mononitogoswami
commented
8 months ago I am facing a very similar issue with the same version of VS code and Jupyter.
Closed AlSzmigiel closed 8 months ago
mononitogoswami
commented
8 months ago I am facing a very similar issue with the same version of VS code and Jupyter.
DonJayamanne
commented
8 months ago Based on the logs, you seem to be deleting some of the cells while execution is in progress Please can you verify this is the case.
Disposing request as the cell was deleted /work/Master_Project/bash_scripts/analysis.ipynb 16:34:38.812 [info] Dispose Kernel '/work/Master_Project/bash_scripts/analysis.ipynb' associated with '/work/Master_Project/bash_scripts/analysis.ipynb'
AlSzmigiel
commented
8 months ago No, it happened many times, at some point syntax is not being highlighted anymore and then after running the next cell it's pending forever and it's impossible to interrupt the process. I have to restart the SSH connection to be able to stop the process.
DonJayamanne
commented
8 months ago Working on creating a custom build of the VSIX to get some more logs
DonJayamanne
commented
8 months ago ms-toolsai-jupyter-insiders.vsix.zip
Install from VSIX@mononitogoswami Please coul you also try the above, Please ensure you enable verbose logging as follows Please could you enable logging as follows:
Jupyter->LoggingverboseJupyter output panel.
varevshatyan
commented
8 months ago Facing the same issue with Jupyter randomly disposing the kernel.
AlSzmigiel
commented
8 months ago I noticed that it happens when I copy some content from one cell to another (ctrl+c), but after some time of using the notebook. Right after I connect and copy-paste everything is good.
There you go:
Visual Studio Code (1.83.1, ssh-remote, desktop) Jupyter Extension Version: 2023.11.100. Python Extension Version: 2023.18.0. Platform: linux (x64). Workspace folder /work/Master_Project, Home = /home/ucloud 10:09:27.272 [debug] Get Custom Env Variables, Class name = um (started execution), Arg 1: undefined, Arg 2: "RunPythonCode" 10:09:27.274 [info] Start refreshing Kernel Picker (1698829767274) 10:09:27.301 [info] Using Pylance 10:09:29.425 [debug] Get Custom Env Variables, Class name = um, completed in 2153ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunPythonCode" 10:09:29.425 [debug] Jupyter Paths /kernels: 10:09:29.426 [debug] Kernel Spec Root Paths, /usr/share/jupyter/kernels, /usr/local/share/jupyter/kernels, ~/.local/share/jupyter/kernels 10:09:29.478 [debug] Search for KernelSpecs in Interpreter /work/Master_Project/miniconda3/envs/singlecell2/bin/python 10:09:29.479 [debug] Finding Global Python KernelSpecs 10:09:29.481 [debug] Search for KernelSpecs in Interpreter /work/Master_Project/miniconda3/bin/python 10:09:29.482 [debug] Search for KernelSpecs in Interpreter /bin/python 10:09:29.483 [debug] Search for KernelSpecs in Interpreter /usr/bin/python 10:09:29.484 [debug] Full interpreter list is length: 4, /work/Master_Project/miniconda3/bin/python::Conda:/work/Master_Project/miniconda3/bin/python, /bin/python::Unknown:/bin/python, /usr/bin/python::Unknown:/usr/bin/python, /work/Master_Project/miniconda3/envs/singlecell2/bin/python::Conda:/work/Master_Project/miniconda3/envs/singlecell2/bin/python 10:09:29.487 [debug] Getting activated env variables, Class name = td (started execution), Arg 1: "/work/Master_Project", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 10:09:29.487 [debug] Get Custom Env Variables, Class name = um (started execution), Arg 1: "/work/Master_Project", Arg 2: "RunPythonCode" 10:09:29.487 [debug] Get Custom Env Variables, Class name = um, completed in 0ms, has a truthy return value, Arg 1: "/work/Master_Project", Arg 2: "RunPythonCode" 10:09:29.504 [debug] Kernels for interpreter /work/Master_Project/miniconda3/bin/python are .jvsc74a57bd0b3acb5aa85d39e2947cc826f82cb93fda52035c027d60cb6fdb7a8b0e9b99f0f./work/Master_Project/miniconda3/python./work/Master_Project/miniconda3/python.-m#ipykernel_launcher 10:09:29.504 [debug] Kernels for interpreter /bin/python are .jvsc74a57bd0e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a./bin/python./bin/python.-m#ipykernel_launcher 10:09:29.505 [debug] Kernels for interpreter /usr/bin/python are .jvsc74a57bd0767d51c1340bd893661ea55ea3124f6de3c7a262a8b4abca0554b478b1e2ff90./usr/bin/python./usr/bin/python.-m#ipykernel_launcher 10:09:29.509 [debug] Loading kernelspec from /usr/share/jupyter/kernels/xonsh/kernel.json 10:09:29.509 [debug] Loading kernelspec from /work/Master_Project/miniconda3/envs/singlecell2/share/jupyter/kernels/python3/kernel.json for /work/Master_Project/miniconda3/envs/singlecell2/bin/python 10:09:29.521 [debug] Kernel Specs found in interpreter /work/Master_Project/miniconda3/envs/singlecell2/bin/python are [{"specFile":"/work/Master_Project/miniconda3/envs/singlecell2/share/jupyter/kernels/python3/kernel.json","interpreterPath":"/work/Master_Project/miniconda3/envs/singlecell2/bin/python","isRegisteredByVSC":"registeredByNewVersionOfExt","name":"pythonjvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589","argv":["/work/Master_Project/miniconda3/envs/singlecell2/bin/python","-m","ipykernel_launcher","-f","{connection_file}"],"language":"python","executable":"/work/Master_Project/miniconda3/envs/singlecell2/bin/python","display_name":"Python 3 (ipykernel)","metadata":{"debugger":false,"vscode":{"originalSpecFile":"/work/Master_Project/miniconda3/envs/singlecell2/share/jupyter/kernels/python3/kernel.json","originalDisplayName":"Python 3 (ipykernel)"}}}] 10:09:29.521 [debug] Hiding default kernel spec 'Python 3 (ipykernel)', 'pythonjvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589', /work/Master_Project/miniconda3/envs/singlecell2/bin/python for interpreter /work/Master_Project/miniconda3/envs/singlecell2/bin/python and spec /work/Master_Project/miniconda3/envs/singlecell2/share/jupyter/kernels/python3/kernel.json 10:09:29.521 [debug] Kernels for interpreter /work/Master_Project/miniconda3/envs/singlecell2/bin/python are .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher 10:09:29.579 [debug] KernelProvider switched kernel to id = .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher 10:09:29.579 [debug] start the kernel, options.disableUI=true for /work/Master_Project/bash_scripts/analysis.ipynb 10:09:29.581 [debug] Initialize notebook communications for editor /work/Master_Project/bash_scripts/analysis.ipynb 10:09:29.581 [debug] Resolving notebook UI Comms (resolve) for /work/Master_Project/bash_scripts/analysis.ipynb 10:09:29.581 [debug] initialize CommonMessageCoordinator 10:09:29.611 [debug] Registering commtarget jupyter.widget 10:09:29.611 [debug] IPyWidgetMessageDispatcher.initialize 10:09:29.612 [debug] Attempting to determine version of IPyWidgets 10:09:29.613 [debug] Controller selection change completed 10:09:29.613 [debug] Waiting for IPyWidgets version 10:09:29.613 [debug] Waiting for IPyWidgets version promise 10:09:29.615 [info] Starting Kernel startUsingPythonInterpreter, .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher (Python Path: /work/Master_Project/miniconda3/envs/singlecell2/bin/python, Conda, 3.11.6) for '/work/Master_Project/bash_scripts/analysis.ipynb' (disableUI=true) 10:09:29.616 [debug] Creating raw notebook for resource '/work/Master_Project/bash_scripts/analysis.ipynb' 10:09:29.620 [debug] Kernel Launcher. launch, Class name = uo (started execution), Arg 1: ".jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher", Arg 2: 60000, Arg 3: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 4: "/work/Master_Project/bash_scripts", Arg 5: "" 10:09:29.628 [debug] Getting activated env variables, Class name = td (started execution), Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 10:09:29.628 [debug] Get Custom Env Variables, Class name = um (started execution), Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "RunPythonCode" 10:09:29.628 [debug] Get Custom Env Variables, Class name = um, completed in 0ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "RunPythonCode" 10:09:29.669 [debug] Launching kernel in kernelProcess.ts, Class name = ly (started execution), Arg 1: "/work/Master_Project/bash_scripts", Arg 2: "" 10:09:29.827 [debug] Conda file returned by Python Extension is conda 10:09:29.935 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 448ms 10:09:29.937 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 10:09:29.937 [debug] Prepend PATH with python bin for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is ~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 10:09:29.937 [debug] Activated Env Variables for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is /work/Master_Project/miniconda3/envs/singlecell2/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 10:09:29.938 [debug] Getting activated env variables, Class name = td, completed in 452ms, has a truthy return value, Arg 1: "/work/Master_Project", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 10:09:29.956 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m pip list 10:09:29.971 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 343ms 10:09:29.972 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 10:09:29.972 [debug] Prepend PATH with python bin for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is ~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 10:09:29.972 [debug] Activated Env Variables for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is /work/Master_Project/miniconda3/envs/singlecell2/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 10:09:29.973 [debug] Getting activated env variables, Class name = td, completed in 345ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 10:09:29.987 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -c "import ipykernel; print(ipykernel.version); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.file)" 10:09:29.988 [debug] Kernel Env Variables for ~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/temp/jupyter/kernels/pythonjvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589/kernel.json, PATH value is /work/Master_Project/miniconda3/envs/singlecell2/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 10:09:30.004 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9003 --control=9001 --hb=9000 --Session.signature_scheme="hmac-sha256" --Session.key=b"c16de57f-a806-4767-a3c9-371557772151" --shell=9002 --transport="tcp" --iopub=9004 --f=~/.local/share/jupyter/runtime/kernel-v2-4264cXTeIYyyJxMu.json
cwd: /work/Master_Project/bash_scripts 10:09:30.005 [debug] Launching kernel in kernelProcess.ts, Class name = ly, completed in 336ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts", Arg 2: "" 10:09:30.485 [info] End refreshing Kernel Picker (1698829767274) 10:09:30.768 [info] ipykernel version & path 6.25.0, /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/ipykernel/init.py for /work/Master_Project/miniconda3/envs/singlecell2/bin/python 10:09:32.267 [warn] StdErr from Kernel Process 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 10:09:32.268 [debug] KernelProcess error: 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
10:09:32.486 [debug] Kernel Output: To connect another client to this kernel, use: --existing kernel-v2-4264cXTeIYyyJxMu.json
10:09:32.486 [debug] KernelProcess output: NOTE: When using the ipython kernel entry point, Ctrl-C will not work.
To exit, you will have to explicitly quit this process, by either sending "quit" from a client, or using Ctrl-\ in UNIX-like environments.
To read more about this, see https://github.com/ipython/ipython/issues/2049
To connect another client to this kernel, use: --existing kernel-v2-4264cXTeIYyyJxMu.json
10:09:32.680 [debug] Kernel Launcher. launch, Class name = uo, completed in 3060ms, has a truthy return value, Arg 1: ".jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher", Arg 2: 60000, Arg 3: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 4: "/work/Master_Project/bash_scripts", Arg 5: ""
10:09:32.872 [debug] Waiting for Raw Session to be ready in postStartRawSession
10:09:32.872 [debug] Waiting for Raw session to be ready, currently connected
10:09:32.872 [debug] Raw session connected
10:09:32.872 [debug] Waiting for Raw session to be ready for 30s
10:09:32.873 [debug] Waited for Raw session to be ready & got connected
10:09:32.873 [debug] Successfully waited for Raw Session to be ready in postStartRawSession
10:09:32.873 [debug] Kernel status before requesting kernel info and after ready is unknown
10:09:32.873 [debug] Sending request for kernelInfo
10:09:32.878 [debug] Got response for requestKernelInfo
10:09:32.878 [debug] Successfully completed postStartRawSession
10:09:32.881 [debug] Begin sendTelemetryForPythonKernelExecutable
10:09:32.881 [debug] Executing silently Code (idle) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys
10:09:32.957 [debug] Executing silently Code (completed) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys with 1 output(s)
10:09:32.958 [debug] End sendTelemetryForPythonKernelExecutable
10:09:32.959 [debug] Started running kernel initialization for /work/Master_Project/bash_scripts/analysis.ipynb
10:09:32.961 [debug] Executing silently Code (idle) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy
10:09:32.971 [debug] Executing silently Code (completed) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy with 0 output(s)
10:09:32.972 [debug] Determined IPyWidgets Version as undefined and event fired
10:09:32.974 [debug] Executing silently Code (idle) = import os as _VSCODE_os\nimport sys as _VSCODE_sys\n%cd "//work/Master_Project/bash_scripts"\nif _VSCOD
10:09:32.986 [debug] Executing silently Code (completed) = import os as _VSCODE_os\nimport sys as _VSCODE_sys\n%cd "//work/Master_Project/bash_scripts"\nif _VSCOD with 1 output(s)
10:09:32.986 [debug] Requesting Kernel info
10:09:32.987 [debug] Got Kernel info
10:09:32.987 [debug] End running kernel initialization, now waiting for idle
10:09:32.987 [debug] Waiting for 60000ms idle on (kernel): def622d4-ae51-4534-9264-ac15ccb9c2ea -> idle
10:09:32.988 [debug] Finished waiting for idle on (kernel): def622d4-ae51-4534-9264-ac15ccb9c2ea -> idle
10:09:32.988 [debug] End running kernel initialization, session is idle
10:09:32.990 [debug] IPyWidgetScriptSource.initialize
10:09:32.990 [debug] IPyWidgetMessageDispatcher.initialize
10:09:32.993 [debug] getDataDirsImpl, Class name = en (started execution), Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python"
10:09:32.993 [debug] Get Custom Env Variables, Class name = um (started execution), Arg 1: undefined, Arg 2: "RunPythonCode"
10:09:32.994 [debug] Get Custom Env Variables, Class name = um, completed in 1ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunPythonCode"
10:09:32.994 [debug] Jupyter Paths :
10:09:33.064 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/pythonFiles/printJupyterDataDir.py
10:09:33.089 [debug] getDataDirsImpl, Class name = en, completed in 96ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python"
10:09:44.522 [debug] Updating cache with Local kernels startUsingLocalKernelSpec:'.xonsh./usr/bin/python3././usr/bin/python3#-m#xonsh.jupyter_kernel#-f#{connection_file} (interpreter id = )', Added = , Updated = , Removed =
10:10:11.883 [debug] notebook communications already initialized for editor /work/Master_Project/bash_scripts/analysis.ipynb
10:10:11.883 [info] Start refreshing Interpreter Kernel Picker
10:10:11.883 [info] Start refreshing Kernel Picker (1698829811883)
10:10:12.179 [debug] Python API env change detected, update => '/work/Master_Project/miniconda3/bin/python'
10:10:12.197 [debug] Full interpreter list is length: 4, /work/Master_Project/miniconda3/bin/python::Conda:/work/Master_Project/miniconda3/bin/python, /bin/python::Unknown:/bin/python, /usr/bin/python::Unknown:/usr/bin/python, /work/Master_Project/miniconda3/envs/singlecell2/bin/python::Conda:/work/Master_Project/miniconda3/envs/singlecell2/bin/python
10:10:12.197 [debug] Refreshed Environments
10:10:13.197 [info] End refreshing Kernel Picker (1698829811883)
10:10:27.198 [debug] Updating cache with Local kernels startUsingLocalKernelSpec:'.xonsh./usr/bin/python3././usr/bin/python3#-m#xonsh.jupyter_kernel#-f#{connection_file} (interpreter id = )', Added = , Updated = , Removed =
10:10:38.037 [info] Handle Execution of Cells 0 for /work/Master_Project/bash_scripts/analysis.ipynb
10:10:38.039 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:10:38.043 [debug] Execution Request Sent to Kernel for cell 0
10:10:38.059 [debug] Start cell 0 execution @ 1698829838057 (clear output)
10:10:38.060 [info] Kernel acknowledged execution of cell 0 @ 1698829838057
10:10:40.859 [info] End cell 0 execution @ 1698829840858, started @ 1698829838057, elapsed time = 2.801s
10:10:40.861 [debug] Cell 0 executed with state Success
10:10:56.325 [info] Handle Execution of Cells 3 for /work/Master_Project/bash_scripts/analysis.ipynb
10:10:56.326 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:10:56.329 [debug] Execution Request Sent to Kernel for cell 3
10:10:56.338 [debug] Start cell 3 execution @ 1698829856338 (clear output)
10:10:56.338 [info] Kernel acknowledged execution of cell 3 @ 1698829856338
10:11:14.162 [info] End cell 3 execution @ 1698829874162, started @ 1698829856338, elapsed time = 17.824s
10:11:14.165 [debug] Cell 3 executed with state Success
10:11:17.018 [info] Handle Execution of Cells 4 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:17.020 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:17.022 [debug] Execution Request Sent to Kernel for cell 4
10:11:17.036 [debug] Start cell 4 execution @ 1698829877036 (clear output)
10:11:17.036 [info] Kernel acknowledged execution of cell 4 @ 1698829877036
10:11:17.039 [info] End cell 4 execution @ 1698829877039, started @ 1698829877036, elapsed time = 0.003s
10:11:17.039 [debug] Cell 4 executed with state Success
10:11:19.530 [info] Handle Execution of Cells 5 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:19.532 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:19.536 [debug] Execution Request Sent to Kernel for cell 5
10:11:19.543 [debug] Start cell 5 execution @ 1698829879543 (clear output)
10:11:19.543 [info] Kernel acknowledged execution of cell 5 @ 1698829879543
10:11:19.547 [info] End cell 5 execution @ 1698829879547, started @ 1698829879543, elapsed time = 0.004s
10:11:19.548 [debug] Cell 5 executed with state Success
10:11:21.454 [info] Handle Execution of Cells 6 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:21.457 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:21.460 [debug] Execution Request Sent to Kernel for cell 6
10:11:21.473 [debug] Start cell 6 execution @ 1698829881473 (clear output)
10:11:21.473 [info] Kernel acknowledged execution of cell 6 @ 1698829881473
10:11:21.476 [info] End cell 6 execution @ 1698829881476, started @ 1698829881473, elapsed time = 0.003s
10:11:21.476 [debug] Cell 6 executed with state Success
10:11:23.766 [info] Handle Execution of Cells 8 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:23.767 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:23.768 [debug] Execution Request Sent to Kernel for cell 8
10:11:23.773 [debug] Start cell 8 execution @ 1698829883772 (clear output)
10:11:23.773 [info] Kernel acknowledged execution of cell 8 @ 1698829883772
10:11:25.161 [info] End cell 8 execution @ 1698829885160, started @ 1698829883772, elapsed time = 1.388s
10:11:25.161 [debug] Cell 8 executed with state Success
10:11:27.767 [info] Handle Execution of Cells 9 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:27.768 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:27.769 [debug] Execution Request Sent to Kernel for cell 9
10:11:27.775 [debug] Start cell 9 execution @ 1698829887775 (clear output)
10:11:27.775 [info] Kernel acknowledged execution of cell 9 @ 1698829887775
10:11:31.045 [info] End cell 9 execution @ 1698829891045, started @ 1698829887775, elapsed time = 3.27s
10:11:31.046 [debug] Cell 9 executed with state Success
10:11:32.404 [info] Handle Execution of Cells 10 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:32.406 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:32.409 [debug] Execution Request Sent to Kernel for cell 10
10:11:32.418 [debug] Start cell 10 execution @ 1698829892418 (clear output)
10:11:32.418 [info] Kernel acknowledged execution of cell 10 @ 1698829892418
10:11:35.231 [info] End cell 10 execution @ 1698829895231, started @ 1698829892418, elapsed time = 2.813s
10:11:35.232 [debug] Cell 10 executed with state Success
10:11:37.982 [info] Handle Execution of Cells 13 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:37.983 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:37.984 [debug] Execution Request Sent to Kernel for cell 13
10:11:37.991 [debug] Start cell 13 execution @ 1698829897991 (clear output)
10:11:37.991 [info] Kernel acknowledged execution of cell 13 @ 1698829897991
10:11:37.993 [info] End cell 13 execution @ 1698829897993, started @ 1698829897991, elapsed time = 0.002s
10:11:37.993 [debug] Cell 13 executed with state Success
10:11:39.814 [info] Handle Execution of Cells 14 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:39.815 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:39.817 [debug] Execution Request Sent to Kernel for cell 14
10:11:39.825 [debug] Start cell 14 execution @ 1698829899825 (clear output)
10:11:39.825 [info] Kernel acknowledged execution of cell 14 @ 1698829899825
10:11:47.032 [info] End cell 14 execution @ 1698829907032, started @ 1698829899825, elapsed time = 7.207s
10:11:47.033 [debug] Cell 14 executed with state Success
10:11:49.423 [info] Handle Execution of Cells 15 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:49.424 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:49.427 [debug] Execution Request Sent to Kernel for cell 15
10:11:49.436 [debug] Start cell 15 execution @ 1698829909436 (clear output)
10:11:49.436 [info] Kernel acknowledged execution of cell 15 @ 1698829909436
10:11:49.438 [info] End cell 15 execution @ 1698829909438, started @ 1698829909436, elapsed time = 0.002s
10:11:49.438 [debug] Cell 15 executed with state Success
10:11:55.469 [info] Handle Execution of Cells 16 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:55.471 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:55.472 [debug] Execution Request Sent to Kernel for cell 16
10:11:55.478 [debug] Start cell 16 execution @ 1698829915478 (clear output)
10:11:55.478 [info] Kernel acknowledged execution of cell 16 @ 1698829915478
10:11:55.481 [info] End cell 16 execution @ 1698829915480, started @ 1698829915478, elapsed time = 0.002s
10:11:55.481 [debug] Cell 16 executed with state Success
10:11:58.220 [info] Handle Execution of Cells 17 for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:58.220 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:11:58.222 [debug] Execution Request Sent to Kernel for cell 17
10:11:58.236 [debug] Start cell 17 execution @ 1698829918236 (clear output)
10:11:58.236 [info] Kernel acknowledged execution of cell 17 @ 1698829918236
10:11:58.241 [info] End cell 17 execution @ 1698829918241, started @ 1698829918236, elapsed time = 0.005s
10:11:58.242 [debug] Cell 17 executed with state Success
10:12:01.286 [info] Handle Execution of Cells 19 for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:01.287 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:01.289 [debug] Execution Request Sent to Kernel for cell 19
10:12:01.296 [debug] Start cell 19 execution @ 1698829921295 (clear output)
10:12:01.296 [info] Kernel acknowledged execution of cell 19 @ 1698829921295
10:12:01.300 [info] End cell 19 execution @ 1698829921299, started @ 1698829921295, elapsed time = 0.004s
10:12:01.300 [debug] Cell 19 executed with state Success
10:12:03.106 [info] Handle Execution of Cells 20 for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:03.107 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:03.110 [debug] Execution Request Sent to Kernel for cell 20
10:12:03.118 [debug] Start cell 20 execution @ 1698829923118 (clear output)
10:12:03.118 [info] Kernel acknowledged execution of cell 20 @ 1698829923118
10:12:05.191 [info] End cell 20 execution @ 1698829925191, started @ 1698829923118, elapsed time = 2.073s
10:12:05.191 [debug] Cell 20 executed with state Success
10:12:07.683 [info] Handle Execution of Cells 21 for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:07.684 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:07.685 [debug] Execution Request Sent to Kernel for cell 21
10:12:07.690 [debug] Start cell 21 execution @ 1698829927690 (clear output)
10:12:07.690 [info] Kernel acknowledged execution of cell 21 @ 1698829927690
10:12:07.693 [info] End cell 21 execution @ 1698829927693, started @ 1698829927690, elapsed time = 0.003s
10:12:07.693 [debug] Cell 21 executed with state Success
10:12:11.308 [info] Handle Execution of Cells 22 for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:11.309 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:11.311 [debug] Execution Request Sent to Kernel for cell 22
10:12:11.322 [debug] Start cell 22 execution @ 1698829931322 (clear output)
10:12:11.322 [info] Kernel acknowledged execution of cell 22 @ 1698829931322
10:12:11.326 [info] End cell 22 execution @ 1698829931326, started @ 1698829931322, elapsed time = 0.004s
10:12:11.327 [debug] Cell 22 executed with state Success
10:12:14.367 [info] Handle Execution of Cells 23 for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:14.368 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb
10:12:14.369 [debug] Execution Request Sent to Kernel for cell 23
10:12:14.375 [debug] Start cell 23 execution @ 1698829934375 (clear output)
10:12:14.375 [info] Kernel acknowledged execution of cell 23 @ 1698829934375
10:12:14.378 [info] End cell 23 execution @ 1698829934377, started @ 1698829934375, elapsed time = 0.002s
10:12:14.378 [debug] Cell 23 executed with state Success
10:12:26.544 [info] Disposing request as the cell (0) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.545 [info] Disposing request as the cell (3) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.546 [info] Disposing request as the cell (4) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.546 [info] Disposing request as the cell (6) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.547 [info] Disposing request as the cell (8) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.547 [info] Disposing request as the cell (10) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.548 [info] Disposing request as the cell (13) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.548 [info] Disposing request as the cell (14) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.548 [info] Disposing request as the cell (16) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.549 [info] Disposing request as the cell (17) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.549 [info] Disposing request as the cell (19) was deleted /work/Master_Project/bash_scripts/analysis.ipynb
10:12:26.549 [debug] Disposing kernel associated with /work/Master_Project/bash_scripts/analysis.ipynb, isClosed=true
10:12:26.549 [info] Dispose Kernel '/work/Master_Project/bash_scripts/analysis.ipynb' associated with '/work/Master_Project/bash_scripts/analysis.ipynb'
10:12:26.550 [debug] Cancel pending cells
10:12:26.550 [debug] Shutdown session def622d4-ae51-4534-9264-ac15ccb9c2ea, .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher - start called from Error:
at hT.shutdown (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/dist/extension.node.js:256:3409)
at hT.disposeAsync (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/dist/extension.node.js:256:2887)
at e (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/dist/extension.node.js:232:27399)
at WD.dispose (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/dist/extension.node.js:232:27633)
at Zv.disposeOldKernel (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.11.100/dist/extension.node.js:232:18994)
at Zv.
BlackCloud37
commented
8 months ago Same issue, open the .ipynb for a while and the kernel just randomly disposed. After that, run cell only shows a clock icon in the left-bottom cornor of the cell w/o elpased seconds. Reopen the .ipynb file won't reset this situation, so I need to reload the vscode window.
Versions: vscode Jupyter extension: v2023.10.1003070148 ipykernel: 5.5.5 Python 3.6.13 :: Anaconda, Inc.
Log: 11:28:34.219 [info] Kernel acknowledged execution of cell 15 @ 1698895714219 11:28:34.222 [info] End cell 15 execution @ 1698895714221, started @ 1698895714219, elapsed time = 0.002s 11:28:36.797 [info] Dispose Kernel '~/stat.ipynb' associated with '~/stat.ipynb' 11:28:36.798 [info] Dispose Kernel process 11824. 11:29:01.117 [error] Notebook not found for Cell ~/stat.ipynb 11:29:01.226 [error] Notebook not found for Cell ~/stat.ipynb 11:29:01.382 [error] Notebook not found for Cell ~/stat.ipynb 11:29:01.614 [error] Notebook not found for Cell ~/stat.ipynb 11:29:01.711 [error] Notebook not found for Cell ~/stat.ipynb
SaneBow
commented
8 months ago Encounter exactly the same issue starting from 2 days ago. Even connecting to an external jupyter server (launched with jupyter notebook) or switch insider/stable version of vscode doesn't help
Mai0313
commented
8 months ago Exactly same thing; log is the same with others.
stnbSim
commented
8 months ago my case is like the kernel disposed itself when I Ctrl + C on a code
DonJayamanne
commented
8 months ago Please can everyone try the following
Let me know if the problem still persists even after that. Others have had luck, but I'd like to identify the extension thats causing this issue.
Purewhite2019
commented
8 months ago Please can everyone try the following
- Disable all extensions except for Python, Jupyter and Notebook Renderers Especially extensions like Pylint, flake8, Pylance, Ruff and the like
Let me know if the problem still persists even after that. Others have had luck, but I'd like to identify the extension thats causing this issue.
Yes, the only enabled extensions are ms-toolsai.jupyter@2023.10.1003070148, ms-python.python@2023.20.0, ms-python.vscode-pylance@2023.10.50 and ms-vscode-remote.remote-ssh
Purewhite2019
commented
8 months ago https://github.com/microsoft/pylance-release/issues/5034
It seems that this problem may relate to pylance. :thinking:
After downgrading it from v2023.10.50 (released 6 days ago) to v2023.10.40 (released 1 week ago), my jupyter now works correctly.
Hope this information can help.
DonJayamanne
commented
8 months ago @luabud @rchiodo
DonJayamanne
commented
8 months ago Please downgrade Pylance to v2023.10.40
AlSzmigiel
commented
8 months ago I downgraded Pylance and in my case now it looks like Pylance randomly stops working (syntax stops being highlighted randomly, and I don't see 'Python' in the bottom right corner), and in this case executing cells takes much much longer time than it normally would. Even with print("hello world"). After a long execution time syntax is highlighted again, and the time of execution shown in the logs is in milliseconds. If you try to call the variable that does not exist when Pylance is not in the "working mode" then kernel get disposed and the problem occurs again. Not very helpful.
edit: Disabling Pylance completely seems to be working for me.
rchiodo
commented
8 months ago We've been having trouble reproducing this with the steps provided. In https://github.com/microsoft/vscode/issues/196740 I was able to cause something similar using goto def, but not with just copying cells.
The curious part is that the root cause seems to be Pylance returning URIs for cells that don't match the URI originally sent for a request. How does this break the Jupyter extension though? Where would the jupyter extension be using the URI, especially with something like a copy (language server shouldn't be involved here).
DonJayamanne
commented
8 months ago for a request. How does this break the Jupyter extension though? Where would the jupyter extension be using the URI, especially with something like a copy (language server shouldn't be involved here).
@rchiodo Jupyter extension doesn't use anyhting from Pylance. Somehow VS Code detects some change and triggers events indicating the editor associated with the cell has been closed and similarly vscode triggers events for the notebook being closed. When notebooks are closed Jupyter extension disposes the kernels.
Ie somehow VS Code is using the data from pylance and triggering closing of notebooks and cells.
luabud
commented
8 months ago We have just shipped a new version of Pylance that potentially fixes this issue: 2023.11.10
If someone is able to still reproduce it on this new version while also using the latest version of VS Code and the Jupyter extension, please let us know at https://github.com/microsoft/pylance-release!
SaneBow
commented
8 months ago Confirmed in my case the issue no longer occurs after upgrading to 2023.11.10
DonJayamanne
commented
8 months ago @SaneBow It should be the pylance extension that needs to be updated, not Jupyter Either way, great to know its resolved
DonJayamanne
commented
8 months ago Closing this issue as resolved Please ensure you updated too the latest version of pylance
Environment data
Expected behaviour
Kernel not being disposed at random points
Actual behaviour
Kernel is being disposed after running some cells, but at different times and with different operations.
Logs
Output for
Jupyterin theOutputpanel (View→Output, change the drop-down the upper-right of theOutputpanel toJupyter)Visual Studio Code (1.83.1, ssh-remote, desktop) Jupyter Extension Version: 2023.9.1102792234. Python Extension Version: 2023.18.0. Platform: linux (x64). Workspace folder /work/Master_Project, Home = /home/ucloud 16:24:20.751 [info] User belongs to experiment group 'NewJupyterSession' 16:24:21.505 [info] Start refreshing Kernel Picker (1698765861505) 16:24:21.510 [info] Using Pylance 16:24:23.080 [info] Starting Kernel startUsingPythonInterpreter, .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher (Python Path: /work/Master_Project/miniconda3/envs/singlecell2/bin/python, Conda, 3.11.6) for '/work/Master_Project/bash_scripts/analysis.ipynb' (disableUI=true) 16:24:23.484 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 569ms 16:24:23.487 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 16:24:23.554 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m pip list 16:24:23.565 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 467ms 16:24:23.567 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 16:24:23.600 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)" 16:24:23.662 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9003 --control=9001 --hb=9000 --Session.signature_scheme="hmac-sha256" --Session.key=b"8b39c960-d595-4836-9c06-b898c33d95a6" --shell=9002 --transport="tcp" --iopub=9004 --f=~/.local/share/jupyter/runtime/kernel-v2-8212aR5VmPI9BOkl.json > cwd: /work/Master_Project/bash_scripts 16:24:23.944 [info] End refreshing Kernel Picker (1698765861505) 16:24:24.990 [info] ipykernel version & path 6.25.0, /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/ipykernel/__init__.py for /work/Master_Project/miniconda3/envs/singlecell2/bin/python 16:24:26.755 [warn] StdErr from Kernel Process 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 16:24:26.756 [warn] StdErr from Kernel Process 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 16:24:27.072 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2544: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5. warn( 16:24:27.072 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2495: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '8b39c960-d595-4836-9c06-b898c33d95a6' instead of 'b"8b39c960-d595-4836-9c06-b898c33d95a6"'. warn( 16:24:27.854 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/pythonFiles/printJupyterDataDir.py 16:25:38.052 [info] Restart requested /work/Master_Project/bash_scripts/analysis.ipynb 16:25:38.055 [info] Dispose Kernel process 8670. 16:25:38.129 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 36ms 16:25:38.132 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 16:25:38.155 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)" 16:25:38.184 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9008 --control=9006 --hb=9005 --Session.signature_scheme="hmac-sha256" --Session.key=b"c7c3cdb4-1978-4f67-8e0e-f68c75bd9e82" --shell=9007 --transport="tcp" --iopub=9009 --f=~/.local/share/jupyter/runtime/kernel-v2-8212hnF9ye829tQU.json > cwd: /work/Master_Project/bash_scripts 16:25:38.532 [info] ipykernel version & path 6.25.0, /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/ipykernel/__init__.py for /work/Master_Project/miniconda3/envs/singlecell2/bin/python 16:25:39.019 [warn] StdErr from Kernel Process 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 16:25:39.108 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2544: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5. warn( 16:25:39.108 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2495: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use 'c7c3cdb4-1978-4f67-8e0e-f68c75bd9e82' instead of 'b"c7c3cdb4-1978-4f67-8e0e-f68c75bd9e82"'. warn( 16:25:39.237 [info] Restarted 8d0f22ea-992e-4e9c-84c0-e7fc35433b05 16:26:12.167 [info] Handle Execution of Cells 0 for /work/Master_Project/bash_scripts/analysis.ipynb 16:26:12.183 [info] Kernel acknowledged execution of cell 0 @ 1698765972181 16:26:15.343 [info] End cell 0 execution @ 1698765975343, started @ 1698765972181, elapsed time = 3.162s 16:31:43.829 [debug] notebook communications already initialized for editor /work/Master_Project/bash_scripts/analysis.ipynb 16:31:43.830 [info] Start refreshing Interpreter Kernel Picker 16:31:43.831 [info] Start refreshing Kernel Picker (1698766303831) 16:31:43.845 [debug] Full interpreter list is length: 4, /work/Master_Project/miniconda3/bin/python::Conda:/work/Master_Project/miniconda3/bin/python, /bin/python::Unknown:/bin/python, /usr/bin/python::Unknown:/usr/bin/python, /work/Master_Project/miniconda3/envs/singlecell2/bin/python::Conda:/work/Master_Project/miniconda3/envs/singlecell2/bin/python 16:31:43.845 [debug] Refreshed Environments 16:31:44.846 [info] End refreshing Kernel Picker (1698766303831) 16:31:48.682 [debug] Restart kernel command handler for /work/Master_Project/bash_scripts/analysis.ipynb 16:31:49.830 [debug] restart the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:31:49.832 [info] Restart requested /work/Master_Project/bash_scripts/analysis.ipynb 16:31:49.834 [debug] Cancel pending cells 16:31:49.836 [info] Dispose Kernel process 8905. 16:31:49.862 [debug] Kernel Launcher. launch, Class name = ty (started execution), Arg 1: ".jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher", Arg 2: 60000, Arg 3: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 4: "/work/Master_Project/bash_scripts", Arg 5: "" 16:31:49.866 [debug] Getting activated env variables, Class name = za (started execution), Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 16:31:49.866 [debug] Get Custom Env Variables, Class name = Kl (started execution), Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "RunPythonCode" 16:31:49.869 [debug] Get Custom Env Variables, Class name = Kl, completed in 3ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "RunPythonCode" 16:31:49.876 [debug] Disposed Kernel process 8905. 16:31:49.882 [debug] Launching kernel in kernelProcess.ts, Class name = Zv (started execution), Arg 1: "/work/Master_Project/bash_scripts", Arg 2: "" 16:31:49.910 [debug] KernelProcess Exited, Exit Code - undefined 16:31:49.965 [error] Failed to get activated conda env vars for /work/Master_Project/miniconda3/envs/singlecell2/bin/python in 99ms 16:31:49.968 [error] Unable to determine site packages path for python /work/Master_Project/miniconda3/envs/singlecell2/bin/python (Conda) 16:31:49.968 [debug] Prepend PATH with python bin for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is ~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 16:31:49.968 [debug] Activated Env Variables for /work/Master_Project/miniconda3/envs/singlecell2/bin/python, PATH value is /work/Master_Project/miniconda3/envs/singlecell2/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin and Path value is undefined 16:31:49.969 [debug] Getting activated env variables, Class name = za, completed in 103ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 2: "/work/Master_Project/miniconda3/envs/singlecell2/bin/python", Arg 3: undefined 16:31:49.993 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)" 16:31:49.993 [debug] Kernel Env Variables for ~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/temp/jupyter/kernels/pythonjvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589/kernel.json, PATH value is /work/Master_Project/miniconda3/envs/singlecell2/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/bin/remote-cli:~/.local/bin:/usr/lib/code-server/bin:~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 16:31:50.010 [info] Process Execution: /work/Master_Project/miniconda3/envs/singlecell2/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9003 --control=9001 --hb=9000 --Session.signature_scheme="hmac-sha256" --Session.key=b"32685e07-c1dd-4868-a9e1-4a8295c7506c" --shell=9002 --transport="tcp" --iopub=9004 --f=~/.local/share/jupyter/runtime/kernel-v2-8212NvyG5ziL7KVs.json > cwd: /work/Master_Project/bash_scripts 16:31:50.010 [debug] Launching kernel in kernelProcess.ts, Class name = Zv, completed in 128ms, has a truthy return value, Arg 1: "/work/Master_Project/bash_scripts", Arg 2: "" 16:31:50.304 [info] ipykernel version & path 6.25.0, /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/ipykernel/__init__.py for /work/Master_Project/miniconda3/envs/singlecell2/bin/python 16:31:50.813 [debug] KernelProcess error: 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 16:31:50.814 [warn] StdErr from Kernel Process 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 16:31:50.898 [debug] KernelProcess error: /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2544: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5. warn( 16:31:50.899 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2544: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5. warn( 16:31:50.899 [debug] KernelProcess error: /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2495: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '32685e07-c1dd-4868-a9e1-4a8295c7506c' instead of 'b"32685e07-c1dd-4868-a9e1-4a8295c7506c"'. warn( 16:31:50.899 [warn] StdErr from Kernel Process /work/Master_Project/miniconda3/envs/singlecell2/lib/python3.11/site-packages/traitlets/traitlets.py:2495: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '32685e07-c1dd-4868-a9e1-4a8295c7506c' instead of 'b"32685e07-c1dd-4868-a9e1-4a8295c7506c"'. warn( 16:31:50.910 [debug] KernelProcess output: NOTE: When using the `ipython kernel` entry point, Ctrl-C will not work. To exit, you will have to explicitly quit this process, by either sending "quit" from a client, or using Ctrl-\ in UNIX-like environments. To read more about this, see https://github.com/ipython/ipython/issues/2049 To connect another client to this kernel, use: --existing kernel-v2-8212NvyG5ziL7KVs.json 16:31:50.910 [debug] Kernel Output: To connect another client to this kernel, use: --existing kernel-v2-8212NvyG5ziL7KVs.json 16:31:51.020 [debug] Kernel Launcher. launch, Class name = ty, completed in 1158ms, has a truthy return value, Arg 1: ".jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher", Arg 2: 60000, Arg 3: "/work/Master_Project/bash_scripts/analysis.ipynb", Arg 4: "/work/Master_Project/bash_scripts", Arg 5: "" 16:31:51.027 [debug] Waiting for Raw Session to be ready in postStartRawSession 16:31:51.027 [debug] Waiting for Raw session to be ready, currently connected 16:31:51.027 [debug] Raw session connected 16:31:51.027 [debug] Waiting for Raw session to be ready for 30s 16:31:51.027 [debug] Waited for Raw session to be ready & got connected 16:31:51.027 [debug] Successfully waited for Raw Session to be ready in postStartRawSession 16:31:51.027 [debug] Kernel status before requesting kernel info and after ready is unknown 16:31:51.027 [debug] Sending request for kernelInfo 16:31:51.035 [debug] Got response for requestKernelInfo 16:31:51.035 [debug] Successfully completed postStartRawSession 16:31:51.037 [info] Restarted 8d0f22ea-992e-4e9c-84c0-e7fc35433b05 16:31:51.037 [debug] Begin sendTelemetryForPythonKernelExecutable 16:31:51.037 [debug] Executing silently Code (idle) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys 16:31:51.056 [debug] Executing silently Code (completed) = import sys as _VSCODE_sys\nprint(_VSCODE_sys.executable); del _VSCODE_sys with 1 output(s) 16:31:51.057 [debug] End sendTelemetryForPythonKernelExecutable 16:31:51.057 [debug] Started running kernel initialization for /work/Master_Project/bash_scripts/analysis.ipynb 16:31:51.057 [debug] Executing silently Code (idle) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy 16:31:51.068 [debug] Executing silently Code (completed) = try:\nimport ipywidgets as _VSCODE_ipywidgets\nprint("e976ee50-99ed-4aba-9b6b-9dcd5634d07d:IPy with 0 output(s) 16:31:51.069 [debug] Determined IPyWidgets Version as undefined and event fired 16:31:51.071 [debug] Executing silently Code (idle) = import os as _VSCODE_os\nimport sys as _VSCODE_sys\n%cd "//work/Master_Project/bash_scripts"\nif _VSCOD 16:31:51.089 [debug] Executing silently Code (completed) = import os as _VSCODE_os\nimport sys as _VSCODE_sys\n%cd "//work/Master_Project/bash_scripts"\nif _VSCOD with 1 output(s) 16:31:51.090 [debug] Requesting Kernel info 16:31:51.091 [debug] Got Kernel info 16:31:51.091 [debug] End running kernel initialization, now waiting for idle 16:31:51.091 [debug] Waiting for 60000ms idle on (kernel): 8d0f22ea-992e-4e9c-84c0-e7fc35433b05 -> idle 16:31:51.091 [debug] Finished waiting for idle on (kernel): 8d0f22ea-992e-4e9c-84c0-e7fc35433b05 -> idle 16:31:51.091 [debug] End running kernel initialization, session is idle 16:31:51.092 [debug] Registering commtarget jupyter.widget 16:31:58.847 [debug] Updating cache with Local kernels startUsingLocalKernelSpec:'.xonsh./usr/bin/python3././usr/bin/python3#-m#xonsh.jupyter_kernel#-f#{connection_file} (interpreter id = )', Added = , Updated = , Removed = 16:33:40.880 [info] Handle Execution of Cells 0,1,2,4,5,6,7,9,10,11,14,15,16,17,18,20,21,22,23,24 for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.886 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.887 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.888 [debug] start the kernel, options.disableUI=false for /work/Master_Project/bash_scripts/analysis.ipynb 16:33:40.905 [debug] Execution Request Sent to Kernel for cell 0 16:33:40.912 [debug] Start cell 0 execution @ 1698766420911 (clear output) 16:33:40.912 [info] Kernel acknowledged execution of cell 0 @ 1698766420911 16:33:44.004 [info] End cell 0 execution @ 1698766424003, started @ 1698766420911, elapsed time = 3.092s 16:33:44.004 [debug] Execution Request Sent to Kernel for cell 1 16:33:44.004 [debug] Cell 0 executed with state Success 16:33:44.008 [debug] Start cell 1 execution @ 1698766424008 (clear output) 16:33:44.008 [info] Kernel acknowledged execution of cell 1 @ 1698766424008 16:33:44.011 [info] End cell 1 execution @ 1698766424011, started @ 1698766424008, elapsed time = 0.003s 16:33:44.011 [debug] Execution Request Sent to Kernel for cell 2 16:33:44.012 [debug] Cell 1 executed with state Success 16:33:44.015 [debug] Start cell 2 execution @ 1698766424015 (clear output) 16:33:44.015 [info] Kernel acknowledged execution of cell 2 @ 1698766424015 16:33:44.066 [info] End cell 2 execution @ 1698766424065, started @ 1698766424015, elapsed time = 0.05s 16:33:44.066 [debug] Execution Request Sent to Kernel for cell 4 16:33:44.067 [debug] Cell 2 executed with state Success 16:33:44.074 [debug] Start cell 4 execution @ 1698766424074 (clear output) 16:33:44.074 [info] Kernel acknowledged execution of cell 4 @ 1698766424074 16:34:04.140 [info] End cell 4 execution @ 1698766444139, started @ 1698766424074, elapsed time = 20.065s 16:34:04.140 [debug] Execution Request Sent to Kernel for cell 5 16:34:04.142 [debug] Cell 4 executed with state Success 16:34:04.153 [debug] Start cell 5 execution @ 1698766444153 (clear output) 16:34:04.153 [info] Kernel acknowledged execution of cell 5 @ 1698766444153 16:34:04.156 [info] End cell 5 execution @ 1698766444156, started @ 1698766444153, elapsed time = 0.003s 16:34:04.157 [debug] Execution Request Sent to Kernel for cell 6 16:34:04.158 [debug] Cell 5 executed with state Success 16:34:04.165 [debug] Start cell 6 execution @ 1698766444165 (clear output) 16:34:04.165 [info] Kernel acknowledged execution of cell 6 @ 1698766444165 16:34:04.178 [info] End cell 6 execution @ 1698766444178, started @ 1698766444165, elapsed time = 0.013s 16:34:04.179 [debug] Execution Request Sent to Kernel for cell 7 16:34:04.180 [debug] Cell 6 executed with state Success 16:34:04.188 [debug] Start cell 7 execution @ 1698766444188 (clear output) 16:34:04.188 [info] Kernel acknowledged execution of cell 7 @ 1698766444188 16:34:04.207 [info] End cell 7 execution @ 1698766444207, started @ 1698766444188, elapsed time = 0.019s 16:34:04.207 [debug] Execution Request Sent to Kernel for cell 9 16:34:04.208 [debug] Cell 7 executed with state Success 16:34:04.212 [debug] Start cell 9 execution @ 1698766444212 (clear output) 16:34:04.212 [info] Kernel acknowledged execution of cell 9 @ 1698766444212 16:34:05.548 [info] End cell 9 execution @ 1698766445547, started @ 1698766444212, elapsed time = 1.335s 16:34:05.549 [debug] Execution Request Sent to Kernel for cell 10 16:34:05.550 [debug] Cell 9 executed with state Success 16:34:05.558 [debug] Start cell 10 execution @ 1698766445558 (clear output) 16:34:05.559 [info] Kernel acknowledged execution of cell 10 @ 1698766445558 16:34:08.890 [info] End cell 10 execution @ 1698766448890, started @ 1698766445558, elapsed time = 3.332s 16:34:08.890 [debug] Execution Request Sent to Kernel for cell 11 16:34:08.890 [debug] Cell 10 executed with state Success 16:34:08.895 [debug] Start cell 11 execution @ 1698766448895 (clear output) 16:34:08.895 [info] Kernel acknowledged execution of cell 11 @ 1698766448895 16:34:11.654 [info] End cell 11 execution @ 1698766451654, started @ 1698766448895, elapsed time = 2.759s 16:34:11.655 [debug] Execution Request Sent to Kernel for cell 14 16:34:11.655 [debug] Cell 11 executed with state Success 16:34:11.674 [debug] Start cell 14 execution @ 1698766451673 (clear output) 16:34:11.674 [info] Kernel acknowledged execution of cell 14 @ 1698766451673 16:34:11.678 [info] End cell 14 execution @ 1698766451678, started @ 1698766451673, elapsed time = 0.005s 16:34:11.679 [debug] Execution Request Sent to Kernel for cell 15 16:34:11.680 [debug] Cell 14 executed with state Success 16:34:11.687 [debug] Start cell 15 execution @ 1698766451687 (clear output) 16:34:11.687 [info] Kernel acknowledged execution of cell 15 @ 1698766451687 16:34:19.664 [info] End cell 15 execution @ 1698766459664, started @ 1698766451687, elapsed time = 7.977s 16:34:19.664 [debug] Execution Request Sent to Kernel for cell 16 16:34:19.665 [debug] Cell 15 executed with state Success 16:34:19.672 [debug] Start cell 16 execution @ 1698766459672 (clear output) 16:34:19.672 [info] Kernel acknowledged execution of cell 16 @ 1698766459672 16:34:19.675 [info] End cell 16 execution @ 1698766459675, started @ 1698766459672, elapsed time = 0.003s 16:34:19.676 [debug] Execution Request Sent to Kernel for cell 17 16:34:19.677 [debug] Cell 16 executed with state Success 16:34:19.682 [debug] Start cell 17 execution @ 1698766459682 (clear output) 16:34:19.682 [info] Kernel acknowledged execution of cell 17 @ 1698766459682 16:34:19.698 [info] End cell 17 execution @ 1698766459698, started @ 1698766459682, elapsed time = 0.016s 16:34:19.698 [debug] Execution Request Sent to Kernel for cell 18 16:34:19.699 [debug] Cell 17 executed with state Success 16:34:19.702 [debug] Start cell 18 execution @ 1698766459701 (clear output) 16:34:19.702 [info] Kernel acknowledged execution of cell 18 @ 1698766459701 16:34:19.749 [info] End cell 18 execution @ 1698766459748, started @ 1698766459701, elapsed time = 0.047s 16:34:19.750 [debug] Execution Request Sent to Kernel for cell 20 16:34:19.752 [debug] Cell 18 executed with state Success 16:34:19.759 [debug] Start cell 20 execution @ 1698766459759 (clear output) 16:34:19.759 [info] Kernel acknowledged execution of cell 20 @ 1698766459759 16:34:19.770 [info] End cell 20 execution @ 1698766459770, started @ 1698766459759, elapsed time = 0.011s 16:34:19.771 [debug] Execution Request Sent to Kernel for cell 21 16:34:19.771 [debug] Cell 20 executed with state Success 16:34:19.779 [debug] Start cell 21 execution @ 1698766459779 (clear output) 16:34:19.779 [info] Kernel acknowledged execution of cell 21 @ 1698766459779 16:34:21.759 [info] End cell 21 execution @ 1698766461759, started @ 1698766459779, elapsed time = 1.98s 16:34:21.760 [debug] Execution Request Sent to Kernel for cell 22 16:34:21.761 [debug] Cell 21 executed with state Success 16:34:21.774 [debug] Start cell 22 execution @ 1698766461774 (clear output) 16:34:21.774 [info] Kernel acknowledged execution of cell 22 @ 1698766461774 16:34:21.779 [info] End cell 22 execution @ 1698766461778, started @ 1698766461774, elapsed time = 0.004s 16:34:21.779 [debug] Execution Request Sent to Kernel for cell 23 16:34:21.779 [debug] Cell 22 executed with state Success 16:34:21.785 [debug] Start cell 23 execution @ 1698766461785 (clear output) 16:34:21.785 [info] Kernel acknowledged execution of cell 23 @ 1698766461785 16:34:21.814 [info] End cell 23 execution @ 1698766461814, started @ 1698766461785, elapsed time = 0.029s 16:34:21.815 [debug] Start cell 24 execution @ undefined (clear output) 16:34:21.815 [info] End cell 24 execution @ undefined, started @ undefined, elapsed time = 0s 16:34:21.815 [debug] Cell 23 executed with state Success 16:34:21.816 [debug] Cell 24 executed with state Idle 16:34:38.812 [debug] Disposing request as the cell was deleted /work/Master_Project/bash_scripts/analysis.ipynb 16:34:38.812 [info] Dispose Kernel '/work/Master_Project/bash_scripts/analysis.ipynb' associated with '/work/Master_Project/bash_scripts/analysis.ipynb' 16:34:38.812 [debug] Cancel pending cells 16:34:38.813 [debug] Shutdown session 8d0f22ea-992e-4e9c-84c0-e7fc35433b05, .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher - start called from Error: at xy.shutdown (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:24:123857) at xy.disposeAsync (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:24:123279) at ~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:17:236128 at Qg.dispose (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:17:236342) at pv.disposeOldKernel (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:17:228606) at pv. (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:17:226939)
at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.A (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1972)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2188)
at Oc. (~/.vscode-server/extensions/ms-toolsai.jupyter-2023.9.1102792234-linux-x64/out/extension.node.js:2:2352412)
at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.A (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1972)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2188)
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at i.S (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:135:10827)
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at i.M (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:135:9683)
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at s.value (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:135:7565)
at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2119)
at g.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:96:14010)
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at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2119)
at g.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:96:14010)
at r.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:96:17075)
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at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2119)
at s.acceptChunk (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:96:11784)
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at c.z (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:1902)
at c.fire (~/.vscode-server/bin/f1b07bd25dfad64b0167beb15359ae573aecd2cc/out/vs/workbench/api/node/extensionHostProcess.js:80:2119)
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16:34:38.813 [info] Dispose Kernel process 9081.
16:34:38.831 [debug] Kernel got disposed, hence there is no longer a kernel associated with /work/Master_Project/bash_scripts/analysis.ipynb
16:34:38.836 [debug] Cancel executions after closing notebook /work/Master_Project/bash_scripts/analysis.ipynb
16:34:38.836 [debug] Cancel executions after closing notebook /work/Master_Project/bash_scripts/analysis.ipynb
16:34:38.841 [debug] Shutdown session 8d0f22ea-992e-4e9c-84c0-e7fc35433b05, .jvsc74a57bd0642515480be6c57b33e96e50f66250cab74fdf12f6be7d10bb335971f436f589./work/Master_Project/miniconda3/envs/singlecell2/python./work/Master_Project/miniconda3/envs/singlecell2/python.-m#ipykernel_launcher - shutdown complete
16:34:38.846 [debug] Disposed Kernel process 9081.
16:34:39.165 [debug] KernelProcess Exited, Exit Code - undefined