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arayabrain / barebone-studio

pipeline tool
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Freeze on suite2p_registration with docker #365

Open milesAraya opened 5 months ago

milesAraya commented 5 months ago

追加機能についての概要 Fails when using suite2p_registration. Reproduction steps:

1. git checkout develop-main
2. docker compose -f docker-compose.dev.yml up
3. “Documentation” -> “Import sample data”
4. RECORD “Reproduce” tutorial1
5. “RUN ALL”

Error message:

2024-06-25 18:00:40,806 : ERROR - smk_status_logger.py - {'level': 'debug', 'msg': 'Full Traceback (most recent call last):\n File "/usr/local/lib/python3.8/site-packages/snakemake/executors/init.py", line 2561, in run_wrapper\n run(\n File "/app/studio/app/Snakefile", line 101, in __rule_4\n File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 1567, in script\n executor.evaluate()\n File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 455, in evaluate\n self.execute_script(fd.name, edit=edit)\n File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 683, in execute_script\n self._execute_cmd(\n File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 486, in _executecmd\n return shell(\n File "/usr/local/lib/python3.8/site-packages/snakemake/shell.py", line 294, in new\n raise sp.CalledProcessError(retcode, cmd)\nsubprocess.CalledProcessError: Command \'source /opt/miniconda3/bin/activate \'/app/.snakemake/conda/0f05ef6e0614bb486f644bea8d4b33d4\'; set -euo pipefail; python /app/.snakemake/scripts/tmp8_ru4hde.func.py\' died with <Signals.SIGSEGV: 11>.\n', 'timestamp': 1719306040.8063872}

Terminal log from 1st occurance

studio.log from 2nd occurance

重要度 中: この機能は開発要件に含まれているが、早急に対応する必要はない。

ブランチ名 feature/update-multiuser-settings develop-main

その他 caiman_mc is working.

環境: Test case spreadsheet: Link

Native steps:

1. RECORD “Reproduce” tutorial1
2. “RUN ALL”

Image

milesAraya commented 5 months ago

Docker version

docker version Version: 26.1.4 API version: 1.45 Go version: go1.21.11 Git commit: 5650f9b Built: Wed Jun 5 11:26:02 2024 OS/Arch: darwin/arm64 Context: desktop-linux Server: Docker Desktop 4.31.0 (153195) Engine: Version: 26.1.4 API version: 1.45 (minimum version 1.24) Go version: go1.21.11 Git commit: de5c9cf Built: Wed Jun 5 11:29:12 2024 OS/Arch: linux/arm64 Experimental: false containerd: Version: 1.6.33 GitCommit: d2d58213f83a351ca8f528a95fbd145f5654e957 runc: Version: 1.1.12 GitCommit: v1.1.12-0-g51d5e94 docker-init: Version: 0.19.0 GitCommit: de40ad0

docker snakemake conda env for suite2p_registration

docker compose -f docker-compose.dev.yml up tutorial1 reproduce Find snakemake env for suite2p:

studio-dev-be-1 | Activating conda environment: .snakemake/conda/0f05ef6e0614bb486f644bea8d4b33d4_

docker exec -it barebone-studio-studio-dev-be-1 /bin/bash conda activate /app/.snakemake/conda/0f05ef6e0614bb486f644bea8d4b33d4_ Check the log for the conda env ID conda list

Name Version Build Channel _libgcc_mutex 0.1 main _openmp_mutex 5.1 1_gnu bcrypt 4.1.3 pypi_0 pypi ca-certificates 2024.3.11 h06a4308_0 cffi 1.16.0 pypi_0 pypi contourpy 1.1.1 pypi_0 pypi cryptography 42.0.8 pypi_0 pypi cycler 0.12.1 pypi_0 pypi filelock 3.15.4 pypi_0 pypi fonttools 4.53.0 pypi_0 pypi fsspec 2024.6.1 pypi_0 pypi h5py 3.11.0 pypi_0 pypi importlib-metadata 8.0.0 pypi_0 pypi importlib-resources 6.4.0 pypi_0 pypi jinja2 3.1.4 pypi_0 pypi joblib 1.4.2 pypi_0 pypi kiwisolver 1.4.5 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1 libffi 3.4.4 h6a678d5_1 libgcc-ng 11.2.0 h1234567_1 libgomp 11.2.0 h1234567_1 libstdcxx-ng 11.2.0 h1234567_1 llvmlite 0.41.1 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.7.5 pypi_0 pypi mpmath 1.3.0 pypi_0 pypi natsort 8.4.0 pypi_0 pypi ncurses 6.4 h6a678d5_0 networkx 3.1 pypi_0 pypi numba 0.58.1 pypi_0 pypi numpy 1.23.5 pypi_0 pypi nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi nvidia-curand-cu12 10.3.2.106 pypi_0 pypi nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi nvidia-nccl-cu12 2.20.5 pypi_0 pypi nvidia-nvjitlink-cu12 12.5.40 pypi_0 pypi nvidia-nvtx-cu12 12.1.105 pypi_0 pypi openssl 3.0.14 h5eee18b_0 packaging 24.1 pypi_0 pypi pandas 1.5.3 pypi_0 pypi paramiko 3.4.0 pypi_0 pypi pillow 10.3.0 pypi_0 pypi pip 24.0 py38h06a4308_0 pycparser 2.22 pypi_0 pypi pynacl 1.5.0 pypi_0 pypi pyparsing 3.1.2 pypi_0 pypi pyqt5 5.15.9 pypi_0 pypi pyqt5-qt5 5.15.2 pypi_0 pypi pyqt5-sip 12.11.1 pypi_0 pypi pyqtgraph 0.12.4 pypi_0 pypi python 3.8.19 h955ad1f_0 python-dateutil 2.9.0.post0 pypi_0 pypi pytz 2024.1 pypi_0 pypi rastermap 0.1.3 pypi_0 pypi readline 8.2 h5eee18b_0 sbxreader 0.2.2 pypi_0 pypi scanimage-tiff-reader 1.4.1.4 pypi_0 pypi scikit-learn 1.3.2 pypi_0 pypi scipy 1.10.1 pypi_0 pypi setuptools 69.5.1 py38h06a4308_0 six 1.16.0 pypi_0 pypi sqlite 3.45.3 h5eee18b_0 suite2p 0.10.3 pypi_0 pypi sympy 1.12.1 pypi_0 pypi threadpoolctl 3.5.0 pypi_0 pypi tifffile 2022.3.25 pypi_0 pypi tk 8.6.14 h39e8969_0 torch 2.3.1 pypi_0 pypi triton 2.3.1 pypi_0 pypi typing-extensions 4.12.2 pypi_0 pypi wheel 0.43.0 py38h06a4308_0 xz 5.4.6 h5eee18b_1 zipp 3.19.2 pypi_0 pypi zlib 1.2.13 h5eee18b_1

milesAraya commented 3 months ago

Dockerのlog:


> 2024-08-22 15:31:09 Skipping virtualenv creation, as specified in config file.
> 2024-08-22 15:31:26 2024-08-22 15:31:26,147 INFO:     [uvicorn.error] __init__():339 - Will watch for changes in these directories: ['/app/studio']
> 2024-08-22 15:31:26 2024-08-22 15:31:26,148 INFO:     [uvicorn.error] bind_socket():571 - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
> 2024-08-22 15:31:26 2024-08-22 15:31:26,149 INFO:     [uvicorn.error] startup():77 - Started reloader process [1] using StatReload
> 2024-08-22 15:31:36 2024-08-22 15:31:36,365 INFO:     [uvicorn.error] serve():76 - Started server process [27]
> 2024-08-22 15:31:36 2024-08-22 15:31:36,365 INFO:     [uvicorn.error] startup():46 - Waiting for application startup.
> 2024-08-22 15:31:36 2024-08-22 15:31:36,374 INFO:     [optinist] startup_event():95 - "Studio" application startup complete. [mode: standalone]
> 2024-08-22 15:31:36 2024-08-22 15:31:36,375 INFO:     [uvicorn.error] startup():60 - Application startup complete.
> 2024-08-22 15:32:56 2024-08-22 15:32:56,505 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60346 - "GET /js/main.7a24960b.js HTTP/1.1" 200
> 2024-08-22 15:32:57 2024-08-22 15:32:57,453 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60346 - "GET /is_standalone HTTP/1.1" 200
> 2024-08-22 15:32:57 2024-08-22 15:32:57,609 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60352 - "GET /algolist HTTP/1.1" 200
> 2024-08-22 15:32:57 2024-08-22 15:32:57,887 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60366 - "GET /workflow/fetch/1 HTTP/1.1" 200
> 2024-08-22 15:32:57 2024-08-22 15:32:57,889 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60346 - "GET /media/logo.e44efe3246aecc6d6219.png HTTP/1.1" 200
> 2024-08-22 15:32:58 2024-08-22 15:32:58,255 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60346 - "GET /experiments/1 HTTP/1.1" 200
> 2024-08-22 15:33:29 2024-08-22 15:33:29,185 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60890 - "GET /params/suite2p_file_convert HTTP/1.1" 200
> 2024-08-22 15:33:40 2024-08-22 15:33:40,405 INFO:     [optinist] run_id():44 - run snakemake
> 2024-08-22 15:33:40 2024-08-22 15:33:40,405 INFO:     [optinist] run_id():45 - forcerun list: [ForceRun(nodeId='suite2p_file_convert_tjmj285n2r', name='suite2p_file_convert')]
> 2024-08-22 15:33:40 2024-08-22 15:33:40,408 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60646 - "POST /run/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:33:40 2024-08-22 15:33:40,552 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60646 - "GET /experiments/1 HTTP/1.1" 200
> 2024-08-22 15:33:41 Building DAG of jobs...
> 2024-08-22 15:33:41 2024-08-22 15:33:41,919 WARNING:  [snakemake.logging] text_handler():578 - Building DAG of jobs...
> 2024-08-22 15:33:44 Using shell: /usr/bin/bash
> 2024-08-22 15:33:44 2024-08-22 15:33:44,930 WARNING:  [snakemake.logging] text_handler():578 - Using shell: /usr/bin/bash
> 2024-08-22 15:33:44 Provided cores: 2
> 2024-08-22 15:33:44 2024-08-22 15:33:44,933 WARNING:  [snakemake.logging] text_handler():586 - Provided cores: 2
> 2024-08-22 15:33:44 Rules claiming more threads will be scaled down.
> 2024-08-22 15:33:44 2024-08-22 15:33:44,935 WARNING:  [snakemake.logging] text_handler():586 - Rules claiming more threads will be scaled down.
> 2024-08-22 15:33:44 Job stats:
> 2024-08-22 15:33:44 job                                count    min threads    max threads
> 2024-08-22 15:33:44 -------------------------------  -------  -------------  -------------
> 2024-08-22 15:33:44 all                                    1              1              1
> 2024-08-22 15:33:44 suite2p_file_convert_tjmj285n2r        1              1              1
> 2024-08-22 15:33:44 total                                  2              1              1
> 2024-08-22 15:33:44 
> 2024-08-22 15:33:44 2024-08-22 15:33:44,966 WARNING:  [snakemake.logging] text_handler():588 - Job stats:
> 2024-08-22 15:33:44 job                                count    min threads    max threads
> 2024-08-22 15:33:44 -------------------------------  -------  -------------  -------------
> 2024-08-22 15:33:44 all                                    1              1              1
> 2024-08-22 15:33:44 suite2p_file_convert_tjmj285n2r        1              1              1
> 2024-08-22 15:33:44 total                                  2              1              1
> 2024-08-22 15:33:44 
> 2024-08-22 15:33:44 Select jobs to execute...
> 2024-08-22 15:33:44 2024-08-22 15:33:44,967 WARNING:  [snakemake.logging] text_handler():578 - Select jobs to execute...
> 2024-08-22 15:33:45 
> 2024-08-22 15:33:45 2024-08-22 15:33:45,009 INFO:     [snakemake.logging] text_handler():496 - 
> 2024-08-22 15:33:45 [Thu Aug 22 15:33:45 2024]
> 2024-08-22 15:33:45 2024-08-22 15:33:45,014 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:33:45 2024]
> 2024-08-22 15:33:45 rule suite2p_file_convert_tjmj285n2r:
> 2024-08-22 15:33:45     input: /app/studio_data/output/1/tutorial2/input_0/sample_mouse2p_image.pkl
> 2024-08-22 15:33:45     output: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:33:45     jobid: 1
> 2024-08-22 15:33:45     reason: Missing output files: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:33:45     resources: tmpdir=/tmp
> 2024-08-22 15:33:45 2024-08-22 15:33:45,016 INFO:     [snakemake.logging] text_handler():503 - rule suite2p_file_convert_tjmj285n2r:
> 2024-08-22 15:33:45     input: /app/studio_data/output/1/tutorial2/input_0/sample_mouse2p_image.pkl
> 2024-08-22 15:33:45     output: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:33:45     jobid: 1
> 2024-08-22 15:33:45     reason: Missing output files: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:33:45     resources: tmpdir=/tmp
> 2024-08-22 15:33:45 
> 2024-08-22 15:33:45 2024-08-22 15:33:45,020 INFO:     [snakemake.logging] text_handler():510 - 
> 2024-08-22 15:33:45 2024-08-22 15:33:45,579 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61634 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:33:45 Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:33:45 2024-08-22 15:33:45,623 WARNING:  [snakemake.logging] text_handler():578 - Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:33:47 Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:33:47 2024-08-22 15:33:47,638 WARNING:  [snakemake.logging] text_handler():578 - Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:33:50 2024-08-22 15:33:50,830 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61642 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:33:55 2024-08-22 15:33:55,610 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55436 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:01 2024-08-22 15:34:01,934 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55440 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:05 2024-08-22 15:34:05,477 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55508 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:10 2024-08-22 15:34:10,464 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55520 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:15 2024-08-22 15:34:15,562 INFO:     [uvicorn.access] send():478 - 172.18.0.1:62250 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:20 2024-08-22 15:34:20,781 INFO:     [uvicorn.access] send():478 - 172.18.0.1:62264 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:25 2024-08-22 15:34:25,482 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55018 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:30 2024-08-22 15:34:30,561 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55020 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:35 2024-08-22 15:34:35,431 INFO:     [optinist] run():32 - start rule runner
> 2024-08-22 15:34:35 2024-08-22 15:34:35,494 INFO:     [uvicorn.access] send():478 - 172.18.0.1:57878 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:40 2024-08-22 15:34:40,526 INFO:     [uvicorn.access] send():478 - 172.18.0.1:57886 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:45 2024-08-22 15:34:45,525 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60926 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:50 2024-08-22 15:34:50,545 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60938 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:34:55 2024-08-22 15:34:55,500 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60108 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:01 2024-08-22 15:35:01,098 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60110 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:05 2024-08-22 15:35:05,496 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61214 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:10 2024-08-22 15:35:10,507 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61228 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:15 2024-08-22 15:35:15,800 INFO:     [uvicorn.access] send():478 - 172.18.0.1:63924 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:20 2024-08-22 15:35:20,563 INFO:     [uvicorn.access] send():478 - 172.18.0.1:63936 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:25 2024-08-22 15:35:25,810 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55978 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:30 2024-08-22 15:35:30,589 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55992 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:34 /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_/lib/python3.8/site-packages/paramiko/pkey.py:100: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.
> 2024-08-22 15:35:34   "cipher": algorithms.TripleDES,
> 2024-08-22 15:35:34 /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_/lib/python3.8/site-packages/paramiko/transport.py:259: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.
> 2024-08-22 15:35:34   "class": algorithms.TripleDES,
> 2024-08-22 15:35:34 2024-08-22 15:35:34,115 INFO:     [optinist] suite2p_file_convert():24 - start suite2p_file_convert: suite2p_file_convert_tjmj285n2r
> 2024-08-22 15:35:35 2024-08-22 15:35:35,653 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61196 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:40 2024-08-22 15:35:40,573 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61202 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:45 2024-08-22 15:35:45,544 INFO:     [uvicorn.access] send():478 - 172.18.0.1:57688 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:49 2024-08-22 15:35:49,782 INFO:     [optinist] suite2p_file_convert():51 - ['/app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r']
> 2024-08-22 15:35:49 2024-08-22 15:35:49,784 INFO:     [optinist] suite2p_file_convert():52 - ['sample_mouse2p_image.tiff']
> 2024-08-22 15:35:50 2024-08-22 15:35:50,537 INFO:     [uvicorn.access] send():478 - 172.18.0.1:57700 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:55 2024-08-22 15:35:55,537 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60888 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:35:57 2024-08-22 15:35:57,809 INFO:     [optinist] run():74 - rule output: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:03 2024-08-22 15:36:03,399 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60898 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:36:03 2024-08-22 15:36:03,627 INFO:     [uvicorn.access] send():478 - 172.18.0.1:60898 - "GET /experiments/1 HTTP/1.1" 200
> 2024-08-22 15:36:04 [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 2024-08-22 15:36:04,496 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 Finished job 1.
> 2024-08-22 15:36:04 2024-08-22 15:36:04,546 INFO:     [snakemake.logging] text_handler():602 - Finished job 1.
> 2024-08-22 15:36:04 1 of 2 steps (50%) done
> 2024-08-22 15:36:04 2024-08-22 15:36:04,562 INFO:     [snakemake.logging] text_handler():592 - 1 of 2 steps (50%) done
> 2024-08-22 15:36:04 Select jobs to execute...
> 2024-08-22 15:36:04 2024-08-22 15:36:04,566 WARNING:  [snakemake.logging] text_handler():578 - Select jobs to execute...
> 2024-08-22 15:36:04 
> 2024-08-22 15:36:04 2024-08-22 15:36:04,579 INFO:     [snakemake.logging] text_handler():496 - 
> 2024-08-22 15:36:04 [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 2024-08-22 15:36:04,582 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 localrule all:
> 2024-08-22 15:36:04     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:04     jobid: 0
> 2024-08-22 15:36:04     reason: Input files updated by another job: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:04     resources: tmpdir=/tmp
> 2024-08-22 15:36:04 2024-08-22 15:36:04,587 INFO:     [snakemake.logging] text_handler():503 - localrule all:
> 2024-08-22 15:36:04     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:04     jobid: 0
> 2024-08-22 15:36:04     reason: Input files updated by another job: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:04     resources: tmpdir=/tmp
> 2024-08-22 15:36:04 
> 2024-08-22 15:36:04 2024-08-22 15:36:04,598 INFO:     [snakemake.logging] text_handler():510 - 
> 2024-08-22 15:36:04 [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 2024-08-22 15:36:04,605 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:36:04 2024]
> 2024-08-22 15:36:04 Finished job 0.
> 2024-08-22 15:36:04 2024-08-22 15:36:04,607 INFO:     [snakemake.logging] text_handler():602 - Finished job 0.
> 2024-08-22 15:36:04 2 of 2 steps (100%) done
> 2024-08-22 15:36:04 2024-08-22 15:36:04,611 INFO:     [snakemake.logging] text_handler():592 - 2 of 2 steps (100%) done
> 2024-08-22 15:36:04 Complete log: .snakemake/log/2024-08-22T153340.624227.snakemake.log
> 2024-08-22 15:35:57 Warning: cellpose did not import
> 2024-08-22 15:35:57 No module named 'cellpose'
> 2024-08-22 15:35:57 cannot use anatomical mode, but otherwise suite2p will run normally
> 2024-08-22 15:35:57 NOTE: ScanImageTiffReader not working for this tiff type, using tifffile
> 2024-08-22 15:35:57 tif
> 2024-08-22 15:35:57 ** Found 1 tifs - converting to binary **
> 2024-08-22 15:35:57 2000 frames of binary, time 5.74 sec.
> 2024-08-22 15:36:04 2024-08-22 15:36:04,682 WARNING:  [snakemake.logging] text_handler():578 - Complete log: .snakemake/log/2024-08-22T153340.624227.snakemake.log
> 2024-08-22 15:36:09 2024-08-22 15:36:09,229 INFO:     [uvicorn.access] send():478 - 172.18.0.1:64428 - "GET /params/suite2p_registration HTTP/1.1" 200
> 2024-08-22 15:36:16 2024-08-22 15:36:16,913 INFO:     [optinist] run_id():44 - run snakemake
> 2024-08-22 15:36:16 2024-08-22 15:36:16,914 INFO:     [optinist] run_id():45 - forcerun list: [ForceRun(nodeId='suite2p_registration_9ho5xvv9qn', name='suite2p_registration')]
> 2024-08-22 15:36:16 2024-08-22 15:36:16,916 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61364 - "POST /run/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:36:17 2024-08-22 15:36:17,098 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61364 - "GET /experiments/1 HTTP/1.1" 200
> 2024-08-22 15:36:17 Building DAG of jobs...
> 2024-08-22 15:36:17 2024-08-22 15:36:17,844 WARNING:  [snakemake.logging] text_handler():578 - Building DAG of jobs...
> 2024-08-22 15:36:18 Using shell: /usr/bin/bash
> 2024-08-22 15:36:18 2024-08-22 15:36:18,013 WARNING:  [snakemake.logging] text_handler():578 - Using shell: /usr/bin/bash
> 2024-08-22 15:36:18 Provided cores: 2
> 2024-08-22 15:36:18 2024-08-22 15:36:18,015 WARNING:  [snakemake.logging] text_handler():586 - Provided cores: 2
> 2024-08-22 15:36:18 Rules claiming more threads will be scaled down.
> 2024-08-22 15:36:18 2024-08-22 15:36:18,018 WARNING:  [snakemake.logging] text_handler():586 - Rules claiming more threads will be scaled down.
> 2024-08-22 15:36:18 Job stats:
> 2024-08-22 15:36:18 job                                count    min threads    max threads
> 2024-08-22 15:36:18 -------------------------------  -------  -------------  -------------
> 2024-08-22 15:36:18 all                                    1              1              1
> 2024-08-22 15:36:18 suite2p_registration_9ho5xvv9qn        1              1              1
> 2024-08-22 15:36:18 total                                  2              1              1
> 2024-08-22 15:36:18 
> 2024-08-22 15:36:18 2024-08-22 15:36:18,034 WARNING:  [snakemake.logging] text_handler():588 - Job stats:
> 2024-08-22 15:36:18 job                                count    min threads    max threads
> 2024-08-22 15:36:18 -------------------------------  -------  -------------  -------------
> 2024-08-22 15:36:18 all                                    1              1              1
> 2024-08-22 15:36:18 suite2p_registration_9ho5xvv9qn        1              1              1
> 2024-08-22 15:36:18 total                                  2              1              1
> 2024-08-22 15:36:18 
> 2024-08-22 15:36:18 Select jobs to execute...
> 2024-08-22 15:36:18 2024-08-22 15:36:18,036 WARNING:  [snakemake.logging] text_handler():578 - Select jobs to execute...
> 2024-08-22 15:36:18 
> 2024-08-22 15:36:18 2024-08-22 15:36:18,042 INFO:     [snakemake.logging] text_handler():496 - 
> 2024-08-22 15:36:18 [Thu Aug 22 15:36:18 2024]
> 2024-08-22 15:36:18 2024-08-22 15:36:18,045 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:36:18 2024]
> 2024-08-22 15:36:18 rule suite2p_registration_9ho5xvv9qn:
> 2024-08-22 15:36:18     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:18     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:36:18     jobid: 1
> 2024-08-22 15:36:18     reason: Missing output files: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:36:18     resources: tmpdir=/tmp
> 2024-08-22 15:36:18 2024-08-22 15:36:18,051 INFO:     [snakemake.logging] text_handler():503 - rule suite2p_registration_9ho5xvv9qn:
> 2024-08-22 15:36:18     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:36:18     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:36:18     jobid: 1
> 2024-08-22 15:36:18     reason: Missing output files: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:36:18     resources: tmpdir=/tmp
> 2024-08-22 15:36:18 
> 2024-08-22 15:36:18 2024-08-22 15:36:18,063 INFO:     [snakemake.logging] text_handler():510 - 
> 2024-08-22 15:36:18 Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:36:18 2024-08-22 15:36:18,165 WARNING:  [snakemake.logging] text_handler():578 - Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:36:20 Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:36:20 2024-08-22 15:36:20,026 WARNING:  [snakemake.logging] text_handler():578 - Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:36:55 2024-08-22 15:36:55,754 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61370 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:36:59 2024-08-22 15:36:59,288 INFO:     [uvicorn.access] send():478 - 172.18.0.1:61370 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:04 2024-08-22 15:37:04,274 INFO:     [uvicorn.access] send():478 - 172.18.0.1:56920 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:09 2024-08-22 15:37:09,165 INFO:     [uvicorn.access] send():478 - 172.18.0.1:58198 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:14 2024-08-22 15:37:14,171 INFO:     [uvicorn.access] send():478 - 172.18.0.1:58208 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:17 2024-08-22 15:37:17,226 INFO:     [optinist] run():32 - start rule runner
> 2024-08-22 15:37:19 2024-08-22 15:37:19,266 INFO:     [uvicorn.access] send():478 - 172.18.0.1:63682 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:24 2024-08-22 15:37:24,234 INFO:     [uvicorn.access] send():478 - 172.18.0.1:63686 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:29 2024-08-22 15:37:29,458 INFO:     [uvicorn.access] send():478 - 172.18.0.1:56784 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:34 2024-08-22 15:37:34,249 INFO:     [uvicorn.access] send():478 - 172.18.0.1:56796 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:39 2024-08-22 15:37:39,218 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55250 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:44 2024-08-22 15:37:44,202 INFO:     [uvicorn.access] send():478 - 172.18.0.1:55258 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:45 /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_/lib/python3.8/site-packages/paramiko/pkey.py:100: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.
> 2024-08-22 15:37:45   "cipher": algorithms.TripleDES,
> 2024-08-22 15:37:45 /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_/lib/python3.8/site-packages/paramiko/transport.py:259: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.
> 2024-08-22 15:37:45   "class": algorithms.TripleDES,
> 2024-08-22 15:37:45 2024-08-22 15:37:45,004 INFO:     [optinist] suite2p_registration():15 - start suite2p registration: suite2p_registration_9ho5xvv9qn
> 2024-08-22 15:37:45 2024-08-22 15:37:45,801 ERROR:    [tutorial2] smk_logger():91 - {'level': 'debug', 'msg': 'Full Traceback (most recent call last):\n  File "/usr/local/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2561, in run_wrapper\n    run(\n  File "/app/studio/app/Snakefile", line 101, in __rule_4\n  File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 1567, in script\n    executor.evaluate()\n  File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 455, in evaluate\n    self.execute_script(fd.name, edit=edit)\n  File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 683, in execute_script\n    self._execute_cmd(\n  File "/usr/local/lib/python3.8/site-packages/snakemake/script.py", line 486, in _execute_cmd\n    return shell(\n  File "/usr/local/lib/python3.8/site-packages/snakemake/shell.py", line 294, in __new__\n    raise sp.CalledProcessError(retcode, cmd)\nsubprocess.CalledProcessError: Command \'source /opt/miniconda3/bin/activate \'/app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_\'; set -euo pipefail;  python /app/.snakemake/scripts/tmpdm4fofqg.func.py\' died with <Signals.SIGSEGV: 11>.\n', 'timestamp': 1724308665.799362}
> 2024-08-22 15:37:45 [Thu Aug 22 15:37:45 2024]
> 2024-08-22 15:37:45 2024-08-22 15:37:45,816 INFO:     [snakemake.logging] timestamp():490 - [Thu Aug 22 15:37:45 2024]
> 2024-08-22 15:37:45 Error in rule suite2p_registration_9ho5xvv9qn:
> 2024-08-22 15:37:45     jobid: 1
> 2024-08-22 15:37:45     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:37:45     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:37:45     conda-env: /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:37:45 
> 2024-08-22 15:37:45 2024-08-22 15:37:45,819 ERROR:    [snakemake.logging] text_handler():550 - Error in rule suite2p_registration_9ho5xvv9qn:
> 2024-08-22 15:37:45     jobid: 1
> 2024-08-22 15:37:45     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
> 2024-08-22 15:37:45     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
> 2024-08-22 15:37:45     conda-env: /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 2024-08-22 15:37:45 
> 2024-08-22 15:37:45 Shutting down, this might take some time.
> 2024-08-22 15:37:45 2024-08-22 15:37:45,843 WARNING:  [snakemake.logging] text_handler():578 - Shutting down, this might take some time.
> 2024-08-22 15:37:45 Exiting because a job execution failed. Look above for error message
> 2024-08-22 15:37:45 2024-08-22 15:37:45,845 ERROR:    [snakemake.logging] text_handler():582 - Exiting because a job execution failed. Look above for error message
> 2024-08-22 15:37:45 Complete log: .snakemake/log/2024-08-22T153616.981367.snakemake.log
> 2024-08-22 15:37:45 2024-08-22 15:37:45,869 WARNING:  [snakemake.logging] text_handler():578 - Complete log: .snakemake/log/2024-08-22T153616.981367.snakemake.log
> 2024-08-22 15:37:49 2024-08-22 15:37:49,195 INFO:     [uvicorn.access] send():478 - 172.18.0.1:56796 - "POST /run/result/1/tutorial2 HTTP/1.1" 200
> 2024-08-22 15:37:49 2024-08-22 15:37:49,354 INFO:     [uvicorn.access] send():478 - 172.18.0.1:56796 - "GET /experiments/1 HTTP/1.1" 200

Snakemake log:


> Building DAG of jobs...
> Using shell: /usr/bin/bash
> Provided cores: 2
> Rules claiming more threads will be scaled down.
> Job stats:
> job                                count    min threads    max threads
> -------------------------------  -------  -------------  -------------
> all                                    1              1              1
> suite2p_registration_9ho5xvv9qn        1              1              1
> total                                  2              1              1
> 
> Select jobs to execute...
> 
> [Thu Aug 22 15:36:18 2024]
> rule suite2p_registration_9ho5xvv9qn:
>     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
>     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
>     jobid: 1
>     reason: Missing output files: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
>     resources: tmpdir=/tmp
> 
> Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> Activating conda environment: .snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> [Thu Aug 22 15:37:45 2024]
> Error in rule suite2p_registration_9ho5xvv9qn:
>     jobid: 1
>     input: /app/studio_data/output/1/tutorial2/suite2p_file_convert_tjmj285n2r/suite2p_file_convert.pkl
>     output: /app/studio_data/output/1/tutorial2/suite2p_registration_9ho5xvv9qn/suite2p_registration.pkl
>     conda-env: /app/.snakemake/conda/dfb585ac3f9cac0bb52f4fb61a2aac2d_
> 
> Shutting down, this might take some time.
> Exiting because a job execution failed. Look above for error message
> Complete log: .snakemake/log/2024-08-22T153616.981367.snakemake.log
milesAraya commented 3 months ago

conda list of downloaded problem env 


> (base) milesd@Miless-MacBook-Pro Downloads % cd dfb585ac3f9cac0bb52f4fb61a2aac2d_
> (base) milesd@Miless-MacBook-Pro dfb585ac3f9cac0bb52f4fb61a2aac2d_ % conda activate
> (base) milesd@Miless-MacBook-Pro dfb585ac3f9cac0bb52f4fb61a2aac2d_ % conda list
> # packages in environment at /opt/anaconda3:
> #
> # Name                    Version                   Build  Channel
> _anaconda_depends         2024.06         py312_openblas_2  
> abseil-cpp                20230802.0           h61975a4_2  
> aiobotocore               2.12.3          py312hecd8cb5_0  
> aiohttp                   3.9.5           py312h6c40b1e_0  
> aioitertools              0.7.1              pyhd3eb1b0_0  
> aiosignal                 1.2.0              pyhd3eb1b0_0  
> alabaster                 0.7.16          py312hecd8cb5_0  
> altair                    5.0.1           py312hecd8cb5_0  
> anaconda-anon-usage       0.4.4           py312hfb7c958_100  
> anaconda-catalogs         0.2.0           py312hecd8cb5_1  
> anaconda-client           1.12.3          py312hecd8cb5_0  
> anaconda-cloud-auth       0.5.1           py312hecd8cb5_0  
> anaconda-navigator        2.6.0           py312hecd8cb5_0  
> anaconda-project          0.11.1          py312hecd8cb5_0  
> annotated-types           0.6.0           py312hecd8cb5_0  
> anyio                     4.2.0           py312hecd8cb5_0  
> aom                       3.6.0                hcec6c5f_0  
> appdirs                   1.4.4              pyhd3eb1b0_0  
> applaunchservices         0.3.0           py312hecd8cb5_0  
> appnope                   0.1.3           py312hecd8cb5_1001  
> appscript                 1.1.2           py312h6c40b1e_0  
> archspec                  0.2.3              pyhd3eb1b0_0  
> argon2-cffi               21.3.0             pyhd3eb1b0_0  
> argon2-cffi-bindings      21.2.0          py312h6c40b1e_0  
> arrow                     1.2.3           py312hecd8cb5_1  
> arrow-cpp                 14.0.2               h3ade35f_1  
> astroid                   2.14.2          py312hecd8cb5_0  
> astropy                   6.1.0           py312ha2b695f_0  
> astropy-iers-data         0.2024.6.3.0.31.14 py312hecd8cb5_0  
> asttokens                 2.0.5              pyhd3eb1b0_0  
> async-lru                 2.0.4           py312hecd8cb5_0  
> atomicwrites              1.4.0                      py_0  
> attrs                     23.1.0          py312hecd8cb5_0  
> automat                   20.2.0                     py_0  
> autopep8                  2.0.4              pyhd3eb1b0_0  
> aws-c-auth                0.6.19               h6c40b1e_0  
> aws-c-cal                 0.5.20               h3333b6a_0  
> aws-c-common              0.8.5                h6c40b1e_0  
> aws-c-compression         0.2.16               h6c40b1e_0  
> aws-c-event-stream        0.2.15               hcec6c5f_0  
> aws-c-http                0.6.25               h6c40b1e_0  
> aws-c-io                  0.13.10              h6c40b1e_0  
> aws-c-mqtt                0.7.13               h6c40b1e_0  
> aws-c-s3                  0.1.51               h6c40b1e_0  
> aws-c-sdkutils            0.1.6                h6c40b1e_0  
> aws-checksums             0.1.13               h6c40b1e_0  
> aws-crt-cpp               0.18.16              hcec6c5f_0  
> aws-sdk-cpp               1.10.55              h61975a4_0  
> babel                     2.11.0          py312hecd8cb5_0  
> bcrypt                    3.2.0           py312h6c40b1e_1  
> beautifulsoup4            4.12.3          py312hecd8cb5_0  
> binaryornot               0.4.4              pyhd3eb1b0_1  
> black                     24.4.2          py312hecd8cb5_0  
> blas                      1.0                    openblas  
> bleach                    4.1.0              pyhd3eb1b0_0  
> blinker                   1.6.2           py312hecd8cb5_0  
> blosc                     1.21.3               hcec6c5f_0  
> bokeh                     3.4.1           py312h8e4b320_0  
> boltons                   23.0.0          py312hecd8cb5_0  
> boost-cpp                 1.82.0               ha357a0b_2  
> botocore                  1.34.69         py312hecd8cb5_0  
> bottleneck                1.3.7           py312h32608ca_0  
> brotli                    1.0.9                h6c40b1e_8  
> brotli-bin                1.0.9                h6c40b1e_8  
> brotli-python             1.0.9           py312hcec6c5f_8  
> brunsli                   0.1                  h23ab428_0  
> bzip2                     1.0.8                h6c40b1e_6  
> c-ares                    1.19.1               h6c40b1e_0  
> c-blosc2                  2.12.0               hcf5af9b_0  
> ca-certificates           2024.7.4             h8857fd0_0    conda-forge
> cachetools                5.3.3           py312hecd8cb5_0  
> cctools                   949.0.1             h9abeeb2_25  
> cctools_osx-64            949.0.1             hc7db93f_25  
> certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
> cffi                      1.16.0          py312h6c40b1e_1  
> cfitsio                   3.470                hbd21bf8_7  
> chardet                   4.0.0           py312hecd8cb5_1003  
> charls                    2.2.0                h23ab428_0  
> charset-normalizer        2.0.4              pyhd3eb1b0_0  
> click                     8.1.7           py312hecd8cb5_0  
> cloudpickle               2.2.1           py312hecd8cb5_0  
> colorama                  0.4.6           py312hecd8cb5_0  
> colorcet                  3.1.0           py312hecd8cb5_0  
> comm                      0.2.1           py312hecd8cb5_0  
> conda                     24.7.1          py312hb401068_0    conda-forge
> conda-build               24.5.1          py312hecd8cb5_0  
> conda-content-trust       0.2.0           py312hecd8cb5_1  
> conda-index               0.5.0           py312hecd8cb5_0  
> conda-libmamba-solver     24.1.0             pyhd3eb1b0_0  
> conda-pack                0.7.1           py312hecd8cb5_0  
> conda-package-handling    2.3.0           py312hecd8cb5_0  
> conda-package-streaming   0.10.0          py312hecd8cb5_0  
> conda-repo-cli            1.0.88          py312hecd8cb5_0  
> conda-token               0.5.0              pyhd3eb1b0_0  
> constantly                23.10.4         py312hecd8cb5_0  
> contourpy                 1.2.0           py312ha357a0b_0  
> cookiecutter              2.6.0           py312hecd8cb5_0  
> cryptography              42.0.5          py312h30e54ef_1  
> cssselect                 1.2.0           py312hecd8cb5_0  
> curl                      8.7.1                h04015c4_0  
> cycler                    0.11.0             pyhd3eb1b0_0  
> cyrus-sasl                2.1.28               h3973f50_1  
> cytoolz                   0.12.2          py312h6c40b1e_0  
> dask                      2024.5.0        py312hecd8cb5_0  
> dask-core                 2024.5.0        py312hecd8cb5_0  
> dask-expr                 1.1.0           py312hecd8cb5_0  
> datashader                0.16.2          py312hecd8cb5_0  
> dav1d                     1.2.1                h6c40b1e_0  
> debugpy                   1.6.7           py312hcec6c5f_0  
> decorator                 5.1.1              pyhd3eb1b0_0  
> defusedxml                0.7.1              pyhd3eb1b0_0  
> diff-match-patch          20200713           pyhd3eb1b0_0  
> dill                      0.3.8           py312hecd8cb5_0  
> distributed               2024.5.0        py312hecd8cb5_0  
> distro                    1.9.0           py312hecd8cb5_0  
> docstring-to-markdown     0.11            py312hecd8cb5_0  
> docutils                  0.18.1          py312hecd8cb5_3  
> entrypoints               0.4             py312hecd8cb5_0  
> et_xmlfile                1.1.0           py312hecd8cb5_1  
> executing                 0.8.3              pyhd3eb1b0_0  
> expat                     2.6.2                hcec6c5f_0  
> filelock                  3.13.1          py312hecd8cb5_0  
> flake8                    7.0.0           py312hecd8cb5_0  
> flask                     3.0.3           py312hecd8cb5_0  
> fmt                       10.2.1               h7728843_0    conda-forge
> fonttools                 4.51.0          py312h6c40b1e_0  
> freetype                  2.12.1               hd8bbffd_0  
> frozendict                2.4.2           py312hecd8cb5_0  
> frozenlist                1.4.0           py312h6c40b1e_0  
> fsspec                    2024.3.1        py312hecd8cb5_0  
> gensim                    4.3.2           py312he282a81_0  
> gettext                   0.22.5               h5ff76d1_2    conda-forge
> gettext-tools             0.22.5               h5ff76d1_2    conda-forge
> gflags                    2.2.2                hcec6c5f_1  
> giflib                    5.2.1                h6c40b1e_3  
> gitdb                     4.0.7              pyhd3eb1b0_0  
> gitpython                 3.1.37          py312hecd8cb5_0  
> glib                      2.78.4               hcec6c5f_0  
> glib-tools                2.78.4               hcec6c5f_0  
> glog                      0.5.0                hcec6c5f_1  
> greenlet                  3.0.1           py312hcec6c5f_0  
> grpc-cpp                  1.48.2               hbe2b35a_4  
> gst-plugins-base          1.14.1               hcec6c5f_1  
> gstreamer                 1.14.1               h6c40b1e_1  
> gtest                     1.14.0               ha357a0b_1  
> h5py                      3.11.0          py312h79b7918_0  
> hdf5                      1.12.1               ha01d115_3  
> hdmf                      3.14.3                   pypi_0    pypi
> heapdict                  1.0.1              pyhd3eb1b0_0  
> holoviews                 1.19.0          py312hecd8cb5_0  
> hvplot                    0.10.0          py312hecd8cb5_0  
> hyperlink                 21.0.0             pyhd3eb1b0_0  
> icu                       73.2                 hf5e326d_0    conda-forge
> idna                      3.7             py312hecd8cb5_0  
> imagecodecs               2023.1.23       py312h724c009_1  
> imageio                   2.33.1          py312hecd8cb5_0  
> imagesize                 1.4.1           py312hecd8cb5_0  
> imbalanced-learn          0.12.3          py312hecd8cb5_1  
> importlib-metadata        7.0.1           py312hecd8cb5_0  
> incremental               22.10.0            pyhd3eb1b0_0  
> inflection                0.5.1           py312hecd8cb5_1  
> iniconfig                 1.1.1              pyhd3eb1b0_0  
> intake                    0.7.0           py312hecd8cb5_0  
> intervaltree              3.1.0              pyhd3eb1b0_0  
> ipykernel                 6.28.0          py312hecd8cb5_0  
> ipython                   8.25.0          py312hecd8cb5_0  
> ipython_genutils          0.2.0              pyhd3eb1b0_1  
> ipywidgets                7.8.1           py312hecd8cb5_0  
> isort                     5.13.2          py312hecd8cb5_0  
> itemadapter               0.3.0              pyhd3eb1b0_0  
> itemloaders               1.1.0           py312hecd8cb5_0  
> itsdangerous              2.2.0           py312hecd8cb5_0  
> jaraco.classes            3.2.1              pyhd3eb1b0_0  
> jedi                      0.18.1          py312hecd8cb5_1  
> jellyfish                 1.0.1           py312haa3eb71_0  
> jinja2                    3.1.4           py312hecd8cb5_0  
> jmespath                  1.0.1           py312hecd8cb5_0  
> joblib                    1.4.2           py312hecd8cb5_0  
> jpeg                      9e                   h6c40b1e_1  
> jq                        1.6               h9ed2024_1000  
> json5                     0.9.6              pyhd3eb1b0_0  
> jsonpatch                 1.33            py312hecd8cb5_1  
> jsonpointer               2.1                pyhd3eb1b0_0  
> jsonschema                4.19.2          py312hecd8cb5_0  
> jsonschema-specifications 2023.7.1        py312hecd8cb5_0  
> jupyter                   1.0.0           py312hecd8cb5_9  
> jupyter-lsp               2.2.0           py312hecd8cb5_0  
> jupyter_client            8.6.0           py312hecd8cb5_0  
> jupyter_console           6.6.3           py312hecd8cb5_1  
> jupyter_core              5.7.2           py312hecd8cb5_0  
> jupyter_events            0.10.0          py312hecd8cb5_0  
> jupyter_server            2.14.1          py312hecd8cb5_0  
> jupyter_server_terminals  0.4.4           py312hecd8cb5_1  
> jupyterlab                4.0.11          py312hecd8cb5_0  
> jupyterlab-variableinspector 3.1.0           py312hecd8cb5_0  
> jupyterlab_pygments       0.1.2                      py_0  
> jupyterlab_server         2.25.1          py312hecd8cb5_0  
> jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
> jxrlib                    1.1                  haf1e3a3_2  
> keyring                   24.3.1          py312hecd8cb5_0  
> kiwisolver                1.4.4           py312hcec6c5f_0  
> krb5                      1.20.1               h428f121_1  
> lazy-object-proxy         1.10.0          py312h6c40b1e_0  
> lazy_loader               0.4             py312hecd8cb5_0  
> lcms2                     2.12                 hf1fd2bf_0  
> ld64                      530                 h20443b4_25  
> ld64_osx-64               530                 h70f3046_25  
> ldid                      2.1.5                hc58f1be_3  
> lerc                      3.0                  he9d5cce_0  
> libaec                    1.0.4                hb1e8313_1  
> libarchive                3.7.2                hd35d340_1    conda-forge
> libasprintf               0.22.5               h5ff76d1_2    conda-forge
> libasprintf-devel         0.22.5               h5ff76d1_2    conda-forge
> libavif                   0.11.1               h6c40b1e_0  
> libblas                   3.9.0           16_osx64_openblas    conda-forge
> libboost                  1.82.0               hf53b9f2_2  
> libbrotlicommon           1.0.9                h6c40b1e_8  
> libbrotlidec              1.0.9                h6c40b1e_8  
> libbrotlienc              1.0.9                h6c40b1e_8  
> libcblas                  3.9.0           16_osx64_openblas    conda-forge
> libclang                  14.0.6          default_hd95374b_1  
> libclang13                14.0.6          default_habbcc1a_1  
> libcurl                   8.7.1                hf20ceda_0  
> libcxx                    18.1.8               hef8daea_1    conda-forge
> libdeflate                1.17                 hb664fd8_1  
> libedit                   3.1.20230828         h6c40b1e_0  
> libev                     4.33                 h9ed2024_1  
> libevent                  2.1.12               h04015c4_1  
> libexpat                  2.6.2                h73e2aa4_0    conda-forge
> libffi                    3.4.4                hecd8cb5_1  
> libgettextpo              0.22.5               h5ff76d1_2    conda-forge
> libgettextpo-devel        0.22.5               h5ff76d1_2    conda-forge
> libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
> libgfortran5              13.2.0               h2873a65_3    conda-forge
> libglib                   2.78.4               h19e1a8f_0  
> libiconv                  1.17                 hd75f5a5_2    conda-forge
> libintl                   0.22.5               h5ff76d1_2    conda-forge
> libintl-devel             0.22.5               h5ff76d1_2    conda-forge
> liblapack                 3.9.0           16_osx64_openblas    conda-forge
> liblief                   0.12.3               hcec6c5f_0  
> libllvm14                 14.0.6               h91fad77_3  
> libmamba                  1.5.8                ha449628_0    conda-forge
> libmambapy                1.5.8           py312h67f5953_0    conda-forge
> libnghttp2                1.57.0               h9beae6a_0  
> libopenblas               0.3.21               h54e7dc3_0  
> libpng                    1.6.39               h6c40b1e_0  
> libpq                     12.17                h04015c4_0  
> libprotobuf               3.20.3               hfff2838_0  
> libsodium                 1.0.18               h1de35cc_0  
> libsolv                   0.7.24               hfff2838_1  
> libspatialindex           1.9.3                h23ab428_0  
> libsqlite                 3.46.0               h1b8f9f3_0    conda-forge
> libssh2                   1.11.0               hf20ceda_0  
> libthrift                 0.15.0               h70b4b81_2  
> libtiff                   4.5.1                hcec6c5f_0  
> libwebp-base              1.3.2                h6c40b1e_0  
> libxml2                   2.12.7               h3e169fe_1    conda-forge
> libxslt                   1.1.39               h03b04e6_0    conda-forge
> libzlib                   1.2.13               h87427d6_6    conda-forge
> libzopfli                 1.0.3                hb1e8313_0  
> linkify-it-py             2.0.0           py312hecd8cb5_0  
> llvm-openmp               14.0.6               h0dcd299_0  
> llvmlite                  0.42.0          py312hcec6c5f_0  
> locket                    1.0.0           py312hecd8cb5_0  
> lxml                      5.2.2           py312h1aa9a54_0    conda-forge
> lz4                       4.3.2           py312h6c40b1e_0  
> lz4-c                     1.9.4                hcec6c5f_1  
> lzo                       2.10                 haf1e3a3_2  
> mamba                     1.5.8           py312ha12221d_0    conda-forge
> markdown                  3.4.1           py312hecd8cb5_0  
> markdown-it-py            2.2.0           py312hecd8cb5_1  
> markupsafe                2.1.3           py312h6c40b1e_0  
> matplotlib                3.8.4           py312hecd8cb5_0  
> matplotlib-base           3.8.4           py312h7f12edd_0  
> matplotlib-inline         0.1.6           py312hecd8cb5_0  
> mccabe                    0.7.0              pyhd3eb1b0_0  
> mdit-py-plugins           0.3.0           py312hecd8cb5_0  
> mdurl                     0.1.0           py312hecd8cb5_0  
> menuinst                  2.1.1           py312hecd8cb5_0  
> mistune                   2.0.4           py312hecd8cb5_0  
> more-itertools            10.1.0          py312hecd8cb5_0  
> mpmath                    1.3.0           py312hecd8cb5_0  
> msgpack-python            1.0.3           py312ha357a0b_0  
> multidict                 6.0.4           py312h6c40b1e_0  
> multipledispatch          0.6.0           py312hecd8cb5_0  
> mypy                      1.10.0          py312h46256e1_0  
> mypy_extensions           1.0.0           py312hecd8cb5_0  
> mysql                     5.7.24               h1a8d504_2  
> navigator-updater         0.5.1           py312hecd8cb5_0  
> nbclient                  0.8.0           py312hecd8cb5_0  
> nbconvert                 7.10.0          py312hecd8cb5_0  
> nbformat                  5.9.2           py312hecd8cb5_0  
> ncurses                   6.4                  hcec6c5f_0  
> nest-asyncio              1.6.0           py312hecd8cb5_0  
> networkx                  3.2.1           py312hecd8cb5_0  
> nltk                      3.8.1           py312hecd8cb5_0  
> notebook                  7.0.8           py312hecd8cb5_0  
> notebook-shim             0.2.3           py312hecd8cb5_0  
> numba                     0.59.1          py312he282a81_0  
> numexpr                   2.8.7           py312h7d6adbd_0  
> numpy                     1.26.4          py312h7d6adbd_0  
> numpy-base                1.26.4          py312hbb3573c_0  
> numpydoc                  1.7.0           py312hecd8cb5_0  
> oniguruma                 6.9.7.1              h9ed2024_0  
> openjpeg                  2.4.0                h66ea3da_0  
> openpyxl                  3.1.2           py312h6c40b1e_0  
> openssl                   3.3.1                h87427d6_2    conda-forge
> orc                       1.7.4                h995b336_1  
> overrides                 7.4.0           py312hecd8cb5_0  
> packaging                 23.2            py312hecd8cb5_0  
> pandas                    2.2.2           py312h77d3abe_0  
> pandocfilters             1.5.0              pyhd3eb1b0_0  
> panel                     1.4.4           py312hecd8cb5_0  
> param                     2.1.0           py312hecd8cb5_0  
> parsel                    1.8.1           py312hecd8cb5_0  
> parso                     0.8.3              pyhd3eb1b0_0  
> partd                     1.4.1           py312hecd8cb5_0  
> patch                     2.7.6             h1de35cc_1001  
> pathspec                  0.10.3          py312hecd8cb5_0  
> patsy                     0.5.6           py312hecd8cb5_0  
> pcre2                     10.42                h9b97e30_1  
> pexpect                   4.8.0              pyhd3eb1b0_3  
> pickleshare               0.7.5           pyhd3eb1b0_1003  
> pillow                    10.3.0          py312h6c40b1e_0  
> pip                       24.1.2                   pypi_0    pypi
> pkce                      1.0.3           py312hecd8cb5_0  
> pkginfo                   1.10.0          py312hecd8cb5_0  
> platformdirs              3.10.0          py312hecd8cb5_0  
> plotly                    5.22.0          py312h8e4b320_0  
> pluggy                    1.0.0           py312hecd8cb5_1  
> ply                       3.11            py312hecd8cb5_1  
> prometheus_client         0.14.1          py312hecd8cb5_0  
> prompt-toolkit            3.0.43          py312hecd8cb5_0  
> prompt_toolkit            3.0.43               hd3eb1b0_0  
> protego                   0.1.16                     py_0  
> protobuf                  3.20.3          py312hcec6c5f_0  
> psutil                    5.9.0           py312h6c40b1e_0  
> ptyprocess                0.7.0              pyhd3eb1b0_2  
> pure_eval                 0.2.2              pyhd3eb1b0_0  
> py-cpuinfo                9.0.0           py312hecd8cb5_0  
> py-lief                   0.12.3          py312hcec6c5f_0  
> pyarrow                   14.0.2          py312h0b9b6c3_0  
> pyasn1                    0.4.8              pyhd3eb1b0_0  
> pyasn1-modules            0.2.8                      py_0  
> pybind11-abi              4                    hd8ed1ab_3    conda-forge
> pycodestyle               2.11.1          py312hecd8cb5_0  
> pycosat                   0.6.6           py312h6c40b1e_1  
> pycparser                 2.21               pyhd3eb1b0_0  
> pyct                      0.5.0           py312hecd8cb5_0  
> pycurl                    7.45.2          py312h04015c4_1  
> pydantic                  2.5.3           py312hecd8cb5_0  
> pydantic-core             2.14.6          py312hf2ad997_0  
> pydeck                    0.8.0           py312hecd8cb5_2  
> pydispatcher              2.0.5           py312hecd8cb5_3  
> pydocstyle                6.3.0           py312hecd8cb5_0  
> pyerfa                    2.0.1.4         py312ha2b695f_0  
> pyflakes                  3.2.0           py312hecd8cb5_0  
> pygments                  2.15.1          py312hecd8cb5_1  
> pyjwt                     2.8.0           py312hecd8cb5_0  
> pylint                    2.16.2          py312hecd8cb5_0  
> pylint-venv               3.0.3           py312hecd8cb5_0  
> pyls-spyder               0.4.0              pyhd3eb1b0_0  
> pynwb                     2.8.1                    pypi_0    pypi
> pyobjc-core               10.1            py312h46256e1_0  
> pyobjc-framework-cocoa    10.1            py312h9205ec4_0  
> pyobjc-framework-coreservices 10.1            py312h46256e1_0  
> pyobjc-framework-fsevents 10.1            py312hecd8cb5_0  
> pyodbc                    5.0.1           py312hcec6c5f_0  
> pyopenssl                 24.0.0          py312hecd8cb5_0  
> pyparsing                 3.0.9           py312hecd8cb5_0  
> pyqt                      5.15.10         py312hcec6c5f_0  
> pyqt5-sip                 12.13.0         py312h6c40b1e_0  
> pyqtwebengine             5.15.10         py312hcec6c5f_0  
> pysocks                   1.7.1           py312hecd8cb5_0  
> pytables                  3.9.2           py312ha921439_0  
> pytest                    7.4.4           py312hecd8cb5_0  
> python                    3.12.2          h9f0c242_0_cpython    conda-forge
> python-dateutil           2.9.0post0      py312hecd8cb5_2  
> python-dotenv             0.21.0          py312hecd8cb5_0  
> python-fastjsonschema     2.16.2          py312hecd8cb5_0  
> python-json-logger        2.0.7           py312hecd8cb5_0  
> python-libarchive-c       2.9                pyhd3eb1b0_1  
> python-lmdb               1.4.1           py312hcec6c5f_0  
> python-lsp-black          2.0.0           py312hecd8cb5_0  
> python-lsp-jsonrpc        1.1.2              pyhd3eb1b0_0  
> python-lsp-server         1.10.0          py312hecd8cb5_0  
> python-slugify            5.0.2              pyhd3eb1b0_0  
> python-snappy             0.6.1           py312hcec6c5f_0  
> python-tzdata             2023.3             pyhd3eb1b0_0  
> python.app                3               py312h6c40b1e_0  
> python_abi                3.12                    4_cp312    conda-forge
> pytoolconfig              1.2.6           py312hecd8cb5_0  
> pytz                      2024.1          py312hecd8cb5_0  
> pyviz_comms               3.0.2           py312hecd8cb5_0  
> pywavelets                1.5.0           py312h32608ca_0  
> pyyaml                    6.0.1           py312h6c40b1e_0  
> pyzmq                     25.1.2          py312hcec6c5f_0  
> qdarkstyle                3.2.3              pyhd3eb1b0_0  
> qstylizer                 0.2.2           py312hecd8cb5_0  
> qt-main                   5.15.2              hf83fbd5_10  
> qt-webengine              5.15.9               h90a370e_7  
> qtawesome                 1.2.2           py312hecd8cb5_0  
> qtconsole                 5.5.1           py312hecd8cb5_0  
> qtpy                      2.4.1           py312hecd8cb5_0  
> queuelib                  1.6.2           py312hecd8cb5_0  
> re2                       2022.04.01           he9d5cce_0  
> readline                  8.2                  hca72f7f_0  
> referencing               0.30.2          py312hecd8cb5_0  
> regex                     2023.10.3       py312h6c40b1e_0  
> reproc                    14.2.4               hcec6c5f_2  
> reproc-cpp                14.2.4               hcec6c5f_2  
> requests                  2.32.2          py312hecd8cb5_0  
> requests-file             1.5.1              pyhd3eb1b0_0  
> requests-toolbelt         1.0.0           py312hecd8cb5_0  
> rfc3339-validator         0.1.4           py312hecd8cb5_0  
> rfc3986-validator         0.1.1           py312hecd8cb5_0  
> rich                      13.3.5          py312hecd8cb5_1  
> rope                      1.12.0          py312hecd8cb5_0  
> rpds-py                   0.10.6          py312hf2ad997_0  
> rtree                     1.0.1           py312hecd8cb5_0  
> ruamel.yaml               0.17.21         py312h6c40b1e_0  
> ruamel_yaml               0.17.21         py312h6c40b1e_0  
> s3fs                      2024.3.1        py312hecd8cb5_0  
> scikit-image              0.23.2          py312h77d3abe_0  
> scikit-learn              1.4.2           py312he282a81_1  
> scipy                     1.14.0          py312hb9702fa_1    conda-forge
> scrapy                    2.11.1          py312hecd8cb5_0  
> seaborn                   0.13.2          py312hecd8cb5_0  
> semver                    3.0.2           py312hecd8cb5_0  
> send2trash                1.8.2           py312hecd8cb5_0  
> service_identity          18.1.0             pyhd3eb1b0_1  
> setuptools                69.5.1          py312hecd8cb5_0  
> sip                       6.7.12          py312hcec6c5f_0  
> six                       1.16.0             pyhd3eb1b0_1  
> smart_open                5.2.1           py312hecd8cb5_0  
> smmap                     4.0.0              pyhd3eb1b0_0  
> snappy                    1.1.10               hcec6c5f_1  
> sniffio                   1.3.0           py312hecd8cb5_0  
> snowballstemmer           2.2.0              pyhd3eb1b0_0  
> sortedcontainers          2.4.0              pyhd3eb1b0_0  
> soupsieve                 2.5             py312hecd8cb5_0  
> sphinx                    7.3.7           py312hecd8cb5_0  
> sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
> sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
> sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
> sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
> sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
> sphinxcontrib-serializinghtml 1.1.10          py312hecd8cb5_0  
> spyder                    5.5.1           py312hecd8cb5_0  
> spyder-kernels            2.5.0           py312hecd8cb5_0  
> sqlalchemy                2.0.30          py312h46256e1_0  
> sqlite                    3.45.3               h6c40b1e_0  
> stack_data                0.2.0              pyhd3eb1b0_0  
> statsmodels               0.14.2          py312ha2b695f_0  
> streamlit                 1.32.0          py312hecd8cb5_0  
> sympy                     1.12            py312hecd8cb5_0  
> tabulate                  0.9.0           py312hecd8cb5_0  
> tapi                      1000.10.8            ha1b3eb9_0  
> tbb                       2021.8.0             ha357a0b_0  
> tblib                     1.7.0              pyhd3eb1b0_0  
> tenacity                  8.2.2           py312hecd8cb5_1  
> terminado                 0.17.1          py312hecd8cb5_0  
> text-unidecode            1.3                pyhd3eb1b0_0  
> textdistance              4.2.1              pyhd3eb1b0_0  
> threadpoolctl             2.2.0              pyh0d69192_0  
> three-merge               0.1.1              pyhd3eb1b0_0  
> tifffile                  2023.4.12       py312hecd8cb5_0  
> tinycss2                  1.2.1           py312hecd8cb5_0  
> tk                        8.6.14               h4d00af3_0  
> tldextract                3.2.0              pyhd3eb1b0_0  
> toml                      0.10.2             pyhd3eb1b0_0  
> tomli                     2.0.1           py312hecd8cb5_1  
> tomlkit                   0.11.1          py312hecd8cb5_0  
> toolz                     0.12.0          py312hecd8cb5_0  
> tornado                   6.4.1           py312h46256e1_0  
> tqdm                      4.66.4          py312h8e4b320_0  
> traitlets                 5.14.3          py312hecd8cb5_0  
> truststore                0.8.0           py312hecd8cb5_0  
> twisted                   23.10.0         py312hecd8cb5_0  
> typing-extensions         4.11.0          py312hecd8cb5_0  
> typing_extensions         4.11.0          py312hecd8cb5_0  
> tzdata                    2024a                h04d1e81_0  
> uc-micro-py               1.0.1           py312hecd8cb5_0  
> ujson                     5.10.0          py312h6d0c2b6_0  
> unicodedata2              15.1.0          py312h6c40b1e_0  
> unidecode                 1.2.0              pyhd3eb1b0_0  
> unixodbc                  2.3.11               hb456775_0  
> urllib3                   2.2.2           py312hecd8cb5_0  
> utf8proc                  2.6.1                h6c40b1e_1  
> w3lib                     2.1.2           py312hecd8cb5_0  
> watchdog                  4.0.1           py312h3333b6a_0  
> wcwidth                   0.2.5              pyhd3eb1b0_0  
> webencodings              0.5.1           py312hecd8cb5_2  
> websocket-client          1.8.0           py312hecd8cb5_0  
> werkzeug                  3.0.3           py312hecd8cb5_0  
> whatthepatch              1.0.2           py312hecd8cb5_0  
> wheel                     0.43.0          py312hecd8cb5_0  
> widgetsnbextension        3.6.6           py312hecd8cb5_0  
> wrapt                     1.14.1          py312h6c40b1e_0  
> wurlitzer                 3.0.2           py312hecd8cb5_0  
> xarray                    2023.6.0        py312hecd8cb5_0  
> xlwings                   0.31.4          py312hecd8cb5_0  
> xyzservices               2022.9.0        py312hecd8cb5_1  
> xz                        5.4.6                h6c40b1e_1  
> yaml                      0.2.5                haf1e3a3_0  
> yaml-cpp                  0.8.0                hcec6c5f_1  
> yapf                      0.40.2          py312hecd8cb5_0  
> yarl                      1.9.3           py312h6c40b1e_0  
> zeromq                    4.3.5                hcec6c5f_0  
> zfp                       1.0.0                hcec6c5f_0  
> zict                      3.0.0           py312hecd8cb5_0  
> zipp                      3.17.0          py312hecd8cb5_0  
> zlib                      1.2.13               h87427d6_6    conda-forge
> zlib-ng                   2.0.7                h6c40b1e_0  
> zope                      1.0             py312hecd8cb5_1  
> zope.interface            5.4.0           py312h6c40b1e_0  
> zstandard                 0.22.0          py312h2d76c9a_0  
> zstd                      1.5.5                hc035e20_2
itutu-tienday commented 3 months ago

Additional information

In docker-compose, the .snakemake directory is volume mounted, but in some cases the volume mount on Mac M* can be quite slow, so this situation may be affecting the issue.

Try to improve the performance of the volume mount on Mac + docker and check if the issue is resolved.

Note