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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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create_cistopic_object_from_fragments run forever #465

Closed Quentin-bioinfo closed 2 weeks ago

Quentin-bioinfo commented 2 weeks ago

I followed the tutorial of pycisTopic and it works well until i reach the function create_cistopic_object_from_fragments.

When I run the command as written in the tutorial, it shows : "2024-09-12 10:16:32,539 cisTopic INFO Reading data for 21_069"

But then just run forever without showing anything else.

The first part of the command work 

sample_metrics = pl.read_parquet(
        os.path.join(pycistopic_qc_output_dir, f'{sample_id}.fragments_stats_per_cb.parquet')
    ).to_pandas().set_index("CB").loc[ sample_id_to_barcodes_passing_filters[sample_id] ]

But then again if i run the create_cistopic_object_from_fragments command after that it runs forever.

Pycistopic version: '2.0a0'

Any ideas?