Meghan Franklin
10/31/2022, 7:04 PMimport matplotlib; matplotlib.use('agg')
I get a segfault like this:
./run_local.sh: line 14: 34109 Segmentation fault: 11 python cli.py local -pfile developer/test_input.json
make: *** [run_local] Error 139
(p39_ngs) MB-MFRANKLIN:amplicon-analysis meghanfranklin$ /Users/meghanfranklin/opt/anaconda3/envs/p39_ngs/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
but if I don’t use that, python crashes 🙃
/Users/meghanfranklin/opt/anaconda3/envs/p39_ngs/lib/python3.9/site-packages/amp_analysis/plots.py:425: UserWarning: Starting a Matplotlib GUI outside of the main thread will likely fail.
fig, ax = plt.subplots()
[2022-10-31 15:02:54-0400] INFO - prefect.TaskRunner | Task 'create_pipeline_run': Finished task run for task with final state: 'Success'
2022-10-31 15:02:54.121 python[34449:328037] *** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'NSWindow drag regions should only be invalidated on the Main Thread!'
*** First throw call stack:
(
0 CoreFoundation 0x00007ff80bf1e7c3 __exceptionPreprocess + 242
1 libobjc.A.dylib 0x00007ff80bc7ebc3 objc_exception_throw + 48
2 CoreFoundation 0x00007ff80bf47076 -[NSException raise] + 9
[a lot more lines here]
)
libc++abi: terminating with uncaught exception of type NSException
./run_local.sh: line 14: 34449 Abort trap: 6 python cli.py local -pfile developer/test_input.json
make: *** [run_local] Error 134
(p39_ngs) MB-MFRANKLIN:amplicon-analysis meghanfranklin$ /Users/meghanfranklin/opt/anaconda3/envs/p39_ngs/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
-> cue Mac popup window about sending crash report to apple
[2022-10-31 19:07:35+0000] ERROR - prefect.TaskRunner | Unexpected error: Done(<matplotlib.backends.backend_agg.RendererAgg object at 0x7f337ba30c10>)
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/prefect/engine/runner.py", line 48, in inner
new_state = method(self, state, *args, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 876, in get_task_run_state
value = prefect.utilities.executors.run_task_with_timeout(
File "/opt/conda/lib/python3.9/site-packages/prefect/utilities/executors.py", line 467, in run_task_with_timeout
return task.run(*args, **kwargs) # type: ignore
File "/opt/conda/lib/python3.9/site-packages/amp_analysis/analyze.py", line 48, in analyze_sam_info
process_sam_stats(sample[0], sam_df, summary_folder, graph_folder)
File "/opt/conda/lib/python3.9/site-packages/amp_analysis/sam.py", line 103, in process_sam_stats
phred_histogram(mut_phreds, f"{graph_base}.Qscores_mismatches.png")
File "/opt/conda/lib/python3.9/site-packages/amp_analysis/plots.py", line 71, in phred_histogram
plt.savefig(outfile)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/pyplot.py", line 958, in savefig
res = fig.savefig(*args, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/figure.py", line 3019, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 2319, in print_figure
result = print_method(
File "/opt/conda/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 1648, in wrapper
return func(*args, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/_api/deprecation.py", line 412, in wrapper
return func(*inner_args, **inner_kwargs)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/backends/backend_agg.py", line 540, in print_png
FigureCanvasAgg.draw(self)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/opt/conda/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 1533, in _draw
def _draw(renderer): raise Done(renderer)
matplotlib.backend_bases._get_renderer.<locals>.Done: <matplotlib.backends.backend_agg.RendererAgg object at 0x7f337ba30c10>
[2022-10-31 19:07:35+0000] ERROR - prefect.TaskRunner | Task 'analyze_sam_info[1]': Unexpected error while running task: Done(<matplotlib.backends.backend_agg.RendererAgg object at 0x7f337ba30c10>)
At least there’s no segfault??Zanie
10/31/2022, 7:24 PMMeghan Franklin
10/31/2022, 7:37 PMZanie
11/01/2022, 3:05 PMasync
task or flow will run things in the main thread.Meghan Franklin
11/01/2022, 3:27 PMJeff Hale
11/01/2022, 3:33 PM