cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2275-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 10173 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 10e5fd209f) cellbender:remove-background: 2024-06-06 15:05:08 cellbender:remove-background: Running remove-background cellbender:remove-background: Loading data from /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2275-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 30978 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1784 cellbender:remove-background: Prior on counts for empty droplets is 93 cellbender:remove-background: Excluding 7069 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23909 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 46 cellbender:remove-background: Using 10173 probable cell barcodes, plus an additional 9827 barcodes, and 27480 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 91 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp6jdlg17c cellbender:remove-background: No saved checkpoint. cellbender:remove-background: No checkpoint loaded. cellbender:remove-background: Running inference... cellbender:remove-background: [epoch 001] average training loss: 4736.6845 cellbender:remove-background: [epoch 002] average training loss: 3887.1572 (6.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 65 epochs cellbender:remove-background: [epoch 003] average training loss: 3374.2779 cellbender:remove-background: [epoch 004] average training loss: 3052.8659 cellbender:remove-background: [epoch 005] average training loss: 2946.7643 cellbender:remove-background: [epoch 005] average test loss: 2970.8539 cellbender:remove-background: [epoch 006] average training loss: 2917.9716 cellbender:remove-background: [epoch 007] average training loss: 2869.5400 cellbender:remove-background: [epoch 008] average training loss: 2838.7617 cellbender:remove-background: [epoch 009] average training loss: 2844.9210 cellbender:remove-background: [epoch 010] average training loss: 2811.7893 cellbender:remove-background: [epoch 010] average test loss: 2821.1063 cellbender:remove-background: [epoch 011] average training loss: 2818.9306 cellbender:remove-background: [epoch 012] average training loss: 2769.3724 cellbender:remove-background: [epoch 013] average training loss: 2684.9226 cellbender:remove-background: [epoch 014] average training loss: 2689.4615 cellbender:remove-background: [epoch 015] average training loss: 2654.5850 cellbender:remove-background: [epoch 015] average test loss: 2692.0525 cellbender:remove-background: [epoch 016] average training loss: 2642.3978 cellbender:remove-background: [epoch 017] average training loss: 2656.2093 cellbender:remove-background: [epoch 018] average training loss: 2644.9350 cellbender:remove-background: [epoch 019] average training loss: 2628.0379 cellbender:remove-background: [epoch 020] average training loss: 2608.2131 cellbender:remove-background: [epoch 020] average test loss: 2648.8168 cellbender:remove-background: [epoch 021] average training loss: 2609.4914 cellbender:remove-background: [epoch 022] average training loss: 2608.5204 cellbender:remove-background: [epoch 023] average training loss: 2605.3304 cellbender:remove-background: [epoch 024] average training loss: 2586.2088 cellbender:remove-background: [epoch 025] average training loss: 2574.1693 cellbender:remove-background: [epoch 025] average test loss: 2584.1187 cellbender:remove-background: [epoch 026] average training loss: 2540.3506 cellbender:remove-background: [epoch 027] average training loss: 2528.8667 cellbender:remove-background: [epoch 028] average training loss: 2519.9873 cellbender:remove-background: [epoch 029] average training loss: 2500.9658 cellbender:remove-background: [epoch 030] average training loss: 2486.0848 cellbender:remove-background: [epoch 030] average test loss: 2489.9000 cellbender:remove-background: [epoch 031] average training loss: 2479.5573 cellbender:remove-background: [epoch 032] average training loss: 2471.8385 cellbender:remove-background: [epoch 033] average training loss: 2459.7611 cellbender:remove-background: [epoch 034] average training loss: 2453.8094 cellbender:remove-background: [epoch 035] average training loss: 2446.7197 cellbender:remove-background: [epoch 035] average test loss: 2426.7865 cellbender:remove-background: [epoch 036] average training loss: 2443.4732 cellbender:remove-background: [epoch 037] average training loss: 2437.6477 cellbender:remove-background: [epoch 038] average training loss: 2440.9204 cellbender:remove-background: [epoch 039] average training loss: 2440.4432 cellbender:remove-background: [epoch 040] average training loss: 2442.7118 cellbender:remove-background: [epoch 040] average test loss: 2443.1218 cellbender:remove-background: [epoch 041] average training loss: 2444.6021 cellbender:remove-background: [epoch 042] average training loss: 2442.5625 cellbender:remove-background: [epoch 043] average training loss: 2438.0043 cellbender:remove-background: [epoch 044] average training loss: 2443.7042 cellbender:remove-background: [epoch 045] average training loss: 2443.9872 cellbender:remove-background: [epoch 045] average test loss: 2453.4131 cellbender:remove-background: [epoch 046] average training loss: 2444.8613 cellbender:remove-background: [epoch 047] average training loss: 2446.2734 cellbender:remove-background: [epoch 048] average training loss: 2443.5844 cellbender:remove-background: [epoch 049] average training loss: 2447.9604 cellbender:remove-background: [epoch 050] average training loss: 2446.0407 cellbender:remove-background: [epoch 050] average test loss: 2452.1033 cellbender:remove-background: [epoch 051] average training loss: 2448.5656 cellbender:remove-background: [epoch 052] average training loss: 2443.4938 cellbender:remove-background: [epoch 053] average training loss: 2446.5625 cellbender:remove-background: [epoch 054] average training loss: 2444.9453 cellbender:remove-background: [epoch 055] average training loss: 2449.0288 cellbender:remove-background: [epoch 055] average test loss: 2446.9086 cellbender:remove-background: [epoch 056] average training loss: 2449.8655 cellbender:remove-background: [epoch 057] average training loss: 2446.0053 cellbender:remove-background: [epoch 058] average training loss: 2447.7342 cellbender:remove-background: [epoch 059] average training loss: 2446.4531 cellbender:remove-background: [epoch 060] average training loss: 2443.7108 cellbender:remove-background: [epoch 060] average test loss: 2462.9524 cellbender:remove-background: [epoch 061] average training loss: 2443.8222 cellbender:remove-background: [epoch 062] average training loss: 2443.0210 cellbender:remove-background: [epoch 063] average training loss: 2443.6101 cellbender:remove-background: [epoch 064] average training loss: 2445.2555 cellbender:remove-background: [epoch 065] average training loss: 2442.2427 cellbender:remove-background: [epoch 065] average test loss: 2440.2501 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 066] average training loss: 2445.5756 cellbender:remove-background: [epoch 067] average training loss: 2442.9732 cellbender:remove-background: [epoch 068] average training loss: 2442.4994 cellbender:remove-background: [epoch 069] average training loss: 2445.3995 cellbender:remove-background: [epoch 070] average training loss: 2441.2387 cellbender:remove-background: [epoch 070] average test loss: 2454.3276 cellbender:remove-background: [epoch 071] average training loss: 2441.4280 cellbender:remove-background: [epoch 072] average training loss: 2438.9761 cellbender:remove-background: [epoch 073] average training loss: 2441.7842 cellbender:remove-background: [epoch 074] average training loss: 2440.4201 cellbender:remove-background: [epoch 075] average training loss: 2438.4279 cellbender:remove-background: [epoch 075] average test loss: 2457.5140 cellbender:remove-background: [epoch 076] average training loss: 2441.2722 cellbender:remove-background: [epoch 077] average training loss: 2437.7363 cellbender:remove-background: [epoch 078] average training loss: 2436.1176 cellbender:remove-background: [epoch 079] average training loss: 2434.2001 cellbender:remove-background: [epoch 080] average training loss: 2440.2041 cellbender:remove-background: [epoch 080] average test loss: 2436.2776 cellbender:remove-background: [epoch 081] average training loss: 2439.6339 cellbender:remove-background: [epoch 082] average training loss: 2435.7017 cellbender:remove-background: [epoch 083] average training loss: 2437.5010 cellbender:remove-background: [epoch 084] average training loss: 2435.1156 cellbender:remove-background: [epoch 085] average training loss: 2436.0905 cellbender:remove-background: [epoch 085] average test loss: 2439.1248 cellbender:remove-background: [epoch 086] average training loss: 2433.8177 cellbender:remove-background: [epoch 087] average training loss: 2435.2729 cellbender:remove-background: [epoch 088] average training loss: 2436.6753 cellbender:remove-background: [epoch 089] average training loss: 2435.2220 cellbender:remove-background: [epoch 090] average training loss: 2436.0020 cellbender:remove-background: [epoch 090] average test loss: 2444.5711 cellbender:remove-background: [epoch 091] average training loss: 2434.2382 cellbender:remove-background: [epoch 092] average training loss: 2436.4729 cellbender:remove-background: [epoch 093] average training loss: 2432.3603 cellbender:remove-background: [epoch 094] average training loss: 2431.2910 cellbender:remove-background: [epoch 095] average training loss: 2431.9366 cellbender:remove-background: [epoch 095] average test loss: 2444.9606 cellbender:remove-background: [epoch 096] average training loss: 2432.2621 cellbender:remove-background: [epoch 097] average training loss: 2429.6542 cellbender:remove-background: [epoch 098] average training loss: 2431.0964 cellbender:remove-background: [epoch 099] average training loss: 2429.6353 cellbender:remove-background: [epoch 100] average training loss: 2431.5006 cellbender:remove-background: [epoch 100] average test loss: 2433.3306 cellbender:remove-background: [epoch 101] average training loss: 2426.2752 cellbender:remove-background: [epoch 102] average training loss: 2431.6534 cellbender:remove-background: [epoch 103] average training loss: 2425.4591 cellbender:remove-background: [epoch 104] average training loss: 2429.7281 cellbender:remove-background: [epoch 105] average training loss: 2427.1164 cellbender:remove-background: [epoch 105] average test loss: 2448.8643 cellbender:remove-background: [epoch 106] average training loss: 2431.0580 cellbender:remove-background: [epoch 107] average training loss: 2427.5705 cellbender:remove-background: [epoch 108] average training loss: 2426.0114 cellbender:remove-background: [epoch 109] average training loss: 2427.9893 cellbender:remove-background: [epoch 110] average training loss: 2428.1480 cellbender:remove-background: [epoch 110] average test loss: 2425.3399 cellbender:remove-background: [epoch 111] average training loss: 2427.8543 cellbender:remove-background: [epoch 112] average training loss: 2426.6169 cellbender:remove-background: [epoch 113] average training loss: 2423.2289 cellbender:remove-background: [epoch 114] average training loss: 2426.8846 cellbender:remove-background: [epoch 115] average training loss: 2425.7048 cellbender:remove-background: [epoch 115] average test loss: 2438.3259 cellbender:remove-background: [epoch 116] average training loss: 2423.6433 cellbender:remove-background: [epoch 117] average training loss: 2426.2053 cellbender:remove-background: [epoch 118] average training loss: 2426.1104 cellbender:remove-background: [epoch 119] average training loss: 2425.1123 cellbender:remove-background: [epoch 120] average training loss: 2425.8092 cellbender:remove-background: [epoch 120] average test loss: 2435.1045 cellbender:remove-background: [epoch 121] average training loss: 2423.3001 cellbender:remove-background: [epoch 122] average training loss: 2425.3386 cellbender:remove-background: [epoch 123] average training loss: 2424.5262 cellbender:remove-background: [epoch 124] average training loss: 2422.5716 cellbender:remove-background: [epoch 125] average training loss: 2423.4131 cellbender:remove-background: [epoch 125] average test loss: 2443.6007 cellbender:remove-background: [epoch 126] average training loss: 2422.9101 cellbender:remove-background: [epoch 127] average training loss: 2422.2637 cellbender:remove-background: [epoch 128] average training loss: 2421.6795 cellbender:remove-background: [epoch 129] average training loss: 2422.5125 cellbender:remove-background: [epoch 130] average training loss: 2425.8376 cellbender:remove-background: [epoch 130] average test loss: 2434.9907 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 131] average training loss: 2420.5214 cellbender:remove-background: [epoch 132] average training loss: 2419.6531 cellbender:remove-background: [epoch 133] average training loss: 2421.3270 cellbender:remove-background: [epoch 134] average training loss: 2419.1862 cellbender:remove-background: [epoch 135] average training loss: 2420.4780 cellbender:remove-background: [epoch 135] average test loss: 2439.3881 cellbender:remove-background: [epoch 136] average training loss: 2419.7332 cellbender:remove-background: [epoch 137] average training loss: 2420.7653 cellbender:remove-background: [epoch 138] average training loss: 2421.5929 cellbender:remove-background: [epoch 139] average training loss: 2420.1200 cellbender:remove-background: [epoch 140] average training loss: 2418.5568 cellbender:remove-background: [epoch 140] average test loss: 2442.8335 cellbender:remove-background: [epoch 141] average training loss: 2419.5098 cellbender:remove-background: [epoch 142] average training loss: 2420.2812 cellbender:remove-background: [epoch 143] average training loss: 2420.4726 cellbender:remove-background: [epoch 144] average training loss: 2420.1512 cellbender:remove-background: [epoch 145] average training loss: 2420.1347 cellbender:remove-background: [epoch 145] average test loss: 2438.9737 cellbender:remove-background: [epoch 146] average training loss: 2418.6570 cellbender:remove-background: [epoch 147] average training loss: 2420.2542 cellbender:remove-background: [epoch 148] average training loss: 2419.3559 cellbender:remove-background: [epoch 149] average training loss: 2421.1751 cellbender:remove-background: [epoch 150] average training loss: 2419.4094 cellbender:remove-background: [epoch 150] average test loss: 2442.0064 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:25:23 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp851g6_0y cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp851g6_0y /tmp/tmp851g6_0y/10e5fd209f_random.pyro /tmp/tmp851g6_0y/10e5fd209f_random.cuda /tmp/tmp851g6_0y/10e5fd209f_model.torch /tmp/tmp851g6_0y/10e5fd209f_optim.torch /tmp/tmp851g6_0y/10e5fd209f_optim.pyro /tmp/tmp851g6_0y/10e5fd209f_params.pyro /tmp/tmp851g6_0y/10e5fd209f_train.loaderstate /tmp/tmp851g6_0y/10e5fd209f_test.loaderstate /tmp/tmp851g6_0y/10e5fd209f_args.npy cellbender:remove-background: Posterior not currently included in checkpoint. cellbender:remove-background: Computing posterior noise count probabilities in mini-batches. cellbender:remove-background: Working on chunk (1/109) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/109) cellbender:remove-background: Working on chunk (3/109) cellbender:remove-background: Working on chunk (4/109) cellbender:remove-background: Working on chunk (5/109) cellbender:remove-background: Working on chunk (6/109) cellbender:remove-background: Working on chunk (7/109) cellbender:remove-background: Working on chunk (8/109) cellbender:remove-background: Working on chunk (9/109) cellbender:remove-background: Working on chunk (10/109) cellbender:remove-background: Working on chunk (11/109) cellbender:remove-background: Working on chunk (12/109) cellbender:remove-background: Working on chunk (13/109) cellbender:remove-background: Working on chunk (14/109) cellbender:remove-background: Working on chunk (15/109) cellbender:remove-background: Working on chunk (16/109) cellbender:remove-background: Working on chunk (17/109) cellbender:remove-background: Working on chunk (18/109) cellbender:remove-background: Working on chunk (19/109) cellbender:remove-background: Working on chunk (20/109) cellbender:remove-background: Working on chunk (21/109) cellbender:remove-background: Working on chunk (22/109) cellbender:remove-background: Working on chunk (23/109) cellbender:remove-background: Working on chunk (24/109) cellbender:remove-background: Working on chunk (25/109) cellbender:remove-background: Working on chunk (26/109) cellbender:remove-background: Working on chunk (27/109) cellbender:remove-background: Working on chunk (28/109) cellbender:remove-background: Working on chunk (29/109) cellbender:remove-background: Working on chunk (30/109) cellbender:remove-background: Working on chunk (31/109) cellbender:remove-background: Working on chunk (32/109) cellbender:remove-background: Working on chunk (33/109) cellbender:remove-background: Working on chunk (34/109) cellbender:remove-background: Working on chunk (35/109) cellbender:remove-background: Working on chunk (36/109) cellbender:remove-background: Working on chunk (37/109) cellbender:remove-background: Working on chunk (38/109) cellbender:remove-background: Working on chunk (39/109) cellbender:remove-background: Working on chunk (40/109) cellbender:remove-background: Working on chunk (41/109) cellbender:remove-background: Working on chunk (42/109) cellbender:remove-background: Working on chunk (43/109) cellbender:remove-background: Working on chunk (44/109) cellbender:remove-background: Working on chunk (45/109) cellbender:remove-background: Working on chunk (46/109) cellbender:remove-background: Working on chunk (47/109) cellbender:remove-background: Working on chunk (48/109) cellbender:remove-background: Working on chunk (49/109) cellbender:remove-background: Working on chunk (50/109) cellbender:remove-background: Working on chunk (51/109) cellbender:remove-background: Working on chunk (52/109) cellbender:remove-background: Working on chunk (53/109) cellbender:remove-background: Working on chunk (54/109) cellbender:remove-background: Working on chunk (55/109) cellbender:remove-background: Working on chunk (56/109) cellbender:remove-background: Working on chunk (57/109) cellbender:remove-background: Working on chunk (58/109) cellbender:remove-background: Working on chunk (59/109) cellbender:remove-background: Working on chunk (60/109) cellbender:remove-background: Working on chunk (61/109) cellbender:remove-background: Working on chunk (62/109) cellbender:remove-background: Working on chunk (63/109) cellbender:remove-background: Working on chunk (64/109) cellbender:remove-background: Working on chunk (65/109) cellbender:remove-background: Working on chunk (66/109) cellbender:remove-background: Working on chunk (67/109) cellbender:remove-background: Working on chunk (68/109) cellbender:remove-background: Working on chunk (69/109) cellbender:remove-background: Working on chunk (70/109) cellbender:remove-background: Working on chunk (71/109) cellbender:remove-background: Working on chunk (72/109) cellbender:remove-background: Working on chunk (73/109) cellbender:remove-background: Working on chunk (74/109) cellbender:remove-background: Working on chunk (75/109) cellbender:remove-background: Working on chunk (76/109) cellbender:remove-background: Working on chunk (77/109) cellbender:remove-background: Working on chunk (78/109) cellbender:remove-background: Working on chunk (79/109) cellbender:remove-background: Working on chunk (80/109) cellbender:remove-background: Working on chunk (81/109) cellbender:remove-background: Working on chunk (82/109) cellbender:remove-background: Working on chunk (83/109) cellbender:remove-background: Working on chunk (84/109) cellbender:remove-background: Working on chunk (85/109) cellbender:remove-background: Working on chunk (86/109) cellbender:remove-background: Working on chunk (87/109) cellbender:remove-background: Working on chunk (88/109) cellbender:remove-background: Working on chunk (89/109) cellbender:remove-background: Working on chunk (90/109) cellbender:remove-background: Working on chunk (91/109) cellbender:remove-background: Working on chunk (92/109) cellbender:remove-background: Working on chunk (93/109) cellbender:remove-background: Working on chunk (94/109) cellbender:remove-background: Working on chunk (95/109) cellbender:remove-background: Working on chunk (96/109) cellbender:remove-background: Working on chunk (97/109) cellbender:remove-background: Working on chunk (98/109) cellbender:remove-background: Working on chunk (99/109) cellbender:remove-background: Working on chunk (100/109) cellbender:remove-background: Working on chunk (101/109) cellbender:remove-background: Working on chunk (102/109) cellbender:remove-background: Working on chunk (103/109) cellbender:remove-background: Working on chunk (104/109) cellbender:remove-background: Working on chunk (105/109) cellbender:remove-background: Working on chunk (106/109) cellbender:remove-background: Working on chunk (107/109) cellbender:remove-background: Working on chunk (108/109) cellbender:remove-background: Working on chunk (109/109) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:30:48 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.44 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 15:41:27 Total MCKP estimation time = 615.15 sec cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-Hippocampus/2275-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:41:44