Question: hicPlotMatrix memory error
gravatar for foxjuly
6 months ago by
foxjuly0 wrote:

Hi, I am using hicExplorer to plot the .h5 file generated with hicBuildMatrix, but I always encouted "memory error" problem. My computer setup is: intel i7 4 GHz (8 cores), 32 GB internal memory. here is my command: hicPlotMatrix -m ./contact_matrix/trackloop_GM12878_300K.h5 -o ./plots/Trackloop_GM12878_300k.png -t 'Trackloop_GM12878_300k' --log1p --clearMaskedBins --chromosomeOrder chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX --perChromosome

I always encoutered the following report: INFO:hicexplorer.hicPlotMatrix:min: 1, max: 694

Traceback (most recent call last): File "/home/jiang/miniconda3/bin/hicPlotMatrix", line 7, in <module> main() File "/home/jiang/miniconda3/lib/python3.6/site-packages/hicexplorer/", line 528, in main matrix = np.asarray(ma.getMatrix().astype(float)) File "/home/jiang/miniconda3/lib/python3.6/site-packages/hicexplorer/", line 491, in getMatrix matrix = self.matrix.todense() File "/home/jiang/miniconda3/lib/python3.6/site-packages/scipy/sparse/", line 846, in todense return np.asmatrix(self.toarray(order=order, out=out)) File "/home/jiang/miniconda3/lib/python3.6/site-packages/scipy/sparse/", line 947, in toarray out = self._process_toarray_args(order, out) File "/home/jiang/miniconda3/lib/python3.6/site-packages/scipy/sparse/", line 1184, in _process_toarray_args return np.zeros(self.shape, dtype=self.dtype, order=order) MemoryError

So, does anyone know what is the cause of the problem?

hicexplorer hicplotmatrix • 302 views
ADD COMMENTlink modified 4 months ago by wolffj.bioinf10 • written 6 months ago by foxjuly0
gravatar for wolffj.bioinf
4 months ago by
wolffj.bioinf10 wrote:


the problem is quite simple: You have too less memory to plot it. Unfortunately, matplotlib is demanding a lot of memory to plot images.

A solution would be to plot fewer chromosomes, to plot with a lower resolution or to switch to a more powerful machine. For more resources we offer our web server: with unlimited (up to 240GB so far, will be increased beginning of next year) RAM and CPU resources. Feel free to register there an account.

I hope I could help you.



ADD COMMENTlink written 4 months ago by wolffj.bioinf10
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