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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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error for export_pseudobulk #255

Open leogg738 opened 7 months ago

leogg738 commented 7 months ago

Describe the bug when i run export_pseudobulk , jupyter shows kernel restarting, 'The kernel for Untitled.ipynb appears to have died. It will restart automatically.'

To Reproduce from pycisTopic.pseudobulk_peak_calling import export_pseudobulk bw_paths, bed_paths = export_pseudobulk(input_data = cell_data, variable = 'celltype', # variable by which to generate pseubulk profiles, in this case we want pseudobulks per celltype sample_id_col = 'sample_id', chromsizes = chromsizes, bed_path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/pseudobulk_bed_files/'), # specify where pseudobulk_bed_files should be stored bigwig_path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/pseudobulk_bw_files/'),# specify where pseudobulk_bw_files should be stored path_to_fragments = fragments_dict, # location of fragment fiels n_cpu = 1, # specify the number of cores to use, we use ray for multi processing normalize_bigwig = True, remove_duplicates = True, _temp_dir = os.path.join(tmp_dir, 'ray_spill'), split_pattern = '-')

Error output kernel restarting, 'The kernel for Untitled.ipynb appears to have died. It will restart automatically.'

Expected behavior run successfully

SeppeDeWinter commented 7 months ago

Hi @leogg738

You might be running out of memory. How much do you have available?

All the best,

Seppe

leogg738 commented 7 months ago

Hi @SeppeDeWinter

Thank you for your response. I have 256G available memoey. Recently I have not tried it again. So I do not konw whether it can run. If you give me some solutions, I am very pleasure to try.

Best wishes,

leo