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jenniening / deltaVinaXGB

This is a machine-learning based protein-ligand scoring function.
https://www.nyu.edu/projects/yzhang/DeltaVina/
GNU General Public License v3.0
48 stars 14 forks source link

issue with running the test command: "python run_DXGB.py --help" #7

Closed Sinsilcobio closed 3 years ago

Sinsilcobio commented 3 years ago

Hello Jenniening,

I installed all the packages and dependencies according to the procedure mentioned in the "readme.md" file. However, when I tried to run the first test command, the following error popped up.

Could you please give me a clue what I am missing?

Thank you, Sajjad

(DXGB) sajads-air:DXGB sajadahrari$ conda activate DXGB (DXGB) sajads-air:DXGB sajadahrari$ python run_DXGB.py --help Traceback (most recent call last): File "run_DXGB.py", line 6, in from DXGB.convert_file import RF20_main as RF20_main ModuleNotFoundError: No module named 'DXGB'

jenniening commented 3 years ago

HI, did you run 'python setup.py install' ? Also, when you run 'python run_DXGB.py --help', could you check if you are in deltaVInaXGB package?

Sinsilcobio commented 3 years ago

Hi Jenniening,

I re-run the "python setup.py install".

The issue was resolved yet the following error popped up (I have numbered it as error number 1) which seems to be related to "Open Babel" installation.

I tried to reinstall "Open Babel with "conda install -c openbabel openbabel" command and error number 2 showed up (which seems to be related to packaging incompatibility).

I am installing it on my Mac and was wondering if it is the source of the issue?

Thank you, Sajjad

Error 1

(DXGB) sajads-air:DXGB sajadahrari$ conda activate DXGB (DXGB) sajads-air:DXGB sajadahrari$ python run_DXGB.py --help Traceback (most recent call last): File "run_DXGB.py", line 7, in from DXGB.run_features import run_features as run_features File "", line 259, in load_module File "/Users/sajadahrari/opt/anaconda3/lib/python3.8/site-packages/DXGB-0.1.0-py3.8.egg/DXGB/run_features.py", line 16, in import DXGB.cal_sasa File "", line 259, in load_module File "/Users/sajadahrari/opt/anaconda3/lib/python3.8/site-packages/DXGB-0.1.0-py3.8.egg/DXGB/cal_sasa.py", line 7, in from DXGB.featureSASA import sasa File "", line 259, in load_module File "/Users/sajadahrari/opt/anaconda3/lib/python3.8/site-packages/DXGB-0.1.0-py3.8.egg/DXGB/featureSASA.py", line 4, in import os, sys, pybel ModuleNotFoundError: No module named 'pybel'

========================================================================================== Error 2

(DXGB) sajads-air:DXGB sajadahrari$ conda install -c openbabel openbabel Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed - /

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

Output in format: Requested package -> Available versions

Package blis conflicts for: libblas -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0'] libcblas -> libblas==3.9.0=11_osx64_blis -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0'] liblapack -> libblas=3.9.0 -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0'] numpy -> libblas[version='>=3.8.0,<4.0a0'] -> blis[version='0.5.1.|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0'] scipy -> libblas[version='>=3.8.0,<4.0a0'] -> blis[version='0.5.1.*|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0']

Package numpy conflicts for: py-xgboost -> numpy py-xgboost -> scikit-learn -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.18.1,<2.0a0|>=1.11|>=1.15.1,<2.0a0'] scikit-learn -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.9.3,<2.0a0|>=1.9'] numpy scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.15.1,<2.0a0'] xgboost=0.80.0 -> numpy scikit-learn -> scipy -> numpy[version='>=1.11|>=1.18.1,<2.0a0|>=1.15.1,<2.0a0'] xgboost=0.80.0 -> scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.15.1,<2.0a0']

Package llvm-openmp conflicts for: libopenblas -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=12.0.1|>=9.0.1|>=9.0.0'] libblas -> libopenblas[version='>=0.3.17,<0.3.18.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=12.0.1|>=8.0.0|>=8.0.1|>=9.0.1|>=9.0.0'] xgboost=0.80.0 -> py-xgboost==0.80=py36h0a44026_1001 -> llvm-openmp[version='8.0.0|8.0.0|8.0.1|>=4.0.1',build='h770b8ee_1|h770b8ee_0|h770b8ee_0'] llvm-openmp liblapack -> libgfortran5[version='>=9.3.0'] -> llvm-openmp[version='>=10.0.1|>=8.0.0|>=8.0.1'] libopenblas -> libgfortran5[version='>=9.3.0'] -> llvm-openmp[version='>=8.0.0|>=8.0.1'] py-xgboost -> libxgboost==1.4.0=he49afe7_0 -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=9.0.1'] libcblas -> libgfortran5[version='>=9.3.0'] -> llvm-openmp[version='>=10.0.1|>=8.0.0|>=8.0.1'] scikit-learn -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=9.0.1|>=9.0.0'] numpy -> openblas[version='>=0.2.15'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=12.0.1|>=9.0.1|>=9.0.0'] libgfortran -> libgfortran5 -> llvm-openmp[version='>=10.0.1'] py-xgboost -> llvm-openmp[version='>=10.0.0|>=4.0.1|>=9.0.0|>=8.0.1'] libgfortran -> llvm-openmp[version='>=8.0.0|>=8.0.1'] libxgboost -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1|>=8.0.1'] libgfortran5 -> llvm-openmp[version='>=10.0.1|>=8.0.0'] scipy -> libgfortran5[version='>=9.3.0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=8.0.0|>=8.0.1|>=11.1.0|>=12.0.1|>=11.0.0|>=9.0.1|>=9.0.0']

Package ca-certificates conflicts for: openbabel -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates scikit-learn -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates joblib -> python -> ca-certificates pip -> python -> ca-certificates scipy -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates setuptools -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates xgboost=0.80.0 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates python_abi -> python=2.7 -> ca-certificates ca-certificates py-xgboost -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates numpy -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates openssl -> ca-certificates wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> ca-certificates python=3.7 -> openssl[version='>=1.1.1j,<1.1.2a'] -> ca-certificates

Package readline conflicts for: python_abi -> python=3.9 -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] scipy -> python[version='>=3.7,<3.8.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] py-xgboost -> python[version='>=3.7,<3.8.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] joblib -> python[version='>=3.6'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] python=3.7 -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0'] wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.0.|7.'] pip -> python[version='>=3.6'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] threadpoolctl -> python[version='>=3.6'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.'] openbabel -> python[version='>=3.7,<3.8.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|7.|7.0.|>=8.1,<9.0a0'] readline setuptools -> python[version='>=3.8,<3.9.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|7.|>=8.1,<9.0a0|7.0.'] numpy -> python[version='>=3.7,<3.8.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|7.0.'] sqlite -> readline[version='6.2.|7.0|7.0.|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0'] python=3.7 -> sqlite[version='>=3.34.0,<4.0a0'] -> readline[version='>=8.1,<9.0a0'] scikit-learn -> python[version='>=3.7,<3.8.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|7.|>=8.1,<9.0a0|7.0.'] xgboost=0.80.0 -> python[version='>=3.6,<3.7.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|7.|7.0.*']

Package ncurses conflicts for: wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] scikit-learn -> pypy3.7[version='>=7.3.5'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] xgboost=0.80.0 -> python[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] sqlite -> ncurses[version='5.9|5.9.|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] python=3.7 -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] python_abi -> python=3.9 -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] sqlite -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='6.0.|>=6.0,<7.0a0|>=6.1,<7.0a0'] numpy -> pypy3.7[version='>=7.3.5'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] scipy -> pypy3.7[version='>=7.3.5'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] setuptools -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0'] joblib -> python[version='>=3.6'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] py-xgboost -> pypy3.7[version='>=7.3.4'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] readline -> ncurses[version='5.9.|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] openbabel -> python[version='>=3.7,<3.8.0a0'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0'] pip -> python[version='>=3.6'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] python=3.7 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='5.9.|>=6.1,<6.3.0a0|>=6.0,<7.0a0|6.0.'] threadpoolctl -> python[version='>=3.6'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0'] ncurses

Package scipy conflicts for: scikit-learn -> scipy[version='>=0.19.1'] xgboost=0.80.0 -> scipy py-xgboost -> scikit-learn -> scipy[version='>=0.19.1'] py-xgboost -> scipy scipy ....

jenniening commented 3 years ago

Thanks for the update! Could you try 'pip install openbabel' to install openbable?

Sinsilcobio commented 3 years ago

Thank you very much for your reply.

I tried to install with pip. However, the following list of errors showed up.

It seems that openbabel has already been installed with anaconda3 as I can see it running by typing "obabel" in the terminal.

Could you please give me a clue what I am missing? Thank you

(DXGB) sajads-air:DXGB sajadahrari$ pip install openbabel Collecting openbabel Using cached openbabel-3.1.1.1.tar.gz (82 kB) Building wheels for collected packages: openbabel Building wheel for openbabel (setup.py) ... error ERROR: Command errored out with exit status 1: command: /Users/sajadahrari/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9p/fr8j3_555dn5p5zyrwpzk5h80000gn/T/pip-install-3jgav96a/openbabel/setup.py'"'"'; file='"'"'/private/var/folders/9p/fr8j3_555dn5p5zyrwpzk5h80000gn/T/pip-install-3jgav96a/openbabel/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/9p/fr8j3_555dn5p5zyrwpzk5h80000gn/T/pip-wheel-www7swdi cwd: /private/var/folders/9p/fr8j3_555dn5p5zyrwpzk5h80000gn/T/pip-install-3jgav96a/openbabel/ Complete output (16 lines): running bdist_wheel running build running build_ext Warning: invalid version number '3.1.1.1'. Guessing Open Babel location:

jenniening commented 3 years ago

Thanks for the update. Could you check the version of openbabel installed? Also, could you try bellow two sets of commands in python and share the outputs?

first: from openbabel import openbabel as ob from openbabel import pybel

second: import openbabel as ob import pybel

Thanks!

Sinsilcobio commented 3 years ago

Thank you very much for your follow-up.

Following you can find the output of all your mentioned commands. It seems that except for "pybel", others are working fine.

I also checked the version of openable and it is Open Babel-3.1.0.

Thank you!

**(DXGB) sajads-air:DXGB sajadahrari$ python Python 3.8.3 (default, Jul 2 2020, 11:26:31) [Clang 10.0.0 ] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information.

from openbabel import openbabel as ob from openbabel import pybel

import openbabel as ob import pybel Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pybel'

exit() (DXGB) sajads-air:DXGB sajadahrari$ obabel No input file or format spec or possibly a misplaced option. Most options must come after the input files. (-i -o -O -m can be anywhwere.)

Open Babel 3.1.0 -- May 8 2020 -- 19:21:06 Usage: obabel [-i] [-o] -O [Options] Try -H option for more information. (DXGB) sajads-air:DXGB sajadahrari$**

Sinsilcobio commented 3 years ago

Hello Jenniening, I was wondering if you had a chance to look at the last post? Thank you

jenniening commented 3 years ago

Hi, sorry i forgot to comment. Thanks for sharing the testing result. Yeah, actually the issue is related to openbable version, in 3.x, pybel is needed to be imported through openbable but in 2.x it can be directly imported. Please see this link for reference: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html One thing we can try is instead directly 'import pybel' in script, just change that line to 'from openbabel import pybel'. Two files needed to be changed are: https://github.com/jenniening/deltaVinaXGB/blob/Light/DXGB/featureSASA.py and https://github.com/jenniening/deltaVinaXGB/blob/Light/DXGB/pharma.py. Please change the corresponding line in your local, and after making that change, please rerun the python setup.py file, the updated package should be installed again.

Sinsilcobio commented 3 years ago

Hi Jenniening, Thank you very much for your help. I belive the issue with the first test command (python run_DXGB.py --help) was resolved (see following for the out put). However, for the second test command (python run_DXGB.py --runfeatures --datadir ../Test_2al5 --pdbid 2al5 --average), I faced the following error. Could you please give me a clue what I am missing?

Thank you, Sajjad

first test command: (DXGB) sajads-air:DXGB sajadahrari$ python run_DXGB.py --help Usage: run_DXGB.py [OPTIONS]

Options: --model TEXT model name [default: DXGB] --modeldir TEXT absolute model directory [default: ../Model] --datadir TEXT absolute data directory [default: ../Test] --pdbid TEXT pdbid, ligand input should be pdbid_ligand.mol2 or sdf, protein input should be pdbid_protein_all.pdb --outfile TEXT output filename [default: score.csv] --runfeatures run features calculation [default: False] --water TEXT water type --opt TEXT opt type --rewrite rewrite protein part water generation, ligand optimization, ligand conformation generation or not --average average for 10 models --modelidx TEXT model index [default: 1] --featuretype TEXT which feature will be calculated, options:all,Vina,SASA,BW,Ion,dE [default: all] --runrf get deltaVinaRF20 scores --help Show this message and exit. (DXGB) sajads-air:DXGB sajadahrari$

second test command:

(DXGB) sajads-air:DXGB sajadahrari$ python run_DXGB.py --runfeatures --datadir ../Test_2al5 --pdbid 2al5 --average pdb index: 2al5 file directory: /Users/sajadahrari/Documents/GitHub/deltaVinaXGB/Test_2al5 feature will be calculated:all output filename : score.csv 1 molecule converted Ligand for conformation stability:2al5_ligand.mol2 Ligand for Vina, SASA, BA, ION:2al5_ligand_rename.pdb Protein without water molecules:2al5_protein.pdb Protein with water molecules:2al5_protein_all.pdb Finish Input Preparation No Consideration of Water No Optimized Ligand C Finish Vina Finish SASA No Ion Finish Ion Input Type:mol2 mol has been read The total number of conformers before clustering: 52 The total number of conformers after clustring: 12 The lowest energy: 26.35273201345399 Input Type:mol2 Finish Feature Calculation 1 Traceback (most recent call last): File "run_DXGB.py", line 103, in main() File "/Users/sajadahrari/opt/anaconda3/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/Users/sajadahrari/opt/anaconda3/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/Users/sajadahrari/opt/anaconda3/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/sajadahrari/opt/anaconda3/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "run_DXGB.py", line 74, in main test_new = run_model(inf,datadir,i,model_dir = modeldir, model_name = model, average = average, model_index = modelidx)
File "/Users/sajadahrari/opt/anaconda3/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_models.py", line 37, in run_model mod = pickle.load(open(modeldir + "/pima.pickle" + str(i) + ".dat", "rb")) FileNotFoundError: [Errno 2] No such file or directory: '/Users/sajadahrari/Documents/GitHub/deltaVinaXGB/Model/DXGB/pima.pickle_1.dat' (DXGB) sajads-air:DXGB sajadahrari$

Sinsilcobio commented 3 years ago

Hi Jenniening, The issue is resolved. There was a problem with file access and permissions. Thank you!

jenniening commented 3 years ago

Thanks for updating, sounds great!