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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Pipeline Fails while ICE Normalization #349

Closed rkash closed 3 years ago

rkash commented 4 years ago

Hi,

I have the following libraries installed.

bx==0.3.0 bx-python==0.8.9 iced==0.5.7 numpy==1.16.6 pandas==0.24.2 pysam==0.16.0.1 python-dateutil==2.8.1 pytz==2020.1 scipy==1.2.3 ice_500000.log

six==1.15.0

While running ICE normalization I am facing the following error. I am running the pipeline on test data provided in the software

Traceback (most recent call last): File "/usr/local/bin/HiC-Pro_2.11.1/scripts/ice", line 83, in counts = sparse.coo_matrix((data, (i - 1, j - 1)), shape=(N, N), dtype=float) File "/home/kaustavs/.local/lib/python2.7/site-packages/scipy/sparse/coo.py", line 154, in init self._shape = check_shape((M, N)) File "/home/kaustavs/.local/lib/python2.7/site-packages/scipy/sparse/sputils.py", line 286, in check_shape new_shape = tuple(operator.index(arg) for arg in args) File "/home/kaustavs/.local/lib/python2.7/site-packages/scipy/sparse/sputils.py", line 286, in new_shape = tuple(operator.index(arg) for arg in args) TypeError: 'numpy.float64' object cannot be interpreted as an index

Thanks in advance

nservant commented 4 years ago

@NelleV , any idea ? @rkash , anyway I would advice to move to the last HiC-Pro stable version 2.11.4 (or even 3.0.0 from the devel branch which is not yet release). The main difference is that these versions are now simply using iced and no longer include it within HiC-Pro.

NelleV commented 4 years ago

This error should have been fixed in recent version of iced. Indeed, upgrading to the last version of HiC-pro should fix the issue.