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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hic-pro mistake, zero-size array to reduction operation minimum which has no identity #407

Closed jimie0311 closed 3 years ago

jimie0311 commented 3 years ago

Hi everyone, I am using hic-pro to see hic connection map. Here is an error:

ice --results_filename hic_results/matrix/91scaffolds/iced/20000/91scaffolds_20000_iced.matrix --filter_low_counts_perc 0.02 --filter_high_counts_perc --max_iter 100 --eps 0.1 --remove-all-zeros-loci --output-bias 1 --verbose 1 hic_results/matrix/91scaffolds/raw/20000/91scaffolds_20000.matrix Using iced version 0.4.2 Loading files... Traceback (most recent call last): File "/data/Liangjunmin/.local/bin/ice", line 76, in if min(i.min(), j.min()) == 0: File "/data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/hicpro/lib/python2.7/site-packages/numpy/core/_methods.py", line 32, in _amin return umr_minimum(a, axis, None, out, keepdims, initial) ValueError: zero-size array to reduction operation minimum which has no identity

This issue is similar to mistake #206, however, the files of hic_results/matrix/91scaffolds/raw/20000/91scaffolds_20000.matrix in my case are empty!

Anybody know how to resolve it? Your help will be appreciate.

nservant commented 3 years ago

Hi, If the matrix file is empty, it means that something went wrong before. What about the .validPairs file ? are they empty too ?

jimie0311 commented 3 years ago

Hi Nservant, Thanks for your reply. The .validParis file are not empty. The problem is that I input a wrong path for size file. It was run succesuffully now. Thanks.