"cctyper -h" error information, about pkg_resources, XGBoost

[ShuqingL]

Software installation command in Miniconda3(with Python 3.8): conda create -n CRISPRCasTyper -c conda-forge -c bioconda -c russel88 cctyper
There were no error or warning messages prompted during CRISPRCasTyper installation process.
After installation, the following error message appears when using. Can anyone provide assistance?
run:
conda activate CRISPRCasTyper
cctyper -h

/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/bin/cctyper:7: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
Traceback (most recent call last):
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/bin/cctyper", line 14, in
from cctyper.xgb import XGB
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/cctyper/xgb.py", line 8, in
import xgboost as xgb
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/xgboost/init.py", line 6, in
from . import tracker # noqa
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/xgboost/tracker.py", line 9, in
from .core import _LIB, _check_call, make_jcargs
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/xgboost/core.py", line 269, in
_LIB = _load_lib()
File "/share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages/xgboost/core.py", line 222, in _load_lib
raise XGBoostError(
xgboost.core.XGBoostError:
XGBoost Library (libxgboost.so) could not be loaded.
Likely causes:

• OpenMP runtime is not installed

  • vcomp140.dll or libgomp-1.dll for Windows
  • libomp.dylib for Mac OSX
  • libgomp.so for Linux and other UNIX-like OSes
    Mac OSX users: Run brew install libomp to install OpenMP runtime.

• You are running 32-bit Python on a 64-bit OS

Error message(s): ['dlopen: cannot load any more object with static TLS']

run:
pip show xgboost
Name: xgboost
Version: 2.1.1
Summary: XGBoost Python Package
Home-page:
Author:
Author-email: Hyunsu Cho [email protected], Jiaming Yuan [email protected]
License: Apache-2.0
Location: /share/Software/Miniconda3-py38/envs/CRISPRCasTyper/lib/python3.8/site-packages
Requires: numpy, scipy
Required-by: cctyper

run:
conda list xgboost
packages in environment at /share/Software/Miniconda3-py38/envs/CRISPRCasTyper:

Name Version Build Channel
_py-xgboost-mutex 2.0 cpu_0 conda-forge
libxgboost 2.1.1 cpu_h3a1dfae_2 conda-forge
py-xgboost 2.1.1 cpu_pyh1941385_2 conda-forge

[samnooij]

I'm not sure if this is the same problem as I ran into, but if you're trying to get CCTyper to work from conda, I suggest you try the versions as I posted in #55 :

name: cctyper

dependencies:
 - cctyper=1.8.0
 - biopython=1.79
 - libxgboost=1.7.1
 - py-xgboost=1.7.1

channels:
 - conda-forge
 - bioconda
 - russel88

If you save this as a file, for example cctyper.yaml and then run conda env create -f cctyper.yaml it should create a functional installation of CCTyper. Hope that helps, good luck!