https://github.com/multimeric/miniwdlbug
https://github.com/multimeric/miniwdlbug
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/multimeric/miniwdlbug
- Owner: multimeric
- Created: 2025-04-03T01:18:30.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2025-04-03T01:21:21.000Z (12 months ago)
- Last Synced: 2025-05-05T14:52:11.659Z (11 months ago)
- Language: WDL
- Size: 13.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
```bash
uv run miniwdl run wf.wdl --cfg conf.cfg
```
```
2025-04-03 12:20:25.917 wdl.w:wf NOTICE workflow start :: name: "wf", source: "wf.wdl", line: 10, column: 1, dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf"
2025-04-03 12:20:25.931 wdl.w:wf NOTICE miniwdl :: version: "v1.12.1", uname: "Linux slurm-login02.hpc.wehi.edu.au 5.14.0-362.24.1.el9_3.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Feb 15 07:18:13 EST 2024 x86_64"
2025-04-03 12:20:25.938 wdl.w:wf NOTICE ready :: job: "call-my_task", callee: "my_task"
2025-04-03 12:20:25.945 wdl.w:wf.t:call-my_task NOTICE task setup :: name: "my_task", source: "wf.wdl", line: 1, column: 1, dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task", thread: 22525751285312
2025-04-03 12:20:26.368 wdl.w:wf.t:call-my_task NOTICE Singularity runtime initialized (BETA) :: singularity_version: "apptainer version 1.3.3"
2025-04-03 12:20:26.376 wdl.w:wf.t:call-my_task ERROR task my_task (wf.wdl Ln 1 Col 1) failed :: dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task", error: "KeyError", message: "'docker'", traceback: ["Traceback (most recent call last):", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\", line 207, in run_local_task", " _try_task(cfg, task, logger, container, command, terminating)", " ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\", line 608, in _try_task", " return container.run(logger, command)", " ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task_container.py\", line 323, in run", " exit_code = self._run(logger, terminating, command)", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 67, in _run", " image = self._pull(logger, cleanup)", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 186, in _pull", " image, invocation = self._pull_invocation(logger, cleanup)", " ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/singularity.py\", line 62, in _pull_invocation", " image, invocation = super()._pull_invocation(logger, cleanup)", " ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 132, in _pull_invocation", " \"docker\", self.cfg.get_dict(\"task_runtime\", \"defaults\")[\"docker\"]", " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^", "KeyError: 'docker'"]
2025-04-03 12:20:26.394 wdl.w:wf ERROR call failure propagating :: from: "call-my_task", dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf"
2025-04-03 12:20:26.394 wdl.w:wf NOTICE aborting workflow
2025-04-03 12:20:26.400 miniwdl-run ERROR 'docker' :: error: "KeyError", traceback: ["Traceback (most recent call last):", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\", line 207, in run_local_task", " _try_task(cfg, task, logger, container, command, terminating)", " ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\", line 608, in _try_task", " return container.run(logger, command)", " ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task_container.py\", line 323, in run", " exit_code = self._run(logger, terminating, command)", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 67, in _run", " image = self._pull(logger, cleanup)", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 186, in _pull", " image, invocation = self._pull_invocation(logger, cleanup)", " ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/singularity.py\", line 62, in _pull_invocation", " image, invocation = super()._pull_invocation(logger, cleanup)", " ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\", line 132, in _pull_invocation", " \"docker\", self.cfg.get_dict(\"task_runtime\", \"defaults\")[\"docker\"]", " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^", "KeyError: 'docker'", "", "The above exception was the direct cause of the following exception:", "", "Traceback (most recent call last):", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\", line 1046, in _workflow_main_loop", " __, outputs = future.result()", " ~~~~~~~~~~~~~^^", " File \"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/_base.py\", line 449, in result", " return self.__get_result()", " ~~~~~~~~~~~~~~~~~^^", " File \"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/_base.py\", line 401, in __get_result", " raise self._exception", " File \"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py\", line 59, in run", " result = self.fn(*self.args, **self.kwargs)", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\", line 275, in run_local_task", " raise wrapper from exn", "WDL.runtime.error.RunFailed: task my_task (wf.wdl Ln 1 Col 1) failed", "", "The above exception was the direct cause of the following exception:", "", "Traceback (most recent call last):", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/CLI.py\", line 821, in runner", " rundir, output_env = runtime.run(cfg, target, input_env, run_dir=run_dir, _cache=cache)", " ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/__init__.py\", line 63, in run", " return entrypoint(cfg, exe, inputs, **run_kwargs) # type: ignore", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\", line 934, in run_local_workflow", " outputs = _workflow_main_loop(", " cfg,", " ...<9 lines>...", " _test_pickle,", " )", " File \"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\", line 1113, in _workflow_main_loop", " raise wrapper from exn", "WDL.runtime.error.RunFailed: workflow wf (wf.wdl Ln 10 Col 1) failed"], dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf", from_dir: "/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task"
```