Main tool: checkm2
Code repository: https://github.com/chklovski/CheckM2
Additional tools installed via micromamba:
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.2.0 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_3 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
checkm2 1.1.0 pyh7e72e81_1 bioconda
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
diamond 2.1.11 h5ca1c30_2 bioconda
flatbuffers 24.3.25 h59595ed_0 conda-forge
gast 0.6.0 pyhd8ed1ab_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
google-pasta 0.2.0 pyhd8ed1ab_2 conda-forge
grpcio 1.65.5 py312h374181b_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.13.0 nompi_py312hedeef09_100 conda-forge
hdf5 1.14.3 nompi_h2d575fe_109 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_1 conda-forge
keras 3.9.2 pyh753f3f9_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libabseil 20240722.0 cxx17_hbbce691_4 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libboost 1.86.0 h6c02f8c_3 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgrpc 1.65.5 hf5c653b_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblightgbm 4.6.0 cpu_h2211129_1 conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libprotobuf 5.27.5 h5b01275_2 conda-forge
libre2-11 2024.07.02 hbbce691_2 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lightgbm 4.6.0 cpu_py_1 conda-forge
markdown 3.8 pyhd8ed1ab_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py312h178313f_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
ml_dtypes 0.4.0 py312hf9745cd_2 conda-forge
namex 0.0.9 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
opencl-headers 2024.10.24 h5888daf_0 conda-forge
openssl 3.5.0 h7b32b05_0 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
optree 0.15.0 py312h68727a3_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.2.3 py312hf9745cd_3 conda-forge
pip 25.1 pyh8b19718_0 conda-forge
prodigal 2.6.3 h7b50bb2_10 bioconda
protobuf 5.27.5 py312h2ec8cdc_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.10 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-flatbuffers 25.2.10 pyhbc23db3_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 7_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
re2 2024.07.02 h9925aae_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
scikit-learn 1.6.1 py312h7a48858_0 conda-forge
scipy 1.15.2 py312ha707e6e_0 conda-forge
setuptools 80.1.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
tensorboard 2.17.1 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py312hda17c39_2 conda-forge
tensorflow 2.17.0 cpu_py312h69ecde4_3 conda-forge
tensorflow-base 2.17.0 cpu_py312h4c54302_3 conda-forge
tensorflow-estimator 2.17.0 cpu_py312h4f468f2_3 conda-forge
termcolor 3.1.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typing-extensions 4.13.2 h0e9735f_0 conda-forge
typing_extensions 4.13.2 pyh29332c3_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py312h66e93f0_0 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zstandard 0.23.0 py312h66e93f0_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Basic information on how to use this tool:
- executable: checkm2
- help: -h, --help
- version: --version
- description: Rapid assessment of genome bin quality using machine learning.
Additional information:
CheckM2 relies on a external diamond database (~1.7 GB) for rapid annotation. the database can be downloaded via checkm2 database --download command or obtained directly from: https://zenodo.org/records/14897628
Full documentation: https://github.com/chklovski/CheckM2
checkm2 predict --threads 8 fasta --input ./input_folder --output-directory ./output_folder --database_path /path/to/database/CheckM2_database/uniref100.KO.1.dmnd