Python errors when launching niceGUI #31
Description
System: macOSX Sequoia 16.6.1, running on M2 Pro.
Environment: Conda robin_0_6 directly from osx yaml file as instructed.
ROBIN launches, but fails to properly serve the niceGUI webpage. visiting localhost:8080 gives a 500 server error, displaying "ValueError: [TypeError("'coroutine' object is not iterable"), TypeError('vars() argument must have dict attribute')]"
ROBIN seems to be running just fine in the background, just unable to serve to the webserver.
(robin_0_6) MU00155730X:littlejohn jste0021$ robin workflow /Volumes/dnascreen_joshua_2/MOLBI24065 -w target,cnv,fusion,mgmt,sturgeon,nanodx,pannanodx,random_forest --reference /Users/jste0021/Documents/Projects/ont_cns2_mess/Homo_sapiens_assembly38.fasta --center test --target-panel rCNS2 --work-dir /Volumes/dnascreen_joshua_2/ROBIN_WORK
Validating reference genome: /Users/jste0021/Documents/Projects/ont_cns2_mess/Homo_sapiens_assembly38.fasta
✓ Reference genome validated and indexed: /Users/jste0021/Documents/Projects/ont_cns2_mess/Homo_sapiens_assembly38.fasta
DISCLAIMER:
This report and the data contained within it are intended for research use only and should not be used for direct diagnostic purposes. The methylation-based classification and other analyses provided here may be considered by neuropathologists as supplementary information in the context of comprehensive diagnostic assessment, which should include clinical history, radiological findings, and complete histopathological and molecular evaluation. The final interpretation and diagnosis should always be made by qualified healthcare professionals based on all available information.
The authors of this software note that:
Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.
To proceed, please type 'I agree' (exactly as shown):
I agree
2025-12-03 13:14:22,156 INFO worker.py:2003 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8265
/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/ray/_private/worker.py:2051: FutureWarning: Tip: In future versions of Ray, Ray will no longer override accelerator visible devices env var if num_gpus=0 or num_gpus=None (default). To enable this behavior and turn off this error message, set RAY_ACCEL_ENV_VAR_OVERRIDE_ON_ZERO=0
warnings.warn(
Center: test
Starting workflow on /Volumes/dnascreen_joshua_2/MOLBI24065 for BAM files (will process existing files first)...
Output directory: /Volumes/dnascreen_joshua_2/ROBIN_WORK
Workflow plan (simplified): ['preprocessing', 'bed_conversion', 'target', 'cnv', 'fusion', 'mgmt', 'sturgeon', 'nanodx', 'pannanodx', 'random_forest']
Auto-assigned queues: ['preprocessing:preprocessing', 'bed_conversion:bed_conversion', 'target:target', 'cnv:cnv', 'fusion:fusion', 'mgmt:mgmt', 'classification:sturgeon', 'classification:nanodx', 'classification:pannanodx', 'slow:random_forest']
Note: bed_conversion was automatically added as it's required for other jobs
Commands: {}
Log_level: ERROR
Distributed computing: Ray (experimental)
- Ray CPUs: auto-detect
- Analysis workers per type: 1 (distributed across Ray cluster)
- Log level: ERROR (applied to all Ray actors)
Press Ctrl+C to stop
Running The Workflow!
Launching GUI early to ensure immediate availability...
NiceGUI ready to go on http://localhost:8081, and http://49.127.80.68:8081
GUI launched successfully on http://0.0.0.0:8081
GUI monitoring started - workflow status will be updated in real-time
Preprocessing: 0%| | 0/64 [00:14<?, ?jobs/s, PBG47499_pass_24301271...(14s) | PBG47499_pass2025-12-03 13:14:54 - nicegui - ERROR - [TypeError("'coroutine' object is not iterable"), TypeError('vars() argument must have __dict__ attribute')]
Traceback (most recent call last):00:14<?, ?jobs/s]
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 337, in jsonable_encoder
data = dict(obj) | 0/0 [00:14<?, ?jobs/s]
TypeError: 'coroutine' object is not iterable?jobs/s]
Classification: | | 0/0 [00:14<?, ?jobs/s]
During handling of the above exception, another exception occurred:
Overall Progress: 0%| | 0/64 [00:14<?, ?jobs/s, Act:64 | Done:0 | Fail:0 | Skip:1 | Tot:65]
Traceback (most recent call last):
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 342, in jsonable_encoder
data = vars(obj)
TypeError: vars() argument must have __dict__ attribute
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/sessions.py", line 85, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/storage.py", line 33, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/middlewares.py", line 23, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/middlewares.py", line 13, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 29, in __call__
await responder(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 130, in __call__
await super().__call__(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 46, in __call__
await self.app(scope, receive, self.send_with_compression)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/exceptions.py", line 63, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
await self.app(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 716, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 736, in app
await route.handle(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 290, in handle
await self.app(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 119, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 105, in app
response = await f(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 407, in app
content = await serialize_response(
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 273, in serialize_response
return jsonable_encoder(response_content)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 345, in jsonable_encoder
raise ValueError(errors) from e
ValueError: [TypeError("'coroutine' object is not iterable"), TypeError('vars() argument must have __dict__ attribute')]
ERROR: Exception in ASGI application
Traceback (most recent call last):
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 337, in jsonable_encoder
data = dict(obj)
TypeError: 'coroutine' object is not iterable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 342, in jsonable_encoder
data = vars(obj)
TypeError: vars() argument must have __dict__ attribute
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/uvicorn/protocols/http/httptools_impl.py", line 409, in run_asgi
result = await app( # type: ignore[func-returns-value]
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 60, in __call__
return await self.app(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/applications.py", line 1139, in __call__
await super().__call__(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/applications.py", line 113, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/sessions.py", line 85, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/storage.py", line 33, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/middlewares.py", line 23, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 196, in __call__
recv_stream.close()
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 193, in __call__
response = await self.dispatch_func(request, call_next)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/nicegui/middlewares.py", line 13, in dispatch
response = await call_next(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 168, in call_next
raise app_exc from app_exc.__cause__ or app_exc.__context__
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/base.py", line 144, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 29, in __call__
await responder(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 130, in __call__
await super().__call__(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/gzip.py", line 46, in __call__
await self.app(scope, receive, self.send_with_compression)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/middleware/exceptions.py", line 63, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
await self.app(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 716, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 736, in app
await route.handle(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/routing.py", line 290, in handle
await self.app(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 119, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 105, in app
response = await f(request)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 407, in app
content = await serialize_response(
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/routing.py", line 273, in serialize_response
return jsonable_encoder(response_content)
File "/Users/jste0021/miniconda3/envs/robin_0_6/lib/python3.9/site-packages/fastapi/encoders.py", line 345, in jsonable_encoder
raise ValueError(errors) from e
ValueError: [TypeError("'coroutine' object is not iterable"), TypeError('vars() argument must have __dict__ attribute')]