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uw-ipd / RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction
MIT License
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Solving environment hangs on Ubuntu 22.04 #37

Open ronboger opened 1 year ago

ronboger commented 1 year ago

Hello! I'm trying to install the code on a standard t2.2xlarge AWS instance with Ubuntu 22.04 LTS installed. These are the steps I've taken:

Install microconda

https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Clone and create the RF2na environment:

git clone https://github.com/uw-ipd/RoseTTAFold2NA.git
cd RoseTTAFold2NA
conda env create -f RF2na-linux.yml

The following then happens:

Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

and then

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc conflicts for:
bioconda::blast -> libgcc
bioconda::cd-hit -> libgcc
dglteam::dgl-cuda11.3 -> scipy -> libgcc
bioconda::infernal -> libgcc

Package libgcc-ng conflicts for:
bioconda::cd-hit -> libgcc-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.3.0|>=4.9']
bioconda::mafft -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0']
bioconda::hhsuite -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0']
conda-forge::tqdm -> python[version='>=2.7'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0|>=12|>=9.4.0|>=9.3.0|>=4.9']
bioconda::blast -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
bioconda::cd-hit -> zlib[version='>=1.2.12,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.2.0']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0']
bioconda::hmmer[version='>=3.3'] -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0|>=7.3.0']
requests -> python[version='>=3.8,<3.9.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=12|>=9.4.0|>=9.3.0|>=7.2.0|>=4.9']
conda-forge::psutil -> python[version='>=3.9,<3.10.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.2.0']
bioconda::hhsuite -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5] -> libgcc-ng[version='>=11.2.0|>=7.2.0|>=4.9']
bioconda::blast -> curl[version='>=7.83.1,<8.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.2.0']
bioconda::infernal -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5] -> libgcc-ng[version='>=11.2.0|>=9.4.0|>=7.2.0']
conda-forge::psutil -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
bioconda::csblast -> libgcc-ng[version='>=10.3.0|>=9.3.0']
python=3.8 -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=12|>=9.4.0|>=9.3.0']
dglteam::dgl-cuda11.3 -> numpy -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0|>=12|>=9.4.0|>=9.3.0|>=4.9']
bioconda::infernal -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
pytorch::pytorch -> blas=[build=mkl] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=7.2.0|>=4.9']

Package numpy conflicts for:
bioconda::blast -> boost[version='>=1.68.0,<1.68.1.0a0'] -> numpy[version='1.11.*|1.12.*|1.13.*|>=1.11|>=1.8|>=1.9.3,<2.0a0|>=1.9|>=1.7|>=1.23.4,<2.0a0|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.21.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.16.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.14.6,<2.0a0']
pytorch::pytorch -> numpy[version='>=1.11|>=1.19']
dglteam::dgl-cuda11.3 -> networkx -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16,<1.23|>=1.19,<1.25.0|>=1.19|>=1.19,<1.26.0|>=1.21,<1.26.0|>=1.21,<1.25.0|>=1.21,<1.23|>=1.16.6,<1.23.0|>=1.21.2,<1.23.0|>=1.16.6,<2.0a0|>=1.15.1,<2.0a0|>=1.9.3,<2.0a0|>=1.21.6,<1.26|>=1.21.6,<2.0a0|>=1.23.4,<1.26|>=1.23.4,<2.0a0|>=1.20.3,<1.26|>=1.20.3,<2.0a0|>=1.19.5,<2.0a0|>=1.20.3,<1.25|>=1.21.6,<1.25|>=1.18.5,<2.0a0|>=1.21.5,<2.0a0|>=1.20.3,<1.23|>=1.21.6,<1.23|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9']
dglteam::dgl-cuda11.3 -> numpy

Package tzdata conflicts for:
conda-forge::psutil -> python[version='>=3.11,<3.12.0a0'] -> tzdata
bioconda::hhsuite -> python[version='>=3.10,<3.11.0a0'] -> tzdata
conda-forge::tqdm -> python[version='>=2.7'] -> tzdata
dglteam::dgl-cuda11.3 -> python[version='>=3.9,<3.10.0a0'] -> tzdata
pytorch::pytorch -> python[version='>=3.10,<3.11.0a0'] -> tzdata
requests -> python[version='>=3.10,<3.11.0a0'] -> tzdata

Package ncurses conflicts for:
python=3.8 -> ncurses[version='>=6.1,<7.0.0a0|>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0']
python=3.8 -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='5.9.*|6.0.*|>=6.0,<7.0a0']

Package _libgcc_mutex conflicts for:
bioconda::csblast -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1|0.1',build='conda_forge|main']
bioconda::cd-hit -> _openmp_mutex[version='>=4.5'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']
bioconda::hmmer[version='>=3.3'] -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1|0.1',build='conda_forge|main']
bioconda::infernal -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1|0.1',build='conda_forge|main']
python=3.8 -> libgcc-ng[version='>=11.2.0'] -> _libgcc_mutex[version='*|0.1|0.1',build='conda_forge|main']
conda-forge::psutil -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']
bioconda::mafft -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']
bioconda::blast -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']
bioconda::hhsuite -> _openmp_mutex[version='>=4.5'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']

Package libffi conflicts for:
pytorch::pytorch -> python[version='>=3.10,<3.11.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0|>=3.3|<3.3.0.a0']
dglteam::dgl-cuda11.3 -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0']
python=3.8 -> libffi[version='>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0']
requests -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0']
conda-forge::psutil -> python[version='>=3.11,<3.12.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4.2,<3.5.0a0|>=3.4,<4.0a0|>=3.2.1,<3.3a0']
bioconda::hhsuite -> python[version='>=3.10,<3.11.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0']
conda-forge::tqdm -> python[version='>=2.7'] -> libffi[version='3.2.*|>=3.2.1,<3.3a0|>=3.3,<3.4.0a0|>=3.4,<3.5|>=3.4,<4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3.0a0']

Package libblas conflicts for:
pytorch::pytorch -> blas=[build=mkl] -> libblas[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|>=3.9.0,<4.0a0|>=3.8.0,<4.0a0',build='4_mkl|6_mkl|7_mkl|8_mkl|9_mkl|12_mkl|13_mkl|18_mkl|19_mkl|6_mkl|7_mkl|8_mkl|10_mkl|14_linux64_mkl|15_linux64_mkl|16_linux64_mkl|13_linux64_mkl|12_linux64_mkl|11_linux64_mkl|9_mkl|5_mkl|21_mkl|20_mkl|16_mkl|15_mkl|14_mkl|11_mkl|10_mkl|5_mkl']
dglteam::dgl-cuda11.3 -> numpy -> libblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']

Package gmp conflicts for:
bioconda::blast -> gnutls[version='>=3.6.5,<3.7.0a0'] -> gmp[version='6.1.*|>=6.1.2|>=4.2']
bioconda::cd-hit -> libgcc -> gmp[version='>=4.2']
bioconda::blast -> gmp[version='>=6.1.2,<7.0a0']
bioconda::infernal -> libgcc -> gmp[version='>=4.2']

Package libsqlite conflicts for:
python=3.8 -> libsqlite[version='>=3.40.0,<4.0a0']
python=3.8 -> sqlite[version='>=3.40.0,<4.0a0'] -> libsqlite[version='3.39.2|3.39.3|3.39.4|3.40.0|>=3.39.4,<4.0a0|>=3.39.2,<4.0a0',build='h753d276_0|h753d276_1']

Package _openmp_mutex conflicts for:
bioconda::csblast -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
bioconda::blast -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
python=3.8 -> libgcc-ng[version='>=11.2.0'] -> _openmp_mutex[version='>=4.5']
bioconda::infernal -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
bioconda::cd-hit -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex
pytorch::pytorch -> blas=[build=mkl] -> _openmp_mutex[version='*|>=4.5',build=*_llvm]
bioconda::hhsuite -> _openmp_mutex[version='>=4.5']
bioconda::mafft -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
bioconda::hmmer[version='>=3.3'] -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
conda-forge::psutil -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
bioconda::hhsuite -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex
bioconda::cd-hit -> _openmp_mutex[version='>=4.5']

Package ca-certificates conflicts for:
conda-forge::psutil -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
requests -> python -> ca-certificates
pytorch::pytorch -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
conda-forge::tqdm -> python[version='>=2.7'] -> ca-certificates
bioconda::blast -> gnutls[version='>=3.6.5,<3.7.0a0'] -> ca-certificates
bioconda::hhsuite -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.8 -> openssl[version='>=1.1.1s,<1.1.2a'] -> ca-certificates

Package python conflicts for:
dglteam::dgl-cuda11.3 -> networkx -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5|>=3.6|>=3.7|>=3.8|>=3.5,<3.6.0a0|3.4.*|>=3.11,<3.12.0a0|>=3.7,<4.0|>=3.6,<4.0|>=2.7']
dglteam::dgl-cuda11.3 -> python[version='>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
python=3.8
conda-forge::psutil -> python_abi=3.11[build=*_cp311] -> python[version='3.10.*|3.11.*|3.9.*|3.8.*|3.7.*']
conda-forge::tqdm -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=2.7|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|3.4.*']
conda-forge::tqdm -> colorama -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|>=3.7|>=3.6']
pytorch::pytorch -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
requests -> certifi[version='>=2017.4.17'] -> python[version='3.7.*|3.8.*|<4.0|>=3.5|>=3.7']
bioconda::hhsuite -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0']
conda-forge::psutil -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.*']
pytorch::pytorch -> typing_extensions -> python[version='2.7.*|3.5.*|3.6.*|3.9.*|>=3.11,<3.12.0a0|>=3.5|>=3.6|>=3.7|>=3.6,<3.7|3.4.*|3.9.10|3.8.12|3.7.12|3.7.10|3.7.10|3.6.12|3.7.9|3.6.12|3.6.9|3.6.9|3.6.9|3.6.9|>=3.8|>=3',build='0_73_pypy|2_73_pypy|4_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|5_73_pypy|5_73_pypy|3_73_pypy|1_73_pypy']
bioconda::hhsuite -> python_abi=3.10[build=*_cp310] -> python[version='2.7.*|3.10.*|3.8.*|3.7.*|3.9.*|3.6.*']
requests -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.6|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.7,<4.0|>=3.6,<4.0|3.4.*']
bioconda::blast -> boost[version='>=1.68.0,<1.68.1.0a0'] -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.11,<3.12.0a0']

Package mkl conflicts for:
pytorch::pytorch -> mkl[version='>=2018']
pytorch::pytorch -> blas=[build=mkl] -> mkl[version='>=2018.0.0,<2019.0a0|>=2018.0.1,<2019.0a0|>=2018.0.2,<2019.0a0|>=2018.0.3,<2019.0a0|>=2019.1,<2021.0a0|>=2019.3,<2021.0a0|>=2019.4,<2021.0a0|>=2021.2.0,<2022.0a0|>=2021.3.0,<2022.0a0|>=2021.4.0,<2022.0a0|>=2019.4,<2020.0a0']

Package libzlib conflicts for:
bioconda::cd-hit -> zlib[version='>=1.2.12,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_2|h166bdaf_3|h166bdaf_4|h166bdaf_1|h166bdaf_1014|h36c2ea0_1012']
python=3.8 -> zlib[version='>=1.2.13,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.12,<1.3.0a0',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_2|h166bdaf_3|h166bdaf_4|h166bdaf_1|h166bdaf_1014|h36c2ea0_1012']
python=3.8 -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0']
conda-forge::psutil -> python[version='>=3.11,<3.12.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::blast -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::cd-hit -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::hhsuite -> python[version='>=3.10,<3.11.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::blast -> curl[version='>=7.83.1,<8.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.13,<1.3.0a0',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_2|h166bdaf_3|h166bdaf_4|h166bdaf_1|h166bdaf_1014|h36c2ea0_1012']
requests -> python[version='>=3.8,<3.9.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']
conda-forge::tqdm -> python[version='>=2.7'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
pytorch::pytorch -> python[version='>=3.10,<3.11.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
dglteam::dgl-cuda11.3 -> python[version='>=3.8,<3.9.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']

Package sqlite conflicts for:
python=3.8 -> sqlite[version='>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.31.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.35.4,<4.0a0|>=3.36.0,<4.0a0|>=3.38.0,<4.0a0|>=3.39.3,<4.0a0|>=3.40.0,<4.0a0|>=3.37.1,<4.0a0|>=3.37.0,<4.0a0|>=3.35.5,<4.0a0|>=3.34.0,<4.0a0']
python=3.8 -> pypy3.8=7.3.9 -> sqlite[version='>=3.38.2,<4.0a0|>=3.39.1,<4.0a0|>=3.39.2,<4.0a0']

Package perl conflicts for:
bioconda::blast -> entrez-direct -> perl[version='>=5.22.0,<5.23.0|>=5.26.2,<5.27.0a0|>=5.32.1,<6.0a0',build=*_perl5]
bioconda::blast -> perl[version='5.22.0.*|>=5.26.2,<5.26.3.0a0']
bioconda::hhsuite -> perl[version='>=5.26.2,<5.26.3.0a0|>=5.32.1,<5.33.0a0',build=*_perl5]
bioconda::infernal -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5]

Package pypy3.6 conflicts for:
requests -> certifi[version='>=2017.4.17'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
pytorch::pytorch -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.3|>=7.3.2']
bioconda::blast -> boost -> pypy3.6[version='>=7.3.3']
bioconda::hhsuite -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
dglteam::dgl-cuda11.3 -> numpy -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
conda-forge::psutil -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
conda-forge::tqdm -> python[version='>=2.7'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
conda-forge::psutil -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']

Package xz conflicts for:
python=3.8 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0|>=5.2.6,<6.0a0|>=5.2.5,<5.3.0a0']
python=3.8 -> pypy3.8=7.3.9 -> xz[version='>=5.2.6,<5.3.0a0']

Package blas conflicts for:
pytorch::pytorch -> numpy[version='>=1.19'] -> blas[version='*|1.0|1.0|1.1',build='openblas|mkl|openblas|openblas']
pytorch::pytorch -> blas=[build=mkl]

Package requests conflicts for:
dglteam::dgl-cuda11.3 -> requests
requests

Package expat conflicts for:
python=3.8 -> pypy3.8=7.3.9 -> expat[version='>=2.4.7,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0']
conda-forge::psutil -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.7,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0']

Package psutil conflicts for:
dglteam::dgl-cuda11.3 -> psutil
conda-forge|conda-forge::psutil
conda-forge::psutil

Package libnsl conflicts for:
conda-forge::tqdm -> python[version='>=2.7'] -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::hhsuite -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5] -> libnsl[version='>=2.0.0,<2.1.0a0']
conda-forge::psutil -> python[version='>=3.11,<3.12.0a0'] -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::infernal -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5] -> libnsl[version='>=2.0.0,<2.1.0a0']
pytorch::pytorch -> python[version='>=3.10,<3.11.0a0'] -> libnsl[version='>=2.0.0,<2.1.0a0']
requests -> python[version='>=3.8,<3.9.0a0'] -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::blast -> perl -> libnsl[version='>=2.0.0,<2.1.0a0']
python=3.8 -> libnsl[version='>=2.0.0,<2.1.0a0']
dglteam::dgl-cuda11.3 -> python[version='>=3.8,<3.9.0a0'] -> libnsl[version='>=2.0.0,<2.1.0a0']

Package cudatoolkit conflicts for:
conda-forge|conda-forge::cudatoolkit=11.3
pytorch::pytorch -> cudatoolkit[version='8.*|>=10.0,<10.1|>=10.1,<10.2|>=10.2,<10.3|>=11.3,<11.4|>=11.6,<11.7|>=11.5,<11.6|>=11.1,<11.2|>=11.0,<11.1|>=9.2,<9.3|>=9.0,<9.1|>=8.0,<8.1|9.*']
conda-forge::cudatoolkit=11.3

Package setuptools conflicts for:
python=3.8 -> pip -> setuptools
dglteam::dgl-cuda11.3 -> networkx -> setuptools

Package gdbm conflicts for:
bioconda::blast -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']
python=3.8 -> pypy3.8=7.3.9 -> gdbm[version='>=1.18,<1.19.0a0']
conda-forge::psutil -> pypy3.9[version='>=7.3.9'] -> gdbm[version='>=1.18,<1.19.0a0']

Package clangdev conflicts for:
bioconda::cd-hit -> openmp -> clangdev[version='4.0.0|4.0.0|4.0.0.*|5.0.0|5.0.0.*']
bioconda::hhsuite -> openmp -> clangdev[version='4.0.0|4.0.0|4.0.0.*|5.0.0|5.0.0.*']

Package llvm-openmp conflicts for:
pytorch::pytorch -> blas=[build=mkl] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=15.0.6|>=14.0.3|>=9.0.1']
bioconda::cd-hit -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='8.0.0|8.0.0|8.0.1|>=9.0.1',build='hc9558a2_0|hc9558a2_0|hc9558a2_1']
bioconda::hhsuite -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='8.0.0|8.0.0|8.0.1|>=9.0.1',build='hc9558a2_0|hc9558a2_0|hc9558a2_1']

Package tqdm conflicts for:
dglteam::dgl-cuda11.3 -> tqdm
conda-forge::tqdm
conda-forge|conda-forge::tqdm

Package libstdcxx-ng conflicts for:
python=3.8 -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=9.4.0|>=9.3.0']
python=3.8 -> libffi[version='>=3.2.1,<3.3a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0']

Package zlib conflicts for:
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
python=3.8 -> pypy3.8=7.3.9 -> zlib

Package blast-legacy conflicts for:
biocore::blast-legacy=2.2.26
biocore|biocore::blast-legacy=2.2.26
biocore::psipred=4.01 -> blast-legacy==2.2.26The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - feature:|@/linux-64::__glibc==2.35=0
  - bioconda::blast -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::cd-hit -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::csblast -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::hhsuite -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::hmmer[version='>=3.3'] -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::infernal -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::mafft -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::cudatoolkit=11.3 -> __glibc[version='>=2.17,<3.0.a0']
  - conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::psutil -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - pytorch::pytorch -> cudatoolkit[version='>=11.3,<11.4'] -> __glibc[version='>=2.17,<3.0.a0']

Your installed version is: 2.35

Note that strict channel priority may have removed packages required for satisfiability.

I've also tried doing the same on the standard Pytorch 13.1 deep learning AMI for AWS and have run into the same issue. What am I doing wrong here?

stianale commented 7 months ago

I get these same errors when following the exact procedure listed in the readme. I have Ubuntu 22.04.

Edit. Got around it by first creating a clean conda env, then adding channels, and then running the command conda config --set channel_priority flexible, before running conda env update -n RF2NA -f RF2na-linux.yml

SuhasSrinivasan commented 3 months ago

Potential solution #105