Installation error due to medaka 2.0.0

[Jia340]

Hi,

Thank you for developing the amazing pipeline! I was following the instruction to install the pipeline. The dependencies can be installed without error and I got the following packages in my conda environment. However, a new medaka version (v2.0.0) was just released several weeks ago and with the current .yml file it's automatically installed, and I got the following error when running snakemake -j 1 -pr --configfile config.yml:

RuntimeError: Error validating model from '--model' argument: Model 'r941_min_high_g360' is deprecated in medaka v2.0. Please use medaka version 1.x..

I tried installing an older version of medaka, but it always has conflict with some packages. Could you please suggest a way to fix it, or provide the version of dependencies? Thank you!

_openmp_mutex             4.5                       2_gnu    conda-forge
aioeasywebdav             2.4.0           py38h578d9bd_1001    conda-forge
aiohappyeyeballs          2.4.3              pyhd8ed1ab_0    conda-forge
aiohttp                   3.10.5           py38h2019614_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.12               h4ab18f5_0    conda-forge
amply                     0.1.6              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attmap                    0.13.2             pyhd8ed1ab_0    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
bcftools                  1.21                 h8b25389_0    bioconda
bcrypt                    4.2.0            py38h4005ec7_0    conda-forge
bedtools                  2.31.1               hf5e1c6e_2    bioconda
biopython                 1.83                     pypi_0    pypi
boto3                     1.35.30            pyhd8ed1ab_0    conda-forge
botocore                  1.35.31         pyge38_1234567_0    conda-forge
brotli-python             1.1.0            py38h17151c0_1    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.32.3               h4bc722e_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.5.0              pyhd8ed1ab_0    conda-forge
cairo                     1.18.0               hebfffa5_3    conda-forge
catfishq                  1.4.0                    pypi_0    pypi
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.0           py38heb5c249_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
coin-or-cbc               2.10.12              h8b142ea_1    conda-forge
coin-or-cgl               0.60.9               h1d3f3f2_0    conda-forge
coin-or-clp               1.17.10              h07f2a63_0    conda-forge
coin-or-osi               0.108.11             h6514dde_1    conda-forge
coin-or-utils             2.11.12              h99da652_1    conda-forge
coincbc                   2.10.12           1_metapackage    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
configargparse            1.7                pyhd8ed1ab_0    conda-forge
connection_pool           0.0.3              pyhd3deb0d_0    conda-forge
contourpy                 1.1.1                    pypi_0    pypi
cryptography              43.0.0           py38hf793753_0    conda-forge
cycler                    0.12.1                   pypi_0    pypi
datrie                    0.8.2            py38h01eb140_7    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.20.1           py38h578d9bd_3    conda-forge
dpath                     2.2.0              pyha770c72_0    conda-forge
dropbox                   12.0.2             pyhd8ed1ab_0    conda-forge
eido                      0.2.2              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
expat                     2.6.3                h5888daf_0    conda-forge
filechunkio               1.8                        py_2    conda-forge
filelock                  3.16.1             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.54.1                   pypi_0    pypi
freetype                  2.12.1               h267a509_2    conda-forge
frozenlist                1.4.1            py38h01eb140_0    conda-forge
fsspec                    2024.9.0           pyhff2d567_0    conda-forge
ftputil                   5.1.0              pyhd8ed1ab_0    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
gitdb                     4.0.11             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.43             pyhd8ed1ab_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
gmpy2                     2.1.5            py38h6a1700d_1    conda-forge
google-api-core           2.20.0             pyhd8ed1ab_0    conda-forge
google-api-python-client  2.147.0            pyhd8ed1ab_0    conda-forge
google-auth               2.35.0             pyhff2d567_0    conda-forge
google-auth-httplib2      0.2.0              pyhd8ed1ab_0    conda-forge
google-cloud-core         2.4.1              pyhd8ed1ab_0    conda-forge
google-cloud-storage      2.18.2             pyhff2d567_0    conda-forge
google-crc32c             1.1.2            py38hf9d55a7_5    conda-forge
google-resumable-media    2.7.2              pyhd8ed1ab_1    conda-forge
googleapis-common-protos  1.65.0             pyhd8ed1ab_0    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
grpcio                    1.62.2           py38h94a1851_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
h5py                      3.11.0          nompi_py38h55b5aab_102    conda-forge
harfbuzz                  9.0.0                hda332d3_1    conda-forge
hdf5                      1.14.3          nompi_hdf9ad27_105    conda-forge
htslib                    1.21                 h5efdd21_0    bioconda
httplib2                  0.22.0             pyhd8ed1ab_0    conda-forge
humanfriendly             10.0               pyhd8ed1ab_6    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
intervaltree              3.1.0              pyhd8ed1ab_1    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
k8                        1.2                  h6618dc6_1    bioconda
kernel-headers_linux-64   3.10.0              he073ed8_17    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.7                    pypi_0    pypi
krb5                      1.21.3               h659f571_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_1    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20240116.2      cxx17_he02047a_1    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libblas                   3.9.0           24_linux64_openblas    conda-forge
libcblas                  3.9.0           24_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.10.1               hbbe4b11_0    conda-forge
libdeflate                1.21                 h4bc722e_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.3                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.1.0               h77fa898_1    conda-forge
libgcc-ng                 14.1.0               h69a702a_1    conda-forge
libgfortran               14.1.0               h69a702a_1    conda-forge
libgfortran-ng            14.1.0               h69a702a_1    conda-forge
libgfortran5              14.1.0               hc5f4f2c_1    conda-forge
libglib                   2.82.1               h2ff4ddf_0    conda-forge
libgomp                   14.1.0               h77fa898_1    conda-forge
libgrpc                   1.62.2               h15f2491_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           24_linux64_openblas    conda-forge
liblapacke                3.9.0           24_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libpng                    1.6.44               hadc24fc_0    conda-forge
libprotobuf               4.25.3               hd5b35b9_1    conda-forge
libre2-11                 2023.09.01           h5a48ba9_2    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.1               hadc24fc_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx                 14.1.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.1.0               h4852527_1    conda-forge
libtiff                   4.7.0                h6565414_0    conda-forge
libtorch                  2.3.1           cpu_generic_h970db74_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.49.0               hb9d3cd8_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
logmuse                   0.2.6              pyh8c360ce_0    conda-forge
mappy                     2.28             py38h6bfa29d_2    bioconda
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5            py38h01eb140_0    conda-forge
matplotlib                3.7.5                    pypi_0    pypi
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
medaka                    2.0.0            py38h8774169_0    bioconda
minimap2                  2.28                 he4a0461_3    bioconda
mpc                       1.3.1                h24ddda3_1    conda-forge
mpfr                      4.2.1                h90cbb55_3    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
multidict                 6.0.5            py38h01eb140_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numpy                     1.24.4           py38h59b608b_0    conda-forge
oauth2client              4.1.3                      py_0    conda-forge
ont-fast5-api             4.1.3              pyhdfd78af_0    bioconda
openjdk                   22.0.1               h8651b0f_1    conda-forge
openssl                   3.3.2                hb9d3cd8_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.0.3            py38h01efb38_1    conda-forge
paramiko                  3.5.0              pyhd8ed1ab_0    conda-forge
parasail-python           1.3.4            py38h40d3509_2    bioconda
pcre2                     10.44                hba22ea6_2    conda-forge
peppy                     0.40.7             pyhd8ed1ab_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pillow                    10.4.0                   pypi_0    pypi
pip                       24.2               pyh8b19718_1    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
plac                      1.4.3              pyhd8ed1ab_0    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_0    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
ply                       3.11               pyhd8ed1ab_2    conda-forge
prettytable               3.11.0             pyhd8ed1ab_0    conda-forge
progressbar33             2.4                        py_0    conda-forge
proto-plus                1.23.0             pyhd8ed1ab_0    conda-forge
protobuf                  4.25.3           py38hb5c7596_0    conda-forge
psutil                    6.0.0            py38hfb59056_0    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
pulp                      2.7.0            py38h578d9bd_1    conda-forge
pyabpoa                   1.5.3            py38h6bfa29d_0    bioconda
pyasn1                    0.6.1              pyhd8ed1ab_1    conda-forge
pyasn1-modules            0.4.1              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pynacl                    1.5.0            py38h01eb140_3    conda-forge
pyopenssl                 24.2.1             pyhd8ed1ab_2    conda-forge
pyparsing                 3.1.4              pyhd8ed1ab_0    conda-forge
pysam                     0.22.1           py38h2d19e03_2    bioconda
pysftp                    0.2.9                      py_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pyspoa                    0.2.1            py38hd638cd3_3    bioconda
pytest                    8.3.3              pyhd8ed1ab_0    conda-forge
python                    3.8.16          he550d4f_1_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-edlib              1.3.9.post1      py38h2123bcc_0    bioconda
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-irodsclient        2.1.0              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      5_cp38    conda-forge
pytorch                   2.3.1           cpu_generic_py38h1fa1760_0    conda-forge
pytz                      2024.2             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2            py38h2019614_0    conda-forge
re2                       2023.09.01           h7f4b329_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
reretry                   0.11.8             pyhd8ed1ab_0    conda-forge
rich                      13.9.1             pyhd8ed1ab_0    conda-forge
rpds-py                   0.20.0           py38h4005ec7_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
s3transfer                0.10.2             pyhd8ed1ab_0    conda-forge
samtools                  1.21                 h50ea8bc_0    bioconda
seaborn                   0.13.2                   pypi_0    pypi
seqkit                    2.8.2                h9ee0642_1    bioconda
setuptools                75.1.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
slacker                   0.14.0                     py_0    conda-forge
sleef                     3.7                  h1b44611_0    conda-forge
smart_open                7.0.4              pyhd8ed1ab_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
snakemake                 7.32.4               hdfd78af_1    bioconda
snakemake-minimal         7.32.4             pyhdfd78af_1    bioconda
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
stone                     3.3.2              pyhd8ed1ab_0    conda-forge
stopit                    1.1.2                      py_0    conda-forge
sympy                     1.13.3          pypyh2585a3b_103    conda-forge
sysroot_linux-64          2.17                h4a8ded7_17    conda-forge
tabix                     1.11                 hdfd78af_0    bioconda
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tar                       1.34                 hb2e2bae_1    conda-forge
throttler                 1.2.2              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toposort                  1.10               pyhd8ed1ab_0    conda-forge
tqdm                      4.66.5             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
tzdata                    2024a                h8827d51_1    conda-forge
ubiquerg                  0.8.0              pyhd8ed1ab_0    conda-forge
umi-amplicon-tools        1.0.0                    pypi_0    pypi
uritemplate               4.1.1              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.19            pyhd8ed1ab_0    conda-forge
varscan                   2.4.6                hdfd78af_0    bioconda
veracitools               0.1.3                      py_0    conda-forge
vsearch                   2.29.0               h6a68c12_0    bioconda
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0           py38h01eb140_0    conda-forge
wurlitzer                 3.1.1              pyhd8ed1ab_0    conda-forge
xorg-libice               1.1.1                hb9d3cd8_1    conda-forge
xorg-libsm                1.2.4                he73a12e_1    conda-forge
xorg-libx11               1.8.10               h4f16b4b_0    conda-forge
xorg-libxau               1.0.11               hb9d3cd8_1    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
xorg-libxext              1.3.6                hb9d3cd8_0    conda-forge
xorg-libxfixes            6.0.1                hb9d3cd8_0    conda-forge
xorg-libxi                1.8.2                hb9d3cd8_0    conda-forge
xorg-libxrender           0.9.11               hb9d3cd8_1    conda-forge
xorg-libxt                1.3.0                hb9d3cd8_2    conda-forge
xorg-libxtst              1.2.5                hb9d3cd8_1    conda-forge
xorg-xorgproto            2024.1               hb9d3cd8_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yarl                      1.9.4            py38h01eb140_0    conda-forge
yte                       1.5.4              pyha770c72_0    conda-forge
zipp                      3.20.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge```