@ -1,9 +1,52 @@
-*************************************
+##################################################
 ``babs-status``: Check job status
-*************************************
+##################################################
+
+.. contents:: Table of Contents
+
+**********************
+Command-Line Arguments
+**********************
 
 .. argparse::
    :ref: babs.cli.babs_status_cli
    :prog: babs-status
    :nodefault:
-   :nodefaultconst:
\ No newline at end of file
+   :nodefaultconst:
+
+
+**********************
+Example commands
+**********************
+
+Basic use: you'll only get job summary (number of jobs finished/pending/running/failed):
+
+.. code-block:: bash
+
+    babs-status \
+        --project-root /path/to/my_BABS_project
+
+Failed job auditing: only using alert messages in log files:
+
+.. code-block:: bash
+
+    babs-status \
+        --project-root /path/to/my_BABS_project \
+        --container-config-yaml-file /path/to/container_config.yaml
+
+Failed job auditing: using alert messages in log files + performing job account for jobs
+without alert messages in log files:
+
+.. code-block:: bash
+
+    babs-status \
+        --project-root /path/to/my_BABS_project \
+        --container-config-yaml-file /path/to/container_config.yaml \
+        --job-account
+
+When using ``--job-account``, you should also use ``--container-config-yaml-file``.
+
+.. developer's note: seems like if only using `--job-account` without `--container-config-yaml-file`,
+..  although job account commands will be called (taking more time),
+..  it won't report the message e.g., "Among job(s) that are failed and don't have alert message in log files:"
+..  This is probably because the "alert_message" was cleared up, so no job has "BABS: No alert message found in log files."
diff --git a/docs/source/preparation_config_yaml_file.rst b/docs/source/preparation_config_yaml_file.rst
index 757cf8d5..3e93c588 100644
--- a/docs/source/preparation_config_yaml_file.rst
+++ b/docs/source/preparation_config_yaml_file.rst
@@ -239,18 +239,19 @@ Advanced - Manual of writing section ``singularity_run``
 
 * Can I use a job environment variable, e.g., number of CPUs?
 
-    * Yes you can! For number of CPUs (e.g., ``--n_cpus`` in QSIPrep), for *SGE* clusters,
-      you can use environment variable ``$NSLOTS``, and you can specify it as::
+    * Yes you can! For number of CPUs (e.g., ``--n_cpus`` in QSIPrep), 
+      if you also use ``number_of_cpus`` in **cluster_resources** section (see below),
+      then you can use environment variable for this Singularity run argument.
+    * For *SGE* clusters, you can use environment variable ``$NSLOTS``, and you can specify it as::
 
         --n_cpus: "$NSLOTS"
       
-      as long as you also set ``number_of_cpus`` in **cluster_resources** section (see below).
-    
-    * :octicon:`alert-fill` :bdg-warning:`warning` However *Slurm* clusters probably have different environment variable name
-      for this - please check out its manual!
+    * For *Slurm* clusters, you can use environment variable ``$NSLOTS``, and you can specify it as::
 
-.. developer's note: for Slurm it might be ``$SLURM_NTASKS`` (below ref), however did not find for MSI cluster..
-.. ref: https://docs.mpcdf.mpg.de/doc/computing/clusters/aux/migration-from-sge-to-slurm
+        --n_cpus: "$SLURM_CPUS_PER_TASK"
+    
+.. developer's note: for Slurm: ref: https://login.scg.stanford.edu/faqs/cores/
+..  other ref: https://docs.mpcdf.mpg.de/doc/computing/clusters/aux/migration-from-sge-to-slurm
 
 * When **more than one** input BIDS dataset: You need to specify which dataset goes to the positional argument 
   ``input_dataset`` in the BIDS App, which dataset goes to another named argument.
@@ -416,11 +417,10 @@ Example section **cluster_resources** for ``QSIPrep``::
         temporary_disk_space: 200G
         number_of_cpus: "6" 
 
-These will be turned into options in the preambles of ``participant_job.sh`` on an SGE cluster
+These will be turned into options in the directives (at the beginning) of ``participant_job.sh`` on an SGE cluster
 (this script could be found at: ``/path/to/my_BABS_project/analysis/code``) shown as below::
 
     #!/bin/bash
-    #$ -S /bin/bash
     #$ -l h_vmem=32G
     #$ -l tmpfree=200G
     #$ -pe threaded 6
@@ -429,6 +429,13 @@ For example, a job requires no more than 32 GB of memory,
 i.e., on SGE clusters, ``-l h_vmem=32G``.
 You may simply specify: ``hard_memory_limit: 32G``.
 
+.. warning::
+    Make sure you add ``interpreting_shell``!
+    It is very important.
+    For SGE, you might need: ``interpreting_shell: /bin/bash``;
+    For Slurm, you might need: ``interpreting_shell: /bin/bash -l``.
+    Check what it should be like in the manual of your cluster!
+
 The table below lists all the named cluster resources requests that BABS supports.
 You may not need all of them.
 BABS will replace ``$VALUE`` with the value you provide.
@@ -447,28 +454,33 @@ The second row in each cell, which is also in (), is an example.
 ..       - ``interpreting_shell: /bin/bash``
 ..       - ``-S /bin/bash``
 
-+------------------------------------------+---------------------------------------+
-| | Section ``cluster_resources`` in YAML  | | Generated preamble for SGE clusters |
-| |         (example key-value)            | |           (example outcome)         |
-+==========================================+=======================================+
-| | ``interpreting_shell: $VALUE``         | | ``-S $VALUE``                       |
-| | (``interpreting_shell: /bin/bash``)    | | (``-S /bin/bash``)                  |
-+------------------------------------------+---------------------------------------+
-| | ``hard_memory_limit: $VALUE``          | | ``-l h_vmem=$VALUE``                |
-| | (``hard_memory_limit: 25G``)           | | (``-l h_vmem=25G``)                 |
-+------------------------------------------+---------------------------------------+
-| | ``soft_memory_limit: $VALUE``          | | ``-l s_vmem=$VALUE``                |
-| | (``soft_memory_limit: 23.5G``)         | | (``-l s_vmem=23.5G``)               |
-+------------------------------------------+---------------------------------------+
-| | ``temporary_disk_space: $VALUE``       | | ``-l tmpfree=$VALUE``               |
-| | (``temporary_disk_space: 200G``)       | | (``-l tmpfree=200G``)               |
-+------------------------------------------+---------------------------------------+
-| | ``number_of_cpus: "$VALUE"``           | | ``-pe threaded $VALUE``             |
-| | (``number_of_cpus: "6"``)              | | (``-pe threaded 6``)                |
-+------------------------------------------+---------------------------------------+
-| | ``hard_runtime_limit: "$VALUE"``       | | ``-l h_rt=$VALUE``                  |
-| | (``hard_runtime_limit: "24:00:00"``)   | | (``-l h_rt=24:00:00``)              |
-+------------------------------------------+---------------------------------------+
+.. developer's note: actually the width is not working here....
+..  tried `||` and `| |` for each row's beginning but did not help...
+.. table::
+    :widths: 60 40 40
+
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | Section ``cluster_resources`` in YAML  | | Generated directives for SGE clusters  | | Generated directives for Slurm clusters |
+    | |         (example key-value)            | |           (example outcome)            | |           (example outcome)             |
+    +==========================================+==========================================+===========================================+
+    | | ``interpreting_shell: $VALUE``         | | ``#!$VALUE``                           | | ``#!$VALUE``                            |
+    | | (``interpreting_shell: /bin/bash``)    | | (``#!/bin/bash``)                      | | (``#!/bin/bash``)                       |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | ``hard_memory_limit: $VALUE``          | | ``#$ -l h_vmem=$VALUE``                | | ``#SBATCH --mem=$VALUE``                |
+    | | (``hard_memory_limit: 25G``)           | | (``#$ -l h_vmem=25G``)                 | | (``#SBATCH --mem=25G``)                 |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | ``soft_memory_limit: $VALUE``          | | ``#$ -l s_vmem=$VALUE``                | Not applicable.                           |
+    | | (``soft_memory_limit: 23.5G``)         | | (``#$ -l s_vmem=23.5G``)               |                                           |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | ``temporary_disk_space: $VALUE``       | | ``#$ -l tmpfree=$VALUE``               | | ``#SBATCH --tmp=$VALUE``                |
+    | | (``temporary_disk_space: 200G``)       | | (``#$ -l tmpfree=200G``)               | | (``#SBATCH --tmp=200G``)                |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | ``number_of_cpus: "$VALUE"``           | | ``#$ -pe threaded $VALUE``             | | ``#SBATCH --cpus-per-task=$VALUE``      |
+    | | (``number_of_cpus: "6"``)              | | (``#$ -pe threaded 6``)                | | (``#SBATCH --cpus-per-task=6``)         |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
+    | | ``hard_runtime_limit: "$VALUE"``       | | ``#$ -l h_rt=$VALUE``                  | | ``#SBATCH --time=$VALUE``               |
+    | | (``hard_runtime_limit: "24:00:00"``)   | | (``#$ -l h_rt=24:00:00``)              | | (``#SBATCH --time=24:00:00``)           |
+    +------------------------------------------+------------------------------------------+-------------------------------------------+
 
 If you cannot find the one you want in the above table, you can still add it by ``customized_text``.
 Below is an example for SGE cluster::
diff --git a/notebooks/README.md b/notebooks/README.md
new file mode 100644
index 00000000..c21c6e9f
--- /dev/null
+++ b/notebooks/README.md
@@ -0,0 +1,8 @@
+# Notebooks folder
+
+## Example container configuration YAML files
+* Naming convention: `eg_<bidsapp-0-0-0>_<task>_<system>_<cluster_name>.yaml`
+    * `<bidsapp-0-0-0>`: BIDS App name and version
+    * `<task>`:  For what application of BIDS App? Full run? Sloppy mode?
+    * `<system>`: `sge` or `slurm`
+    * `<cluster_name>`: name of example cluster where the YAML file was tested
diff --git a/notebooks/docs_developer.md b/notebooks/docs_developer.md
index be466229..8c97bf90 100644
--- a/notebooks/docs_developer.md
+++ b/notebooks/docs_developer.md
@@ -74,12 +74,29 @@ when `print(df)` by python:
 # Testing
 ## Create pending, failed, or stalled jobs
 Change/Add these in `participant_job.sh`:
-- failed: add `-l h_rt=0:0:20` (hard runtime limit is 20 sec)
+- failed: see next section
 - pending: increase `-l h_vmem` and `-l s_vmem`; increase `-pe threaded N`
 - stalled (`eqw`): see Bergman email 12/20/22
 
 After these changes, `datalad save -m "message"` and `datalad push --to input`
 
+## Create failed cases for testing `babs-status` failed job auditing
+* Add `sleep 3600` to `container_zip.sh`; make sure you `datalad save` the changes
+* Change hard runtime limit to 20min (on SGE: `-l h_rt=0:20:00`)
+* Create failed cases:
+    * when the job is pending, manually kill it
+        * For Slurm cluster: you'll see normal msg from `State` column of `sacct` msg when `--job-account`
+        * For SGE cluster: you'll see warning that `qacct` failed for this job - this is normal. See PR #98 for more details.
+    * when the job is running, manually kill it
+    * wait until the job is running out of time, killed by the cluster
+        * if you don't want to wait for that long, just set the hard runtime limit to very low value, e.g., 20 sec
+* Perform job auditing using `--container-config-yaml-file`:
+    * add some msg into the `alert_log_messages`, which can be seen in the "failed" jobs - for testing purpose
+        * although they can be normal msg seen in successful jobs
+* Perform job auditing using `--job-account` (and `--container-config-yaml-file`):
+    * delete the `alert_log_messages` from the yaml file;
+    * Now, you should see job account for these failed jobs
+
 # Terminology
 
 - "<jobname>.o<jobid>": standard output stream of the job
diff --git a/notebooks/example_container_fmriprep_anatonly.yaml b/notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_fmriprep_anatonly.yaml
rename to notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml
diff --git a/notebooks/example_container_fmriprep.yaml b/notebooks/eg_fmriprep-20-2-3_full_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_fmriprep.yaml
rename to notebooks/eg_fmriprep-20-2-3_full_sge_cubic.yaml
diff --git a/notebooks/example_container_fmriprep_ingressed_fs.yaml b/notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_fmriprep_ingressed_fs.yaml
rename to notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml
diff --git a/notebooks/example_container_fmriprep_sloppyFlag.yaml b/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
similarity index 60%
rename from notebooks/example_container_fmriprep_sloppyFlag.yaml
rename to notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
index 4ea199ea..81c5919f 100644
--- a/notebooks/example_container_fmriprep_sloppyFlag.yaml
+++ b/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
@@ -1,27 +1,33 @@
-# This is an example config yaml file for fMRIPrep version 20.2.3,
-#   but in `--sloppy` mode, i.e., test mode, and there is no FreeSurfer recon either.
-# This should NOT be used to produce real outputs you need.
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 20.2.3
+#   Task:             `--sloppy` mode + without FreeSurfer reconstruction
+#   Which system:     SGE
+#   Tested on which cluster:  Penn Med CUBIC cluster
+# fMRIPrep's Docker image is publicly available at: https://hub.docker.com/r/nipreps/fmriprep/
 
-# Warning!!!
+# WARNING!!!
 #   This is only an example, which may not necessarily fit your purpose,
 #   or be an optimized solution for your case,
-#   or be compatible to the fMRIPrep version you're using.
+#   or be compatible to the BIDS App version you're using.
 #   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of fMRIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
 
 # Arguments when executing the BIDS App using `singularity run`:
-# You should not have flags of : `--participant-label`, or `--bids-filter-file`!
 singularity_run:
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
     --n_cpus: '1'
     --stop-on-first-crash: ""
-    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # path to FS license file
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
     --skip-bids-validation: Null  # Null or NULL is also a placeholder
-    --output-spaces: "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"   # e.g., two output spaces
+    --output-spaces: "MNI152NLin6Asym:res-2"   # for two output spaces: e.g., "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"
     --force-bbr: ""
-    #--cifti-output: 91k   # ADD THIS WHEN FULL RUN!
     -v: '-v'   # this is for double "-v"
-    --sloppy: ''      # TEST RUN!
-    --fs-no-reconall: ''   # TEST RUN!
+    --sloppy: ''      # WARNING: use this only when testing
+    --fs-no-reconall: ''   # WARNING: use this only when testing
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
 #   per `--fs-no-reconall`, there won't be an output folder called `freesurfer`
@@ -29,9 +35,9 @@ zip_foldernames:
     fmriprep: "20-2-3"   # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-20-2-3.zip'
 
 cluster_resources:
-    interpreting_shell: /bin/bash   # "-S /bin/bash" on cubic
-    hard_memory_limit: 25G   # "-l h_vmem=25G" on cubic
-    temporary_disk_space: 200G   # "-l tmpfree=200G" on cubic  # this is highly-recommended on cubic
+    interpreting_shell: /bin/bash   # --> "#!/bin/bash"
+    hard_memory_limit: 25G   # --> "#$ -l h_vmem=25G"
+    temporary_disk_space: 200G   # --> "#$ -l tmpfree=200G"  # this is highly-recommended on CUBIC cluster
     customized_text: |
         #$ -R y
         #$ -l hostname=!compute-fed*
@@ -42,8 +48,8 @@ cluster_resources:
 #   they will be used as preambles in `participant_job.sh`
 #   the commands should not be quoted!
 script_preamble: |
-    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
-    echo "I am running BABS."   # this is an example command to show how to add another line; not necessary to include.
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+    echo "I am running BABS."   # [FIX ME] this is an example command to show how to add another line; not necessary to include.
 
 # ^^ conda env above: where the scripts generated by BABS will run
 #   not necessary the same one for running `babs-init`
@@ -51,7 +57,7 @@ script_preamble: |
 # for MSI, might need to add command e.g., "module_load"
 
 # Where to run the jobs:
-job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
 
 # Below is to filter out subjects (or sessions)
 #   right now we only filter based on unzipped dataset
diff --git a/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml b/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml
new file mode 100644
index 00000000..0d877816
--- /dev/null
+++ b/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml
@@ -0,0 +1,82 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 20.2.3
+#   Task:             `--sloppy` mode + without FreeSurfer reconstruction
+#   Which system:     Slurm
+#   Tested on which cluster:  MSI cluster
+# fMRIPrep's Docker image is publicly available at: https://hub.docker.com/r/nipreps/fmriprep/
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of fMRIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+# Arguments when executing the BIDS App using `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder. BABS will replace it with `${PWD}/.git/tmp/wkdir`
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/home/faird/zhaoc/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: Null  # Null or NULL is also a placeholder
+    --output-spaces: "MNI152NLin6Asym:res-2"   # for two output spaces: e.g., "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"
+    --force-bbr: ""
+    -v: '-v'   # this is for double "-v"
+    --sloppy: ''      # WARNING: use this only when testing
+    --fs-no-reconall: ''   # WARNING: use this only when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   per `--fs-no-reconall`, there won't be an output folder called `freesurfer`
+zip_foldernames:
+    fmriprep: "20-2-3"   # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-20-2-3.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"   # --> "#!/bin/bash -l"
+    # number_of_cpus: "1"     # --> "#SBATCH --cpus-per-task=1"
+    hard_memory_limit: 25G   # --> "#SBATCH --mem=25G"
+    temporary_disk_space: 200G    # --> "#SBATCH --tmp=200G"
+    hard_runtime_limit: "72:00:00"    # --> "--time=72:00:00", i.e., 3 days.  Should NOT large than partition's time limit!
+    customized_text: |
+        #SBATCH -p k40
+# Other choices of job partitions on MSI: amd2tb,ram256g,v100,k40
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# ^^ conda env above: where the scripts generated by BABS will run
+#   not necessary the same one for running `babs-init`
+# ^^ based on what you need on your cluster; some people even don't use `conda`...
+# for MSI, might need to add command e.g., "module_load"
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "Exception: No T1w images found for"  # probably not needed, after setting `required_files`
+        - "Excessive topologic defect encountered"
+        - "Cannot allocate memory"
+        - "mris_curvature_stats: Could not open file"
+        - "Numerical result out of range"
+        - "fMRIPrep failed"
+    # stderr:
+    #     - "xxxxx"
diff --git a/notebooks/example_container_fmriprepfake.yaml b/notebooks/eg_fmriprepfake-0-1-1_full_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_fmriprepfake.yaml
rename to notebooks/eg_fmriprepfake-0-1-1_full_sge_cubic.yaml
diff --git a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml
new file mode 100644
index 00000000..43e9ec53
--- /dev/null
+++ b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml
@@ -0,0 +1,60 @@
+# This is an example config yaml file for:
+#   BIDS App:         QSIPrep ("qsiprep")
+#   BIDS App version: 0.16.0RC3
+#   Task:             `--sloppy` mode
+#   Which system:     SGE
+#   Tested on which cluster:  Penn Med CUBIC cluster
+# QSIPrep's Docker image is publicly available at: https://hub.docker.com/r/pennbbl/qsiprep
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of QSIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+singularity_run:
+    -v: "-v"
+    -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
+    --n_cpus: "$NSLOTS"   # `$NSLOTS` can be recognized by SGE
+    --omp-nthreads: "3"   # without this, only run single-threaded jobs (N=`--n_cpus`) at once
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: Null  # Null or NULL is also a placeholder
+    --unringing-method: "mrdegibbs"
+    --output-resolution: "2.0"
+    --sloppy: ""    # WARNING: only use this when testing
+    --hmc-model: "none"   # WARNING: only use this when testing
+    --dwi-only: ""   # WARNING: only use this when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    qsiprep: "0-16-0RC3"     # folder 'qsiprep' will be zipped into 'sub-xx_ses-yy_qsiprep-0-16-0RC3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash   # --> "#!/bin/bash"
+    hard_memory_limit: 32G   # --> `#$ -l h_vmem=32G`
+    temporary_disk_space: 200G   # --> `#$ -l tmpfree=200G`
+    number_of_cpus: "6"    # --> `#$ -pe threaded 6`
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+    echo "I am running BABS."   # [FIX ME] this is an example command to show how to add another line; not necessary to include.
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
+
+required_files:
+    $INPUT_DATASET_#1:
+        - "dwi/*_dwi.nii*"   # QSIPrep
diff --git a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml
new file mode 100644
index 00000000..e292b7bf
--- /dev/null
+++ b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml
@@ -0,0 +1,63 @@
+# This is an example config yaml file for:
+#   BIDS App:         QSIPrep ("qsiprep")
+#   BIDS App version: 0.16.0RC3
+#   Task:             `--sloppy` mode
+#   Which system:     Slurm
+#   Tested on which cluster:  MSI cluster
+# QSIPrep's Docker image is publicly available at: https://hub.docker.com/r/pennbbl/qsiprep
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of QSIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+singularity_run:
+    -v: "-v"
+    -w: "$BABS_TMPDIR"   # this is a placeholder. BABS will replace it with `${PWD}/.git/tmp/wkdir`
+    --n_cpus: "$SLURM_CPUS_PER_TASK"   # Slurm env variable, taking value from `--cpus-per-task`, i.e., "number_of_cpus" in section "cluster_resources"
+    --omp-nthreads: "3"   # without this, only run single-threaded jobs (N=`--n_cpus`) at once
+    --stop-on-first-crash: ""
+    --fs-license-file: "/home/faird/zhaoc/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: Null  # Null or NULL is also a placeholder
+    --unringing-method: "mrdegibbs"
+    --output-resolution: "2.0"
+    --sloppy: ""    # WARNING: only use this when testing
+    --hmc-model: "none"   # WARNING: only use this when testing
+    --dwi-only: ""   # WARNING: only use this when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    qsiprep: "0-16-0RC3"     # folder 'qsiprep' will be zipped into 'sub-xx_ses-yy_qsiprep-0-16-0RC3.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"   # --> "#!/bin/bash -l"
+    hard_memory_limit: 32G   # --> "#SBATCH --mem=32G"
+    temporary_disk_space: 200G   # --> "#SBATCH --tmp=200G"
+    number_of_cpus: "6"    # --> "#SBATCH --cpus-per-task=6"
+    hard_runtime_limit: "48:00:00"    # --> "--time=48:00:00", i.e., 2 days. Should NOT large than partition's time limit!
+    customized_text: |
+        #SBATCH -p ram256g
+# Other choices of job partitions on MSI: amd2tb,ram256g,v100,k40
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "dwi/*_dwi.nii*"   # QSIPrep
diff --git a/notebooks/example_container_toybidsapp.yaml b/notebooks/eg_toybidsapp-0-0-7_rawBIDS_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_toybidsapp.yaml
rename to notebooks/eg_toybidsapp-0-0-7_rawBIDS_sge_cubic.yaml
diff --git a/notebooks/eg_toybidsapp-0-0-7_rawBIDS_slurm_msi.yaml b/notebooks/eg_toybidsapp-0-0-7_rawBIDS_slurm_msi.yaml
new file mode 100644
index 00000000..fb4df255
--- /dev/null
+++ b/notebooks/eg_toybidsapp-0-0-7_rawBIDS_slurm_msi.yaml
@@ -0,0 +1,59 @@
+# This is an example config yaml file for:
+#   BIDS App:         toy BIDS App ("toy_bids_app")
+#   BIDS App version: 0.0.7
+#   Task:             for raw BIDS dataset ("unzipped")
+#   Which system:     Slurm
+#   Tested on which cluster:  MSI cluster
+# Toy BIDS App's Docker image is publicly available at: https://hub.docker.com/r/pennlinc/toy_bids_app
+# This BIDS App counts number of non-hidden files in a subject's (or a session's) folder;
+#     More details please see: https://github.com/PennLINC/babs_tests/blob/main/docker/README.md#toy-bids-app-toy_bids_app
+# How to prepare a container DataLad dataset of this toy BIDS App? See docs here: https://pennlinc-babs.readthedocs.io/en/latest/preparation_container.html
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+singularity_run:
+    --no-zipped: ""  # for raw BIDS dataset
+    --dummy: "2"   # this is a dummy variable, accepting values
+    -v: ""    # this is also a dummy variable, not accepting values
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    toybidsapp: "0-0-7"   # folder 'toybidsapp' will be zipped into 'sub-xx_ses-yy_toybidsapp-0-0-7.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"   # --> "#!/bin/bash -l"
+    number_of_cpus: "1"     # --> "#SBATCH --cpus-per-task=1"
+    temporary_disk_space: 20G    # --> "#SBATCH --tmp=20G"
+    hard_memory_limit: 2G   # --> "#SBATCH --mem=2G"
+    hard_runtime_limit: "20"    # --> "--time=20", i.e., 20min. Should NOT large than partition's time limit!
+    customized_text: |
+        #SBATCH -p ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+# Other things to test:
+# #SBATCH --ntasks=1
+# #SBATCH -p amd2tb,ram256g,v100,k40
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# 'required_files' section is not needed for toy BIDS App.
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "xxxx"   # this is a dummy alert message.
+    stderr:
+        - "xxx"    # this is a dummy alert message.
diff --git a/notebooks/example_container_zipped_toybidsapp.yaml b/notebooks/eg_toybidsapp-0-0-7_zipped_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_zipped_toybidsapp.yaml
rename to notebooks/eg_toybidsapp-0-0-7_zipped_sge_cubic.yaml
diff --git a/notebooks/example_container_xcpd.yaml b/notebooks/eg_xcpd-0-3-0_full_sge_cubic.yaml
similarity index 100%
rename from notebooks/example_container_xcpd.yaml
rename to notebooks/eg_xcpd-0-3-0_full_sge_cubic.yaml
diff --git a/notebooks/example_container_qsiprep.yaml b/notebooks/example_container_qsiprep.yaml
deleted file mode 100644
index c93183d9..00000000
--- a/notebooks/example_container_qsiprep.yaml
+++ /dev/null
@@ -1,56 +0,0 @@
-# Below is example config yaml file for QSIPrep:
-
-cli_call: |
-    -v -v \
-    -w ${PWD}/.git/tmp/wkdir \
-    --n_cpus $NSLOTS \
-    --stop-on-first-crash \
-    --fs-license-file code/license.txt \
-    --skip-bids-validation \
-    --unringing-method mrdegibbs \
-    --output-resolution 2.0
-
-# You should not have flags of : `--participant-label`, or `--bids-filter-file`!
-
-singularity_run:
-    -v: "-v"
-    -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
-    --n_cpus: "$NSLOTS"   # `$NSLOTS` can be recognized by SGE; if you're using Slurm clusters please change to Slurm version!
-    --omp-nthreads: "3"   # without this, only run single-threaded jobs (N=`--n_cpus`) at once
-    --stop-on-first-crash: ""
-    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # path to FS license file
-    --skip-bids-validation: Null  # Null or NULL is also a placeholder
-    --unringing-method: "mrdegibbs"
-    --output-resolution: "2.0"
-    --sloppy: ""    # ADD THIS WHEN TESTING
-    --hmc-model: "none"   # ADD THIS WHEN TESTING
-    --dwi-only: ""   # ADD THIS WHEN TESTING
-
-# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
-zip_foldernames:
-    qsiprep: "0-16-0RC3"     # folder 'qsiprep' will be zipped into 'sub-xx_ses-yy_qsiprep-0-16-0RC3.zip'
-
-cluster_resources:
-    interpreting_shell: /bin/bash  # `#$ -S /bin/bash` on cubic
-    hard_memory_limit: 32G   # `#$ -l h_vmem=32G` on cubic
-    temporary_disk_space: 200G   # `#$ -l tmpfree=200G` on cubic
-    number_of_cpus: "6"    # `#$ -pe threaded 6` on cubic
-    customized_text: |
-        #$ -R y
-        #$ -l hostname=!compute-fed*
-# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
-#   So it's probably not relevant for other clusters
-
-# Users need to add their customized bash command below,
-#   they will be used as preambles in `participant_job.sh`
-#   the commands should not be quoted!
-script_preamble: |
-    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
-    echo "I am running BABS."   # this is an example command to show how to add another line; not necessary to include.
-
-# Where to run the jobs:
-job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
-
-required_files:
-    $INPUT_DATASET_#1:
-        - "dwi/*_dwi.nii*"   # QSIPrep
diff --git a/notebooks/show_babs_init_InputBIDS.ipynb b/notebooks/show_babs_init_InputBIDS.ipynb
index 337a68d1..aa6d1b9b 100644
--- a/notebooks/show_babs_init_InputBIDS.ipynb
+++ b/notebooks/show_babs_init_InputBIDS.ipynb
@@ -42,18 +42,34 @@
             "cell_type": "code",
             "execution_count": 2,
             "metadata": {},
-            "outputs": [],
+            "outputs": [
+                {
+                    "name": "stdout",
+                    "output_type": "stream",
+                    "text": [
+                        "/cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml\n"
+                    ]
+                }
+            ],
             "source": [
-                "# This notebook only accepts toybidsapp, qsiprep or fmriprep\n",
+                "# This notebook only accepts toybidsapp_rawBIDS, qsiprep or fmriprep\n",
                 "#   or fmriprep_anatonly or 'fmriprep_sloppyFlag' or fmriprepfake (input ds: BIDS)\n",
                 "# ++++++++++++++++++++++++++++++++++\n",
-                "flag_instance = \"toybidsapp\"\n",
+                "bidsapp = \"qsiprep\"\n",
+                "task_name = \"sloppy\"   # for fmriprep: 'anatonly', 'sloppy'; for toybidsapp: 'rawBIDS'\n",
                 "type_session = \"multi-ses\"\n",
-                "which_dataset = \"toy_fake\"    # \"toy_fake\", \"toy_real\", \"HBN\"\n",
+                "which_dataset = \"toy_real\"    # \"toy_fake\", \"toy_real\", \"HBN\", \"PNC\"\n",
                 "\n",
-                "flag_where = \"cubic\"     # \"cubic\" or \"local\"\n",
+                "flag_where = \"cubic\"     # \"cubic\" or \"local\" or \"msi\"\n",
+                "type_system = \"sge\"   # \"sge\" or \"slurm\"\n",
                 "# ++++++++++++++++++++++++++++++++++\n",
                 "\n",
+                "# sanity checks:\n",
+                "if flag_where == \"cubic\":\n",
+                "    assert type_system == \"sge\"\n",
+                "elif flag_where == \"msi\":\n",
+                "    assert type_system == \"slurm\"\n",
+                "\n",
                 "# where:\n",
                 "if flag_where == \"cubic\":\n",
                 "    where_root = \"/cbica/projects/BABS\"\n",
@@ -63,15 +79,21 @@
                 "    where_root = \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper\"\n",
                 "    where_project = op.join(where_root, \"data\")\n",
                 "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+                "elif flag_where == \"msi\":\n",
+                "    where_root = \"/home/faird/zhaoc\"\n",
+                "    where_project = \"/home/faird/zhaoc/data\"\n",
+                "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
                 "else:\n",
                 "    raise Exception(\"not valid `flag_where`!\")\n",
                 "\n",
                 "# Input dataset:\n",
                 "if which_dataset == \"toy_fake\":\n",
                 "    if type_session == \"multi-ses\":\n",
-                "        input_ds = op.join(where_project, \"w2nu3\")\n",
+                "        input_ds = \"https://osf.io/w2nu3/\"\n",
+                "        # input_ds = op.join(where_project, \"w2nu3\")\n",
                 "    elif type_session == \"single-ses\":\n",
-                "        input_ds = op.join(where_project, \"t8urc\")\n",
+                "        input_ds = \t\"https://osf.io/t8urc/\"\n",
+                "        # input_ds = op.join(where_project, \"t8urc\")\n",
                 "elif which_dataset == \"toy_real\":  # real data:\n",
                 "    if type_session == \"multi-ses\":\n",
                 "        # input_ds = \"/cbica/projects/RBC/chenying_practice/data_for_babs/NKI/data_hashedID_bids\"\n",
@@ -79,34 +101,34 @@
                 "    elif type_session == \"single-ses\":\n",
                 "        raise Exception(\"not supported yet!\")\n",
                 "elif which_dataset == \"HBN\":  # HBN data:\n",
-                "    if type_session == \"single-ses\":\n",
+                "    assert type_session == \"single-ses\"\n",
+                "    if flag_where == \"cubic\":\n",
                 "        input_ds = \"/cbica/projects/BABS/data/rawdata_HBN\"   # datalad sibling in BABS cubic project\n",
-                "    elif type_session == \"multi-ses\":\n",
-                "        raise Exception(\"HBN is a single-ses data!\")\n",
+                "    elif flag_where == \"msi\":\n",
+                "        input_ds = \"/home/faird/zhaoc/data/HBN_BIDS\"\n",
+                "elif which_dataset == \"PNC\":   # PNC data:\n",
+                "    assert type_session == \"single-ses\"\n",
+                "    input_ds = \"/home/faird/zhaoc/data/PNC_BIDS\"  # cloned from RBC github account\n",
                 "\n",
                 "\n",
                 "project_name = \"test_babs_\" + type_session\n",
                 "# Based on which dataset:\n",
-                "if which_dataset == \"HBN\":   # HBN data:\n",
-                "    project_name += \"_HBN\"\n",
+                "if which_dataset in [\"HBN\", \"PNC\"]:   # specific real dataset\n",
+                "    project_name += \"_\" + which_dataset\n",
                 "# Based on which BIDS App:\n",
-                "if flag_instance == \"toybidsapp\":\n",
+                "if bidsapp == \"toybidsapp\":\n",
                 "    input_cli = [[\"BIDS\", input_ds]]\n",
-                "    bidsapp = \"toybidsapp\"\n",
                 "    container_name = bidsapp + \"-0-0-7\"\n",
-                "elif flag_instance in [\"fmriprep\", \"fmriprep_anatonly\", \"fmriprep_sloppyFlag\"]:\n",
-                "    bidsapp = \"fmriprep\"\n",
+                "elif bidsapp in [\"fmriprep\", \"fmriprep_anatonly\", \"fmriprep_sloppy\"]:\n",
                 "    container_name = bidsapp + \"-20-2-3\"\n",
-                "elif flag_instance == \"qsiprep\":\n",
-                "    bidsapp = \"qsiprep\"\n",
+                "elif bidsapp == \"qsiprep\":\n",
                 "    container_name = bidsapp + \"-0-16-0RC3\"\n",
-                "elif flag_instance == \"fmriprepfake\":\n",
-                "    bidsapp = \"fmriprepfake\"\n",
+                "elif bidsapp == \"fmriprepfake\":\n",
                 "    container_name = bidsapp + \"-0-1-1\"\n",
                 "else:\n",
-                "    raise Exception(\"`flag_instance` is not QSIPrep or fMRIPrep!\")\n",
+                "    raise Exception(\"Invalid `flag_instance`!\")\n",
                 "\n",
-                "project_name += \"_\" + flag_instance\n",
+                "project_name += \"_\" + bidsapp + \"_\" + task_name\n",
                 "\n",
                 "\n",
                 "# Container:\n",
@@ -114,7 +136,20 @@
                 "if flag_where == \"local\":\n",
                 "    # container_ds += \"-docker\"   # add \"docker\" at the end\n",
                 "    container_ds = op.join(where_project, \"toybidsapp-container-docker\")\n",
-                "container_config_yaml_file = op.join(where_notebooks, \"example_container_\" + flag_instance + \".yaml\")\n",
+                "\n",
+                "container_config_yaml_file = op.join(where_notebooks, \"eg_\" + container_name\n",
+                "    + \"_\" + task_name + \"_\" + type_system)\n",
+                "if flag_where in [\"cubic\", \"msi\"]:\n",
+                "    container_config_yaml_file += \"_\" + flag_where\n",
+                "else:\n",
+                "    if type_system == \"sge\":\n",
+                "        container_config_yaml_file += \"_\" + \"cubic\"\n",
+                "    elif type_system == \"slurm\":\n",
+                "        container_config_yaml_file += \"_\" + \"msi\"\n",
+                "container_config_yaml_file += \".yaml\"\n",
+                "print(container_config_yaml_file)\n",
+                "assert op.exists(container_config_yaml_file)\n",
+                "# container_config_yaml_file = op.join(where_notebooks, \"example_container_\" + flag_instance + \".yaml\")\n",
                 "\n",
                 "# list_sub_file = op.join(where_notebooks, \"initial_sub_list_\" + type_session + \".csv\")\n",
                 "list_sub_file = None"
@@ -139,11 +174,11 @@
                         "The command to execute:\n",
                         "babs-init \\\n",
                         "\t--where_project /cbica/projects/BABS/data \\\n",
-                        "\t--project_name test_babs_multi-ses_toybidsapp \\\n",
-                        "\t--input BIDS /cbica/projects/BABS/data/w2nu3 \\\n",
-                        "\t--container_ds /cbica/projects/BABS/data/toybidsapp-container \\\n",
-                        "\t--container_name toybidsapp-0-0-7 \\\n",
-                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/example_container_toybidsapp.yaml \\\n",
+                        "\t--project_name test_babs_multi-ses_qsiprep_sloppy \\\n",
+                        "\t--input BIDS /cbica/projects/BABS/data/testdata_NKI/data_hashedID_bids \\\n",
+                        "\t--container_ds /cbica/projects/BABS/data/qsiprep-container \\\n",
+                        "\t--container_name qsiprep-0-16-0RC3 \\\n",
+                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml \\\n",
                         "\t--type_session multi-ses \\\n",
                         "\t--type_system sge\n",
                         "WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\n"
@@ -161,7 +196,7 @@
                 "cmd += \"\\t\" + \"--container_name \" + container_name + \" \\\\\\n\"\n",
                 "cmd += \"\\t\" + \"--container_config_yaml_file \" + container_config_yaml_file + \" \\\\\\n\"\n",
                 "cmd += \"\\t\" + \"--type_session \" + type_session + \" \\\\\\n\"\n",
-                "cmd += \"\\t\" + \"--type_system \" + \"sge\"\n",
+                "cmd += \"\\t\" + \"--type_system \" + type_system\n",
                 "\n",
                 "print(\"The command to execute:\")\n",
                 "print(cmd)\n",
diff --git a/tests/get_data.py b/tests/get_data.py
index 42e02848..e0551404 100644
--- a/tests/get_data.py
+++ b/tests/get_data.py
@@ -194,6 +194,59 @@ def container_ds_path(where_now, tmp_path_factory):
 
     return origin_container_ds
 
+def get_container_config_yaml_filename(which_bidsapp,
+                                       which_input, if_two_input,
+                                       type_system):
+    """
+    This is to get the container's config YAML file name,
+    depending on the BIDS App and if there are two inputs (for fMRIPrep)
+
+    Parameters:
+    -------------
+    which_bidsapp: str
+        name of the bidsapp
+    which_input: str
+        "BIDS" for raw BIDS
+        "fmriprep" for zipped BIDS derivates
+    if_two_input: bool
+        whether there are two input BIDS datasets
+    type_system: str
+        "sge" or "slurm"
+
+    Returns:
+    -----------
+    container_config_yaml_filename: str
+        the filename, without the path.
+    """
+    dict_cluster_name = {'sge': 'cubic',
+                         'slurm': 'msi'}
+    dict_bidsapp_version = {"qsiprep": "0-16-0RC3",
+                            "fmriprep": "20-2-3",
+                            "toybidsapp": "0-0-7"}
+    dict_task_name = {"qsiprep": 'sloppy',
+                      "fmriprep": "full",
+                      "toybidsapp": "rawBIDS"}
+
+    # bidsapp and its version:
+    container_config_yaml_filename = "eg_" + which_bidsapp + "-" \
+        + dict_bidsapp_version[which_bidsapp]
+
+    # task:
+    container_config_yaml_filename += "_"
+    if (which_bidsapp == "fmriprep") & if_two_input:
+        container_config_yaml_filename += "ingressed-fs"
+    elif (which_bidsapp == "toybidsapp") & (which_input == "fmriprep"):
+        # the input is zipped BIDS derivatives:
+        container_config_yaml_filename += "zipped"
+    else:
+        container_config_yaml_filename += dict_task_name[which_bidsapp]
+
+    # cluster system type and example name:
+    container_config_yaml_filename += "_" + type_system + "_" \
+        + dict_cluster_name[type_system] + ".yaml"
+
+    return container_config_yaml_filename
+
 
 def if_command_installed(cmd):
     """
diff --git a/tests/test_babs_check_setup.py b/tests/test_babs_check_setup.py
index 5940aa9e..5799434a 100644
--- a/tests/test_babs_check_setup.py
+++ b/tests/test_babs_check_setup.py
@@ -16,6 +16,7 @@
     container_ds_path,
     where_now,
     if_circleci,
+    get_container_config_yaml_filename,
     __location__,
     INFO_2ND_INPUT_DATA,
     LIST_WHICH_BIDSAPP,
@@ -80,8 +81,12 @@ def test_babs_check_setup(
     project_root = op.join(where_project, project_name)
     container_name = which_bidsapp + "-" + TOYBIDSAPP_VERSION_DASH
     container_config_yaml_filename = "example_container_" + which_bidsapp + ".yaml"
+    container_config_yaml_filename = \
+        get_container_config_yaml_filename(which_bidsapp, which_input, if_two_input=False,
+                                           type_system="sge")  # TODO: also test slurm!
     container_config_yaml_file = op.join(op.dirname(__location__), "notebooks",
                                          container_config_yaml_filename)
+    assert op.exists(container_config_yaml_file)
 
     # below are all correct options:
     babs_init_opts = argparse.Namespace(
diff --git a/tests/test_babs_init.py b/tests/test_babs_init.py
index c691339d..b56643ab 100644
--- a/tests/test_babs_init.py
+++ b/tests/test_babs_init.py
@@ -16,6 +16,7 @@
     container_ds_path,
     where_now,
     if_circleci,
+    get_container_config_yaml_filename,
     __location__,
     INFO_2ND_INPUT_DATA,
     LIST_WHICH_BIDSAPP,
@@ -71,6 +72,8 @@ def test_babs_init(which_bidsapp, which_input, type_session, if_input_local, if_
         Path to the container datalad dataset
     if_circleci: fixture; bool
         Whether currently in CircleCI
+
+    TODO: add `type_system` and to test out Slurm version!
     """
     # Sanity checks:
     assert which_bidsapp in LIST_WHICH_BIDSAPP
@@ -94,12 +97,12 @@ def test_babs_init(which_bidsapp, which_input, type_session, if_input_local, if_
 
     # Preparation of freesurfer: for fmriprep and qsiprep:
     # check if `--fs-license-file` is included in YAML file:
-    container_config_yaml_filename = "example_container_" + which_bidsapp + ".yaml"
-    if (which_bidsapp == "fmriprep") & if_two_input:
-        container_config_yaml_filename = \
-            "example_container_" + which_bidsapp + "_ingressed_fs.yaml"
+    container_config_yaml_filename = \
+        get_container_config_yaml_filename(which_bidsapp, which_input, if_two_input,
+                                           type_system="sge")  # TODO: also test slurm!
     container_config_yaml_file = op.join(op.dirname(__location__), "notebooks",
                                          container_config_yaml_filename)
+    assert op.exists(container_config_yaml_file)
     container_config_yaml = read_yaml(container_config_yaml_file)
 
     if "--fs-license-file" in container_config_yaml["singularity_run"]: