Hi All,

If anyone has used CellOracle tool which is used for Gene KO. I have been using the pipeline on my own dataset to create oracle object and construct GRN using the base_GRN = co.data.load_human_promoter_base_GRN(). While constructing links using function:

links = oracle.get_links(cluster_name_for_GRN_unit="substates", alpha=10,n_jobs=1,verbose_level=10)

where substates in a column from the adata.obs

I face the following error:

  0%|          | 0/3 [00:00<?, ?it/s]
Inferring GRN for Fib_3...
  0%|          | 0/2060 [00:00<?, ?it/s]

ValueError Traceback (most recent call last) /tmp/ipykernel_1038868/1750070816.py in <module> ----> 1 links = oracle.get_links(cluster_name_for_GRN_unit="substates", alpha=10,n_jobs=1,verbose_level=10)

~/.local/lib/python3.7/site-packages/celloracle/trajectory/oracle_core.py in get_links(self, cluster_name_for_GRN_unit, alpha, bagging_number, verbose_level, test_mode, model_method, ignore_warning, n_jobs) 1470 verbose_level=verbose_level, test_mode=test_mode, 1471 model_method=model_method, -> 1472 n_jobs=n_jobs) 1473 return links 1474

ValueError: Length of values (2) does not match length of index (3)

Any help would be appreciated. Thanks