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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Too big memory needed in st.normalize #106

Open liushang20 opened 3 years ago

liushang20 commented 3 years ago

Hello, I test stream with the reference dataset (data_Nestorowa.tsv.gz) and follow the steps in the tutorial (https://nbviewer.jupyter.org/github/pinellolab/STREAM/blob/master/tutorial/1.2.use_vis.ipynb?flush_cache=true). However, the memory needs 100g at " st.normalize(adata,method='lib_size') ". Will this happen.

thank you!

huidongchen commented 3 years ago

For the example dataset data_Nestorowa.tsv.gz, it should not take that much memory. There must be something wrong there.

It works on my local laptop with 16 GB memory so it can't take more than 16GB.