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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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No CellPhoneDB interacions found in this input #14

Closed danli349 closed 2 years ago

danli349 commented 2 years ago

I am trying to use CellPhoneDB to analyze mouse data. I got the following error report when I use CellPhoneDB, could anyone give any suggestion? Thanks!

 cellphonedb method statistical_analysis \
> ETV4_meta.tsv \
> ETV4.h5ad \
> --output-path=./statistical_analysis \
> --counts-data hgnc_symbol \
> --iterations=10 \
> --threads=2
[ ][APP][03/02/22-14:14:47][WARNING] Latest local available version is `v2.0.0`, using it
[ ][APP][03/02/22-14:14:47][WARNING] User selected downloaded database `v2.0.0` is available, using it
[ ][CORE][03/02/22-14:14:47][INFO] Initializing SqlAlchemy CellPhoneDB Core
[ ][CORE][03/02/22-14:14:47][INFO] Using custom database at /home/dan/.cpdb/releases/v2.0.0/cellphone.db
[ ][APP][03/02/22-14:14:47][INFO] Launching Method cpdb_statistical_analysis_local_method_launcher
[ ][APP][03/02/22-14:14:47][INFO] Launching Method _set_paths
[ ][APP][03/02/22-14:14:47][INFO] Launching Method _load_meta_counts
[ ][APP][03/02/22-14:14:54][INFO] Launching Method _check_counts_data
[ ][CORE][03/02/22-14:14:54][INFO] Launching Method cpdb_statistical_analysis_launcher
[ ][CORE][03/02/22-14:14:54][INFO] Launching Method _counts_validations
[ ][CORE][03/02/22-14:14:54][INFO] Launching Method get_interactions_genes_complex
[ ][CORE][03/02/22-14:14:58][INFO] [Cluster Statistical Analysis] Threshold:0.1 Iterations:10 Debug-seed:-1 Threads:2 Precision:3
[ ][APP][03/02/22-14:14:59][ERROR] Unexpected error
Traceback (most recent call last):
  File "/home/dan/miniconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/method_terminal_api_endpoints/method_terminal_commands.py", line 150, in statistical_analysis
    debug,
  File "/home/dan/miniconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/local_launchers/local_method_launcher.py", line 75, in cpdb_statistical_analysis_local_method_launcher
    output_path
  File "/home/dan/miniconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/method_launcher.py", line 111, in cpdb_statistical_analysis_launcher
    output_path)
  File "/home/dan/miniconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_method.py", line 43, in call
    output_path
  File "/home/dan/miniconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_complex_method.py", line 57, in call
    raise NoInteractionsFound()
cellphonedb.src.core.exceptions.NoInteractionsFound.NoInteractionsFound: No CellPhoneDB interacions found in this input.
luzgaral commented 2 years ago

Hi,

Thanks for using CellphoneDB.

Could you give us more information about your input? Please note that CellphoneDB database is designed for human data, only human identifiers are accepted.

Best

Luz

danli349 commented 2 years ago

Hi Luz Can we update the CellphoneDB database for mouse data? My ETV4_meta.tsv is generated following the tutorial: https://github.com/ventolab/CellphoneDB/blob/master/notebooks/0_prepare_your_data_from_anndata.ipynb The ETV4.h5ad is generated by anndata.AnnData.write.

Thanks a lot Dan

luzgaral commented 2 years ago

Hi,

You can generate a new database following the instructions here.

Alternatively, you can translate your mouse ids to their human orthologous and use CellphoneDB default database.

Best,

Luz