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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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The timing bar is not updated after closing the Jupyter notebook web page by mistake #528

Closed jljy47 closed 9 months ago

jljy47 commented 9 months ago

Hi,

I accidentally closed the progress bar page in Jupyter notebook (but the terminal is still there). After re-opening, there is no timing, and the terminal displays as shown as follow. I would like to ask if the program is still continuing in the background at this time?

Terminal

[W 14:57:30.569 NotebookApp] Notebook HT_all_20231004.ipynb is not trusted [W 14:57:30.686 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20231004091321 (127.0.0.1) 3.420000ms referer=http://localhost:8888/notebooks/HT_all_20231004.ipynb [I 14:57:30.703 NotebookApp] Discarding 3 buffered messages for 2241b074-00c6-4023-982b-9f7ec468eacc:ec2bed7b0e934be5a939bd14f1472795 [I 16:22:50.489 NotebookApp] Starting buffering for 2241b074-00c6-4023-982b-9f7ec468eacc:3ea932dcf9c4413c8fd48c5ab011b37e [W 16:22:50.810 NotebookApp] Notebook HT_all_20231004.ipynb is not trusted [W 16:22:50.982 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20231004091321 (127.0.0.1) 2.470000ms referer=http://localhost:8888/notebooks/HT_all_20231004.ipynb [I 16:22:51.010 NotebookApp] Discarding 5 buffered messages for 2241b074-00c6-4023-982b-9f7ec468eacc:3ea932dcf9c4413c8fd48c5ab011b37e [I 17:08:10.184 NotebookApp] Starting buffering for 2241b074-00c6-4023-982b-9f7ec468eacc:75da0a1cec2840a5a5e258b3588367b4 ERROR:asyncio:Task exception was never retrieved future: <Task finished coro=<WebSocketProtocol13.write_message..wrapper() done, defined at /home/nku/miniconda3/lib/python3.7/site-packages/tornado/websocket.py:1100> exception=WebSocketClosedError()> Traceback (most recent call last): File "/home/nku/miniconda3/lib/python3.7/site-packages/tornado/websocket.py", line 1102, in wrapper await fut tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/nku/miniconda3/lib/python3.7/site-packages/tornado/websocket.py", line 1104, in wrapper raise WebSocketClosedError() tornado.websocket.WebSocketClosedError [W 17:08:10.623 NotebookApp] Notebook HT_all_20231004.ipynb is not trusted [W 17:08:10.859 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20231004091321 (127.0.0.1) 3.550000ms referer=http://localhost:8888/notebooks/HT_all_20231004.ipynb [I 17:08:10.899 NotebookApp] Discarding 7 buffered messages for 2241b074-00c6-4023-982b-9f7ec468eacc:75da0a1cec2840a5a5e258b3588367b4 [W 17:10:10.248 NotebookApp] Notebook HT_all_20231004.ipynb is not trusted [W 17:10:10.583 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20231004091321 (127.0.0.1) 3.670000ms referer=http://localhost:8888/notebooks/HT_all_20231004.ipynb

isaacovercast commented 9 months ago

Hello there,

This is not an ipyrad issue, it is a question about how jupyter notebooks work. Issues in the ipyrad github repo should be limited to problems with the software itself. If you have general computing questions or issues with coding or jupyter please feel free to ask on the ipyrad gitter channel or join stackflow.

I know the answer to your question but I will leave it as an exercise for you to figure out how to answer for yourself. If you are truly stuck ask it again on the gitter channel in a couple days.

All the best, -isaac

jljy47 commented 9 months ago

Hi, isaac.

Sorry to ask another question not related to ipyrad.

Thank you for pointing me to the area where this problem belongs. I'm going to try and find out the answer.

Thank you very much again.~

Best wishes, -L