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Do no create conda environments within cluster jobs by default #1463

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sebschmi opened this issue Mar 7, 2022 · 5 comments
Closed

Do no create conda environments within cluster jobs by default #1463

sebschmi opened this issue Mar 7, 2022 · 5 comments
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bug Something isn't working

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@sebschmi
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sebschmi commented Mar 7, 2022

Snakemake version
7.1.0

Describe the bug
It seems that in cluster mode, only those conda environments required for local jobs are created locally. The others are created in the cluster jobs. But if there is more than one cluster job with the same conda environment, the jobs try to create the environment at the same time and fail. This happens on a shared distributed file system.

Logs
This is an example log of a cluster job that creates an environment simultaneously with other jobs:

Building DAG of jobs...
Creating conda environment config/conda-biopython-env.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /proj/sebschmi/git/practical-omnitigs/config/conda-biopython-env.yml:
warning  libmamba Cannot lock '/proj/sebschmi/miniforge3/envs/practical-omnitigs/pkgs/cache/497deca9.solv'
    Waiting for other mamba process to finish
warning  libmamba Cannot lock '/proj/sebschmi/miniforge3/envs/practical-omnitigs/pkgs/cache/09cdf8bf.solv'
    Waiting for other mamba process to finish
warning  libmamba Cannot lock '/proj/sebschmi/miniforge3/envs/practical-omnitigs/pkgs/cache/ffeee55f.solv'
    Waiting for other mamba process to finish
warning  libmamba Cannot lock '/proj/sebschmi/miniforge3/envs/practical-omnitigs/pkgs/cache/2a957770.solv'
    Waiting for other mamba process to finish
warning  libmamba Cannot lock '/proj/sebschmi/miniforge3/envs/practical-omnitigs/pkgs/cache/47929eba.solv'
    Waiting for other mamba process to finish
  Package               Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex           0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex           4.5  1_gnu                conda-forge/linux-64     Cached
  + biopython              1.79  py310h6acc77f_1      conda-forge/linux-64     Cached
  + bzip2                 1.0.8  h7f98852_4           conda-forge/linux-64     Cached
  + ca-certificates   2021.10.8  ha878542_0           conda-forge/linux-64     Cached
  + ld_impl_linux-64     2.36.1  hea4e1c9_2           conda-forge/linux-64     Cached
  + libblas               3.9.0  13_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas              3.9.0  13_linux64_openblas  conda-forge/linux-64     Cached
  + libffi                3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc-ng            11.2.0  h1d223b6_13          conda-forge/linux-64     Cached
  + libgfortran-ng       11.2.0  h69a702a_13          conda-forge/linux-64     Cached
  + libgfortran5         11.2.0  h5c6108e_13          conda-forge/linux-64     Cached
  + libgomp              11.2.0  h1d223b6_13          conda-forge/linux-64     Cached
  + liblapack             3.9.0  13_linux64_openblas  conda-forge/linux-64     Cached
  + libnsl                2.0.0  h7f98852_0           conda-forge/linux-64     Cached
  + libopenblas          0.3.18  pthreads_h8fe5266_0  conda-forge/linux-64     Cached
  + libstdcxx-ng         11.2.0  he4da1e4_13          conda-forge/linux-64     Cached
  + libuuid              2.32.1  h7f98852_1000        conda-forge/linux-64     Cached
  + libzlib              1.2.11  h36c2ea0_1013        conda-forge/linux-64     Cached
  + ncurses                 6.3  h9c3ff4c_0           conda-forge/linux-64     Cached
  + numpy                1.22.2  py310h454958d_0      conda-forge/linux-64     Cached
  + openssl               3.0.0  h7f98852_2           conda-forge/linux-64     Cached
  + pip                  22.0.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + python               3.10.2  hc74c709_3_cpython   conda-forge/linux-64     Cached
  + python_abi             3.10  2_cp310              conda-forge/linux-64     Cached
  + readline                8.1  h46c0cb4_0           conda-forge/linux-64     Cached
  + setuptools           60.9.3  py310hff52083_0      conda-forge/linux-64     Cached
  + sqlite               3.37.0  h9cd32fc_0           conda-forge/linux-64     Cached
  + time                    1.8  h516909a_0           conda-forge/linux-64     Cached
  + tk                   8.6.12  h27826a3_0           conda-forge/linux-64     Cached
  + tzdata                2021e  he74cb21_0           conda-forge/noarch       Cached
  + wheel                0.37.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + xz                    5.2.5  h516909a_1           conda-forge/linux-64     Cached
  + zlib                 1.2.11  h36c2ea0_1013        conda-forge/linux-64     Cached

  Summary:

  Install: 34 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────────────────────

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::libgcc-ng-11.2.0-h1d223b6_13'.
Rolling back transaction: ...working... WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/doc/xz/COPYING.GPLv2.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/doc/xz/COPYING.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/doc/xz/AUTHORS.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/vli.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/version.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/stream_flags.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/lzma12.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/index_hash.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/index.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/check.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/block.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma/bcj.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/x509v3err.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/x509v3.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/x509err.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/x509.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/uierr.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/txt_db.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/tserr.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ts.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/tls1.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ssl3.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ssl2.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ssl.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/srtp.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/srp.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/self_test.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/seed.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/safestack.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/rsaerr.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/rc2.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/randerr.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/rand.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/provider.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/proverr.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/pkcs7.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/pkcs12err.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/pkcs12.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/pem2.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/param_build.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ossl_typ.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/opensslv.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/opensslconf.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/ocsp.h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/openssl/mdc2.h.  Please remove this file manually (you may need to reboot to free file handles)

[cut out a few of these to stay within github's limits]

WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/w/wy-99fgt.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vv100.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vtnt.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte-direct.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte-256color.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte-2012.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte-2007.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte+pcfkeys.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vte.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt61.5.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt510pc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt50h.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt50.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt420pcdos.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt420pc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt420f.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt420+lrmm.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt420.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt400.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt340.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt320nam.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt300-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220d.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220-base.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220-8bit.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220+pcedit.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220+keypad.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt220+cvis.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt102-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt102.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100nam.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-w-nam.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-s-bot.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-s.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-putty.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-nav-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vt100-nav.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vscode-direct.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vsc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vp90.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/visa50.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vip-w.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vip-Hw.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vip.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/viewpoint90.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/viewpoint60.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/viewdata-rv.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/viewdata.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vi50.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vi300-old.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vc415.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vc403a.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vc303a.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/vanilla.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/v5410.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/v3220.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v/v200-nam.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/u/ultimaII.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/u/ultima2.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tws-generic.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tw52-color.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tw52.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tw100.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi970-2p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi955.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-vb.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-unk.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-p-vb.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-p-2p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-2p-unk.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-2p-p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-2p-mc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b-2p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b+fn.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920b.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi920.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912cc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-vb-unk.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-vb-p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-vb-mc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-vb.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-mc-2p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-mc.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-2p-unk.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912c-2p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912b-vb-p.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912b-vb.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t/tvi912b-unk-vb.  Please remove this file manually (you may need to reboot to free file handles)
WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/unctrl.h.  Please remove this file manually (you may need to reboot to free file handles)
done

[Errno 17] File exists: 'libatomic.so.1.2.0' -> '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/lib/libatomic.so'
()
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/lib/python3.10/site-packages/pip/_vendor/platformdirs'
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/include/lzma'
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/doc/xz'
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/x'
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/v'
[Errno 116] Stale file handle: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1/share/terminfo/t'
[Errno 2] No such file or directory: '/proj/sebschmi/git/practical-omnitigs/.snakemake/conda/3efc3f3ffb47b458cb13de5605bee1b1'
@sebschmi sebschmi added the bug Something isn't working label Mar 7, 2022
@johanneskoester
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johanneskoester commented Mar 9, 2022

Indeed, that is not intended, all conda envs should be created in the main process before any cluster job is submitted.

@johanneskoester johanneskoester self-assigned this Mar 9, 2022
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johanneskoester commented Mar 9, 2022

I will have a look.

williamrowell added a commit to williamrowell/hifi-deepvariant-snakemake that referenced this issue Mar 10, 2022
current bug in snakemake 7 causes conda environments to build simultaneously within cluster jobs snakemake/snakemake#1463
johanneskoester added a commit that referenced this issue Mar 11, 2022
johanneskoester added a commit that referenced this issue Mar 11, 2022
…file system (fixes issue #1463) (#1472)

* fix: always deploy conda envs in main process when assuming a shared file system (fixes issue #1463)

* fix lint
@johanneskoester
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johanneskoester commented Mar 11, 2022

Fixed with PR #1472

@dlaehnemann
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dlaehnemann commented Mar 11, 2022

I had the same problem and can confirm that PR #1472 fixes this for me.

@sebschmi
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sebschmi commented Mar 14, 2022

Thank you very much!

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