cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2677-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 20000 --total-droplets-included 21000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 6d367b8e59) cellbender:remove-background: 2024-06-06 14:52:18 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/2677-Schizophrenia-DLPFC.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: 31950 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1688 cellbender:remove-background: Prior on counts for empty droplets is 678 cellbender:remove-background: Excluding 3143 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 28807 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 339 cellbender:remove-background: Using 20000 probable cell barcodes, plus an additional 1000 barcodes, and 10524 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 669 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpbu0_ra90 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: 6141.3640 cellbender:remove-background: [epoch 002] average training loss: 5252.1517 (7.4 seconds per epoch) cellbender:remove-background: Will checkpoint every 57 epochs cellbender:remove-background: [epoch 003] average training loss: 4716.1357 cellbender:remove-background: [epoch 004] average training loss: 4372.5730 cellbender:remove-background: [epoch 005] average training loss: 4208.1053 cellbender:remove-background: [epoch 005] average test loss: 4175.9414 cellbender:remove-background: [epoch 006] average training loss: 4104.9887 cellbender:remove-background: [epoch 007] average training loss: 4088.5711 cellbender:remove-background: [epoch 008] average training loss: 4053.8943 cellbender:remove-background: [epoch 009] average training loss: 4028.1770 cellbender:remove-background: [epoch 010] average training loss: 4030.6585 cellbender:remove-background: [epoch 010] average test loss: 4033.5696 cellbender:remove-background: [epoch 011] average training loss: 4014.7090 cellbender:remove-background: [epoch 012] average training loss: 4005.0373 cellbender:remove-background: [epoch 013] average training loss: 4009.7352 cellbender:remove-background: [epoch 014] average training loss: 3990.5326 cellbender:remove-background: [epoch 015] average training loss: 3998.6331 cellbender:remove-background: [epoch 015] average test loss: 3995.7189 cellbender:remove-background: [epoch 016] average training loss: 3995.1057 cellbender:remove-background: [epoch 017] average training loss: 3991.3932 cellbender:remove-background: [epoch 018] average training loss: 3973.1944 cellbender:remove-background: [epoch 019] average training loss: 3937.7380 cellbender:remove-background: [epoch 020] average training loss: 3927.7243 cellbender:remove-background: [epoch 020] average test loss: 3951.1956 cellbender:remove-background: [epoch 021] average training loss: 3923.8480 cellbender:remove-background: [epoch 022] average training loss: 3921.8136 cellbender:remove-background: [epoch 023] average training loss: 3919.5882 cellbender:remove-background: [epoch 024] average training loss: 3921.5496 cellbender:remove-background: [epoch 025] average training loss: 3909.3430 cellbender:remove-background: [epoch 025] average test loss: 3930.7147 cellbender:remove-background: [epoch 026] average training loss: 3909.5683 cellbender:remove-background: [epoch 027] average training loss: 3908.6605 cellbender:remove-background: [epoch 028] average training loss: 3906.3763 cellbender:remove-background: [epoch 029] average training loss: 3904.8032 cellbender:remove-background: [epoch 030] average training loss: 3905.2750 cellbender:remove-background: [epoch 030] average test loss: 3924.3183 cellbender:remove-background: [epoch 031] average training loss: 3899.1312 cellbender:remove-background: [epoch 032] average training loss: 3907.3953 cellbender:remove-background: [epoch 033] average training loss: 3895.4894 cellbender:remove-background: [epoch 034] average training loss: 3894.2817 cellbender:remove-background: [epoch 035] average training loss: 3894.1778 cellbender:remove-background: [epoch 035] average test loss: 3910.1092 cellbender:remove-background: [epoch 036] average training loss: 3893.1253 cellbender:remove-background: [epoch 037] average training loss: 3892.2299 cellbender:remove-background: [epoch 038] average training loss: 3889.3651 cellbender:remove-background: [epoch 039] average training loss: 3882.6258 cellbender:remove-background: [epoch 040] average training loss: 3881.3536 cellbender:remove-background: [epoch 040] average test loss: 3906.4457 cellbender:remove-background: [epoch 041] average training loss: 3883.6423 cellbender:remove-background: [epoch 042] average training loss: 3880.9938 cellbender:remove-background: [epoch 043] average training loss: 3879.0042 cellbender:remove-background: [epoch 044] average training loss: 3873.7382 cellbender:remove-background: [epoch 045] average training loss: 3873.6180 cellbender:remove-background: [epoch 045] average test loss: 3885.2910 cellbender:remove-background: [epoch 046] average training loss: 3869.3687 cellbender:remove-background: [epoch 047] average training loss: 3867.1845 cellbender:remove-background: [epoch 048] average training loss: 3865.2855 cellbender:remove-background: [epoch 049] average training loss: 3864.1134 cellbender:remove-background: [epoch 050] average training loss: 3862.8154 cellbender:remove-background: [epoch 050] average test loss: 3880.9660 cellbender:remove-background: [epoch 051] average training loss: 3863.3598 cellbender:remove-background: [epoch 052] average training loss: 3862.5424 cellbender:remove-background: [epoch 053] average training loss: 3854.6981 cellbender:remove-background: [epoch 054] average training loss: 3854.9049 cellbender:remove-background: [epoch 055] average training loss: 3854.0084 cellbender:remove-background: [epoch 055] average test loss: 3871.0245 cellbender:remove-background: [epoch 056] average training loss: 3852.9523 cellbender:remove-background: [epoch 057] average training loss: 3856.8402 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/2677-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 058] average training loss: 3848.5539 cellbender:remove-background: [epoch 059] average training loss: 3845.7307 cellbender:remove-background: [epoch 060] average training loss: 3850.5007 cellbender:remove-background: [epoch 060] average test loss: 3840.5088 cellbender:remove-background: [epoch 061] average training loss: 3848.3378 cellbender:remove-background: [epoch 062] average training loss: 3850.5952 cellbender:remove-background: [epoch 063] average training loss: 3852.3359 cellbender:remove-background: [epoch 064] average training loss: 3846.8970 cellbender:remove-background: [epoch 065] average training loss: 3850.2513 cellbender:remove-background: [epoch 065] average test loss: 3875.7326 cellbender:remove-background: [epoch 066] average training loss: 3852.9731 cellbender:remove-background: [epoch 067] average training loss: 3852.0494 cellbender:remove-background: [epoch 068] average training loss: 3847.3368 cellbender:remove-background: [epoch 069] average training loss: 3848.0367 cellbender:remove-background: [epoch 070] average training loss: 3850.1186 cellbender:remove-background: [epoch 070] average test loss: 3862.9889 cellbender:remove-background: [epoch 071] average training loss: 3852.5911 cellbender:remove-background: [epoch 072] average training loss: 3851.1945 cellbender:remove-background: [epoch 073] average training loss: 3856.7394 cellbender:remove-background: [epoch 074] average training loss: 3852.1690 cellbender:remove-background: [epoch 075] average training loss: 3856.6976 cellbender:remove-background: [epoch 075] average test loss: 3891.9847 cellbender:remove-background: [epoch 076] average training loss: 3853.0509 cellbender:remove-background: [epoch 077] average training loss: 3855.3852 cellbender:remove-background: [epoch 078] average training loss: 3867.4873 cellbender:remove-background: [epoch 079] average training loss: 3862.8388 cellbender:remove-background: [epoch 080] average training loss: 3867.5386 cellbender:remove-background: [epoch 080] average test loss: 3885.6283 cellbender:remove-background: [epoch 081] average training loss: 3865.7441 cellbender:remove-background: [epoch 082] average training loss: 3866.5209 cellbender:remove-background: [epoch 083] average training loss: 3868.0857 cellbender:remove-background: [epoch 084] average training loss: 3868.5022 cellbender:remove-background: [epoch 085] average training loss: 3872.3801 cellbender:remove-background: [epoch 085] average test loss: 3884.2075 cellbender:remove-background: [epoch 086] average training loss: 3866.4461 cellbender:remove-background: [epoch 087] average training loss: 3865.9014 cellbender:remove-background: [epoch 088] average training loss: 3871.4198 cellbender:remove-background: [epoch 089] average training loss: 3871.6745 cellbender:remove-background: [epoch 090] average training loss: 3871.4746 cellbender:remove-background: [epoch 090] average test loss: 3889.8286 cellbender:remove-background: [epoch 091] average training loss: 3874.7226 cellbender:remove-background: [epoch 092] average training loss: 3872.4366 cellbender:remove-background: [epoch 093] average training loss: 3873.6434 cellbender:remove-background: [epoch 094] average training loss: 3872.1978 cellbender:remove-background: [epoch 095] average training loss: 3873.7173 cellbender:remove-background: [epoch 095] average test loss: 3883.3714 cellbender:remove-background: [epoch 096] average training loss: 3873.4286 cellbender:remove-background: [epoch 097] average training loss: 3877.0161 cellbender:remove-background: [epoch 098] average training loss: 3882.7395 cellbender:remove-background: [epoch 099] average training loss: 3872.2266 cellbender:remove-background: [epoch 100] average training loss: 3874.2097 cellbender:remove-background: [epoch 100] average test loss: 3917.5594 cellbender:remove-background: [epoch 101] average training loss: 3876.4393 cellbender:remove-background: [epoch 102] average training loss: 3876.2517 cellbender:remove-background: [epoch 103] average training loss: 3874.6281 cellbender:remove-background: [epoch 104] average training loss: 3870.2927 cellbender:remove-background: [epoch 105] average training loss: 3871.4678 cellbender:remove-background: [epoch 105] average test loss: 3903.8337 cellbender:remove-background: [epoch 106] average training loss: 3871.4648 cellbender:remove-background: [epoch 107] average training loss: 3874.4261 cellbender:remove-background: [epoch 108] average training loss: 3880.0290 cellbender:remove-background: [epoch 109] average training loss: 3879.2474 cellbender:remove-background: [epoch 110] average training loss: 3873.4757 cellbender:remove-background: [epoch 110] average test loss: 3891.4303 cellbender:remove-background: [epoch 111] average training loss: 3874.7832 cellbender:remove-background: [epoch 112] average training loss: 3872.5913 cellbender:remove-background: [epoch 113] average training loss: 3883.5220 cellbender:remove-background: [epoch 114] average training loss: 3874.9982 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/2677-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 115] average training loss: 3875.0105 cellbender:remove-background: [epoch 115] average test loss: 3898.4567 cellbender:remove-background: [epoch 116] average training loss: 3869.8650 cellbender:remove-background: [epoch 117] average training loss: 3873.5510 cellbender:remove-background: [epoch 118] average training loss: 3878.1346 cellbender:remove-background: [epoch 119] average training loss: 3874.1945 cellbender:remove-background: [epoch 120] average training loss: 3871.8376 cellbender:remove-background: [epoch 120] average test loss: 3901.5068 cellbender:remove-background: [epoch 121] average training loss: 3869.1952 cellbender:remove-background: [epoch 122] average training loss: 3878.4849 cellbender:remove-background: [epoch 123] average training loss: 3870.2658 cellbender:remove-background: [epoch 124] average training loss: 3869.2444 cellbender:remove-background: [epoch 125] average training loss: 3869.2274 cellbender:remove-background: [epoch 125] average test loss: 3915.3517 cellbender:remove-background: [epoch 126] average training loss: 3874.2581 cellbender:remove-background: [epoch 127] average training loss: 3871.8205 cellbender:remove-background: [epoch 128] average training loss: 3875.1921 cellbender:remove-background: [epoch 129] average training loss: 3876.1587 cellbender:remove-background: [epoch 130] average training loss: 3875.7819 cellbender:remove-background: [epoch 130] average test loss: 3906.4394 cellbender:remove-background: [epoch 131] average training loss: 3878.5690 cellbender:remove-background: [epoch 132] average training loss: 3873.2080 cellbender:remove-background: [epoch 133] average training loss: 3871.8218 cellbender:remove-background: [epoch 134] average training loss: 3874.7751 cellbender:remove-background: [epoch 135] average training loss: 3874.3436 cellbender:remove-background: [epoch 135] average test loss: 3903.2770 cellbender:remove-background: [epoch 136] average training loss: 3873.9734 cellbender:remove-background: [epoch 137] average training loss: 3873.4792 cellbender:remove-background: [epoch 138] average training loss: 3874.0399 cellbender:remove-background: [epoch 139] average training loss: 3872.5232 cellbender:remove-background: [epoch 140] average training loss: 3875.4426 cellbender:remove-background: [epoch 140] average test loss: 3908.9848 cellbender:remove-background: [epoch 141] average training loss: 3873.1297 cellbender:remove-background: [epoch 142] average training loss: 3875.5600 cellbender:remove-background: [epoch 143] average training loss: 3876.9428 cellbender:remove-background: [epoch 144] average training loss: 3873.5691 cellbender:remove-background: [epoch 145] average training loss: 3874.1041 cellbender:remove-background: [epoch 145] average test loss: 3905.4235 cellbender:remove-background: [epoch 146] average training loss: 3872.8013 cellbender:remove-background: [epoch 147] average training loss: 3873.0715 cellbender:remove-background: [epoch 148] average training loss: 3874.1693 cellbender:remove-background: [epoch 149] average training loss: 3873.1819 cellbender:remove-background: [epoch 150] average training loss: 3873.9126 cellbender:remove-background: [epoch 150] average test loss: 3904.8045 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/2677-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:16:24 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpp2s0y3vb cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpp2s0y3vb /tmp/tmpp2s0y3vb/6d367b8e59_random.pyro /tmp/tmpp2s0y3vb/6d367b8e59_random.cuda /tmp/tmpp2s0y3vb/6d367b8e59_model.torch /tmp/tmpp2s0y3vb/6d367b8e59_optim.torch /tmp/tmpp2s0y3vb/6d367b8e59_optim.pyro /tmp/tmpp2s0y3vb/6d367b8e59_params.pyro /tmp/tmpp2s0y3vb/6d367b8e59_train.loaderstate /tmp/tmpp2s0y3vb/6d367b8e59_test.loaderstate /tmp/tmpp2s0y3vb/6d367b8e59_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 (1/129) cellbender:remove-background: [0.05 mins per chunk] cellbender:remove-background: Working on chunk (2/129) cellbender:remove-background: Working on chunk (3/129) cellbender:remove-background: Working on chunk (4/129) cellbender:remove-background: Working on chunk (5/129) cellbender:remove-background: Working on chunk (6/129) cellbender:remove-background: Working on chunk (7/129) cellbender:remove-background: Working on chunk (8/129) cellbender:remove-background: Working on chunk (9/129) cellbender:remove-background: Working on chunk (10/129) cellbender:remove-background: Working on chunk (11/129) cellbender:remove-background: Working on chunk (12/129) cellbender:remove-background: Working on chunk (13/129) cellbender:remove-background: Working on chunk (14/129) cellbender:remove-background: Working on chunk (15/129) cellbender:remove-background: Working on chunk (16/129) cellbender:remove-background: Working on chunk (17/129) cellbender:remove-background: Working on chunk (18/129) cellbender:remove-background: Working on chunk (19/129) cellbender:remove-background: Working on chunk (20/129) cellbender:remove-background: Working on chunk (21/129) cellbender:remove-background: Working on chunk (22/129) cellbender:remove-background: Working on chunk (23/129) cellbender:remove-background: Working on chunk (24/129) cellbender:remove-background: Working on chunk (25/129) cellbender:remove-background: Working on chunk (26/129) cellbender:remove-background: Working on chunk (27/129) cellbender:remove-background: Working on chunk (28/129) cellbender:remove-background: Working on chunk (29/129) cellbender:remove-background: Working on chunk (30/129) cellbender:remove-background: Working on chunk (31/129) cellbender:remove-background: Working on chunk (32/129) cellbender:remove-background: Working on chunk (33/129) cellbender:remove-background: Working on chunk (34/129) cellbender:remove-background: Working on chunk (35/129) cellbender:remove-background: Working on chunk (36/129) cellbender:remove-background: Working on chunk (37/129) cellbender:remove-background: Working on chunk (38/129) cellbender:remove-background: Working on chunk (39/129) cellbender:remove-background: Working on chunk (40/129) cellbender:remove-background: Working on chunk (41/129) cellbender:remove-background: Working on chunk (42/129) cellbender:remove-background: Working on chunk (43/129) cellbender:remove-background: Working on chunk (44/129) cellbender:remove-background: Working on chunk (45/129) cellbender:remove-background: Working on chunk (46/129) cellbender:remove-background: Working on chunk (47/129) cellbender:remove-background: Working on chunk (48/129) cellbender:remove-background: Working on chunk (49/129) cellbender:remove-background: Working on chunk (50/129) cellbender:remove-background: Working on chunk (51/129) cellbender:remove-background: Working on chunk (52/129) cellbender:remove-background: Working on chunk (53/129) cellbender:remove-background: Working on chunk (54/129) cellbender:remove-background: Working on chunk (55/129) cellbender:remove-background: Working on chunk (56/129) cellbender:remove-background: Working on chunk (57/129) cellbender:remove-background: Working on chunk (58/129) cellbender:remove-background: Working on chunk (59/129) cellbender:remove-background: Working on chunk (60/129) cellbender:remove-background: Working on chunk (61/129) cellbender:remove-background: Working on chunk (62/129) cellbender:remove-background: Working on chunk (63/129) cellbender:remove-background: Working on chunk (64/129) cellbender:remove-background: Working on chunk (65/129) cellbender:remove-background: Working on chunk (66/129) cellbender:remove-background: Working on chunk (67/129) cellbender:remove-background: Working on chunk (68/129) cellbender:remove-background: Working on chunk (69/129) cellbender:remove-background: Working on chunk (70/129) cellbender:remove-background: Working on chunk (71/129) cellbender:remove-background: Working on chunk (72/129) cellbender:remove-background: Working on chunk (73/129) cellbender:remove-background: Working on chunk (74/129) cellbender:remove-background: Working on chunk (75/129) cellbender:remove-background: Working on chunk (76/129) cellbender:remove-background: Working on chunk (77/129) cellbender:remove-background: Working on chunk (78/129) cellbender:remove-background: Working on chunk (79/129) cellbender:remove-background: Working on chunk (80/129) cellbender:remove-background: Working on chunk (81/129) cellbender:remove-background: Working on chunk (82/129) cellbender:remove-background: Working on chunk (83/129) cellbender:remove-background: Working on chunk (84/129) cellbender:remove-background: Working on chunk (85/129) cellbender:remove-background: Working on chunk (86/129) cellbender:remove-background: Working on chunk (87/129) cellbender:remove-background: Working on chunk (88/129) cellbender:remove-background: Working on chunk (89/129) cellbender:remove-background: Working on chunk (90/129) cellbender:remove-background: Working on chunk (91/129) cellbender:remove-background: Working on chunk (92/129) cellbender:remove-background: Working on chunk (93/129) cellbender:remove-background: Working on chunk (94/129) cellbender:remove-background: Working on chunk (95/129) cellbender:remove-background: Working on chunk (96/129) cellbender:remove-background: Working on chunk (97/129) cellbender:remove-background: Working on chunk (98/129) cellbender:remove-background: Working on chunk (99/129) cellbender:remove-background: Working on chunk (100/129) cellbender:remove-background: Working on chunk (101/129) cellbender:remove-background: Working on chunk (102/129) cellbender:remove-background: Working on chunk (103/129) cellbender:remove-background: Working on chunk (104/129) cellbender:remove-background: Working on chunk (105/129) cellbender:remove-background: Working on chunk (106/129) cellbender:remove-background: Working on chunk (107/129) cellbender:remove-background: Working on chunk (108/129) cellbender:remove-background: Working on chunk (109/129) cellbender:remove-background: Working on chunk (110/129) cellbender:remove-background: Working on chunk (111/129) cellbender:remove-background: Working on chunk (112/129) cellbender:remove-background: Working on chunk (113/129) cellbender:remove-background: Working on chunk (114/129) cellbender:remove-background: Working on chunk (115/129) cellbender:remove-background: Working on chunk (116/129) cellbender:remove-background: Working on chunk (117/129) cellbender:remove-background: Working on chunk (118/129) cellbender:remove-background: Working on chunk (119/129) cellbender:remove-background: Working on chunk (120/129) cellbender:remove-background: Working on chunk (121/129) cellbender:remove-background: Working on chunk (122/129) cellbender:remove-background: Working on chunk (123/129) cellbender:remove-background: Working on chunk (124/129) cellbender:remove-background: Working on chunk (125/129) cellbender:remove-background: Working on chunk (126/129) cellbender:remove-background: Working on chunk (127/129) cellbender:remove-background: Working on chunk (128/129) cellbender:remove-background: Working on chunk (129/129) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.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/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:25:14 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.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: [3.00 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 15:46:51 Total MCKP estimation time = 1250.85 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/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.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/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.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/2677-Schizophrenia-DLPFC/2677-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:47:13