Review of
"Southern Ocean deep mixing band emerges from a competition between winter buoyancy loss and upper stratification strength"

Review of "Southern Ocean deep mixing band emerges from a competition between winter buoyancy loss and upper stratification strength"

Submitted by sbollmann  

June 11, 2024, 2:35 p.m.

Lead reviewer

sbollmann

Review Body

Reproducibility

Did you manage to reproduce it?
Not Reproducible
Reproducibility rating
How much of the paper did you manage to reproduce?
1 / 10
Briefly describe the procedure followed/tools used to reproduce it

I first tried to install the virtual environment with poetry on a Linux x86 machine, but this didn't work.

I was able to download the apptainer image and start this, but the snakemake workflow failed with the subset of the data from zenodo.

I was not able to find where to register for the full data and how to download the full data.

Briefly describe your familiarity with the procedure/tools used by the paper.

I am very familiar with apptainer.

Which type of operating system were you working in?
Linux/FreeBSD or other Open Source Operating system
What additional software did you need to install?

apptainer

What software did you use

apptainer

What were the main challenges you ran into (if any)?

couldn't find full dataset regsitration and download

poetry virtual environment did not install: First problem was permissions:

``` curl -sSL https://install.python-poetry.org | POETRY_HOME=/etc/poetry python3 - --version 1.3.2 Retrieving Poetry metadata

Welcome to Poetry!

This will download and install the latest version of Poetry, a dependency and package manager for Python.

It will add the poetry command to Poetry's bin directory, located at:

/etc/poetry/bin

You can uninstall at any time by executing this script with the --uninstall option, and these changes will be reverted.

Traceback (most recent call last): File "", line 945, in File "", line 923, in main File "", line 532, in run File "", line 776, in ensure_directories File "/opt/conda/lib/python3.11/pathlib.py", line 1116, in mkdir os.mkdir(self, mode) PermissionError: [Errno 13] Permission denied: '/etc/poetry' ``` Then I changed this to: curl -sSL https://install.python-poetry.org | POETRY_HOME=~/reprohack/ python3 - --version 1.3.2

That worked, but the next step "poetry install" failed, so I had to run poetry run pip install "pyproj (==3.2.1)"

the next step then didn't work, due to a typo in the documentation: poetyr install

but fixing that: poetry install

but that then still fails: he currently activated Python version 3.11.6 is not supported by the project (^3.10,<3.11). Trying to find and use a compatible version. Using python3.10 (3.10.12) Collecting pyproj==3.2.1 Downloading pyproj-3.2.1.tar.gz (213 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 213.3/213.3 kB 3.6 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [2 lines of output] :9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html proj executable not found. Please set the PROJ_DIR variable. For more information see: https://pyproj4.github.io/pyproj/stable/installation.html [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[notice] A new release of pip is available: 23.1 -> 24.0 [notice] To update, run: pip install --upgrade pip (base) jovyan@neurodesktop-:~/reprohack/caneill-et-al-OS-SO-DMB$ poetyr install bash: poetyr: command not found (base) jovyan@neurodesktop-:~/reprohack/caneill-et-al-OS-SO-DMB$ poetry install The currently activated Python version 3.11.6 is not supported by the project (^3.10,<3.11). Trying to find and use a compatible version. Using python3.10 (3.10.12) Installing dependencies from lock file

Package operations: 55 installs, 0 updates, 0 removals

• Installing pyproj (3.2.1): Failed

CalledProcessError

Command '['/home/jovyan/.cache/pypoetry/virtualenvs/lib-interplay-buoyancy-stratification-zxGM5zRI-py3.10/bin/python', '-m', 'pip', 'install', '--use-pep517', '--disable-pip-version-check', '--isolated', '--no-input', '--prefix', '/home/jovyan/.cache/pypoetry/virtualenvs/lib-interplay-buoyancy-stratification-zxGM5zRI-py3.10', '--no-deps', '/home/jovyan/.cache/pypoetry/artifacts/7d/a9/51/51ec74ec8db3a411f00b6fe8fbc3d9bfabf430ee528c75cd9627a8ec9c/pyproj-3.2.1.tar.gz']' returned non-zero exit status 1.

at /opt/conda/lib/python3.11/subprocess.py:571 in run 567│ # We don't call process.wait() as .exit does that for us. 568│ raise 569│ retcode = process.poll() 570│ if check and retcode: → 571│ raise CalledProcessError(retcode, process.args, 572│ output=stdout, stderr=stderr) 573│ return CompletedProcess(process.args, retcode, stdout, stderr) 574│ 575│

The following error occurred when trying to handle this error:

EnvCommandError

Command ['/home/jovyan/.cache/pypoetry/virtualenvs/lib-interplay-buoyancy-stratification-zxGM5zRI-py3.10/bin/python', '-m', 'pip', 'install', '--use-pep517', '--disable-pip-version-check', '--isolated', '--no-input', '--prefix', '/home/jovyan/.cache/pypoetry/virtualenvs/lib-interplay-buoyancy-stratification-zxGM5zRI-py3.10', '--no-deps', '/home/jovyan/.cache/pypoetry/artifacts/7d/a9/51/51ec74ec8db3a411f00b6fe8fbc3d9bfabf430ee528c75cd9627a8ec9c/pyproj-3.2.1.tar.gz'] errored with the following return code 1, and output: Processing /home/jovyan/.cache/pypoetry/artifacts/7d/a9/51/51ec74ec8db3a411f00b6fe8fbc3d9bfabf430ee528c75cd9627a8ec9c/pyproj-3.2.1.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [2 lines of output]
    <string>:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    proj executable not found. Please set the PROJ_DIR variable. For more information see: https://pyproj4.github.io/pyproj/stable/installation.html
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

at ~/reprohack/venv/lib/python3.11/site-packages/poetry/utils/env.py:1540 in _run 1536│ output = subprocess.check_output( 1537│ command, stderr=subprocess.STDOUT, env=env, kwargs 1538│ ) 1539│ except CalledProcessError as e: → 1540│ raise EnvCommandError(e, input=input_) 1541│ 1542│ return decode(output) 1543│ 1544│ def execute(self, bin: str, *args: str, kwargs: Any) -> int:

The following error occurred when trying to handle this error:

PoetryException

Failed to install /home/jovyan/.cache/pypoetry/artifacts/7d/a9/51/51ec74ec8db3a411f00b6fe8fbc3d9bfabf430ee528c75cd9627a8ec9c/pyproj-3.2.1.tar.gz

at ~/reprohack/venv/lib/python3.11/site-packages/poetry/utils/pip.py:58 in pip_install 54│ 55│ try: 56│ return environment.run_pip(*args) 57│ except EnvCommandError as e: → 58│ raise PoetryException(f"Failed to install {path.as_posix()}") from e 59│

I did get the apptainer container to run, but the snakemake workflow failed: Building DAG of jobs... Using shell: /bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Job stats: job count

all 1 all_for_paper_plots_columnar_buoyancy_compare_with_constant_alpha 1 all_for_paper_plots_columnar_buoyancy_theta_S 1 all_for_paper_plots_compare_correction_heat_with_ECCO 1 all_for_paper_plots_fb_and_B 1 all_for_paper_plots_fb_and_B_compare_thresholds 1 all_for_paper_plots_fb_and_B_constant_alpha 1 all_for_paper_plots_fb_and_B_sections 1 all_for_paper_plots_fb_and_B_zonal_mean_comparison 1 all_for_paper_plots_fb_components_mean 1 all_for_paper_plots_fb_components_zonal 1 all_for_paper_plots_mld_fronts_climato 1 all_for_paper_plots_tec_vs_theta 1 diags_adjustment_rm_mean 12 diags_heat 12 diags_heat_annual_excess 12 diags_surface_buoyancy_with_ekman_season_climatology_SO 2 diags_tools_time_mean_climatology 5 paper_plots_copy_each_figure 14 total 70

Select jobs to execute...

[Tue Jun 11 13:08:51 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2014.nc jobid: 28 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2014 resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule diags_tools_time_mean_climatology: input: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2005.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2006.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2007.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2008.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2009.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2010.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2011.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2012.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2013.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2014.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2015.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2016.nc output: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_climatology_time_mean.nc jobid: 60 reason: Code has changed since last execution wildcards: path_to_files=data/processed/surface_fluxes_adjusted_rm-mean/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP, filename=buoyancy resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule diags_surface_buoyancy_with_ekman_season_climatology_SO: input: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2005.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2006.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2007.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2008.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2009.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2010.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2011.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2012.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2013.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2014.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2015.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2016.nc output: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc log: logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb jobid: 46 reason: Code has changed since last execution wildcards: raw_adj=adjusted_rm-mean, buoyancy_with_ekman=buoyancy_with_ekman_constant_alpha_-40_degree_north, surf_heat_pname=OAFlux-ISCCP, surf_freshwater_pname=OAFlux-GPCP resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule diags_tools_time_mean_climatology: input: data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2005.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2006.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2007.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2008.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2009.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2010.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2011.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2012.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2013.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2014.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2015.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_2016.nc output: data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_climatology_time_mean.nc jobid: 59 reason: Code has changed since last execution wildcards: path_to_files=data/processed/surface_fluxes_raw/buoyancy/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP, filename=buoyancy resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule all_for_paper_plots_mld_fronts_climato: input: data/raw/ACC_fronts/Park_and_Durand_2019/62985.nc, data/raw/MLD_de_boyer_montegut/mld_dr003_ref10m_v2023.nc output: figures/paper_intermediate/mld_fronts_climato.pdf log: logs/notebooks/figures/paper_intermediate/mld_fronts_climato.ipynb jobid: 2 reason: Missing output files: figures/paper_intermediate/mld_fronts_climato.pdf resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule all_for_paper_plots_columnar_buoyancy_theta_S: input: data/processed/columnar_buoyancy_MIMOC_B250.nc, data/raw/ACC_fronts/Park_and_Durand_2019/62985.nc output: figures/paper_intermediate/columnar_buoyancy_MIMOC/B250_map_SO_theta_S.pdf log: logs/notebooks/figures/paper_intermediate/columnar_buoyancy_MIMOC/columnar_buoyancy_equivalent_flux_plot_theta_S_B250.ipynb jobid: 4 reason: Missing output files: figures/paper_intermediate/columnar_buoyancy_MIMOC/B250_map_SO_theta_S.pdf wildcards: depth=250 resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule diags_tools_time_mean_climatology: input: data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2005.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2006.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2007.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2008.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2009.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2010.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2011.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2012.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2013.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2014.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2015.nc, data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_2016.nc output: data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx/buoyancy_climatology_time_mean.nc jobid: 61 reason: Code has changed since last execution wildcards: path_to_files=data/processed/surface_fluxes_raw/buoyancy/product_heat_ECCO-oceQnet_freshwater_ECCO-oceFWflx, filename=buoyancy resources: tmpdir=/tmp

[Tue Jun 11 13:08:51 2024] rule diags_surface_buoyancy_with_ekman_season_climatology_SO: input: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2005.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2006.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2007.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2008.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2009.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2010.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2011.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2012.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2013.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2014.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2015.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2016.nc output: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc log: logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb jobid: 7 reason: Code has changed since last execution wildcards: raw_adj=adjusted_rm-mean, buoyancy_with_ekman=buoyancy_with_ekman, surf_heat_pname=OAFlux-ISCCP, surf_freshwater_pname=OAFlux-GPCP resources: tmpdir=/tmp

[Tue Jun 11 13:08:55 2024] Error in rule diags_heat: jobid: 28 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2014.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpjus9ya_0.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:08:55 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2013.nc jobid: 26 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2013 resources: tmpdir=/tmp

[Tue Jun 11 13:08:57 2024] Error in rule diags_heat: jobid: 26 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2013.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmp3db5yio2.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:08:57 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2015.nc jobid: 30 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2015 resources: tmpdir=/tmp

[Tue Jun 11 13:08:58 2024] Finished job 61. 1 of 70 steps (1%) done Select jobs to execute...

[Tue Jun 11 13:08:58 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2016.nc jobid: 32 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2016 resources: tmpdir=/tmp

[Tue Jun 11 13:08:58 2024] Finished job 59. 2 of 70 steps (3%) done [Tue Jun 11 13:08:58 2024] Finished job 60. 3 of 70 steps (4%) done Select jobs to execute...

[Tue Jun 11 13:08:58 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2006.nc jobid: 12 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2006 resources: tmpdir=/tmp

[Tue Jun 11 13:08:58 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2007.nc jobid: 14 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2007 resources: tmpdir=/tmp

Select jobs to execute... [Tue Jun 11 13:08:59 2024] Error in rule diags_heat: jobid: 30 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2015.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpif4v8rn5.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run

[Tue Jun 11 13:08:59 2024] rule all_for_paper_plots_tec_vs_theta: output: figures/paper_intermediate/tec_vs_theta.pdf jobid: 54 reason: Missing output files: figures/paper_intermediate/tec_vs_theta.pdf resources: tmpdir=/tmp

[Tue Jun 11 13:09:00 2024] Error in rule diags_heat: jobid: 32 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2016.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmphlwsdkxl.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:00 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2008.nc jobid: 16 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2008 resources: tmpdir=/tmp

[Tue Jun 11 13:09:00 2024] Error in rule diags_heat: jobid: 12 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2006.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpd747fir2.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:00 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2009.nc jobid: 18 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2009 resources: tmpdir=/tmp

[Tue Jun 11 13:09:00 2024] Error in rule diags_heat: jobid: 14 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2007.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpl8qo6arf.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:00 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2010.nc jobid: 20 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2010 resources: tmpdir=/tmp

[Tue Jun 11 13:09:02 2024] Error in rule diags_heat: jobid: 18 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2009.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmphofp9um9.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:02 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2011.nc jobid: 22 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2011 resources: tmpdir=/tmp

[Tue Jun 11 13:09:02 2024] Error in rule diags_heat: jobid: 16 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2008.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpju1f909e.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:02 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2012.nc jobid: 24 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2012 resources: tmpdir=/tmp

[Tue Jun 11 13:09:02 2024] Error in rule diags_heat: jobid: 20 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2010.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpnk0v9ic8.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Select jobs to execute...

[Tue Jun 11 13:09:02 2024] rule diags_heat: output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2005.nc jobid: 9 reason: Code has changed since last execution wildcards: surf_heat_pname=OAFlux-ISCCP, year=2005 resources: tmpdir=/tmp

[Tue Jun 11 13:09:04 2024] Error in rule diags_heat: jobid: 22 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2011.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmp8n7_wat9.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run [Tue Jun 11 13:09:04 2024] Error in rule diags_heat: jobid: 24 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2012.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpr3lznyx9.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run [Tue Jun 11 13:09:04 2024] Error in rule diags_heat: jobid: 9 output: data/processed/surface_fluxes_raw/heat/product_OAFlux-ISCCP/heat_2005.nc

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 98: Command 'set -euo pipefail; /virtual_env/.venv/bin/python /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpdag5xxtq.surface_heat.py' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 98, in __rule_diags_heat File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run [Tue Jun 11 13:09:23 2024] Error in rule all_for_paper_plots_tec_vs_theta: jobid: 54 output: figures/paper_intermediate/tec_vs_theta.pdf

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm, line 36: Command 'set -euo pipefail; jupyter-nbconvert --log-level ERROR --execute --to notebook --ExecutePreprocessor.timeout=-1 /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmpm5tmcmrc.tec_vs_theta.py.ipynb' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm", line 36, in __rule_all_for_paper_plots_tec_vs_theta File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job all_for_paper_plots_tec_vs_theta since they might be corrupted: figures/paper_intermediate/tec_vs_theta.pdf [Tue Jun 11 13:09:24 2024] Error in rule diags_surface_buoyancy_with_ekman_season_climatology_SO: jobid: 7 input: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2005.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2006.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2007.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2008.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2009.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2010.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2011.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2012.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2013.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2014.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2015.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2016.nc output: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc log: logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb (check log file(s) for error details)

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 504: Command 'set -euo pipefail; jupyter-nbconvert --log-level ERROR --execute --output /data/caneill-et-al-OS-SO-DMB/logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb --to notebook --ExecutePreprocessor.timeout=-1 /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmp2dxir8os.surface_buoyancy_with_ekman_season_climatology_SO.py.ipynb' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 504, in __rule_diags_surface_buoyancy_with_ekman_season_climatology_SO File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job diags_surface_buoyancy_with_ekman_season_climatology_SO since they might be corrupted: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc [Tue Jun 11 13:09:25 2024] Error in rule diags_surface_buoyancy_with_ekman_season_climatology_SO: jobid: 46 input: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2005.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2006.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2007.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2008.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2009.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2010.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2011.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2012.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2013.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2014.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2015.nc, data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_2016.nc output: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc log: logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb (check log file(s) for error details)

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm, line 504: Command 'set -euo pipefail; jupyter-nbconvert --log-level ERROR --execute --output /data/caneill-et-al-OS-SO-DMB/logs/notebooks/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/surface_buoyancy_with_ekman_season_climatology_SO.ipynb --to notebook --ExecutePreprocessor.timeout=-1 /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmp763bp4qh.surface_buoyancy_with_ekman_season_climatology_SO.py.ipynb' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/diags/fluxes.skm", line 504, in __rule_diags_surface_buoyancy_with_ekman_season_climatology_SO File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job diags_surface_buoyancy_with_ekman_season_climatology_SO since they might be corrupted: data/processed/surface_fluxes_adjusted_rm-mean/buoyancy_with_ekman_constant_alpha_-40_degree_north/product_heat_OAFlux-ISCCP_freshwater_OAFlux-GPCP/buoyancy_with_ekman_season_climatology_SO.nc [Tue Jun 11 13:09:42 2024] Error in rule all_for_paper_plots_columnar_buoyancy_theta_S: jobid: 4 input: data/processed/columnar_buoyancy_MIMOC_B250.nc, data/raw/ACC_fronts/Park_and_Durand_2019/62985.nc output: figures/paper_intermediate/columnar_buoyancy_MIMOC/B250_map_SO_theta_S.pdf log: logs/notebooks/figures/paper_intermediate/columnar_buoyancy_MIMOC/columnar_buoyancy_equivalent_flux_plot_theta_S_B250.ipynb (check log file(s) for error details)

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm, line 466: Command 'set -euo pipefail; jupyter-nbconvert --log-level ERROR --execute --output /data/caneill-et-al-OS-SO-DMB/logs/notebooks/figures/paper_intermediate/columnar_buoyancy_MIMOC/columnar_buoyancy_equivalent_flux_plot_theta_S_B250.ipynb --to notebook --ExecutePreprocessor.timeout=-1 /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmprqq1p9ra.columnar_buoyancy_equivalent_flux_plot_theta_S.py.ipynb' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm", line 466, in __rule_all_for_paper_plots_columnar_buoyancy_theta_S File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job all_for_paper_plots_columnar_buoyancy_theta_S since they might be corrupted: figures/paper_intermediate/columnar_buoyancy_MIMOC/B250_map_SO_theta_S.pdf [Tue Jun 11 13:09:58 2024] Error in rule all_for_paper_plots_mld_fronts_climato: jobid: 2 input: data/raw/ACC_fronts/Park_and_Durand_2019/62985.nc, data/raw/MLD_de_boyer_montegut/mld_dr003_ref10m_v2023.nc output: figures/paper_intermediate/mld_fronts_climato.pdf log: logs/notebooks/figures/paper_intermediate/mld_fronts_climato.ipynb (check log file(s) for error details)

RuleException: CalledProcessError in file /data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm, line 22: Command 'set -euo pipefail; jupyter-nbconvert --log-level ERROR --execute --output /data/caneill-et-al-OS-SO-DMB/logs/notebooks/figures/paper_intermediate/mld_fronts_climato.ipynb --to notebook --ExecutePreprocessor.timeout=-1 /data/caneill-et-al-OS-SO-DMB/.snakemake/scripts/tmprt9yh0g4.mld_fronts_climato.py.ipynb' returned non-zero exit status 1. File "/data/caneill-et-al-OS-SO-DMB/workflow/rules/plots/all_for_paper.skm", line 22, in __rule_all_for_paper_plots_mld_fronts_climato File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run Removing output files of failed job all_for_paper_plots_mld_fronts_climato since they might be corrupted: figures/paper_intermediate/mld_fronts_climato.pdf Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-06-11T130851.039242.snakemake.log

What were the positive features of this approach?

the apptainer container is a great idea

Any other comments/suggestions on the reproducibility approach?

n/a the snakemake pipeline is super cool!


Documentation

Documentation rating
How well was the material documented?
2 / 10
How could the documentation be improved?

poetyr install has a typo -> poetry install

What do you like about the documentation?

attempt to document everything clearly

After attempting to reproduce, how familiar do you feel with the code and methods used in the paper?
3 / 10
Any suggestions on how the analysis could be made more transparent?

n/a


Reusability

Reusability rating
Rate the project on reusability of the material
3 / 10
Permissive Data license included:  
Permissive Code license included:  

Any suggestions on how the project could be more reusable?


Any final comments