cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1604-Control-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-Hippocampus/1604-Control-Hippocampus.cellbender.output.h5 --cuda --expected-cells 7527 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 43ebc8da6c) cellbender:remove-background: 2024-06-06 15:32:20 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/1604-Control-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: 32364 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3086 cellbender:remove-background: Prior on counts for empty droplets is 312 cellbender:remove-background: Excluding 4618 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 27746 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 156 cellbender:remove-background: Using 7527 probable cell barcodes, plus an additional 12473 barcodes, and 15308 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/tmp4udc8m8g 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: 5738.5231 cellbender:remove-background: [epoch 002] average training loss: 4805.8722 (5.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 76 epochs cellbender:remove-background: [epoch 003] average training loss: 4268.0866 cellbender:remove-background: [epoch 004] average training loss: 3898.6621 cellbender:remove-background: [epoch 005] average training loss: 3784.4876 cellbender:remove-background: [epoch 005] average test loss: 3951.9708 cellbender:remove-background: [epoch 006] average training loss: 3730.8186 cellbender:remove-background: [epoch 007] average training loss: 3669.5828 cellbender:remove-background: [epoch 008] average training loss: 3631.0784 cellbender:remove-background: [epoch 009] average training loss: 3611.6937 cellbender:remove-background: [epoch 010] average training loss: 3514.5588 cellbender:remove-background: [epoch 010] average test loss: 3544.0089 cellbender:remove-background: [epoch 011] average training loss: 3458.5306 cellbender:remove-background: [epoch 012] average training loss: 3431.6933 cellbender:remove-background: [epoch 013] average training loss: 3404.6332 cellbender:remove-background: [epoch 014] average training loss: 3401.3864 cellbender:remove-background: [epoch 015] average training loss: 3371.4658 cellbender:remove-background: [epoch 015] average test loss: 3447.2789 cellbender:remove-background: [epoch 016] average training loss: 3365.2148 cellbender:remove-background: [epoch 017] average training loss: 3366.4550 cellbender:remove-background: [epoch 018] average training loss: 3356.8305 cellbender:remove-background: [epoch 019] average training loss: 3345.3689 cellbender:remove-background: [epoch 020] average training loss: 3327.6974 cellbender:remove-background: [epoch 020] average test loss: 3442.9237 cellbender:remove-background: [epoch 021] average training loss: 3330.4923 cellbender:remove-background: [epoch 022] average training loss: 3332.3847 cellbender:remove-background: [epoch 023] average training loss: 3332.3984 cellbender:remove-background: [epoch 024] average training loss: 3319.0098 cellbender:remove-background: [epoch 025] average training loss: 3325.5401 cellbender:remove-background: [epoch 025] average test loss: 3372.1696 cellbender:remove-background: [epoch 026] average training loss: 3311.6010 cellbender:remove-background: [epoch 027] average training loss: 3312.8614 cellbender:remove-background: [epoch 028] average training loss: 3306.2356 cellbender:remove-background: [epoch 029] average training loss: 3296.0553 cellbender:remove-background: [epoch 030] average training loss: 3291.1686 cellbender:remove-background: [epoch 030] average test loss: 3331.9533 cellbender:remove-background: [epoch 031] average training loss: 3283.7384 cellbender:remove-background: [epoch 032] average training loss: 3265.1249 cellbender:remove-background: [epoch 033] average training loss: 3252.6053 cellbender:remove-background: [epoch 034] average training loss: 3246.5171 cellbender:remove-background: [epoch 035] average training loss: 3247.3170 cellbender:remove-background: [epoch 035] average test loss: 3302.4326 cellbender:remove-background: [epoch 036] average training loss: 3256.0541 cellbender:remove-background: [epoch 037] average training loss: 3261.3979 cellbender:remove-background: [epoch 038] average training loss: 3265.6683 cellbender:remove-background: [epoch 039] average training loss: 3274.2473 cellbender:remove-background: [epoch 040] average training loss: 3277.7665 cellbender:remove-background: [epoch 040] average test loss: 3364.5335 cellbender:remove-background: [epoch 041] average training loss: 3292.9951 cellbender:remove-background: [epoch 042] average training loss: 3289.4615 cellbender:remove-background: [epoch 043] average training loss: 3290.2919 cellbender:remove-background: [epoch 044] average training loss: 3294.0133 cellbender:remove-background: [epoch 045] average training loss: 3296.7270 cellbender:remove-background: [epoch 045] average test loss: 3319.8827 cellbender:remove-background: [epoch 046] average training loss: 3295.1916 cellbender:remove-background: [epoch 047] average training loss: 3298.7957 cellbender:remove-background: [epoch 048] average training loss: 3296.6167 cellbender:remove-background: [epoch 049] average training loss: 3293.2364 cellbender:remove-background: [epoch 050] average training loss: 3289.3196 cellbender:remove-background: [epoch 050] average test loss: 3312.8968 cellbender:remove-background: [epoch 051] average training loss: 3289.7611 cellbender:remove-background: [epoch 052] average training loss: 3286.4946 cellbender:remove-background: [epoch 053] average training loss: 3288.9034 cellbender:remove-background: [epoch 054] average training loss: 3287.6573 cellbender:remove-background: [epoch 055] average training loss: 3287.3037 cellbender:remove-background: [epoch 055] average test loss: 3300.2977 cellbender:remove-background: [epoch 056] average training loss: 3290.4835 cellbender:remove-background: [epoch 057] average training loss: 3294.5651 cellbender:remove-background: [epoch 058] average training loss: 3300.1744 cellbender:remove-background: [epoch 059] average training loss: 3290.8903 cellbender:remove-background: [epoch 060] average training loss: 3288.6720 cellbender:remove-background: [epoch 060] average test loss: 3357.1057 cellbender:remove-background: [epoch 061] average training loss: 3305.5118 cellbender:remove-background: [epoch 062] average training loss: 3294.0890 cellbender:remove-background: [epoch 063] average training loss: 3288.3542 cellbender:remove-background: [epoch 064] average training loss: 3294.8451 cellbender:remove-background: [epoch 065] average training loss: 3301.2113 cellbender:remove-background: [epoch 065] average test loss: 3330.2295 cellbender:remove-background: [epoch 066] average training loss: 3295.3045 cellbender:remove-background: [epoch 067] average training loss: 3293.7376 cellbender:remove-background: [epoch 068] average training loss: 3293.1507 cellbender:remove-background: [epoch 069] average training loss: 3301.7803 cellbender:remove-background: [epoch 070] average training loss: 3297.2727 cellbender:remove-background: [epoch 070] average test loss: 3353.9199 cellbender:remove-background: [epoch 071] average training loss: 3296.8792 cellbender:remove-background: [epoch 072] average training loss: 3310.5556 cellbender:remove-background: [epoch 073] average training loss: 3317.3384 cellbender:remove-background: [epoch 074] average training loss: 3322.3636 cellbender:remove-background: [epoch 075] average training loss: 3329.0275 cellbender:remove-background: [epoch 075] average test loss: 3407.2974 cellbender:remove-background: [epoch 076] average training loss: 3329.3107 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/1604-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 077] average training loss: 3337.3027 cellbender:remove-background: [epoch 078] average training loss: 3328.7065 cellbender:remove-background: [epoch 079] average training loss: 3333.4653 cellbender:remove-background: [epoch 080] average training loss: 3333.3505 cellbender:remove-background: [epoch 080] average test loss: 3391.2793 cellbender:remove-background: [epoch 081] average training loss: 3361.6359 cellbender:remove-background: [epoch 082] average training loss: 3344.7862 cellbender:remove-background: [epoch 083] average training loss: 3331.9507 cellbender:remove-background: [epoch 084] average training loss: 3322.5794 cellbender:remove-background: [epoch 085] average training loss: 3328.3658 cellbender:remove-background: [epoch 085] average test loss: 3406.5891 cellbender:remove-background: [epoch 086] average training loss: 3331.6502 cellbender:remove-background: [epoch 087] average training loss: 3327.7948 cellbender:remove-background: [epoch 088] average training loss: 3315.9421 cellbender:remove-background: [epoch 089] average training loss: 3327.3000 cellbender:remove-background: [epoch 090] average training loss: 3341.1926 cellbender:remove-background: [epoch 090] average test loss: 3415.5453 cellbender:remove-background: [epoch 091] average training loss: 3329.4986 cellbender:remove-background: [epoch 092] average training loss: 3321.3199 cellbender:remove-background: [epoch 093] average training loss: 3331.3927 cellbender:remove-background: [epoch 094] average training loss: 3325.8305 cellbender:remove-background: [epoch 095] average training loss: 3330.1988 cellbender:remove-background: [epoch 095] average test loss: 3404.7046 cellbender:remove-background: [epoch 096] average training loss: 3332.7957 cellbender:remove-background: [epoch 097] average training loss: 3325.6858 cellbender:remove-background: [epoch 098] average training loss: 3316.8474 cellbender:remove-background: [epoch 099] average training loss: 3323.9913 cellbender:remove-background: [epoch 100] average training loss: 3327.7696 cellbender:remove-background: [epoch 100] average test loss: 3398.0117 cellbender:remove-background: [epoch 101] average training loss: 3318.2672 cellbender:remove-background: [epoch 102] average training loss: 3322.0073 cellbender:remove-background: [epoch 103] average training loss: 3316.9868 cellbender:remove-background: [epoch 104] average training loss: 3317.6035 cellbender:remove-background: [epoch 105] average training loss: 3324.5890 cellbender:remove-background: [epoch 105] average test loss: 3436.5290 cellbender:remove-background: [epoch 106] average training loss: 3319.0971 cellbender:remove-background: [epoch 107] average training loss: 3310.3076 cellbender:remove-background: [epoch 108] average training loss: 3317.3623 cellbender:remove-background: [epoch 109] average training loss: 3318.9781 cellbender:remove-background: [epoch 110] average training loss: 3327.0283 cellbender:remove-background: [epoch 110] average test loss: 3454.1710 cellbender:remove-background: [epoch 111] average training loss: 3327.0419 cellbender:remove-background: [epoch 112] average training loss: 3305.4371 cellbender:remove-background: [epoch 113] average training loss: 3316.3404 cellbender:remove-background: [epoch 114] average training loss: 3319.1224 cellbender:remove-background: [epoch 115] average training loss: 3312.2132 cellbender:remove-background: [epoch 115] average test loss: 3390.1673 cellbender:remove-background: [epoch 116] average training loss: 3319.7390 cellbender:remove-background: [epoch 117] average training loss: 3312.0797 cellbender:remove-background: [epoch 118] average training loss: 3314.6628 cellbender:remove-background: [epoch 119] average training loss: 3302.4334 cellbender:remove-background: [epoch 120] average training loss: 3317.3701 cellbender:remove-background: [epoch 120] average test loss: 3411.0113 cellbender:remove-background: [epoch 121] average training loss: 3306.0002 cellbender:remove-background: [epoch 122] average training loss: 3314.5391 cellbender:remove-background: [epoch 123] average training loss: 3307.3434 cellbender:remove-background: [epoch 124] average training loss: 3311.3958 cellbender:remove-background: [epoch 125] average training loss: 3310.6506 cellbender:remove-background: [epoch 125] average test loss: 3423.9891 cellbender:remove-background: [epoch 126] average training loss: 3303.3042 cellbender:remove-background: [epoch 127] average training loss: 3308.9391 cellbender:remove-background: [epoch 128] average training loss: 3301.6673 cellbender:remove-background: [epoch 129] average training loss: 3306.6629 cellbender:remove-background: [epoch 130] average training loss: 3315.3573 cellbender:remove-background: [epoch 130] average test loss: 3416.1343 cellbender:remove-background: [epoch 131] average training loss: 3304.2049 cellbender:remove-background: [epoch 132] average training loss: 3300.1813 cellbender:remove-background: [epoch 133] average training loss: 3311.7571 cellbender:remove-background: [epoch 134] average training loss: 3312.9743 cellbender:remove-background: [epoch 135] average training loss: 3306.6483 cellbender:remove-background: [epoch 135] average test loss: 3405.0352 cellbender:remove-background: [epoch 136] average training loss: 3302.2448 cellbender:remove-background: [epoch 137] average training loss: 3307.9035 cellbender:remove-background: [epoch 138] average training loss: 3305.9947 cellbender:remove-background: [epoch 139] average training loss: 3298.2485 cellbender:remove-background: [epoch 140] average training loss: 3302.7771 cellbender:remove-background: [epoch 140] average test loss: 3410.2272 cellbender:remove-background: [epoch 141] average training loss: 3305.7863 cellbender:remove-background: [epoch 142] average training loss: 3309.0863 cellbender:remove-background: [epoch 143] average training loss: 3305.0675 cellbender:remove-background: [epoch 144] average training loss: 3304.9622 cellbender:remove-background: [epoch 145] average training loss: 3303.9025 cellbender:remove-background: [epoch 145] average test loss: 3406.4277 cellbender:remove-background: [epoch 146] average training loss: 3305.8569 cellbender:remove-background: [epoch 147] average training loss: 3321.2946 cellbender:remove-background: [epoch 148] average training loss: 3301.6315 cellbender:remove-background: [epoch 149] average training loss: 3303.0007 cellbender:remove-background: [epoch 150] average training loss: 3308.5353 cellbender:remove-background: [epoch 150] average test loss: 3404.6658 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/1604-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:48:56 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmplrrur_vu cellbender:remove-background: Successfully unpacked tarball to /tmp/tmplrrur_vu /tmp/tmplrrur_vu/43ebc8da6c_random.pyro /tmp/tmplrrur_vu/43ebc8da6c_random.cuda /tmp/tmplrrur_vu/43ebc8da6c_model.torch /tmp/tmplrrur_vu/43ebc8da6c_optim.torch /tmp/tmplrrur_vu/43ebc8da6c_optim.pyro /tmp/tmplrrur_vu/43ebc8da6c_params.pyro /tmp/tmplrrur_vu/43ebc8da6c_train.loaderstate /tmp/tmplrrur_vu/43ebc8da6c_test.loaderstate /tmp/tmplrrur_vu/43ebc8da6c_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 (1/113) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/113) cellbender:remove-background: Working on chunk (3/113) cellbender:remove-background: Working on chunk (4/113) cellbender:remove-background: Working on chunk (5/113) cellbender:remove-background: Working on chunk (6/113) cellbender:remove-background: Working on chunk (7/113) cellbender:remove-background: Working on chunk (8/113) cellbender:remove-background: Working on chunk (9/113) cellbender:remove-background: Working on chunk (10/113) cellbender:remove-background: Working on chunk (11/113) cellbender:remove-background: Working on chunk (12/113) cellbender:remove-background: Working on chunk (13/113) cellbender:remove-background: Working on chunk (14/113) cellbender:remove-background: Working on chunk (15/113) cellbender:remove-background: Working on chunk (16/113) cellbender:remove-background: Working on chunk (17/113) cellbender:remove-background: Working on chunk (18/113) cellbender:remove-background: Working on chunk (19/113) cellbender:remove-background: Working on chunk (20/113) cellbender:remove-background: Working on chunk (21/113) cellbender:remove-background: Working on chunk (22/113) cellbender:remove-background: Working on chunk (23/113) cellbender:remove-background: Working on chunk (24/113) cellbender:remove-background: Working on chunk (25/113) cellbender:remove-background: Working on chunk (26/113) cellbender:remove-background: Working on chunk (27/113) cellbender:remove-background: Working on chunk (28/113) cellbender:remove-background: Working on chunk (29/113) cellbender:remove-background: Working on chunk (30/113) cellbender:remove-background: Working on chunk (31/113) cellbender:remove-background: Working on chunk (32/113) cellbender:remove-background: Working on chunk (33/113) cellbender:remove-background: Working on chunk (34/113) cellbender:remove-background: Working on chunk (35/113) cellbender:remove-background: Working on chunk (36/113) cellbender:remove-background: Working on chunk (37/113) cellbender:remove-background: Working on chunk (38/113) cellbender:remove-background: Working on chunk (39/113) cellbender:remove-background: Working on chunk (40/113) cellbender:remove-background: Working on chunk (41/113) cellbender:remove-background: Working on chunk (42/113) cellbender:remove-background: Working on chunk (43/113) cellbender:remove-background: Working on chunk (44/113) cellbender:remove-background: Working on chunk (45/113) cellbender:remove-background: Working on chunk (46/113) cellbender:remove-background: Working on chunk (47/113) cellbender:remove-background: Working on chunk (48/113) cellbender:remove-background: Working on chunk (49/113) cellbender:remove-background: Working on chunk (50/113) cellbender:remove-background: Working on chunk (51/113) cellbender:remove-background: Working on chunk (52/113) cellbender:remove-background: Working on chunk (53/113) cellbender:remove-background: Working on chunk (54/113) cellbender:remove-background: Working on chunk (55/113) cellbender:remove-background: Working on chunk (56/113) cellbender:remove-background: Working on chunk (57/113) cellbender:remove-background: Working on chunk (58/113) cellbender:remove-background: Working on chunk (59/113) cellbender:remove-background: Working on chunk (60/113) cellbender:remove-background: Working on chunk (61/113) cellbender:remove-background: Working on chunk (62/113) cellbender:remove-background: Working on chunk (63/113) cellbender:remove-background: Working on chunk (64/113) cellbender:remove-background: Working on chunk (65/113) cellbender:remove-background: Working on chunk (66/113) cellbender:remove-background: Working on chunk (67/113) cellbender:remove-background: Working on chunk (68/113) cellbender:remove-background: Working on chunk (69/113) cellbender:remove-background: Working on chunk (70/113) cellbender:remove-background: Working on chunk (71/113) cellbender:remove-background: Working on chunk (72/113) cellbender:remove-background: Working on chunk (73/113) cellbender:remove-background: Working on chunk (74/113) cellbender:remove-background: Working on chunk (75/113) cellbender:remove-background: Working on chunk (76/113) cellbender:remove-background: Working on chunk (77/113) cellbender:remove-background: Working on chunk (78/113) cellbender:remove-background: Working on chunk (79/113) cellbender:remove-background: Working on chunk (80/113) cellbender:remove-background: Working on chunk (81/113) cellbender:remove-background: Working on chunk (82/113) cellbender:remove-background: Working on chunk (83/113) cellbender:remove-background: Working on chunk (84/113) cellbender:remove-background: Working on chunk (85/113) cellbender:remove-background: Working on chunk (86/113) cellbender:remove-background: Working on chunk (87/113) cellbender:remove-background: Working on chunk (88/113) cellbender:remove-background: Working on chunk (89/113) cellbender:remove-background: Working on chunk (90/113) cellbender:remove-background: Working on chunk (91/113) cellbender:remove-background: Working on chunk (92/113) cellbender:remove-background: Working on chunk (93/113) cellbender:remove-background: Working on chunk (94/113) cellbender:remove-background: Working on chunk (95/113) cellbender:remove-background: Working on chunk (96/113) cellbender:remove-background: Working on chunk (97/113) cellbender:remove-background: Working on chunk (98/113) cellbender:remove-background: Working on chunk (99/113) cellbender:remove-background: Working on chunk (100/113) cellbender:remove-background: Working on chunk (101/113) cellbender:remove-background: Working on chunk (102/113) cellbender:remove-background: Working on chunk (103/113) cellbender:remove-background: Working on chunk (104/113) cellbender:remove-background: Working on chunk (105/113) cellbender:remove-background: Working on chunk (106/113) cellbender:remove-background: Working on chunk (107/113) cellbender:remove-background: Working on chunk (108/113) cellbender:remove-background: Working on chunk (109/113) cellbender:remove-background: Working on chunk (110/113) cellbender:remove-background: Working on chunk (111/113) cellbender:remove-background: Working on chunk (112/113) cellbender:remove-background: Working on chunk (113/113) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-Hippocampus/1604-Control-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/1604-Control-Hippocampus/1604-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:54:19 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-Hippocampus/1604-Control-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-Hippocampus/1604-Control-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: [1.36 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 16:04:09 Total MCKP estimation time = 567.04 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/1604-Control-Hippocampus/1604-Control-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/1604-Control-Hippocampus/1604-Control-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/1604-Control-Hippocampus/1604-Control-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/1604-Control-Hippocampus/1604-Control-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:04:24