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Teichlab / cellphonedb

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No CellPhoneDB interacions found in this input. #360

Closed monikaramos closed 2 years ago

monikaramos commented 2 years ago

Hi there. Can someone please help me understand what I am doing to generate this error message?

[ ][APP][14/01/22-22:02:20][ERROR] Unexpected error Traceback (most recent call last): File "/data/tools/anaconda3/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 "/data/tools/anaconda3/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 "/data/tools/anaconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/method_launcher.py", line 111, in cpdb_statistical_analysis_launcher output_path) File "/data/tools/anaconda3/envs/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_method.py", line 43, in call output_path File "/data/tools/anaconda3/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.

Here is my command: (cpdb) [mramos@hbl23 cellphonedb_test]$ cellphonedb method statistical_analysis kluv_cd40ag_cpdb_meta.txt cpdb_kluv_cd40_counts.txt --project-name=kluv_cd40ag_cpdb --iterations=1000 --threshold=0.10 --counts-data=hgnc_symbol --output-path=/ home/mramos/cellphonedb_test --verbose --threads=6

and this was the log before the error logs

[ ][APP][14/01/22-22:01:54][WARNING] Latest local available version is v2.0.0, using it [ ][APP][14/01/22-22:01:54][WARNING] User selected downloaded database v2.0.0 is available, using it [ ][CORE][14/01/22-22:01:54][INFO] Initializing SqlAlchemy CellPhoneDB Core [ ][CORE][14/01/22-22:01:54][INFO] Using custom database at /home/mramos/.cpdb/releases/v2.0.0/cellphone.db [ ][APP][14/01/22-22:01:54][INFO] Launching Method cpdb_statistical_analysis_local_method_launcher [ ][APP][14/01/22-22:01:54][INFO] Launching Method _set_paths [ ][APP][14/01/22-22:01:54][INFO] Launching Method _load_meta_counts [ ][APP][14/01/22-22:02:19][INFO] Launching Method _check_counts_data [ ][CORE][14/01/22-22:02:19][INFO] Launching Method cpdb_statistical_analysis_launcher [ ][CORE][14/01/22-22:02:19][INFO] Launching Method _counts_validations [ ][CORE][14/01/22-22:02:19][INFO] Launching Method get_interactions_genes_complex [ ][CORE][14/01/22-22:02:20][INFO] [Cluster Statistical Analysis] Threshold:0.1 Iterations:1000 Debug-seed:-1 Threads:6

Any help is greatly appreciated. I ensured that my count.txt and meta.txt files were constructed exactly as the sample prep and example files had them as well to fix invalid count errors I initially received.

monikaramos commented 2 years ago

Here is an example of what my count.txt input looks like image

monikaramos commented 2 years ago

My genes were not in human hgnc format for anyone else that may have this issue