FloatingPointError, run_on_subsamples.py, nested-subsampling

[bruceamm]

Error: Traceback (most recent call last): File "run_on_subsamples.py", line 70, in results = network_reconstructor.reconstructNetwork(config, subsampledData) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructorSingleCell.py", line 531, in reconstructNetwork return self.runPipeline(stages, allData, *kwargs) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructor.py", line 22, in runPipeline stage(allData) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructorSingleCell.py", line 500, in stageComputeCorrelations allData["correlationCoefficients"], allData["correlationPValues"] = calculateCorrelations(config, allData["filteredData"]) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructorSingleCell.py", line 310, in calculateCorrelations correlationResults = treatmentData.groupby("metatreatment").map(calculateForMetatreatment) File "/home/pharmacy/bruceam/miniconda3/envs/python_nw_test_bruce_2/lib/python3.8/site-packages/xarray/core/groupby.py", line 795, in map return self._combine(applied, shortcut=shortcut) File "/home/pharmacy/bruceam/miniconda3/envs/python_nw_test_bruce_2/lib/python3.8/site-packages/xarray/core/groupby.py", line 819, in _combine combined = concat(applied, dim) File "/home/pharmacy/bruceam/miniconda3/envs/python_nw_test_bruce_2/lib/python3.8/site-packages/xarray/core/concat.py", line 238, in concat return f( File "/home/pharmacy/bruceam/miniconda3/envs/python_nw_test_bruce_2/lib/python3.8/site-packages/xarray/core/concat.py", line 427, in _dataset_concat datasets = list(datasets) File "/home/pharmacy/bruceam/miniconda3/envs/python_nw_test_bruce_2/lib/python3.8/site-packages/xarray/core/groupby.py", line 794, in applied = (maybe_wrap_array(arr, func(arr, args, *kwargs)) for arr in grouped) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructorSingleCell.py", line 272, in calculateForMetatreatment methodKwargs, endArgs = methodPrepare(treatmentData) File "/nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/reconstruction/reconstruction/NetworkReconstructorSingleCell.py", line 237, in prepareSpearman spearmanKwargs["coefficient"] = 6.0 / (n (numpy.square(n) - 1)) FloatingPointError: divide by zero encountered in true_divide

Command used: python3 run_on_subsamples.py --data-file /nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/single_cell_test_5-10-23/cd206-gata3-treg/output/all_data_and_metadata.cdf --config-file /nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/single_cell_test_5-10-23/cd206-gata3-treg/config.json --subsample-file /nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/single_cell_test_5-10-23/cd206-gata3-treg/output/cd206-gata3-treg_subsample.json --output-file /nfs3/PHARM/Morgun_Lab/amanda/network_analysis_NWcode/network_calculations/TkNA/single_cell_test_5-10-23/cd206-gata3-treg/output/cd206-gata3-treg.zip -s

[macovskym]

Unable to reproduce.