Thanks for reaching out — we can help, but we’ll need a bit more context to pinpoint the cause. A few quick notes up front: - In Prefect 3.x,

flow.from_source(...).deploy(...)

clones a real git repository onto the worker with a .git directory. If cloning succeeds, commands like

git rev-parse

should work from anywhere under that tree. - The “fatal: not a git repository (or any of the parent directories): .git” message usually means something in your code or dependencies is calling

git

from a directory that isn’t inside the cloned repo, or the code was packaged/installed without the .git metadata. To help you quickly, could you share: 1) Your Prefect version (2.x or 3.x) 2) How you’re deploying: - Prefect 3.x: are you using

flow.from_source(...)

with a Git URL, or passing a

GitRepository(...)

with credentials? - Prefect 2.x: are you using the GitHub storage block or another storage? 3) The exact stack trace around the error and a snippet of your deployment definition (or CLI you used) 4) Your worker type (AWS ECS, EC2, etc.) and the container image you’re running Common causes and quick checks: - Git not installed in the worker image - If you’re using a custom image, make sure

git

is installed. Otherwise

git

calls will fail (often with “git: not found”, but sometimes tools swallow that and show the generic fatal error). - Code or dependencies expect a git repo at runtime - Tools like setuptools_scm, versioneer, or any code that runs

git

(e.g.,

git describe

) will fail if your code was installed from a wheel/zip or if the working directory isn’t within the clone. - If this is your case and you’re on Prefect 2.x with GitHub storage, note that it downloads a zip without .git. In 3.x, switch to

from_source(...)

to guarantee

.git

is present, or configure your package to not require git at runtime (e.g., setuptools_scm fallback via

SETUPTOOLS_SCM_PRETEND_VERSION

). - Running git from the wrong directory - If your code `chdir`s, containers use a non-default working dir, or a subprocess runs elsewhere,

git

will complain. Log

os.getcwd()

at the point of failure to confirm. - Partial/corrupted clone - Rare, but network issues can leave a broken

.git

directory. In 3.x, Prefect retries by re-cloning automatically; still, if you have a shared volume, clear the destination and retry. Recommended setup for Prefect 3.x with GitHub (ensures .git exists and auth is correct):

from prefect import flow
from prefect.runner.storage import GitRepository
from prefect_github.credentials import GitHubCredentials

@flow
def my_flow():
    ...

creds = GitHubCredentials.load("my-gh-creds")

my_flow.from_source(
    source=GitRepository(
        url="<https://github.com/OWNER/REPO.git>",
        branch="main",
        credentials=creds,
        include_submodules=False,
    ),
    entrypoint="path/to/flow_file.py:my_flow",
).deploy(
    name="aws-ecs-deployment",
    work_pool_name="my-aws-ecs-pool",
    job_variables={
        "image": "prefecthq/prefect:3.0-python3.11"
        # ensure your image has git installed if you’re using a custom base
    },
)

Helpful diagnostics: - Temporarily set

PREFECT_LOGGING_LEVEL=DEBUG

on the worker to see the git clone/pull commands in logs. - Log

os.getcwd()

and

__file__

where the error happens to confirm you’re under the cloned repo. - If you use setuptools_scm or similar, try setting

SETUPTOOLS_SCM_PRETEND_VERSION=0.0

to test whether the error disappears. If you can share the items above (version, deployment snippet, worker type/image, and the stack trace/log lines around the error), I’ll zero in on the exact fix.

@Marvin see reply

I don’t see the reply you’re referring to. Could you paste it here or summarize the issue? To help quickly, please share: - Prefect version (2.x or 3.x) and whether you’re on Cloud or self-hosted - How you’re running (worker type, work pool, infra) - Relevant code snippet or CLI command - Full error/traceback or run logs - What you expected vs what happened If it’s easier, you can drop the details into this template:

Prefect version:
Environment (Cloud/Self-hosted):
Worker/Work pool/Infra:
Command or code used:
Error/traceback (full):
Run/deployment link (if available):
Expected vs actual behavior:
Recent changes (if any):

Thanks — that pull step looks right for Prefect 3.x. A few key points for ECS: - The

git_clone

step runs inside your task container and requires

git

to be installed. The

prefecthq/prefect:3-latest

image already includes git, so that’s fine. - When you pass a

github-credentials

block, the runtime needs the

prefect-github

package so Prefect can load that block type and format the URL with your token. If your ECS image doesn’t have

prefect-github

, you’ll typically see errors like “Could not import block type GitHubCredentials” or “No module named prefect_github”. Two ways to make this work: Option A: Keep using the GitHub credentials block - Ensure your worker image has

prefect-github

installed (either bake it into the image or install at startup). - Bake into image:

FROM prefecthq/prefect:3-latest
RUN pip install --no-cache-dir prefect-github

- Or, if you rely on the Prefect image’s startup behavior, set an env var in your ECS task definition/container:

EXTRA_PIP_PACKAGES=prefect-github

- Then your prefect.yaml can look like:

deployments:
- name: my-flow
  entrypoint: flows/my_flow.py:my_flow
  pull:
    - prefect.deployments.steps.git_clone:
        repository: <https://github.com/org/flows.git>
        branch: main
        credentials: "{{ prefect.blocks.github-credentials.pat }}"

Option B: Use a Secret block with

access_token

(no extra package needed) - Store your PAT in a Secret block and reference it:

deployments:
- name: my-flow
  entrypoint: flows/my_flow.py:my_flow
  pull:
    - prefect.deployments.steps.git_clone:
        repository: <https://github.com/org/flows.git>
        branch: main
        access_token: "{{ prefect.blocks.secret.github-pat }}"

Notes and gotchas: - Make sure the repository URL is not wrapped in angle brackets in your YAML (Slack adds them in messages): use

<https://github.com/org/flows.git>

(the

.git

suffix is optional but fine). - The repo is cloned into the container’s current working directory (in the Prefect image, that’s

/opt/prefect

). The local folder name is derived from the repo (and branch, if specified). - If you use submodules, add

include_submodules: true

and ensure the same credentials work for submodules. - If you’re using the credentials block, double-check the block name:

pat

in

{{ prefect.blocks.github-credentials.pat }}

must match the exact block name you created. If it’s still failing, could you share the exact error from the run logs? Common ones: - ModuleNotFoundError for

prefect_github

→ install

prefect-github

(Option A) or switch to

access_token

(Option B) -

fatal: could not read Username

→ token/permissions issue; confirm the PAT scopes and block reference -

git: command not found

→ custom image missing git Happy to look at the specific traceback and your

prefect.yaml

snippet if you can paste them.

Thanks for the details. That “fatal: not a git repository (or any of the parent directories): .git” usually means a git command is being run in a folder that exists but isn’t actually a git repo. With the

git_clone

pull step, this most often happens if: - The target directory already exists from a previous run (or name collision) but does not contain a

.git

folder - The working directory isn’t what you expect, so git commands run in the wrong place Quick fixes you can try: 1) Force a clean working directory before clone - Use

set_working_directory

to a fresh path (e.g.,

/tmp/prefect-work

) and optionally clear it first so the clone step starts clean. - Give the clone step an

id

, and add a short diagnostics script to prove where we cloned and that it’s a git repo. Example prefect.yaml pull section:

pull:
  - prefect.deployments.steps.run_shell_script:
      id: prep
      script: |
        rm -rf /tmp/prefect-work
        mkdir -p /tmp/prefect-work
  - prefect.deployments.steps.set_working_directory:
      directory: /tmp/prefect-work
  - prefect.deployments.steps.git_clone:
      id: clone
      repository: <https://github.com/org/flows.git>
      branch: main
      # EITHER use a credentials block (requires prefect-github in the image)...
      # credentials: "{{ prefect.blocks.github-credentials.pat }}"
      # ...OR use a Secret (no extra package required):
      # access_token: "{{ prefect.blocks.secret.github-pat }}"
  - prefect.deployments.steps.run_shell_script:
      directory: "{{ clone.directory }}"
      script: |
        echo "CWD:"
        pwd
        echo "Repo top-level:"
        git rev-parse --show-toplevel
        echo "Tree:"
        ls -la

2) Double-check the repo URL in your YAML - Don’t include Slack’s angle brackets. It should be

<https://github.com/org/flows.git>

(or without

.git

) — not

<https://...>

. - Make sure

branch: main

exists in that repo. 3) If you’re using a GitHub credentials block - Ensure your ECS image has

prefect-github

installed. Without it, Prefect can’t load/format the block type at runtime. - Bake it in or install via env var:

# Dockerfile
FROM prefecthq/prefect:3-latest
RUN pip install --no-cache-dir prefect-github

or set in the ECS task/container env:

EXTRA_PIP_PACKAGES=prefect-github

- Alternatively, switch to

access_token: "{{ prefect.blocks.secret.github-pat }}"

to avoid the extra package. 4) Get more visibility while it’s “hard to debug” - Add that final

run_shell_script

step (above) to print

pwd

,

.git

presence, and a short tree — those stdout lines will show up in your container logs. - Make sure your ECS task’s CloudWatch log group is configured and you’re looking at the container’s stdout/stderr. - If helpful, temporarily add:

- prefect.deployments.steps.run_shell_script:
    script: |
      echo "Worker CWD before clone:"
      pwd
      echo "Contents:"
      ls -la

Why this happens -

git_clone

clones into the current working directory. If a folder with the derived name already exists but isn’t a git repo (no

.git

), any subsequent git commands (fetch/pull/checkout) will error with “not a git repository”. - Using a dedicated clean directory (e.g.,

/tmp/prefect-work

) avoids collisions with any pre-existing folders in the image or from prior runs. If this still fails after trying the clean working directory, please share: - Your updated

pull:

section (sanitized) - Whether you’re using

credentials:

or

access_token:

- The ECS container logs from the

run_shell_script

diagnostics step We’ll get you unstuck quickly with those details.

Thanks for sharing the task definition — a few likely culprits jump out that can cause the worker to exit (and therefore block flows from starting): Top things to check first 1) Remove the --type flag in Prefect 3.x - In 3.x, worker type is inferred from the work pool. Passing --type ecs can cause the CLI to error and exit. - Update your command to:

command = [
  "/bin/sh",
  "-c",
  "prefect worker start --pool ${var.prefect_work_pool}"
]

2) Ensure your worker image has the AWS integration installed - The ECS worker type lives in prefect-aws. If it’s missing, the worker won’t start for an ECS pool. - Your image should include:

pip install "prefect[aws]"
# or
pip install prefect-aws

- Quick check:

python -c "from prefect_aws.workers.ecs_worker import ECSWorker; print('OK')"

3) Your “secrets” are SSM parameters — the execution role must read them - Because you’re using ECS container “secrets” with SSM Parameter Store, the task’s execution role must allow: - ssm:GetParameters (and kms:Decrypt if parameters are KMS-encrypted) - Without these, PREFECT_API_KEY/URL won’t be injected and the worker will fail to connect to Prefect. - Add a policy like:

{
  "Version": "2012-10-17",
  "Statement": [
    {
      "Effect": "Allow",
      "Action": [
        "ssm:GetParameters",
        "ssm:GetParameter"
      ],
      "Resource": "arn:aws:ssm:REGION:ACCOUNT:parameter/your-path/*"
    },
    {
      "Effect": "Allow",
      "Action": [
        "kms:Decrypt"
      ],
      "Resource": "arn:aws:kms:REGION:ACCOUNT:key/KEY-ID"
    }
  ]
}

4) Verify the work pool exists, is type ecs, and is unpaused - From anywhere with the Prefect CLI:

prefect work-pool view ${var.prefect_work_pool}
# Type should be "ecs" and the pool should be unpaused

5) Make sure the worker’s task role has the ECS/IAM permissions it needs to submit runs - Common minimum set (tune to your environment): - ecs:RunTask, ecs:RegisterTaskDefinition, ecs:DescribeTaskDefinition, ecs:DescribeTasks, ecs:StopTask, ecs:TagResource - iam:PassRole (to pass the task and execution roles you reference) - ec2:DescribeVpcs, ec2:DescribeSubnets (for Fargate networking) - logs:CreateLogGroup, logs:CreateLogStream, logs:PutLogEvents (for CloudWatch log setup) - Sample policy reference: Prefect sample ECS worker policy 6) CloudWatch logs config - Since you set logConfiguration in the task definition, ensure the execution role has logs permissions (CreateLogGroup/CreateLogStream/PutLogEvents) for the specified log group and region. Quick triage steps - Get the exact error from your worker task logs in CloudWatch — that will pinpoint whether it’s: - an “unknown option” (due to --type), - a missing package (prefect-aws not installed), - missing API creds (SSM permissions issue), - or an AWS permission error (ecsRunTask/iamPassRole/etc.). - Run the image locally to confirm the container can start a worker:

docker run --rm \
  -e PREFECT_API_URL=<your-url> \
  -e PREFECT_API_KEY=<your-key> \
  <your-image> \
  prefect worker start --pool ${var.prefect_work_pool}

- Turn on debug logs for more detail:

PREFECT_LOGGING_LEVEL=DEBUG

If you can paste the first 30–50 lines of the worker container logs (especially the error at startup), I can pinpoint which of the above is hitting you. Helpful docs - ECS worker guide: Prefect ECS integration - Example IAM policy: Worker policy example

You’re right—let’s focus on the git error. What’s happening - Prefect 3.x calls a small helper during startup that runs: -

git rev-parse --abbrev-ref HEAD

- and sometimes

git config --get remote.origin.url

- When the container’s working directory is not a git repo, git prints: -

fatal: not a git repository (or any of the parent directories): .git

- Prefect catches the non‑zero exit and proceeds (so it’s harmless), but git still writes that “fatal” line to stderr, which shows up in your worker logs. This message is noisy but not the root cause of flows not starting. Still, if you want to eliminate it, here are practical ways: Ways to silence the git message - Initialize an empty repo in the worker’s working directory before starting the worker: - In your ECS task command:

command = [
    "/bin/sh",
    "-c",
    "git -C /app init -q || true; prefect worker start --pool ${var.prefect_work_pool}"
  ]

Replace

/app

with the actual working dir if different. This makes

git rev-parse

succeed and removes the fatal line. - Or change the working directory to a path where you’ve done a

git init

(same effect). - Alternatively, rebuild your image to include that one-time

git init -q

in the image at the directory you run the worker from. Important note - That git message by itself does not block flow runs. If flows still aren’t starting after we silence it, there’s a separate blocker. Common ones in ECS: - Worker started against the wrong pool type (pool must be type

ecs

) - Missing prefect-aws in the worker image (install

prefect[aws]

) - IAM permissions (ecs:RunTask, ecs:RegisterTaskDefinition, iam:PassRole, ec2:DescribeVpcs/Subnets, logs:*) - SSM/KMS permissions for your

secrets

(so PREFECT_API_KEY/URL actually get injected) - Missing VPC/subnet config for Fargate If you can share the 30–50 lines around the first occurrence of that fatal message (and your Prefect version in the worker image), I’ll pinpoint whether anything else is failing right after it.