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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicAdjustMatrix ValueError: could not convert integer scalar #784

Open cgirardot opened 2 years ago

cgirardot commented 2 years ago

Hi,

I am using the latest 3.7.2 installed via conda and I am having this error (see below) when executing

hicAdjustMatrix-3.7.2 -a keep --interIntraHandling inter -m matrix.h5 -o matrix.transRemoved.h5 --chromosomes chr2L chr2R chr3L chr3R chr4 chrX

The input matrix.h5 is an unmodified raw h5 matrix produced by hicBuildMatrix with a bin size of 1K (note the hicexplorer version is older ie 3.6 as the matrices was generated some time ago). The weird thing is that the error does not occur if I used a lower resolution i.e. binning at 5K generated using hicMergeMatrixBins --numBins 5 (also produced with v3.6)

Would you have an idea of the issue? Actually I am pretty sure this is not the first time I get this kind of error (I was away from HiC for a while) when using the 1K resolution but not with lower resolutions.

Traceback (most recent call last):
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/bin/hicAdjustMatrix", line 7, in <module>
    main()
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/hicexplorer/hicAdjustMatrix.py", line 197, in main
    hic_matrix = adjustMatrix(args)
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/hicexplorer/hicAdjustMatrix.py", line 177, in adjustMatrix
    hic_matrix.matrix[start:end, end:] = 0
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/scipy/sparse/_index.py", line 146, in __setitem__
    self._set_arrayXarray(i, j, x)
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/scipy/sparse/_compressed.py", line 823, in _set_arrayXarray
    self._set_many(i, j, x)
  File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/scipy/sparse/_compressed.py", line 910, in _set_many
    ret = csr_sample_offsets(M, N, self.indptr, self.indices, n_samples,
ValueError: could not convert integer scalar
cgirardot commented 2 years ago

Hi @joachimwolff , I am really stuck with this. Would you be able to help pls?

cgirardot commented 2 years ago

could this be related to #787 ?