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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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sparseToDense.py error #387

Closed sunthink closed 3 years ago

sunthink commented 3 years ago

Hi, when I use sparseToDense.py: ./sparseToDense.py -h

I get this error：

Traceback (most recent call last): File "./sparseToDense.py", line 6, in from iced import io File "/public/home/cmsun/.local/lib/python2.7/site-packages/iced/init.py", line 1, in from . import normalization File "/public/home/cmsun/.local/lib/python2.7/site-packages/iced/normalization.py", line 3, in from .normalization import _update_normalization_csr File "init.pxd", line 861, in init iced.normalization (iced/normalization.c:4673) ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

But other scripts work well and don't report any error. I use numpy=1.10.4, hic-pro=2.11.4. Do you have any advice?

Thank you, Chengming

nservant commented 3 years ago

Hi, I'm not an expert, but it looks like you have an installation issue with numpy. Could you try to reinstall it ? Best

sunthink commented 3 years ago

Hi,

When I try to uninstall and reinstall numpy with conda, I still get the same error. But when I use pip to install, it works.

Thank you