SCSA annotation stops with Error
I am running notebook 05_annotation of the ATAC Notebooks. The run_scsa() throws following error:
Found 21646 genes from input ranked genes
Checking if genes are in the database...
Best match between input genes and database were found in column 'gene_name' with 3075 genes (14.2%)
Running SCSA...
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In [33], line 2
1 for column in RESOLUTIONS:
----> 2 run_scsa(genes_adata,
3 gene_column=None,
4 gene_symbol='auto',
5 key=f'rank_genes_groups_SCSA_{column}',
6 column_added=f'SCSA_pred_celltype_{column}',
7 inplace=True,
8 python_path=None,
9 species=None,
10 fc=1.5,
11 pvalue=0.01,
12 tissue='All',
13 user_db=SCSA_CUSTOM_DB_PATH
14 )
15 adata.obs[f'SCSA_pred_celltype_{column}'] = genes_adata.obs[f'SCSA_pred_celltype_{column}']
16 sc.pl.umap(adata, color=[f'SCSA_pred_celltype_{column}', f'cell_types_{column}'], wspace=0.5)
File /mnt/workspace/rwiegan/git/sc_framework/sctoolbox/celltype_annotation.py:210, in run_scsa(adata, gene_column, gene_symbol, key, column_added, inplace, python_path, species, fc, pvalue, tissue, user_db, celltype_column)
208 stdout = p.stdout
209 if p.returncode != 0:
--> 210 raise ValueError(f"SCSA failed with error: {stderr.decode('utf-8')}")
212 # ---- read results_path and assign to adata.obs ---- #
213 df = pd.read_csv(results_path, sep='\t', engine='python')
ValueError: SCSA failed with error: Traceback (most recent call last):
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 386, in <module>
p.run_cmd(args)
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 374, in run_cmd
outs = anno.run_detail_cmd()
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 339, in run_detail_cmd
outs = self.calcu_scanpy_group(self.args.input)
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 162, in calcu_scanpy_group
h_values, colnames = self.get_cell_matrix(newexps, lcol, ncol)
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 257, in get_cell_matrix
cell_value, genenames = self.get_cell_matrix_detail(exps, lcol, ncol)
File "/mnt/workspace/rwiegan/git/sc_framework/sctoolbox/data/SCSA_custom.py", line 279, in get_cell_matrix_detail
cellnum = len(cellnames)
TypeError: object of type 'NoneType' has no len()