cellbender:remove-background: Command: cellbender remove-background --input raw_feature_bc_matrix --output cellbender.h5 --expected-cells 5000 --total-droplets-included 20000 --cuda cellbender:remove-background: 2023-07-04 03:22:16 cellbender:remove-background: Running remove-background cellbender:remove-background: Loading data from directory raw_feature_bc_matrix cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Trimming dataset for inference. cellbender:remove-background: Including 44505 genes that have nonzero counts. cellbender:remove-background: Prior on counts in empty droplets is 80 cellbender:remove-background: Prior on counts for cells is 734 cellbender:remove-background: Excluding barcodes with counts below 40 cellbender:remove-background: Using 5000 probable cell barcodes, plus an additional 15000 barcodes, and 62932 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 101 UMI counts. cellbender:remove-background: Running inference... cellbender:remove-background: [epoch 001] average training loss: 1839.7803 cellbender:remove-background: [epoch 002] average training loss: 1606.6756 (7.0 seconds per epoch) cellbender:remove-background: [epoch 003] average training loss: 1559.3606 cellbender:remove-background: [epoch 004] average training loss: 1546.9541 cellbender:remove-background: [epoch 005] average training loss: 1538.8762 cellbender:remove-background: [epoch 005] average test loss: 1571.9767 cellbender:remove-background: [epoch 006] average training loss: 1535.3019 cellbender:remove-background: [epoch 007] average training loss: 1525.3135 cellbender:remove-background: [epoch 008] average training loss: 1525.8069 cellbender:remove-background: [epoch 009] average training loss: 1515.1827 cellbender:remove-background: [epoch 010] average training loss: 1503.8889 cellbender:remove-background: [epoch 010] average test loss: 1534.3757 cellbender:remove-background: [epoch 011] average training loss: 1496.3033 cellbender:remove-background: [epoch 012] average training loss: 1481.1406 cellbender:remove-background: [epoch 013] average training loss: 1468.0516 cellbender:remove-background: [epoch 014] average training loss: 1447.9933 cellbender:remove-background: [epoch 015] average training loss: 1425.4689 cellbender:remove-background: [epoch 015] average test loss: 1436.0363 cellbender:remove-background: [epoch 016] average training loss: 1409.6657 cellbender:remove-background: [epoch 017] average training loss: 1406.7927 cellbender:remove-background: [epoch 018] average training loss: 1403.9156 cellbender:remove-background: [epoch 019] average training loss: 1398.0895 cellbender:remove-background: [epoch 020] average training loss: 1395.1195 cellbender:remove-background: [epoch 020] average test loss: 1412.4156 cellbender:remove-background: [epoch 021] average training loss: 1394.5283 cellbender:remove-background: [epoch 022] average training loss: 1387.8352 cellbender:remove-background: [epoch 023] average training loss: 1383.1464 cellbender:remove-background: [epoch 024] average training loss: 1382.7609 cellbender:remove-background: [epoch 025] average training loss: 1377.7545 cellbender:remove-background: [epoch 025] average test loss: 1410.0174 cellbender:remove-background: [epoch 026] average training loss: 1373.5085 cellbender:remove-background: [epoch 027] average training loss: 1375.0873 cellbender:remove-background: [epoch 028] average training loss: 1368.9780 cellbender:remove-background: [epoch 029] average training loss: 1370.2570 cellbender:remove-background: [epoch 030] average training loss: 1363.7845 cellbender:remove-background: [epoch 030] average test loss: 1375.5252 cellbender:remove-background: [epoch 031] average training loss: 1360.8675 cellbender:remove-background: [epoch 032] average training loss: 1359.9908 cellbender:remove-background: [epoch 033] average training loss: 1353.2207 cellbender:remove-background: [epoch 034] average training loss: 1349.5297 cellbender:remove-background: [epoch 035] average training loss: 1347.8773 cellbender:remove-background: [epoch 035] average test loss: 1378.8185 cellbender:remove-background: [epoch 036] average training loss: 1345.7755 cellbender:remove-background: [epoch 037] average training loss: 1343.6861 cellbender:remove-background: [epoch 038] average training loss: 1377.5199 cellbender:remove-background: [epoch 039] average training loss: 1400.1338 cellbender:remove-background: [epoch 040] average training loss: 1416.4424 cellbender:remove-background: [epoch 040] average test loss: 1430.0873 cellbender:remove-background: [epoch 041] average training loss: 1406.2739 cellbender:remove-background: [epoch 042] average training loss: 1396.2209 cellbender:remove-background: [epoch 043] average training loss: 1399.2033 cellbender:remove-background: [epoch 044] average training loss: 1385.9686 cellbender:remove-background: [epoch 045] average training loss: 1389.1899 cellbender:remove-background: [epoch 045] average test loss: 1425.9045 cellbender:remove-background: [epoch 046] average training loss: 1414.6875 cellbender:remove-background: [epoch 047] average training loss: 1403.8083 cellbender:remove-background: [epoch 048] average training loss: 1401.6825 cellbender:remove-background: [epoch 049] average training loss: 1374.5472 cellbender:remove-background: [epoch 050] average training loss: 1408.7338 cellbender:remove-background: [epoch 050] average test loss: 1429.4819 cellbender:remove-background: [epoch 051] average training loss: 1409.5616 cellbender:remove-background: [epoch 052] average training loss: 1384.1749 cellbender:remove-background: [epoch 053] average training loss: 1379.9081 cellbender:remove-background: [epoch 054] average training loss: 1356.0950 cellbender:remove-background: [epoch 055] average training loss: 1366.7400 cellbender:remove-background: [epoch 055] average test loss: 1434.0476 cellbender:remove-background: [epoch 056] average training loss: 1348.2958 cellbender:remove-background: [epoch 057] average training loss: 1374.0309 cellbender:remove-background: [epoch 058] average training loss: 1379.1292 cellbender:remove-background: [epoch 059] average training loss: 1368.6477 cellbender:remove-background: [epoch 060] average training loss: 1391.2360 cellbender:remove-background: [epoch 060] average test loss: 1419.7808 cellbender:remove-background: [epoch 061] average training loss: 1391.8145 cellbender:remove-background: [epoch 062] average training loss: 1416.3834 cellbender:remove-background: [epoch 063] average training loss: 1405.2807 cellbender:remove-background: [epoch 064] average training loss: 1411.4242 cellbender:remove-background: [epoch 065] average training loss: 1399.7716 cellbender:remove-background: [epoch 065] average test loss: 1433.4952 cellbender:remove-background: [epoch 066] average training loss: 1393.7801 cellbender:remove-background: [epoch 067] average training loss: 1387.0039 cellbender:remove-background: [epoch 068] average training loss: 1382.7365 cellbender:remove-background: [epoch 069] average training loss: 1390.2767 cellbender:remove-background: [epoch 070] average training loss: 1390.2468 cellbender:remove-background: [epoch 070] average test loss: 1414.3326 cellbender:remove-background: [epoch 071] average training loss: 1364.6932 cellbender:remove-background: [epoch 072] average training loss: 1362.6569 cellbender:remove-background: [epoch 073] average training loss: 1357.2442 cellbender:remove-background: [epoch 074] average training loss: 1375.8493 cellbender:remove-background: [epoch 075] average training loss: 1372.6322 cellbender:remove-background: [epoch 075] average test loss: 1413.2037 cellbender:remove-background: [epoch 076] average training loss: 1365.2212 cellbender:remove-background: [epoch 077] average training loss: 1368.6468 cellbender:remove-background: [epoch 078] average training loss: 1366.3601 cellbender:remove-background: [epoch 079] average training loss: 1395.4389 cellbender:remove-background: [epoch 080] average training loss: 1389.0778 cellbender:remove-background: [epoch 080] average test loss: 1412.8026 cellbender:remove-background: [epoch 081] average training loss: 1369.9274 cellbender:remove-background: [epoch 082] average training loss: 1384.3634 cellbender:remove-background: [epoch 083] average training loss: 1398.8811 cellbender:remove-background: [epoch 084] average training loss: 1385.9747 cellbender:remove-background: [epoch 085] average training loss: 1384.9424 cellbender:remove-background: [epoch 085] average test loss: 1407.5808 cellbender:remove-background: [epoch 086] average training loss: 1386.0715 cellbender:remove-background: [epoch 087] average training loss: 1368.1752 cellbender:remove-background: [epoch 088] average training loss: 1363.6845 cellbender:remove-background: [epoch 089] average training loss: 1367.0767 cellbender:remove-background: [epoch 090] average training loss: 1369.9681 cellbender:remove-background: [epoch 090] average test loss: 1410.5463 cellbender:remove-background: [epoch 091] average training loss: 1366.6794 cellbender:remove-background: [epoch 092] average training loss: 1374.8703 cellbender:remove-background: [epoch 093] average training loss: 1376.8892 cellbender:remove-background: [epoch 094] average training loss: 1382.0735 cellbender:remove-background: [epoch 095] average training loss: 1378.6621 cellbender:remove-background: [epoch 095] average test loss: 1410.8972 cellbender:remove-background: [epoch 096] average training loss: 1384.8759 cellbender:remove-background: [epoch 097] average training loss: 1391.6950 cellbender:remove-background: [epoch 098] average training loss: 1394.7136 cellbender:remove-background: [epoch 099] average training loss: 1387.8714 cellbender:remove-background: [epoch 100] average training loss: 1380.1964 cellbender:remove-background: [epoch 100] average test loss: 1409.7531 cellbender:remove-background: [epoch 101] average training loss: 1380.7902 cellbender:remove-background: [epoch 102] average training loss: 1385.7439 cellbender:remove-background: [epoch 103] average training loss: 1416.2797 cellbender:remove-background: [epoch 104] average training loss: 1408.4560 cellbender:remove-background: [epoch 105] average training loss: 1408.7319 cellbender:remove-background: [epoch 105] average test loss: 1419.2237 cellbender:remove-background: [epoch 106] average training loss: 1404.2980 cellbender:remove-background: [epoch 107] average training loss: 1396.5093 cellbender:remove-background: [epoch 108] average training loss: 1399.0994 cellbender:remove-background: [epoch 109] average training loss: 1404.6550 cellbender:remove-background: [epoch 110] average training loss: 1397.3811 cellbender:remove-background: [epoch 110] average test loss: 1416.7751 cellbender:remove-background: [epoch 111] average training loss: 1391.9918 cellbender:remove-background: [epoch 112] average training loss: 1389.9341 cellbender:remove-background: [epoch 113] average training loss: 1384.6147 cellbender:remove-background: [epoch 114] average training loss: 1383.6831 cellbender:remove-background: [epoch 115] average training loss: 1380.8720 cellbender:remove-background: [epoch 115] average test loss: 1410.0102 cellbender:remove-background: [epoch 116] average training loss: 1382.4118 cellbender:remove-background: [epoch 117] average training loss: 1376.7141 cellbender:remove-background: [epoch 118] average training loss: 1374.9366 cellbender:remove-background: [epoch 119] average training loss: 1378.6141 cellbender:remove-background: [epoch 120] average training loss: 1376.3286 cellbender:remove-background: [epoch 120] average test loss: 1406.5439 cellbender:remove-background: [epoch 121] average training loss: 1374.2178 cellbender:remove-background: [epoch 122] average training loss: 1374.2967 cellbender:remove-background: [epoch 123] average training loss: 1371.3367 cellbender:remove-background: [epoch 124] average training loss: 1370.8417 cellbender:remove-background: [epoch 125] average training loss: 1370.3077 cellbender:remove-background: [epoch 125] average test loss: 1401.6146 cellbender:remove-background: [epoch 126] average training loss: 1368.6911 cellbender:remove-background: [epoch 127] average training loss: 1368.8170 cellbender:remove-background: [epoch 128] average training loss: 1368.4479 cellbender:remove-background: [epoch 129] average training loss: 1368.6175 cellbender:remove-background: [epoch 130] average training loss: 1368.8779 cellbender:remove-background: [epoch 130] average test loss: 1400.7396 cellbender:remove-background: [epoch 131] average training loss: 1368.6768 cellbender:remove-background: [epoch 132] average training loss: 1368.9743 cellbender:remove-background: [epoch 133] average training loss: 1369.1433 cellbender:remove-background: [epoch 134] average training loss: 1367.7166 cellbender:remove-background: [epoch 135] average training loss: 1368.3301 cellbender:remove-background: [epoch 135] average test loss: 1401.0061 cellbender:remove-background: [epoch 136] average training loss: 1366.8240 cellbender:remove-background: [epoch 137] average training loss: 1366.4735 cellbender:remove-background: [epoch 138] average training loss: 1366.8424 cellbender:remove-background: [epoch 139] average training loss: 1366.1574 cellbender:remove-background: [epoch 140] average training loss: 1366.8856 cellbender:remove-background: [epoch 140] average test loss: 1400.4325 cellbender:remove-background: [epoch 141] average training loss: 1366.3798 cellbender:remove-background: [epoch 142] average training loss: 1365.7097 cellbender:remove-background: [epoch 143] average training loss: 1366.3895 cellbender:remove-background: [epoch 144] average training loss: 1365.8775 cellbender:remove-background: [epoch 145] average training loss: 1364.4144 cellbender:remove-background: [epoch 145] average test loss: 1399.7614 cellbender:remove-background: [epoch 146] average training loss: 1367.3143 cellbender:remove-background: [epoch 147] average training loss: 1365.6501 cellbender:remove-background: [epoch 148] average training loss: 1366.3909 cellbender:remove-background: [epoch 149] average training loss: 1366.0899 cellbender:remove-background: [epoch 150] average training loss: 1365.7246 cellbender:remove-background: [epoch 150] average test loss: 1400.2466 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Training succeeded cellbender:remove-background: 2023-07-04 03:41:59 cellbender:remove-background: Preparing to write outputs to file... cellbender:remove-background: Optimal posterior regularization factor = 0.37 cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file cellbender.h5 cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file cellbender_filtered.h5 cellbender:remove-background: Saved cell barcodes in cellbender_cell_barcodes.csv cellbender:remove-background: Saved summary plots as cellbender.pdf cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2023-07-04 03:47:03