Issue Generating Pyscenic GRN adj.csv file

[Su870]

Hello,

So I have uploaded all the appropriate files needed to run pyscenic (TF list, motif, expression file, etc.) but I am still getting an error when I run the command !pyscenic grn {f_loom_path_scenic} {f_tfs} -o adj.csv --num_workers 20.

This is the error I am getting: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for name, col in df.iteritems(): The notebook server will temporarily stop sending output to the client in order to avoid crashing it. To change this limit, set the config variable --NotebookApp.iopub_data_rate_limit.

Current values: NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec) NotebookApp.rate_limit_window=3.0 (secs)

---

My steps for loading the data is as follows in this order: following this protocol https://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.html#Reading-in-expression-data:-from-a-text-file

1. f_loom_path_scenic = "geneexp_scenic.loom"
2. f_exprMat = "all_countsData_csv_transposed.csv" adata=sc.read_text( f_exprMat, delimiter=',', first_column_names=True)

#creating loom file row_attrs = { "Gene": np.array(adata.var.index) , } col_attrs = { "CellID": np.array(adata.obs.index) , "nGene": np.array(np.sum(adata.X.transpose()>0, axis=0)).flatten() , "nUMI": np.array(np.sum(adata.X.transpose(), axis=0)).flatten() , } lp.create(f_loom_path_scenic, adata.X.transpose(), row_attrs, col_attrs)

3. f_tfs = "allTFs_hg38.txt"
4. !pyscenic grn {f_loom_path_scenic} {f_tfs} -o adj.csv --num_workers 20

After letting pyscenic run for about 2hrs, I would get that error message mentioned above. The adj.csv file is created in my working directory but the file is empty. Does anyone have a similar experience or know what to do?

Thank you!