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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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pycisTopic label transfer failure #400

Open hshcao opened 6 months ago

hshcao commented 6 months ago

Describe the bug Hi @SeppeDeWinter and others,

the 'label transfer' step did not go through when i run scenicplus for pycisTopic, I followed the tutorial here: (https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html) I run scenicplus on my own GPU server, which is a standalone server, not on a HPC. the labels are from scanpy, which was run following the tutorial here: https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html

Another question: this label transfer are needed for running the scenic+ Snakemake, right? or the Snakemake has some other ways of transferring labels?

Thanks

To Reproduce label_dict = label_transfer( rna_anndata, atac_anndata, labels_to_transfer = ['Seurat_cell_type'], variable_genes = True, methods = ['ingest', 'harmony', 'bbknn', 'scanorama', 'cca'], return_label_weights = False, _temp_dir= '/scratch/leuven/330/vsc33053/ray_spill/' )

Error output Paste the entire output of the command, including log information prior to the error. WechatIMG1577

Expected behavior A clear and concise description of what you expected to happen.

Screenshots WechatIMG1577

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SeppeDeWinter commented 5 months ago

Hi @hshcao

Could you try again by running the following piece of code first:


import ray
ray.shutdown()