Closed jotech closed 1 year ago
Thank you for creating the issue. I tried to fix it with the above commit Could you try install ing dev version from github or simply modifying the env/dram.yaml file accordingly?
hi @SilasK Thanks a lot for your fast response!
There seems to be another problem to find a fitting version of python:
mamba env create -p [...]/dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_ --file [...]/envs/atlas/lib/python3.10/site-packages/atlas/workflow/envs/dram.yaml
Looking for: ['python=3.11', "dram[version='>=1.4.6,<1.5']", "scikit-bio[version='>=0.5.8,<0.6']", "pandas[version='>=1.5,<2']"]
Could not solve for environment specs
The following packages are incompatible
├─ dram >=1.4.6,<1.5 is installable and it requires
│ └─ scipy <=1.8.1 with the potential options
│ ├─ scipy [0.17.1|0.18.0|...|1.2.1] would require
│ │ └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
│ ├─ scipy [0.17.1|0.18.0|0.18.1|0.19.1] would require
│ │ └─ python 3.4* , which can be installed;
│ ├─ scipy [0.17.1|0.18.0|...|1.1.0] would require
│ │ └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
│ ├─ scipy [0.18.1|0.19.0|0.19.1|1.0.0|1.0.1] would require
│ │ └─ python 3.6* , which can be installed;
│ ├─ scipy [0.19.1|1.0.0|...|1.5.2] would require
│ │ └─ python >=3.6,<3.7.0a0 , which can be installed;
│ ├─ scipy [1.1.0|1.2.0|...|1.7.3] would require
│ │ └─ python >=3.7,<3.8.0a0 , which can be installed;
│ ├─ scipy [1.3.1|1.3.2|...|1.7.3] would require
│ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
│ ├─ scipy [1.4.1|1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ ├─ python >=3.6,<3.7.0a0 , which can be installed;
│ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ ├─ scipy [1.4.1|1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ └─ python_abi 3.6 *_pypy36_pp73, which can be installed;
│ ├─ scipy [1.4.1|1.5.0|...|1.7.3] would require
│ │ ├─ python >=3.7,<3.8.0a0 , which can be installed;
│ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ ├─ scipy [1.4.1|1.5.0|...|1.8.1] would require
│ │ ├─ python >=3.8,<3.9.0a0 , which can be installed;
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ ├─ scipy [1.5.2|1.5.3|...|1.8.1] would require
│ │ ├─ python >=3.9,<3.10.0a0 , which can be installed;
│ │ └─ python_abi 3.9.* *_cp39, which can be installed;
│ ├─ scipy [1.6.0|1.6.1|...|1.7.3] would require
│ │ └─ python_abi 3.7 *_pypy37_pp73, which can be installed;
│ ├─ scipy [1.7.2|1.7.3|1.8.0|1.8.1] would require
│ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
│ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ ├─ scipy 1.8.1 would require
│ │ └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│ ├─ scipy 1.8.1 would require
│ │ └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
│ ├─ scipy [1.5.2|1.6.0|...|1.7.3] would require
│ │ └─ python >=3.9,<3.10.0a0 , which can be installed;
│ └─ scipy 1.7.3 would require
│ └─ python >=3.10,<3.11.0a0 , which can be installed;
└─ python 3.11** is uninstallable because it conflicts with any installable versions previously reported.
Ok let's remove the python requirement. Can you pull the latest commit and re-try?
Could you also telle me which versions you had in the initial env?
run:
conda activate [...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_
conda list python
conda list scipy
conda list scikit-learn
conda deactivate
unfortunately, removing the python requirement does not solve the incompatibility. The only valid solution for this I found was to allow an older version of scikit-bio (0.5.7)
, but this then causes the error reported initially.
Looking for: ['python', "dram[version='>=1.4.6,<1.5']", "scikit-bio[version='>=0.5.8,<0.6']", "pandas[version='>=1.5,<2']"]
Could not solve for environment specs
The following packages are incompatible
├─ dram >=1.4.6,<1.5 is installable and it requires
│ ├─ python >=3.6 with the potential options
│ │ ├─ python [3.8.0|3.8.1] would require
│ │ │ └─ python_abi * *_cp38, which can be installed;
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16] would require
│ │ │ └─ python_abi 3.8 *_pypy38_pp73, which conflicts with any installable versions previously reported;
│ │ ├─ python 3.8.5 would require
│ │ │ └─ python_abi 3.8.* *_graalpy223_38_native, which can be installed;
│ │ ├─ python [3.6.0|3.6.1|...|3.6.7] would require
│ │ │ └─ python_abi * *_cp36m, which can be installed;
│ │ ├─ python [3.6.10|3.6.11|...|3.6.9] would require
│ │ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ │ ├─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported;
│ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6] would require
│ │ │ └─ python_abi * *_cp37m, which can be installed;
│ │ ├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
│ │ ├─ python [3.7.10|3.7.12|...|3.7.9] would require
│ │ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ ├─ python [3.9.10|3.9.12|3.9.16] would require
│ │ │ └─ python_abi 3.9 *_pypy39_pp73, which conflicts with any installable versions previously reported;
│ │ ├─ python [3.10.0|3.10.1|...|3.10.9] conflicts with any installable versions previously reported;
│ │ └─ python [3.11.0|3.11.1|3.11.2|3.11.3|3.11.4] conflicts with any installable versions previously reported;
│ └─ scipy <=1.8.1 with the potential options
│ ├─ scipy [0.17.1|0.18.0|...|1.2.1] would require
│ │ └─ python [2.7* |>=2.7,<2.8.0a0 ], which conflicts with any installable versions previously reported;
│ ├─ scipy [0.17.1|0.18.0|0.18.1|0.19.1] would require
│ │ └─ python 3.4* , which conflicts with any installable versions previously reported;
│ ├─ scipy [0.17.1|0.18.0|...|1.1.0] would require
│ │ └─ python [3.5* |>=3.5,<3.6.0a0 ], which conflicts with any installable versions previously reported;
│ ├─ scipy [0.18.1|0.19.0|0.19.1|1.0.0|1.0.1] would require
│ │ └─ python 3.6* but there are no viable options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.7], which cannot be installed (as previously explained);
│ │ ├─ python [3.6.10|3.6.11|...|3.6.9], which cannot be installed (as previously explained);
│ │ ├─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported;
│ │ └─ python [3.6.0a3|3.6.0a4|...|3.6.0rc1] conflicts with any installable versions previously reported;
│ ├─ scipy [0.19.1|1.0.0|...|1.5.2] would require
│ │ └─ python >=3.6,<3.7.0a0 but there are no viable options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.7], which cannot be installed (as previously explained);
│ │ ├─ python [3.6.10|3.6.11|...|3.6.9], which cannot be installed (as previously explained);
│ │ └─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported;
│ ├─ scipy [1.1.0|1.2.0|...|1.7.3] would require
│ │ └─ python >=3.7,<3.8.0a0 but there are no viable options
│ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6], which cannot be installed (as previously explained);
│ │ ├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
│ │ └─ python [3.7.10|3.7.12|...|3.7.9], which cannot be installed (as previously explained);
│ ├─ scipy [1.3.1|1.3.2|...|1.8.1] would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ │ └─ python 3.8.5, which can be installed (as previously explained);
│ │ └─ python_abi 3.8 *_pypy38_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.4.1|1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ ├─ python >=3.6,<3.7.0a0 but there are no viable options
│ │ │ ├─ python [3.6.0|3.6.1|...|3.6.7], which cannot be installed (as previously explained);
│ │ │ ├─ python [3.6.10|3.6.11|...|3.6.9], which cannot be installed (as previously explained);
│ │ │ └─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported;
│ │ └─ python_abi 3.6.* *_cp36m, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.4.1|1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ ├─ python >=3.6,<3.7.0a0 but there are no viable options
│ │ │ ├─ python [3.6.0|3.6.1|...|3.6.7], which cannot be installed (as previously explained);
│ │ │ ├─ python [3.6.10|3.6.11|...|3.6.9], which cannot be installed (as previously explained);
│ │ │ └─ python [3.6.10|3.6.12|...|3.6.9] conflicts with any installable versions previously reported;
│ │ └─ python_abi 3.6 *_pypy36_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.4.1|1.5.0|...|1.7.3] would require
│ │ ├─ python >=3.7,<3.8.0a0 but there are no viable options
│ │ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6], which cannot be installed (as previously explained);
│ │ │ ├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
│ │ │ └─ python [3.7.10|3.7.12|...|3.7.9], which cannot be installed (as previously explained);
│ │ └─ python_abi 3.7.* *_cp37m, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.4.1|1.5.0|...|1.8.1] would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ │ └─ python 3.8.5, which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.5.2|1.5.3|...|1.8.1] would require
│ │ ├─ python >=3.9,<3.10.0a0 but there are no viable options
│ │ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ │ └─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ │ └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.6.0|1.6.1|...|1.7.3] would require
│ │ ├─ python >=3.7,<3.8.0a0 but there are no viable options
│ │ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6], which cannot be installed (as previously explained);
│ │ │ ├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
│ │ │ └─ python [3.7.10|3.7.12|...|3.7.9], which cannot be installed (as previously explained);
│ │ └─ python_abi 3.7 *_pypy37_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.7.2|1.7.3|1.8.0|1.8.1] would require
│ │ ├─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
│ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ ├─ scipy [1.10.0|1.10.1|...|1.9.3] would require
│ │ ├─ python >=3.9,<3.10.0a0 but there are no viable options
│ │ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ │ └─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ │ └─ python_abi 3.9 *_pypy39_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.3.1|1.3.2|...|1.6.2] would require
│ │ ├─ mkl >=2019.4,<2021.0a0 , which can be installed;
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ └─ python 3.8.5, which can be installed (as previously explained);
│ └─ scipy 1.7.3 would require
│ └─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
├─ pandas >=1.5,<2 is installable with the potential options
│ ├─ pandas [1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ └─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
│ ├─ pandas [1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ └─ python 3.8.5, which can be installed (as previously explained);
│ ├─ pandas [1.5.0|1.5.1|1.5.2|1.5.3] would require
│ │ └─ python >=3.9,<3.10.0a0 but there are no viable options
│ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ └─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ └─ pandas [1.5.1|1.5.2|1.5.3] would require
│ └─ python >=3.11,<3.12.0a0 , which conflicts with any installable versions previously reported;
└─ scikit-bio >=0.5.8,<0.6 is uninstallable because there are no viable options
├─ scikit-bio 0.5.8 would require
│ ├─ python [>=3.10,<3.11.0a0 |>=3.8,<3.9.0a0 |>=3.9,<3.10.0a0 ] with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ ├─ python 3.8.5, which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ ├─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ │ └─ python [3.10.0|3.10.1|...|3.10.9] conflicts with any installable versions previously reported;
│ ├─ python_abi [3.8.* *_cp38|3.9.* *_cp39], which conflicts with any installable versions previously reported;
│ └─ scipy >=1.9.0 but there are no viable options
│ ├─ scipy [1.10.0|1.10.1|...|1.9.3], which cannot be installed (as previously explained);
│ ├─ scipy [1.9.1|1.9.3] would require
│ │ ├─ mkl >=2021.4.0,<2022.0a0 , which conflicts with any installable versions previously reported;
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ └─ python 3.8.5, which can be installed (as previously explained);
│ ├─ scipy [1.10.0|1.10.1|...|1.9.3] would require
│ │ └─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
│ ├─ scipy [1.10.0|1.10.1|...|1.9.3] would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ │ └─ python 3.8.5, which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.10.0|1.10.1|...|1.9.3] would require
│ │ ├─ python >=3.9,<3.10.0a0 but there are no viable options
│ │ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ │ └─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ │ └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported;
│ ├─ scipy [1.10.0|1.10.1|1.9.3] would require
│ │ └─ python >=3.11,<3.12.0a0 , which conflicts with any installable versions previously reported;
│ ├─ scipy [1.10.0|1.10.1] would require
│ │ ├─ pypy3.8 >=7.3.11 , which conflicts with any installable versions previously reported;
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ └─ python 3.8.5, which can be installed (as previously explained);
│ ├─ scipy [1.10.0|1.10.1] would require
│ │ ├─ pypy3.9 >=7.3.11 , which conflicts with any installable versions previously reported;
│ │ └─ python >=3.9,<3.10.0a0 but there are no viable options
│ │ ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
│ │ └─ python [3.9.10|3.9.12|3.9.16], which cannot be installed (as previously explained);
│ ├─ scipy [1.10.0|1.10.1|1.9.1|1.9.3] would require
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ │ └─ python 3.8.5, which can be installed (as previously explained);
│ └─ scipy 1.9.3 would require
│ ├─ mkl >=2023.1.0,<2024.0a0 , which can be installed;
│ └─ python >=3.8,<3.9.0a0 with the potential options
│ ├─ python [3.8.0|3.8.1], which can be installed (as previously explained);
│ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ ├─ python [3.8.12|3.8.13|3.8.16], which cannot be installed (as previously explained);
│ └─ python 3.8.5, which can be installed (as previously explained);
└─ scikit-bio 0.5.8 would require
└─ python >=3.11,<3.12.0a0 , which conflicts with any installable versions previously reported.
Version numbers from the old environment:
conda list python
#
# Name Version Build Channel
ipython 8.14.0 pyh41d4057_0 conda-forge
msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge
python 3.10.11 he550d4f_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
conda list scipy
#
# Name Version Build Channel
scipy 1.8.1 py310hdfbd76f_3 conda-forge
conda list scikit-learn
#
# Name Version Build Channel
scikit-learn 1.2.2 py310hf7d194e_2 conda-forge
Can you try again please with the latest commit?
I tried a fresh install with the latest developmental version, but it still doesn't work. I would assume that the error does not occur in your case because the dram database might be already prepared?
Thank you for your ideas and then let's see what the dram people reply.
I made a new bioconda release of dram (same version but a new build) that should handle all the dependencies. This will prpbalby take some minutes to be available.
I also simplified the environment in atlas on the master-branch. atlas v 2.17
If you prefer not to update to atlas v2.17 you can use the branch fix-664
that has the simplified environment but still atlas v2.16.*
hi @SilasK Thank you for the update! I tried the new version with the new dram, but unfortunately, as far as I can see, the error with the PearsonRConstantInputWarning persists.
conda activate [...]/atlas/conda_envs/bd5b0fdab3853fca343b76be3f6692de_
conda list scikit-learn
# packages in environment at [...]/atlas/conda_envs/bd5b0fdab3853fca343b76be3f6692de_:
#
# Name Version Build Channel
scikit-learn 1.2.2 py310hf7d194e_2 conda-forge
conda list scikit-learn
# packages in environment at [...]/atlas/conda_envs/bd5b0fdab3853fca343b76be3f6692de_:
#
# Name Version Build Channel
scikit-learn 1.2.2 py310hf7d194e_2 conda-forge
conda list python
# packages in environment at [...]/atlas/conda_envs/bd5b0fdab3853fca343b76be3f6692de_:
#
# Name Version Build Channel
ipython 8.14.0 pyh41d4057_0 conda-forge
msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge
python 3.10.11 he550d4f_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
>> from scipy.stats import PearsonRConstantInputWarning
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: cannot import name 'PearsonRConstantInputWarning' from 'scipy.stats' ([...]/.local/lib/python3.10/site-packages/scipy/stats/__init__.py)
I don't know why the package does not work on your server.
What you can try is to enter the conda env and reinstall dram:
conda activate [...]/atlas/conda_envs/bd5b0fdab3853fca343b76be3f6692de_
mamba uninstall dram
mamba install dram=1.4.6
#test dram
DRAM-setup.py --help
conda deactivate
This should limit the version of scipy and scikit-bio (not scikit-learn)
could you test if this is the case.
scipy <=1.8.1 scikit-bio<=0.5.7
Unfortunately, it's still not working. I reinstalled it from scratch and also installed dram=1.4.6 on a fresh system, and the same error occurs.
But I'm still a bit confused, don't we need scikit-bio 0.5.8 as mentioned here scikit-bio/issues/1818
When I just install dram with scikit-bio=0.5.8 in a fresh conda, the error does not occur, although this installs dram-1.3.5 and scipy-1.11. At least then I can download the databases needed by dram, although I don't know if the dram=1.3.5 causes any errors within the atlas pipeline?
I made a new dram build, and it passed all the tests. e.g. it run DRAM-setup.py --help
without error.
Did you already get an error when running DRAM-setup.py --help
?
As you noticed there are some conflicts between versions of scipy and scikit-bio. I tried to solve this at multiple levels.
There are two solutions. keep everything at the latest version when it should work (that's what I tried. sckit-bio < 5.8, scipy < 1.8) https://github.com/WrightonLabCSU/DRAM/issues/191#issuecomment-1201699237
Or update to the most recent version when it should work again.
But scikit-bio 5.8 requires python 3.11, which I think is not compatible with everything.
Yes I'm getting the error already with DRAM-setup.py --help
when using dram=1.4.6 and scikit-bio=0.5.7
with scikit-bio=0.5.8 and dram=1.3.5 it works but some downloads fail here because of the older dram version (ncbi removed some files).
I'm really stuck here, it is really strange that it is not reproducible although we both use conda and the same software versions.
My overall problem is that I cannot continue with the atlas pipeline because the failed dram download causes the whole pipeline to stop even when I exclude dram analysis from the config.yaml
My overall problem is that I cannot continue with the atlas pipeline because the failed dram download causes the whole pipeline to stop even when I exclude dram analysis from the
config.yaml
If you comment both kegg_modules and dram in the annotations file you should be able to run atlas run genomes
annotations:
- gtdb_tree
- gtdb_taxonomy
- genes
# - kegg_modules
# - dram
With dram=1.4.6 and scikit-bio=0.5.7 which version of scipy do you have?
It could be that you re-installed the dram v1.4.6 build 0, and not my new build nr 1. Cou can check whcih build you have with conda list dram however I don't know if there is a way to specify the build. Usually, de-install and reinstall should work.
I managed to install dram on a colab using bioconda and also using the latest version of scikit-bio.. https://colab.research.google.com/drive/1q6OhFD12tZJJznFHCH6uNHQIJh0B4Dke?usp=sharing
With dram=1.4.6 and scikit-bio=0.5.7 which version of scipy do you have?
scipy=1.8.1
Cou can check whcih build you have with conda list dram
# Name Version Build Channel dram 1.4.6 pyhdfd78af_1 bioconda
This should be the latest build, shouldn't it?
yes it is the latest version. I don't know why it doesn't work. In the colab it works with exactly the same versions.
What you can try to delete all atlas-generated conda envs that contain dram, and try again.
to get list of al conda envs with dram:
grep dram [...]/atlas/conda_envs/*.y*
I already tried deleting all conda environments and also a fresh install on a different system, it made no difference.
I was wondering whether there could be another installation of the packages with a higher priority? But the error messages is pointing to the libraries from the conda environment.
Maybe we could try to have exact the same environment if you could provide the list of all packages? (conda list --export > requirements.txt
)
Have a look at the cobal link I send you. It produces the requirements.txt files it also gives a way to isntall Dram with the newest versions of scipy and scikit-bio.
conda config --set channel_priority strict
might have an importance.
thanks for the advice! I will check it out and report back.
As a short reply to your previous advice, by commenting out dram and kegg_modules in config.yaml
I can indeed continue with the pipeline.
Now I can confirm that using strict priorities indeed solved the issue! Many thanks for your assistance!
dram_download
Here is the relevant log output:
Atlas version 2.16.3