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An error about grn inference #7

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Leslie456456 opened this issue Feb 24, 2024 · 0 comments
Open

An error about grn inference #7

Leslie456456 opened this issue Feb 24, 2024 · 0 comments

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@Leslie456456
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Hi,

A very nice tool! I have such an error:
usage: pyscenic ctx [-h] [-o OUTPUT] [-n] [--chunk_size CHUNK_SIZE]
[--mode {custom_multiprocessing,dask_multiprocessing,dask_cluster}]
[-a] [-t] [--rank_threshold RANK_THRESHOLD]
[--auc_threshold AUC_THRESHOLD]
[--nes_threshold NES_THRESHOLD]
[--min_orthologous_identity MIN_ORTHOLOGOUS_IDENTITY]
[--max_similarity_fdr MAX_SIMILARITY_FDR]
--annotations_fname ANNOTATIONS_FNAME
[--num_workers NUM_WORKERS]
[--client_or_address CLIENT_OR_ADDRESS]
[--thresholds THRESHOLDS [THRESHOLDS ...]]
[--top_n_targets TOP_N_TARGETS [TOP_N_TARGETS ...]]
[--top_n_regulators TOP_N_REGULATORS [TOP_N_REGULATORS ...]]
[--min_genes MIN_GENES]
[--expression_mtx_fname EXPRESSION_MTX_FNAME]
[--mask_dropouts] [--cell_id_attribute CELL_ID_ATTRIBUTE]
[--gene_attribute GENE_ATTRIBUTE] [--sparse]
module_fname database_fname [database_fname ...]
pyscenic ctx: error: argument module_fname: can't open 'C:\Users\AppData\Local\Temp\tmpgtaq66d0\grn.csv': [Errno 2] No such file or directory: 'C:\Users\AppData\Local\Temp\tmpgtaq66d0\grn.csv'
When I run this code: grn_df = sn.grn.grn_inference(adata_processed=adata_processed, modules_df=modules_df, module=Mod_, groupby_ = groupby_, anno_name = anno_name, specie=specie_, subsampling_pct=80, n_iteration=n_iteration, num_workers=num_workers)
I am looking forward to your help!

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