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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
142 stars 10 forks source link

I installed the yaml file from github via conda, but put the error in the haphic plot. #54

Closed taotaoyuan closed 2 months ago

taotaoyuan commented 3 months ago

OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 1030610 max Traceback (most recent call last): File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/_core/init.py", line 23, in from . import multiarray File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/_core/multiarray.py", line 10, in from . import overrides File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/_core/overrides.py", line 8, in from numpy._core._multiarray_umath import ( ImportError: PyCapsule_Import could not import module "datetime"

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/init.py", line 114, in from numpy.config import show as show_config File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/config.py", line 4, in from numpy._core._multiarray_umath import ( File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/_core/init.py", line 49, in raise ImportError(msg) ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for many reasons, often due to issues with your setup or how NumPy was installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

and make sure that they are the versions you expect. Please carefully study the documentation linked above for further help.

Original error was: PyCapsule_Import could not import module "datetime"

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

Traceback (most recent call last): File "/home/lx_sky6/yt/soft/HapHiC-main/scripts/HapHiC_plot.py", line 19, in import numpy as np File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/site-packages/numpy/init.py", line 119, in raise ImportError(msg) from e ImportError: Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python interpreter from there. Traceback (most recent call last): File "/home/lx_sky6/yt/soft/HapHiC-main/haphic", line 117, in subprocess.run(commands, check=True) File "/home/lx_sky6/yt/soft/miniconda3/envs/haphic/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/home/lx_sky6/yt/soft/HapHiC-main/scripts/HapHiC_plot.py', '-h']' died with <Signals.SIGSEGV: 11>.

zengxiaofei commented 3 months ago

The numpy version is incorrect. We use numpy < 2.0.0 in all .yml files. However, the numpy version you used is 2.1.0. Please check your environment. There must have been some changes.

zengxiaofei commented 2 months ago

Close this issue as there has been no response for two weeks.