CheckM
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Ecogenomics
SafetyError: The package for checkm-genome located at [anaconda3_path]/pkgs/checkm-genome-1.1.3-py_1 appears to be corrupted. The path 'site-packages/checkm/DATA_CONFIG'
Is there any insight on what causes the SafetyError for bioconda's CheckM v1.1.3?
(base) [jespinoz@exp-15-32 test]$ conda create -n checkm_env -c bioconda 'checkm-genome==1.1.3'
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.14.0
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /expanse/projects/jcl110/anaconda3/envs/checkm_env
added / updated specs:
- checkm-genome==1.1.3
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
ca-certificates conda-forge/linux-64::ca-certificates-2022.6.15-ha878542_0
checkm-genome bioconda/noarch::checkm-genome-1.1.3-py_1
curl conda-forge/linux-64::curl-7.83.1-h2283fc2_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
dendropy bioconda/noarch::dendropy-4.5.2-pyh3252c3a_0
freetype conda-forge/linux-64::freetype-2.12.1-hca18f0e_0
gettext conda-forge/linux-64::gettext-0.19.8.1-h73d1719_1008
hmmer bioconda/linux-64::hmmer-3.3.2-h87f3376_2
icu conda-forge/linux-64::icu-67.1-he1b5a44_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
kiwisolver conda-forge/linux-64::kiwisolver-1.4.4-py37h7cecad7_0
krb5 conda-forge/linux-64::krb5-1.19.3-h08a2579_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libblas conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.83.1-h2283fc2_0
libdeflate bioconda/linux-64::libdeflate-1.0-h14c3975_1
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.1.0-h8d9b700_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.1.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-12.1.0-hdcd56e2_16
libgomp conda-forge/linux-64::libgomp-12.1.0-h8d9b700_16
libidn2 conda-forge/linux-64::libidn2-2.3.3-h166bdaf_0
liblapack conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-hff17c54_1
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_2
libpng conda-forge/linux-64::libpng-1.6.37-h753d276_4
libsqlite conda-forge/linux-64::libsqlite-3.39.2-h753d276_1
libssh2 conda-forge/linux-64::libssh2-1.10.0-hf14f497_3
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.1.0-ha89aaad_16
libunistring conda-forge/linux-64::libunistring-0.9.10-h7f98852_0
libzlib conda-forge/linux-64::libzlib-1.2.12-h166bdaf_2
matplotlib-base conda-forge/linux-64::matplotlib-base-3.2.2-py37h1d35a4c_1
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
numpy conda-forge/linux-64::numpy-1.21.6-py37h976b520_0
openssl conda-forge/linux-64::openssl-3.0.5-h166bdaf_1
pip conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
pplacer bioconda/linux-64::pplacer-1.1.alpha19-h9ee0642_2
prodigal bioconda/linux-64::prodigal-2.6.3-hec16e2b_4
pyparsing conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
pysam bioconda/linux-64::pysam-0.15.3-py37hda2845c_1
python conda-forge/linux-64::python-3.7.12-hf930737_100_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
scipy conda-forge/linux-64::scipy-1.7.3-py37hf2a6cf1_0
setuptools conda-forge/linux-64::setuptools-65.3.0-py37h89c1867_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/linux-64::sqlite-3.39.2-h4ff8645_1
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tornado conda-forge/linux-64::tornado-6.2-py37h540881e_0
typing-extensions conda-forge/noarch::typing-extensions-4.3.0-hd8ed1ab_0
typing_extensions conda-forge/noarch::typing_extensions-4.3.0-pyha770c72_0
wget conda-forge/linux-64::wget-1.20.3-ha35d2d1_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
zlib conda-forge/linux-64::zlib-1.2.12-h166bdaf_2
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: -
SafetyError: The package for checkm-genome located at /expanse/projects/jcl110/anaconda3/pkgs/checkm-genome-1.1.3-py_1
appears to be corrupted. The path 'site-packages/checkm/DATA_CONFIG'
has an incorrect size.
reported size: 215 bytes
actual size: 274 bytes
done
Executing transaction: | checkm data setRoot /expanse/projects/jcl110/anaconda3/envs/checkm_env/checkm_data
done
#
# To activate this environment, use
#
# $ conda activate checkm_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
I have same issue.
Do you have any solution?
CheckM2 is on anaconda cloud now. Have you tried it out yet? I've gotten pretty good results with it so far.
CheckM 1 is no longer in active development and I would recommend moving to CheckM 2. I don't maintain the conda release of CheckM so can't help directly on this front.
CheckM 1 is no longer in active development and I would recommend moving to CheckM 2. I don't maintain the conda release of CheckM so can't help directly on this front.
Thanks! I made the switch a few months back. It's an essential piece of my VEBA metagenomics software package that was just published a few days ago in Nucleic Acids Research:
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae528/7697622