cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1320-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 15890 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 28bc185c91) cellbender:remove-background: 2024-06-06 15:32:36 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/1320-Schizophrenia-dACC.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: 32556 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2254 cellbender:remove-background: Prior on counts for empty droplets is 319 cellbender:remove-background: Excluding 6330 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 26226 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 159 cellbender:remove-background: Using 15890 probable cell barcodes, plus an additional 4110 barcodes, and 4488 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 307 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpgf85f22g 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: 8547.8540 cellbender:remove-background: [epoch 002] average training loss: 6821.6889 (5.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 77 epochs cellbender:remove-background: [epoch 003] average training loss: 5745.0211 cellbender:remove-background: [epoch 004] average training loss: 5063.3273 cellbender:remove-background: [epoch 005] average training loss: 4824.9479 cellbender:remove-background: [epoch 005] average test loss: 4855.6255 cellbender:remove-background: [epoch 006] average training loss: 4724.6456 cellbender:remove-background: [epoch 007] average training loss: 4680.9378 cellbender:remove-background: [epoch 008] average training loss: 4631.5775 cellbender:remove-background: [epoch 009] average training loss: 4626.5238 cellbender:remove-background: [epoch 010] average training loss: 4579.8831 cellbender:remove-background: [epoch 010] average test loss: 4612.1004 cellbender:remove-background: [epoch 011] average training loss: 4586.9986 cellbender:remove-background: [epoch 012] average training loss: 4562.4301 cellbender:remove-background: [epoch 013] average training loss: 4464.2042 cellbender:remove-background: [epoch 014] average training loss: 4419.5703 cellbender:remove-background: [epoch 015] average training loss: 4386.2814 cellbender:remove-background: [epoch 015] average test loss: 4448.3876 cellbender:remove-background: [epoch 016] average training loss: 4374.4215 cellbender:remove-background: [epoch 017] average training loss: 4381.3917 cellbender:remove-background: [epoch 018] average training loss: 4362.7481 cellbender:remove-background: [epoch 019] average training loss: 4353.1334 cellbender:remove-background: [epoch 020] average training loss: 4327.0025 cellbender:remove-background: [epoch 020] average test loss: 4371.9359 cellbender:remove-background: [epoch 021] average training loss: 4323.9472 cellbender:remove-background: [epoch 022] average training loss: 4318.9342 cellbender:remove-background: [epoch 023] average training loss: 4309.5400 cellbender:remove-background: [epoch 024] average training loss: 4300.8171 cellbender:remove-background: [epoch 025] average training loss: 4295.5135 cellbender:remove-background: [epoch 025] average test loss: 4295.3836 cellbender:remove-background: [epoch 026] average training loss: 4280.4556 cellbender:remove-background: [epoch 027] average training loss: 4274.5401 cellbender:remove-background: [epoch 028] average training loss: 4264.2847 cellbender:remove-background: [epoch 029] average training loss: 4243.5591 cellbender:remove-background: [epoch 030] average training loss: 4233.5043 cellbender:remove-background: [epoch 030] average test loss: 4232.7288 cellbender:remove-background: [epoch 031] average training loss: 4224.6048 cellbender:remove-background: [epoch 032] average training loss: 4218.7161 cellbender:remove-background: [epoch 033] average training loss: 4216.2077 cellbender:remove-background: [epoch 034] average training loss: 4212.8375 cellbender:remove-background: [epoch 035] average training loss: 4207.2453 cellbender:remove-background: [epoch 035] average test loss: 4198.2469 cellbender:remove-background: [epoch 036] average training loss: 4199.8644 cellbender:remove-background: [epoch 037] average training loss: 4198.0829 cellbender:remove-background: [epoch 038] average training loss: 4200.2391 cellbender:remove-background: [epoch 039] average training loss: 4201.3722 cellbender:remove-background: [epoch 040] average training loss: 4200.1279 cellbender:remove-background: [epoch 040] average test loss: 4225.8265 cellbender:remove-background: [epoch 041] average training loss: 4199.3701 cellbender:remove-background: [epoch 042] average training loss: 4198.3374 cellbender:remove-background: [epoch 043] average training loss: 4197.9930 cellbender:remove-background: [epoch 044] average training loss: 4208.2318 cellbender:remove-background: [epoch 045] average training loss: 4205.0716 cellbender:remove-background: [epoch 045] average test loss: 4162.8209 cellbender:remove-background: [epoch 046] average training loss: 4204.8190 cellbender:remove-background: [epoch 047] average training loss: 4202.7623 cellbender:remove-background: [epoch 048] average training loss: 4205.5418 cellbender:remove-background: [epoch 049] average training loss: 4204.8992 cellbender:remove-background: [epoch 050] average training loss: 4206.9740 cellbender:remove-background: [epoch 050] average test loss: 4159.5137 cellbender:remove-background: [epoch 051] average training loss: 4204.2429 cellbender:remove-background: [epoch 052] average training loss: 4203.8687 cellbender:remove-background: [epoch 053] average training loss: 4198.7934 cellbender:remove-background: [epoch 054] average training loss: 4201.4033 cellbender:remove-background: [epoch 055] average training loss: 4201.1922 cellbender:remove-background: [epoch 055] average test loss: 4199.3032 cellbender:remove-background: [epoch 056] average training loss: 4199.9084 cellbender:remove-background: [epoch 057] average training loss: 4203.6602 cellbender:remove-background: [epoch 058] average training loss: 4197.9405 cellbender:remove-background: [epoch 059] average training loss: 4203.0195 cellbender:remove-background: [epoch 060] average training loss: 4200.1381 cellbender:remove-background: [epoch 060] average test loss: 4211.5486 cellbender:remove-background: [epoch 061] average training loss: 4198.6590 cellbender:remove-background: [epoch 062] average training loss: 4196.4834 cellbender:remove-background: [epoch 063] average training loss: 4200.2880 cellbender:remove-background: [epoch 064] average training loss: 4203.5852 cellbender:remove-background: [epoch 065] average training loss: 4204.2460 cellbender:remove-background: [epoch 065] average test loss: 4170.3701 cellbender:remove-background: [epoch 066] average training loss: 4196.3509 cellbender:remove-background: [epoch 067] average training loss: 4198.9074 cellbender:remove-background: [epoch 068] average training loss: 4204.7568 cellbender:remove-background: [epoch 069] average training loss: 4204.7624 cellbender:remove-background: [epoch 070] average training loss: 4204.1210 cellbender:remove-background: [epoch 070] average test loss: 4205.2891 cellbender:remove-background: [epoch 071] average training loss: 4202.7637 cellbender:remove-background: [epoch 072] average training loss: 4205.7771 cellbender:remove-background: [epoch 073] average training loss: 4203.6914 cellbender:remove-background: [epoch 074] average training loss: 4202.2359 cellbender:remove-background: [epoch 075] average training loss: 4208.3208 cellbender:remove-background: [epoch 075] average test loss: 4184.2172 cellbender:remove-background: [epoch 076] average training loss: 4206.4743 cellbender:remove-background: [epoch 077] average training loss: 4205.6844 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/1320-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 078] average training loss: 4203.7423 cellbender:remove-background: [epoch 079] average training loss: 4201.7958 cellbender:remove-background: [epoch 080] average training loss: 4204.5037 cellbender:remove-background: [epoch 080] average test loss: 4194.3761 cellbender:remove-background: [epoch 081] average training loss: 4202.7917 cellbender:remove-background: [epoch 082] average training loss: 4207.4772 cellbender:remove-background: [epoch 083] average training loss: 4203.4303 cellbender:remove-background: [epoch 084] average training loss: 4211.7015 cellbender:remove-background: [epoch 085] average training loss: 4211.4742 cellbender:remove-background: [epoch 085] average test loss: 4199.4557 cellbender:remove-background: [epoch 086] average training loss: 4214.8159 cellbender:remove-background: [epoch 087] average training loss: 4221.1201 cellbender:remove-background: [epoch 088] average training loss: 4215.2056 cellbender:remove-background: [epoch 089] average training loss: 4215.5539 cellbender:remove-background: [epoch 090] average training loss: 4218.1671 cellbender:remove-background: [epoch 090] average test loss: 4219.8050 cellbender:remove-background: [epoch 091] average training loss: 4219.2297 cellbender:remove-background: [epoch 092] average training loss: 4224.5313 cellbender:remove-background: [epoch 093] average training loss: 4214.5556 cellbender:remove-background: [epoch 094] average training loss: 4210.6120 cellbender:remove-background: [epoch 095] average training loss: 4217.8654 cellbender:remove-background: [epoch 095] average test loss: 4223.5686 cellbender:remove-background: [epoch 096] average training loss: 4213.7755 cellbender:remove-background: [epoch 097] average training loss: 4209.8819 cellbender:remove-background: [epoch 098] average training loss: 4205.9971 cellbender:remove-background: [epoch 099] average training loss: 4213.8847 cellbender:remove-background: [epoch 100] average training loss: 4218.8927 cellbender:remove-background: [epoch 100] average test loss: 4189.1342 cellbender:remove-background: [epoch 101] average training loss: 4211.6565 cellbender:remove-background: [epoch 102] average training loss: 4206.0089 cellbender:remove-background: [epoch 103] average training loss: 4208.6413 cellbender:remove-background: [epoch 104] average training loss: 4214.0708 cellbender:remove-background: [epoch 105] average training loss: 4212.1165 cellbender:remove-background: [epoch 105] average test loss: 4245.3352 cellbender:remove-background: [epoch 106] average training loss: 4215.4853 cellbender:remove-background: [epoch 107] average training loss: 4215.5578 cellbender:remove-background: [epoch 108] average training loss: 4204.6333 cellbender:remove-background: [epoch 109] average training loss: 4207.7354 cellbender:remove-background: [epoch 110] average training loss: 4206.2648 cellbender:remove-background: [epoch 110] average test loss: 4181.8904 cellbender:remove-background: [epoch 111] average training loss: 4203.1108 cellbender:remove-background: [epoch 112] average training loss: 4213.4786 cellbender:remove-background: [epoch 113] average training loss: 4207.2492 cellbender:remove-background: [epoch 114] average training loss: 4203.9600 cellbender:remove-background: [epoch 115] average training loss: 4208.6478 cellbender:remove-background: [epoch 115] average test loss: 4209.8379 cellbender:remove-background: [epoch 116] average training loss: 4206.1623 cellbender:remove-background: [epoch 117] average training loss: 4206.3748 cellbender:remove-background: [epoch 118] average training loss: 4202.8037 cellbender:remove-background: [epoch 119] average training loss: 4208.4147 cellbender:remove-background: [epoch 120] average training loss: 4210.4887 cellbender:remove-background: [epoch 120] average test loss: 4214.8084 cellbender:remove-background: [epoch 121] average training loss: 4206.9566 cellbender:remove-background: [epoch 122] average training loss: 4204.2141 cellbender:remove-background: [epoch 123] average training loss: 4212.5161 cellbender:remove-background: [epoch 124] average training loss: 4206.2850 cellbender:remove-background: [epoch 125] average training loss: 4208.3376 cellbender:remove-background: [epoch 125] average test loss: 4220.4984 cellbender:remove-background: [epoch 126] average training loss: 4208.2333 cellbender:remove-background: [epoch 127] average training loss: 4203.6223 cellbender:remove-background: [epoch 128] average training loss: 4204.1813 cellbender:remove-background: [epoch 129] average training loss: 4199.8780 cellbender:remove-background: [epoch 130] average training loss: 4201.4275 cellbender:remove-background: [epoch 130] average test loss: 4219.2495 cellbender:remove-background: [epoch 131] average training loss: 4196.0691 cellbender:remove-background: [epoch 132] average training loss: 4203.8107 cellbender:remove-background: [epoch 133] average training loss: 4206.6424 cellbender:remove-background: [epoch 134] average training loss: 4205.0435 cellbender:remove-background: [epoch 135] average training loss: 4201.4553 cellbender:remove-background: [epoch 135] average test loss: 4208.0538 cellbender:remove-background: [epoch 136] average training loss: 4203.6991 cellbender:remove-background: [epoch 137] average training loss: 4202.6982 cellbender:remove-background: [epoch 138] average training loss: 4203.6197 cellbender:remove-background: [epoch 139] average training loss: 4204.1810 cellbender:remove-background: [epoch 140] average training loss: 4204.6021 cellbender:remove-background: [epoch 140] average test loss: 4213.5440 cellbender:remove-background: [epoch 141] average training loss: 4208.9945 cellbender:remove-background: [epoch 142] average training loss: 4202.7525 cellbender:remove-background: [epoch 143] average training loss: 4201.1184 cellbender:remove-background: [epoch 144] average training loss: 4199.3647 cellbender:remove-background: [epoch 145] average training loss: 4202.9872 cellbender:remove-background: [epoch 145] average test loss: 4202.1341 cellbender:remove-background: [epoch 146] average training loss: 4201.0226 cellbender:remove-background: [epoch 147] average training loss: 4204.1261 cellbender:remove-background: [epoch 148] average training loss: 4200.7841 cellbender:remove-background: [epoch 149] average training loss: 4201.5232 cellbender:remove-background: [epoch 150] average training loss: 4203.2311 cellbender:remove-background: [epoch 150] average test loss: 4212.0003 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/1320-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:48:49 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpstf62do4 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpstf62do4 /tmp/tmpstf62do4/28bc185c91_random.pyro /tmp/tmpstf62do4/28bc185c91_random.cuda /tmp/tmpstf62do4/28bc185c91_model.torch /tmp/tmpstf62do4/28bc185c91_optim.torch /tmp/tmpstf62do4/28bc185c91_optim.pyro /tmp/tmpstf62do4/28bc185c91_params.pyro /tmp/tmpstf62do4/28bc185c91_train.loaderstate /tmp/tmpstf62do4/28bc185c91_test.loaderstate /tmp/tmpstf62do4/28bc185c91_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 (1/132) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/132) cellbender:remove-background: Working on chunk (3/132) cellbender:remove-background: Working on chunk (4/132) cellbender:remove-background: Working on chunk (5/132) cellbender:remove-background: Working on chunk (6/132) cellbender:remove-background: Working on chunk (7/132) cellbender:remove-background: Working on chunk (8/132) cellbender:remove-background: Working on chunk (9/132) cellbender:remove-background: Working on chunk (10/132) cellbender:remove-background: Working on chunk (11/132) cellbender:remove-background: Working on chunk (12/132) cellbender:remove-background: Working on chunk (13/132) cellbender:remove-background: Working on chunk (14/132) cellbender:remove-background: Working on chunk (15/132) cellbender:remove-background: Working on chunk (16/132) cellbender:remove-background: Working on chunk (17/132) cellbender:remove-background: Working on chunk (18/132) cellbender:remove-background: Working on chunk (19/132) cellbender:remove-background: Working on chunk (20/132) cellbender:remove-background: Working on chunk (21/132) cellbender:remove-background: Working on chunk (22/132) cellbender:remove-background: Working on chunk (23/132) cellbender:remove-background: Working on chunk (24/132) cellbender:remove-background: Working on chunk (25/132) cellbender:remove-background: Working on chunk (26/132) cellbender:remove-background: Working on chunk (27/132) cellbender:remove-background: Working on chunk (28/132) cellbender:remove-background: Working on chunk (29/132) cellbender:remove-background: Working on chunk (30/132) cellbender:remove-background: Working on chunk (31/132) cellbender:remove-background: Working on chunk (32/132) cellbender:remove-background: Working on chunk (33/132) cellbender:remove-background: Working on chunk (34/132) cellbender:remove-background: Working on chunk (35/132) cellbender:remove-background: Working on chunk (36/132) cellbender:remove-background: Working on chunk (37/132) cellbender:remove-background: Working on chunk (38/132) cellbender:remove-background: Working on chunk (39/132) cellbender:remove-background: Working on chunk (40/132) cellbender:remove-background: Working on chunk (41/132) cellbender:remove-background: Working on chunk (42/132) cellbender:remove-background: Working on chunk (43/132) cellbender:remove-background: Working on chunk (44/132) cellbender:remove-background: Working on chunk (45/132) cellbender:remove-background: Working on chunk (46/132) cellbender:remove-background: Working on chunk (47/132) cellbender:remove-background: Working on chunk (48/132) cellbender:remove-background: Working on chunk (49/132) cellbender:remove-background: Working on chunk (50/132) cellbender:remove-background: Working on chunk (51/132) cellbender:remove-background: Working on chunk (52/132) cellbender:remove-background: Working on chunk (53/132) cellbender:remove-background: Working on chunk (54/132) cellbender:remove-background: Working on chunk (55/132) cellbender:remove-background: Working on chunk (56/132) cellbender:remove-background: Working on chunk (57/132) cellbender:remove-background: Working on chunk (58/132) cellbender:remove-background: Working on chunk (59/132) cellbender:remove-background: Working on chunk (60/132) cellbender:remove-background: Working on chunk (61/132) cellbender:remove-background: Working on chunk (62/132) cellbender:remove-background: Working on chunk (63/132) cellbender:remove-background: Working on chunk (64/132) cellbender:remove-background: Working on chunk (65/132) cellbender:remove-background: Working on chunk (66/132) cellbender:remove-background: Working on chunk (67/132) cellbender:remove-background: Working on chunk (68/132) cellbender:remove-background: Working on chunk (69/132) cellbender:remove-background: Working on chunk (70/132) cellbender:remove-background: Working on chunk (71/132) cellbender:remove-background: Working on chunk (72/132) cellbender:remove-background: Working on chunk (73/132) cellbender:remove-background: Working on chunk (74/132) cellbender:remove-background: Working on chunk (75/132) cellbender:remove-background: Working on chunk (76/132) cellbender:remove-background: Working on chunk (77/132) cellbender:remove-background: Working on chunk (78/132) cellbender:remove-background: Working on chunk (79/132) cellbender:remove-background: Working on chunk (80/132) cellbender:remove-background: Working on chunk (81/132) cellbender:remove-background: Working on chunk (82/132) cellbender:remove-background: Working on chunk (83/132) cellbender:remove-background: Working on chunk (84/132) cellbender:remove-background: Working on chunk (85/132) cellbender:remove-background: Working on chunk (86/132) cellbender:remove-background: Working on chunk (87/132) cellbender:remove-background: Working on chunk (88/132) cellbender:remove-background: Working on chunk (89/132) cellbender:remove-background: Working on chunk (90/132) cellbender:remove-background: Working on chunk (91/132) cellbender:remove-background: Working on chunk (92/132) cellbender:remove-background: Working on chunk (93/132) cellbender:remove-background: Working on chunk (94/132) cellbender:remove-background: Working on chunk (95/132) cellbender:remove-background: Working on chunk (96/132) cellbender:remove-background: Working on chunk (97/132) cellbender:remove-background: Working on chunk (98/132) cellbender:remove-background: Working on chunk (99/132) cellbender:remove-background: Working on chunk (100/132) cellbender:remove-background: Working on chunk (101/132) cellbender:remove-background: Working on chunk (102/132) cellbender:remove-background: Working on chunk (103/132) cellbender:remove-background: Working on chunk (104/132) cellbender:remove-background: Working on chunk (105/132) cellbender:remove-background: Working on chunk (106/132) cellbender:remove-background: Working on chunk (107/132) cellbender:remove-background: Working on chunk (108/132) cellbender:remove-background: Working on chunk (109/132) cellbender:remove-background: Working on chunk (110/132) cellbender:remove-background: Working on chunk (111/132) cellbender:remove-background: Working on chunk (112/132) cellbender:remove-background: Working on chunk (113/132) cellbender:remove-background: Working on chunk (114/132) cellbender:remove-background: Working on chunk (115/132) cellbender:remove-background: Working on chunk (116/132) cellbender:remove-background: Working on chunk (117/132) cellbender:remove-background: Working on chunk (118/132) cellbender:remove-background: Working on chunk (119/132) cellbender:remove-background: Working on chunk (120/132) cellbender:remove-background: Working on chunk (121/132) cellbender:remove-background: Working on chunk (122/132) cellbender:remove-background: Working on chunk (123/132) cellbender:remove-background: Working on chunk (124/132) cellbender:remove-background: Working on chunk (125/132) cellbender:remove-background: Working on chunk (126/132) cellbender:remove-background: Working on chunk (127/132) cellbender:remove-background: Working on chunk (128/132) cellbender:remove-background: Working on chunk (129/132) cellbender:remove-background: Working on chunk (130/132) cellbender:remove-background: Working on chunk (131/132) cellbender:remove-background: Working on chunk (132/132) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.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/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:54:51 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.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: [2.07 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 16:10:18 Total MCKP estimation time = 888.60 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/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.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/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.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/1320-Schizophrenia-dACC/1320-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:10:40