Broken mDeepFRI installation and first prediction

[achousal]

• After running pip install mdeepfri, and mDeepFRI --help, I get error messages like the following:

(deepfri) /mnt/data2/andres/deepfri/databases$ mDeepFRI --help
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 5, in
from mDeepFRI.cli import main
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 7, in
from mDeepFRI.pipeline import predict_protein_function
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 10, in
from tqdm import tqdm

• The modules needed which did not install with the general command are: tqdm, pyopal, pysam, biotite, onnxruntime, MMseq2

• After installing the modules I get the help command working, but the default foldcomp and MMseq2 databases wont install properly after running a prediction.

• Command used:

• mDeepFRI predict-function -i /mnt/data2/andres/data/prediction_mgm/SRR1778453/SRR1778453_mH_fC_mS_genes.fna -d /mnt/data2/andres/deepfri/foldcomp/database -w /mnt/data2/andres/deepfri/weights/ -o /mnt/data2/andres/deepfri/output/ 2> log.txt &

• Note: at first, the prediction error log was asking for mmseq package, so I installed MMseq2 from "conda install -c conda-forge -c bioconda mmseqs2"
  Related error message:

[2024-11-26 13:55:20] cli.predict_function INFO: Minimum length: 60
[2024-11-26 13:55:20] cli.predict_function INFO: Maximum length: 1000
[2024-11-26 13:55:20] pipeline.predict_protein_function INFO: EC number prediction is not supported in version 1.1.
[2024-11-26 13:55:20] pipeline.predict_protein_function INFO: Creating PDB100 database. This may take a bit during a first run.
[2024-11-26 13:55:20] pdb.create_pdb_mmseqs INFO: Downloading PDB100 database.
[2024-11-26 13:55:44] pdb.create_pdb_mmseqs INFO: Creating MMSeqs2 database from PDB100.
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 8, in
sys.exit(main())
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 231, in predict_function
predict_protein_function(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 80, in predict_protein_function
pdb100 = create_pdb_mmseqs()
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pdb.py", line 65, in create_pdb_mmseqs
createdb(compressed_path, pdb100_mmseqs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 43, in createdb
run_command(f"mmseqs createdb {sequences_file} {db_path} --dbtype 1")
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 32, in run_command
completed_process = subprocess.run(command,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 493, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 1720, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mmseqs'

• Second try with MMseq2 installed in enviorment:

[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: EC number prediction is not supported in version 1.1.
[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: Creating PDB100 database. This may take a bit during a first run.
[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: PDB100 database created.
[2024-11-26 14:01:57] database.build_database INFO: Building MMSeqs2 database from /mnt/data2/andres/deepfri/foldcomp/database
[2024-11-26 14:01:57] database.build_database INFO: Found /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz in /mnt/data2/andres/deepfri/foldcomp
[2024-11-26 14:01:57] database.build_database INFO: Skipping extraction of FASTA file from FoldComp database.
[2024-11-26 14:01:57] database.build_database INFO: Creating and indexing MMSeqs2 database.
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 32, in run_command
completed_process = subprocess.run(command,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mmseqs', 'createdb', '/mnt/data2/andres/deepfri/foldcomp/database.fasta.gz', '/mnt/data2/andres/deepfri/foldcomp/database.mmseqsDB', '--dbtype', '1']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 8, in
sys.exit(main())
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 231, in predict_function
predict_protein_function(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 89, in predict_protein_function
db = build_database(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/database.py", line 87, in build_database
create_target_database(output_sequences, mmseqs_path, threads)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 112, in create_target_database
createdb(foldcomp_fasta_path, mmseqs_db_path)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 43, in createdb
run_command(f"mmseqs createdb {sequences_file} {db_path} --dbtype 1")
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 42, in run_command
raise RuntimeError(
RuntimeError: Command 'mmseqs createdb /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz /mnt/data2/andres/deepfri/foldcomp/database.mmseqsDB --dbtype 1' failed with exit code 1
The input files have no entry: - /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz
Please check your input files. Only files in fasta/fastq[.gz|bz2] are supported

• This is how my foldcomp folder looks:

(deepfri) kuanguser@kuanglabnslook:/mnt/data2/andres/deepfri/foldcomp$ ls -hs
total 768K
128K database 0 database.mmseqsDB 0 database.mmseqsDB.index 0 database.mmseqsDB_h 0 database.mmseqsDB_h.index
128K database.fasta.gz 128K database.mmseqsDB.dbtype 128K database.mmseqsDB.source 128K database.mmseqsDB_h.dbtype 128K log.txt

• Trying to create a custom db with afdb_swissprot_v4:

(deepfri) kuanguser@kuanglabnslook:/mnt/data2/andres/deepfri$ foldcomp compress -t 40 afdb_swissprot_v4 databases/afdb_swissprot_v4.tar.gz
foldcomp: command not found

[valentynbez]

Hi @achousal!
Can you share you OS and python version?

I have a strong imprression that pip install failed.
Could you please rerun installation command and share log from it?
pip install mdeepfri --force-reinstall

Thanks for using my software and reporting back!
Valentyn

[achousal]

Hey, thanks for the quick response, seems like it reinstalled properly, although there is a issue with TypeDict, and the command get-models does not exist.

(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ pip install mdeepfri --force-reinstall
Defaulting to user installation because normal site-packages is not writeable
Collecting mdeepfri
Using cached mDeepFRI-1.1.5-cp38-cp38-linux_x86_64.whl
Collecting cython (from mdeepfri)
Using cached Cython-3.0.11-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB)
Collecting numpy (from mdeepfri)
Using cached numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting requests (from mdeepfri)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting charset-normalizer<4,>=2 (from requests->mdeepfri)
Using cached charset_normalizer-3.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
Collecting idna<4,>=2.5 (from requests->mdeepfri)
Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests->mdeepfri)
Using cached urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests->mdeepfri)
Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Using cached Cython-3.0.11-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
Using cached numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Using cached certifi-2025.1.31-py3-none-any.whl (166 kB)
Using cached charset_normalizer-3.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB)
Using cached idna-3.10-py3-none-any.whl (70 kB)
Using cached urllib3-2.2.3-py3-none-any.whl (126 kB)
WARNING: Error parsing dependencies of shredder: Invalid version: '2.9.0.Odd.Olm'
WARNING: Error parsing dependencies of dblatex: Invalid version: '0.3.11py3'
WARNING: Error parsing dependencies of devscripts: Invalid version: '2.20.2ubuntu2'
WARNING: Error parsing dependencies of reportbug: Invalid version: '7.6.0ubuntu1'
Installing collected packages: urllib3, numpy, idna, cython, charset-normalizer, certifi, requests, mdeepfri
Attempting uninstall: urllib3
Found existing installation: urllib3 2.2.3
Uninstalling urllib3-2.2.3:
Successfully uninstalled urllib3-2.2.3
Attempting uninstall: numpy
Found existing installation: numpy 1.23.5
Uninstalling numpy-1.23.5:
Successfully uninstalled numpy-1.23.5
Attempting uninstall: idna
Found existing installation: idna 3.10
Uninstalling idna-3.10:
Successfully uninstalled idna-3.10
Attempting uninstall: cython
Found existing installation: Cython 3.0.11
Uninstalling Cython-3.0.11:
Successfully uninstalled Cython-3.0.11
Attempting uninstall: charset-normalizer
Found existing installation: charset-normalizer 3.4.1
Uninstalling charset-normalizer-3.4.1:
Successfully uninstalled charset-normalizer-3.4.1
Attempting uninstall: certifi
Found existing installation: certifi 2025.1.31
Uninstalling certifi-2025.1.31:
Successfully uninstalled certifi-2025.1.31
Attempting uninstall: requests
Found existing installation: requests 2.32.3
Uninstalling requests-2.32.3:
Successfully uninstalled requests-2.32.3
Attempting uninstall: mdeepfri
Found existing installation: mDeepFRI 1.1.5
Uninstalling mDeepFRI-1.1.5:
Successfully uninstalled mDeepFRI-1.1.5
Successfully installed certifi-2025.1.31 charset-normalizer-3.4.1 cython-3.0.11 idna-3.10 mdeepfri-1.1.5 numpy-1.24.4 requests-2.32.3 urllib3-2.2.3
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ mDeepFRI --help
Traceback (most recent call last):
File "/home/kuanguser/.local/bin/mDeepFRI", line 5, in
from mDeepFRI.cli import main
File "/home/kuanguser/.local/lib/python3.8/site-packages/mDeepFRI/cli.py", line 7, in
from mDeepFRI.pipeline import predict_protein_function
File "/home/kuanguser/.local/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 13, in
from mDeepFRI.alignment import run_alignment
File "/home/kuanguser/.local/lib/python3.8/site-packages/mDeepFRI/alignment.py", line 9, in
from mDeepFRI.bio_utils import (AlignmentResult, load_fasta_as_dict,
File "/home/kuanguser/.local/lib/python3.8/site-packages/mDeepFRI/bio_utils.py", line 8, in
from biotite.sequence import ProteinSequence
File "/home/kuanguser/.local/lib/python3.8/site-packages/biotite/sequence/init.py", line 73, in
from .profile import *
File "/home/kuanguser/.local/lib/python3.8/site-packages/biotite/sequence/profile.py", line 9, in
from .align.alignment import get_codes
File "/home/kuanguser/.local/lib/python3.8/site-packages/biotite/sequence/align/init.py", line 45, in
from .multiple import *
File "src/biotite/sequence/align/multiple.pyx", line 19, in init biotite.sequence.align.multiple
File "/home/kuanguser/.local/lib/python3.8/site-packages/biotite/sequence/phylo/init.py", line 34, in
from .tree import *
File "src/biotite/sequence/phylo/tree.pyx", line 14, in init biotite.sequence.phylo.tree
File "/usr/lib/python3/dist-packages/networkx/init.py", line 112, in
import networkx.generators
File "/usr/lib/python3/dist-packages/networkx/generators/init.py", line 14, in
from networkx.generators.geometric import *
File "/usr/lib/python3/dist-packages/networkx/generators/geometric.py", line 24, in
from scipy.spatial import cKDTree as KDTree
File "/usr/lib/python3/dist-packages/scipy/spatial/init.py", line 99, in
from .kdtree import *
File "/usr/lib/python3/dist-packages/scipy/spatial/kdtree.py", line 8, in
import scipy.sparse
File "/usr/lib/python3/dist-packages/scipy/sparse/init.py", line 229, in
from .base import *
File "/usr/lib/python3/dist-packages/scipy/sparse/base.py", line 8, in
from .sputils import (isdense, isscalarlike, isintlike,
File "/usr/lib/python3/dist-packages/scipy/sparse/sputils.py", line 16, in
supported_dtypes = [np.typeDict[x] for x in supported_dtypes]
File "/usr/lib/python3/dist-packages/scipy/sparse/sputils.py", line 16, in
supported_dtypes = [np.typeDict[x] for x in supported_dtypes]
File "/home/kuanguser/.local/lib/python3.8/site-packages/numpy/init.py", line 320, in getattr
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'typeDict'
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ pip uninstall numpy
Found existing installation: numpy 1.24.4
Uninstalling numpy-1.24.4:
Would remove:
/home/kuanguser/.local/bin/f2py
/home/kuanguser/.local/bin/f2py3
/home/kuanguser/.local/bin/f2py3.8
/home/kuanguser/.local/lib/python3.8/site-packages/numpy-1.24.4.dist-info/*
/home/kuanguser/.local/lib/python3.8/site-packages/numpy.libs/libgfortran-040039e1.so.5.0.0
/home/kuanguser/.local/lib/python3.8/site-packages/numpy.libs/libopenblas64_p-r0-15028c96.3.21.so
/home/kuanguser/.local/lib/python3.8/site-packages/numpy.libs/libquadmath-96973f99.so.0.0.0
/home/kuanguser/.local/lib/python3.8/site-packages/numpy/*
Proceed (Y/n)?
Successfully uninstalled numpy-1.24.4
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ pip install numpy==1.23.5
Defaulting to user installation because normal site-packages is not writeable

Collecting numpy==1.23.5
Using cached numpy-1.23.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Using cached numpy-1.23.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
WARNING: Error parsing dependencies of shredder: Invalid version: '2.9.0.Odd.Olm'
WARNING: Error parsing dependencies of dblatex: Invalid version: '0.3.11py3'
WARNING: Error parsing dependencies of devscripts: Invalid version: '2.20.2ubuntu2'
WARNING: Error parsing dependencies of reportbug: Invalid version: '7.6.0ubuntu1'
Installing collected packages: numpy
Successfully installed numpy-1.23.5
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ pip show numpy

Name: numpy
Version: 1.23.5
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email:
License: BSD
Location: /home/kuanguser/.local/lib/python3.8/site-packages
Requires:
Required-by: astropy, biopython, biotite, bx-python, cupcake, mDeepFRI, onnxruntime, pandas, pyerfa, scikit-learn, wxPython
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ mDeepFRI --help

Usage: mDeepFRI [OPTIONS] COMMAND [ARGS]...

mDeepFRI

Options:
--debug / --no-debug
--version Show the version and exit.
--help Show this message and exit.

Commands:
predict-function Predict protein function from sequence.
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ mDeepFRI get-models --output weights -v 1.1
Usage: mDeepFRI [OPTIONS] COMMAND [ARGS]...
Try "mDeepFRI --help" for help.

Error: No such command "get-models".
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$
(mGWAS) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$

[valentynbez]

Yes, it's correct. The installed version of Deepfri is outdated.
The reason for that is using python 3.8 environment.
We only tested software at Python 3.11, where there were some breaking changes in onnx. Dependency management of DL libraries was somewhat of a nightmare.
Please, create env with python 3.11 and install following

pip install mdeepfri==1.1.8 --force-reinstall

I'll look if it can be better managed now in my free time.

Cheers

[achousal]

Tried with python 3.11 on fresh env, cant seem to find 1.1.8. This is weird since -get models did work on my previous installation?

(base) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ conda activate deepFried
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ python --version
Python 3.11.11
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ python -m ensurepip --default-pip
Looking in links: /tmp/user/1000/tmp6xbawc6z
Requirement already satisfied: setuptools in /home/kuanguser/miniconda3/envs/deepFried/lib/python3.11/site-packages (75.8.0)
Requirement already satisfied: pip in /home/kuanguser/miniconda3/envs/deepFried/lib/python3.11/site-packages (25.0)
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ python -m pip install --upgrade pip
Requirement already satisfied: pip in /home/kuanguser/miniconda3/envs/deepFried/lib/python3.11/site-packages (25.0)
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ python -m pip install deepfri==1.1.8
ERROR: Could not find a version that satisfies the requirement deepfri==1.1.8 (from versions: none)
ERROR: No matching distribution found for deepfri==1.1.8
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$

[valentynbez]

Hello, currently you are running the wrong command.
DeepFRI is the original unoptimized pipeline.
mDeepFRI is this repo.
pip install mdeepfri==1.1.8

[achousal]

installation works but does not install 1.1.8? Sorry about all the trouble
using:
python -m pip install mdeepfri==1.1.8
calls for 1.1.8 succesfully, but version is still 1.1.5 when I check it manually.

(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$ pip install mdeepfri==1.1.8
Defaulting to user installation because normal site-packages is not writeable
ERROR: Could not find a version that satisfies the requirement mdeepfri==1.1.8 (from versions: 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5)
ERROR: No matching distribution found for mdeepfri==1.1.8
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$ pip install mdeepfri==1.1.8 --force-reinstall
Defaulting to user installation because normal site-packages is not writeable
ERROR: Could not find a version that satisfies the requirement mdeepfri==1.1.8 (from versions: 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5)
ERROR: No matching distribution found for mdeepfri==1.1.8
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$ python -m pip install mdeepfri==1.1.8
Collecting mdeepfri==1.1.8
Using cached mDeepFRI-1.1.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting click~=8.0 (from mdeepfri==1.1.8)
Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB)
Collecting numpy~=1.21 (from mdeepfri==1.1.8)
Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting biotite (from mdeepfri==1.1.8)
Using cached biotite-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.2 kB)
Collecting pysam>=0.18 (from mdeepfri==1.1.8)
Using cached pysam-0.22.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (1.5 kB)
Collecting pyopal~=0.5 (from mdeepfri==1.1.8)
Using cached pyopal-0.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting foldcomp (from mdeepfri==1.1.8)
Using cached foldcomp-0.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.3 kB)
Collecting tqdm (from mdeepfri==1.1.8)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting onnxruntime-gpu (from mdeepfri==1.1.8)
Using cached onnxruntime_gpu-1.20.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.5 kB)
Collecting archspec~=0.2.0 (from pyopal~=0.5->mdeepfri==1.1.8)
Using cached archspec-0.2.5-py3-none-any.whl.metadata (4.4 kB)
Collecting scoring-matrices~=0.3.0 (from pyopal~=0.5->mdeepfri==1.1.8)
Using cached scoring_matrices-0.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting biotraj<2.0,>=1.0 (from biotite->mdeepfri==1.1.8)
Using cached biotraj-1.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (32 kB)
Collecting msgpack>=0.5.6 (from biotite->mdeepfri==1.1.8)
Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
Collecting networkx>=2.0 (from biotite->mdeepfri==1.1.8)
Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting requests>=2.12 (from biotite->mdeepfri==1.1.8)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting httpx>=0.23.0 (from foldcomp->mdeepfri==1.1.8)
Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
Collecting coloredlogs (from onnxruntime-gpu->mdeepfri==1.1.8)
Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB)
Collecting flatbuffers (from onnxruntime-gpu->mdeepfri==1.1.8)
Using cached flatbuffers-25.1.24-py2.py3-none-any.whl.metadata (875 bytes)
Collecting packaging (from onnxruntime-gpu->mdeepfri==1.1.8)
Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting protobuf (from onnxruntime-gpu->mdeepfri==1.1.8)
Using cached protobuf-5.29.3-cp38-abi3-manylinux2014_x86_64.whl.metadata (592 bytes)
Collecting sympy (from onnxruntime-gpu->mdeepfri==1.1.8)
Using cached sympy-1.13.3-py3-none-any.whl.metadata (12 kB)
Collecting scipy>=1.13 (from biotraj<2.0,>=1.0->biotite->mdeepfri==1.1.8)
Using cached scipy-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting anyio (from httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached anyio-4.8.0-py3-none-any.whl.metadata (4.6 kB)
Collecting certifi (from httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Collecting httpcore==1.* (from httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached httpcore-1.0.7-py3-none-any.whl.metadata (21 kB)
Collecting idna (from httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.12->biotite->mdeepfri==1.1.8)
Using cached charset_normalizer-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.12->biotite->mdeepfri==1.1.8)
Using cached urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime-gpu->mdeepfri==1.1.8)
Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Collecting mpmath<1.4,>=1.1.0 (from sympy->onnxruntime-gpu->mdeepfri==1.1.8)
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting sniffio>=1.1 (from anyio->httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB)
Collecting typing_extensions>=4.5 (from anyio->httpx>=0.23.0->foldcomp->mdeepfri==1.1.8)
Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Using cached mDeepFRI-1.1.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (48.8 MB)
Using cached click-8.1.8-py3-none-any.whl (98 kB)
Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)
Using cached pyopal-0.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (828 kB)
Using cached pysam-0.22.1-cp311-cp311-manylinux_2_28_x86_64.whl (25.1 MB)
Using cached biotite-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (53.1 MB)
Using cached foldcomp-0.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (266 kB)
Using cached onnxruntime_gpu-1.20.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (291.5 MB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Using cached archspec-0.2.5-py3-none-any.whl (76 kB)
Using cached biotraj-1.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.2 MB)
Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
Using cached httpcore-1.0.7-py3-none-any.whl (78 kB)
Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (403 kB)
Using cached networkx-3.4.2-py3-none-any.whl (1.7 MB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Using cached scoring_matrices-0.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (126 kB)
Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
Using cached flatbuffers-25.1.24-py2.py3-none-any.whl (30 kB)
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Using cached protobuf-5.29.3-cp38-abi3-manylinux2014_x86_64.whl (319 kB)
Using cached sympy-1.13.3-py3-none-any.whl (6.2 MB)
Using cached certifi-2025.1.31-py3-none-any.whl (166 kB)
Using cached charset_normalizer-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 kB)
Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
Using cached idna-3.10-py3-none-any.whl (70 kB)
Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)
Using cached scipy-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.6 MB)
Using cached urllib3-2.3.0-py3-none-any.whl (128 kB)
Using cached anyio-4.8.0-py3-none-any.whl (96 kB)
Using cached h11-0.14.0-py3-none-any.whl (58 kB)
Using cached sniffio-1.3.1-py3-none-any.whl (10 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Installing collected packages: mpmath, flatbuffers, urllib3, typing_extensions, tqdm, sympy, sniffio, scoring-matrices, pysam, protobuf, packaging, numpy, networkx, msgpack, idna, humanfriendly, h11, click, charset-normalizer, certifi, archspec, scipy, requests, pyopal, httpcore, coloredlogs, anyio, onnxruntime-gpu, httpx, biotraj, foldcomp, biotite, mdeepfri
Successfully installed anyio-4.8.0 archspec-0.2.5 biotite-1.1.0 biotraj-1.2.2 certifi-2025.1.31 charset-normalizer-3.4.1 click-8.1.8 coloredlogs-15.0.1 flatbuffers-25.1.24 foldcomp-0.0.7 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 humanfriendly-10.0 idna-3.10 mdeepfri-1.1.8 mpmath-1.3.0 msgpack-1.1.0 networkx-3.4.2 numpy-1.26.4 onnxruntime-gpu-1.20.1 packaging-24.2 protobuf-5.29.3 pyopal-0.7.0 pysam-0.22.1 requests-2.32.3 scipy-1.15.1 scoring-matrices-0.3.0 sniffio-1.3.1 sympy-1.13.3 tqdm-4.67.1 typing_extensions-4.12.2 urllib3-2.3.0
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$ mDeepFRI --help
Usage: mDeepFRI [OPTIONS] COMMAND [ARGS]...

mDeepFRI

Options:
--debug / --no-debug
--version Show the version and exit.
--help Show this message and exit.

Commands:
predict-function Predict protein function from sequence.
(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres$ mDeepFRI --version
mDeepFRI, version 1.1.5

(deepFried) kuanguser@kuanglabnslook:/mnt/data2/andres/mgwas/upstream/deepfri$ mDeepFRI get-models --output weights -v 1.1
Usage: mDeepFRI [OPTIONS] COMMAND [ARGS]...
Try "mDeepFRI --help" for help.

Error: No such command "get-models".

[valentynbez]

No worries, it is expected. This project has a lot of dependencies that are hard to manage. Additionally, I don't have time to maintain it anymore.

Not sure what is going on at PyPI, the version is outdated. Try installing straight from GitHub:
pip install git+https://github.com/bioinf-mcb/[email protected]