prete
commented
3 years ago Hi @YuliaInn, the fact that 500 cells work could mean that it's a memory issue when running 22k cells despite having 400GB.
I can suggest you try the --subsampling option when launching cellphonedb. For example, something like:
cellphonedb method statistical_analysis --subsampling --subsampling-log True --subsampling-num-cells 500 meta.txt count.txtRead more the about optional-parameters here.
Alternatively, you could try moving your counts file to h5ad format and give beta version 2.1.8b3 a try (pip install -U cellphonedb==2.1.8b3).
YuliaInn
I have ~22000 cells in my input file. Whenever I subset the same input to 500 cells and run the same command as below, it works. I am running it in hpc cluster with 400G memory and 12 cpus allocated. I have ~450G storage in my working directory too. I talked to my hpc cluster support, they said it shouldn't be a memory problem.
I did not file any issues here with a similar error "No CellPhoneDB interacions found in this input". What can it be?
cellphonedb method statistical_analysis cellphonedb_metaLEFT_all.txt LeeCRCtumorNormalized_LEFT_all.txt --threads=12 --verboseOUTPUT:
/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.cluster.kmeans module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API. warnings.warn(message, FutureWarning) [ ][APP][12/05/21-11:17:43][WARNING] Latest local available version is
v2.0.0, using it [ ][APP][12/05/21-11:17:43][WARNING] User selected downloaded databasev2.0.0is available, using it [ ][CORE][12/05/21-11:17:43][INFO] Initializing SqlAlchemy CellPhoneDB Core [ ][CORE][12/05/21-11:17:43][INFO] Using custom database at /home/iid49/.cpdb/releases/v2.0.0/cellphone.db [ ][APP][12/05/21-11:17:43][INFO] Launching Method cpdb_statistical_analysis_local_method_launcher [ ][APP][12/05/21-11:17:43][INFO] Launching Method _set_paths [ ][APP][12/05/21-11:17:43][INFO] Launching Method _load_meta_counts [ ][CORE][12/05/21-11:28:08][INFO] Launching Method cpdb_statistical_analysis_launcher [ ][CORE][12/05/21-11:28:08][INFO] Launching Method _counts_validations [ ][CORE][12/05/21-11:28:24][INFO] [Cluster Statistical Analysis] Threshold:0.1 Iterations:1000 Debug-seed:-1 Threads:12 Precision:3 [ ][APP][12/05/21-11:28:27][ERROR] Unexpected error Traceback (most recent call last): File "/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/method_terminal_api_endpoints/method_terminal_commands.py", line 144, in statistical_analysis subsampler, File "/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/cellphonedb/src/local_launchers/local_method_launcher.py", line 64, in cpdb_statistical_analysis_local_method_launcher subsampler File "/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/cellphonedb/src/core/methods/method_launcher.py", line 76, in cpdb_statistical_analysis_launcher self.separator) File "/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_method.py", line 36, in call result_precision, File "/storage/hpc/data/iid49/miniconda/envs/cellphone/lib/python3.7/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_complex_method.py", line 64, in call raise NoInteractionsFound() cellphonedb.src.core.exceptions.NoInteractionsFound.NoInteractionsFound: No CellPhoneDB interacions found in this input.