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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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run_scenicplus error #270

Closed poddan01 closed 11 months ago

poddan01 commented 11 months ago

Hi! Thank you for such a great tool. I am getting an error in the run_scenicplus step. Here is the code I am using : run_scenicplus( scplus_obj = scplus_obj, variable = ['annotation'], species = 'hsapiens', assembly = 'hg38', tf_file = '/data/TF_names_v_1.01.txt', save_path = os.path.join(outDir, 'output3'), biomart_host = biomart_host, upstream = [1000, 150000], downstream = [1000, 150000], calculate_TF_eGRN_correlation = True, calculate_DEGs_DARs = True, export_to_loom_file = True, export_to_UCSC_file = True, n_cpu = 10, _temp_dir = os.path.join(tmpDir, 'ray_spill'))

Here is the error :

scenicplus_error

Could you please help me with this? Thanks.

SeppeDeWinter commented 11 months ago

Hi @poddan01

This is the same issue as this one: https://github.com/aertslab/scenicplus/issues/203. I was not able to reproduce this issue, it is related though to the UMAP and Numba versions you are using.

The good news is that once you reach this step, the complete SCENIC+ analysis has already finished (you just don't have a UMAP of the eRegulon enrichment scores).

So make sure to save your SCENIC+ object, this you can still use for all downstream analysis (except plotting UMAPS).

(closing this issue here, but feel free to comment on https://github.com/aertslab/scenicplus/issues/203).

All the best,

Seppe