cellphonedb.src.core.exceptions.AllCountsFilteredException.AllCountsFilteredException: All counts filtered

[Shaun-66]

Hi,

Firstly, thank you for the nice package.
I met a problem when ran the cpdb_degs_analysis_method.call, my code is like:
cpdb_results = cpdb_degs_analysis_method.call(
cpdb_file_path = cpdb_file_path, # mandatory: CellphoneDB database zip file.
meta_file_path = meta_file_path, # mandatory: tsv file defining barcodes to cell label.
counts_file_path = counts_file_path, # mandatory: normalized count matrix - a path to the counts file, or an in-memory AnnData object
degs_file_path = degs_file_path, # mandatory: tsv file with DEG to account.
counts_data = 'hgnc_symbol', # defines the gene annotation in counts matrix.
score_interactions = True, # optional: whether to score interactions or not.
threshold = 0.1, # defines the min % of cells expressing a gene for this to be employed in the analysis.
result_precision = 3, # Sets the rounding for the mean values in significan_means.
separator = '|', # Sets the string to employ to separate cells in the results dataframes "cellA|CellB".
debug = False, # Saves all intermediate tables emplyed during the analysis in pkl format.
output_path = out_path, # Path to save results
output_suffix = None, # Replaces the timestamp in the output files by a user defined string in the (default: None)
threads = 25
)

and the problem is:
Traceback (most recent call last):
File "script.py", line 16, in
cpdb_results = cpdb_degs_analysis_method.call(
File "/home/hd/hd_hd/hd_uz326/miniconda3/envs/CellphoneDB/lib/python3.8/site-packages/cellphonedb/src/core/methods/cpdb_degs_analysis_method.py", line 110, in call
raise AllCountsFilteredException(hint='Are you using human data?')
cellphonedb.src.core.exceptions.AllCountsFilteredException.AllCountsFilteredException: All counts filtered

Could you help me figure out what was going wrong?

Best,
Shaun