cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2686-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-Hippocampus/2686-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 9132 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash dcf5d7f844) cellbender:remove-background: 2024-06-06 15:50:55 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/2686-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: 32656 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3609 cellbender:remove-background: Prior on counts for empty droplets is 91 cellbender:remove-background: Excluding 8486 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24170 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 45 cellbender:remove-background: Using 9132 probable cell barcodes, plus an additional 10868 barcodes, and 26211 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 89 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpm9mtj8ad 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: 6962.9203 cellbender:remove-background: [epoch 002] average training loss: 5446.3374 (13.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 33 epochs cellbender:remove-background: [epoch 003] average training loss: 4694.6447 cellbender:remove-background: [epoch 004] average training loss: 4236.2821 cellbender:remove-background: [epoch 005] average training loss: 4156.6017 cellbender:remove-background: [epoch 005] average test loss: 4315.7363 cellbender:remove-background: [epoch 006] average training loss: 4112.2258 cellbender:remove-background: [epoch 007] average training loss: 4036.4587 cellbender:remove-background: [epoch 008] average training loss: 3986.7886 cellbender:remove-background: [epoch 009] average training loss: 3962.6629 cellbender:remove-background: [epoch 010] average training loss: 3777.0491 cellbender:remove-background: [epoch 010] average test loss: 3845.1909 cellbender:remove-background: [epoch 011] average training loss: 3688.0182 cellbender:remove-background: [epoch 012] average training loss: 3665.3585 cellbender:remove-background: [epoch 013] average training loss: 3614.9343 cellbender:remove-background: [epoch 014] average training loss: 3609.1202 cellbender:remove-background: [epoch 015] average training loss: 3552.1571 cellbender:remove-background: [epoch 015] average test loss: 3687.2495 cellbender:remove-background: [epoch 016] average training loss: 3539.3322 cellbender:remove-background: [epoch 017] average training loss: 3548.8729 cellbender:remove-background: [epoch 018] average training loss: 3542.2139 cellbender:remove-background: [epoch 019] average training loss: 3518.3962 cellbender:remove-background: [epoch 020] average training loss: 3479.6832 cellbender:remove-background: [epoch 020] average test loss: 3528.6711 cellbender:remove-background: [epoch 021] average training loss: 3451.7458 cellbender:remove-background: [epoch 022] average training loss: 3427.3253 cellbender:remove-background: [epoch 023] average training loss: 3407.9973 cellbender:remove-background: [epoch 024] average training loss: 3375.0270 cellbender:remove-background: [epoch 025] average training loss: 3361.0828 cellbender:remove-background: [epoch 025] average test loss: 3373.3203 cellbender:remove-background: [epoch 026] average training loss: 3338.0377 cellbender:remove-background: [epoch 027] average training loss: 3326.4614 cellbender:remove-background: [epoch 028] average training loss: 3318.6637 cellbender:remove-background: [epoch 029] average training loss: 3302.3713 cellbender:remove-background: [epoch 030] average training loss: 3294.5475 cellbender:remove-background: [epoch 030] average test loss: 3325.3753 cellbender:remove-background: [epoch 031] average training loss: 3284.8198 cellbender:remove-background: [epoch 032] average training loss: 3276.9538 cellbender:remove-background: [epoch 033] average training loss: 3268.9703 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/2686-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 034] average training loss: 3264.7611 cellbender:remove-background: [epoch 035] average training loss: 3260.5300 cellbender:remove-background: [epoch 035] average test loss: 3272.7123 cellbender:remove-background: [epoch 036] average training loss: 3259.0632 cellbender:remove-background: [epoch 037] average training loss: 3252.0238 cellbender:remove-background: [epoch 038] average training loss: 3254.5678 cellbender:remove-background: [epoch 039] average training loss: 3248.8605 cellbender:remove-background: [epoch 040] average training loss: 3249.3003 cellbender:remove-background: [epoch 040] average test loss: 3278.0504 cellbender:remove-background: [epoch 041] average training loss: 3247.6577 cellbender:remove-background: [epoch 042] average training loss: 3246.9286 cellbender:remove-background: [epoch 043] average training loss: 3244.7533 cellbender:remove-background: [epoch 044] average training loss: 3247.6487 cellbender:remove-background: [epoch 045] average training loss: 3242.7383 cellbender:remove-background: [epoch 045] average test loss: 3261.5587 cellbender:remove-background: [epoch 046] average training loss: 3245.7760 cellbender:remove-background: [epoch 047] average training loss: 3239.2655 cellbender:remove-background: [epoch 048] average training loss: 3244.2447 cellbender:remove-background: [epoch 049] average training loss: 3242.8034 cellbender:remove-background: [epoch 050] average training loss: 3244.3746 cellbender:remove-background: [epoch 050] average test loss: 3264.4014 cellbender:remove-background: [epoch 051] average training loss: 3244.6922 cellbender:remove-background: [epoch 052] average training loss: 3243.8430 cellbender:remove-background: [epoch 053] average training loss: 3243.5551 cellbender:remove-background: [epoch 054] average training loss: 3247.3156 cellbender:remove-background: [epoch 055] average training loss: 3248.0613 cellbender:remove-background: [epoch 055] average test loss: 3270.1866 cellbender:remove-background: [epoch 056] average training loss: 3247.3906 cellbender:remove-background: [epoch 057] average training loss: 3241.0001 cellbender:remove-background: [epoch 058] average training loss: 3245.9466 cellbender:remove-background: [epoch 059] average training loss: 3248.3085 cellbender:remove-background: [epoch 060] average training loss: 3238.1358 cellbender:remove-background: [epoch 060] average test loss: 3252.5470 cellbender:remove-background: [epoch 061] average training loss: 3243.5955 cellbender:remove-background: [epoch 062] average training loss: 3245.4607 cellbender:remove-background: [epoch 063] average training loss: 3247.1146 cellbender:remove-background: [epoch 064] average training loss: 3253.4557 cellbender:remove-background: [epoch 065] average training loss: 3245.7287 cellbender:remove-background: [epoch 065] average test loss: 3272.1045 cellbender:remove-background: [epoch 066] average training loss: 3247.7410 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/2686-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 067] average training loss: 3251.3472 cellbender:remove-background: [epoch 068] average training loss: 3258.7589 cellbender:remove-background: [epoch 069] average training loss: 3250.3443 cellbender:remove-background: [epoch 070] average training loss: 3254.3030 cellbender:remove-background: [epoch 070] average test loss: 3303.1639 cellbender:remove-background: [epoch 071] average training loss: 3255.7621 cellbender:remove-background: [epoch 072] average training loss: 3256.6598 cellbender:remove-background: [epoch 073] average training loss: 3264.9938 cellbender:remove-background: [epoch 074] average training loss: 3258.2552 cellbender:remove-background: [epoch 075] average training loss: 3255.5064 cellbender:remove-background: [epoch 075] average test loss: 3286.0147 cellbender:remove-background: [epoch 076] average training loss: 3257.1391 cellbender:remove-background: [epoch 077] average training loss: 3264.9681 cellbender:remove-background: [epoch 078] average training loss: 3251.8714 cellbender:remove-background: [epoch 079] average training loss: 3248.8839 cellbender:remove-background: [epoch 080] average training loss: 3254.3822 cellbender:remove-background: [epoch 080] average test loss: 3295.4758 cellbender:remove-background: [epoch 081] average training loss: 3248.7252 cellbender:remove-background: [epoch 082] average training loss: 3247.4325 cellbender:remove-background: [epoch 083] average training loss: 3246.0320 cellbender:remove-background: [epoch 084] average training loss: 3246.7200 cellbender:remove-background: [epoch 085] average training loss: 3248.6537 cellbender:remove-background: [epoch 085] average test loss: 3288.5555 cellbender:remove-background: [epoch 086] average training loss: 3248.1354 cellbender:remove-background: [epoch 087] average training loss: 3245.2535 cellbender:remove-background: [epoch 088] average training loss: 3252.8903 cellbender:remove-background: [epoch 089] average training loss: 3245.6038 cellbender:remove-background: [epoch 090] average training loss: 3251.3770 cellbender:remove-background: [epoch 090] average test loss: 3274.1199 cellbender:remove-background: [epoch 091] average training loss: 3245.1484 cellbender:remove-background: [epoch 092] average training loss: 3243.8763 cellbender:remove-background: [epoch 093] average training loss: 3245.1286 cellbender:remove-background: [epoch 094] average training loss: 3240.6678 cellbender:remove-background: [epoch 095] average training loss: 3247.1648 cellbender:remove-background: [epoch 095] average test loss: 3292.9870 cellbender:remove-background: [epoch 096] average training loss: 3244.5339 cellbender:remove-background: [epoch 097] average training loss: 3245.7274 cellbender:remove-background: [epoch 098] average training loss: 3242.1896 cellbender:remove-background: [epoch 099] average training loss: 3242.8899 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/2686-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 100] average training loss: 3244.2472 cellbender:remove-background: [epoch 100] average test loss: 3301.0963 cellbender:remove-background: [epoch 101] average training loss: 3242.0782 cellbender:remove-background: [epoch 102] average training loss: 3241.4679 cellbender:remove-background: [epoch 103] average training loss: 3244.5373 cellbender:remove-background: [epoch 104] average training loss: 3241.7108 cellbender:remove-background: [epoch 105] average training loss: 3243.1666 cellbender:remove-background: [epoch 105] average test loss: 3303.1147 cellbender:remove-background: [epoch 106] average training loss: 3239.6934 cellbender:remove-background: [epoch 107] average training loss: 3237.8700 cellbender:remove-background: [epoch 108] average training loss: 3239.1600 cellbender:remove-background: [epoch 109] average training loss: 3242.2844 cellbender:remove-background: [epoch 110] average training loss: 3237.8906 cellbender:remove-background: [epoch 110] average test loss: 3291.8173 cellbender:remove-background: [epoch 111] average training loss: 3237.8989 cellbender:remove-background: [epoch 112] average training loss: 3242.0137 cellbender:remove-background: [epoch 113] average training loss: 3234.6191 cellbender:remove-background: [epoch 114] average training loss: 3239.6493 cellbender:remove-background: [epoch 115] average training loss: 3237.0628 cellbender:remove-background: [epoch 115] average test loss: 3283.8716 cellbender:remove-background: [epoch 116] average training loss: 3234.8192 cellbender:remove-background: [epoch 117] average training loss: 3240.5624 cellbender:remove-background: [epoch 118] average training loss: 3235.4192 cellbender:remove-background: [epoch 119] average training loss: 3240.4959 cellbender:remove-background: [epoch 120] average training loss: 3236.9214 cellbender:remove-background: [epoch 120] average test loss: 3298.8919 cellbender:remove-background: [epoch 121] average training loss: 3240.7397 cellbender:remove-background: [epoch 122] average training loss: 3237.8214 cellbender:remove-background: [epoch 123] average training loss: 3235.2354 cellbender:remove-background: [epoch 124] average training loss: 3238.7570 cellbender:remove-background: [epoch 125] average training loss: 3235.7714 cellbender:remove-background: [epoch 125] average test loss: 3287.2744 cellbender:remove-background: [epoch 126] average training loss: 3235.6775 cellbender:remove-background: [epoch 127] average training loss: 3236.2087 cellbender:remove-background: [epoch 128] average training loss: 3234.8380 cellbender:remove-background: [epoch 129] average training loss: 3239.2354 cellbender:remove-background: [epoch 130] average training loss: 3232.6584 cellbender:remove-background: [epoch 130] average test loss: 3298.9844 cellbender:remove-background: [epoch 131] average training loss: 3236.0268 cellbender:remove-background: [epoch 132] average training loss: 3233.9765 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/2686-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 133] average training loss: 3237.9209 cellbender:remove-background: [epoch 134] average training loss: 3236.6933 cellbender:remove-background: [epoch 135] average training loss: 3237.3683 cellbender:remove-background: [epoch 135] average test loss: 3292.6518 cellbender:remove-background: [epoch 136] average training loss: 3235.6091 cellbender:remove-background: [epoch 137] average training loss: 3233.2755 cellbender:remove-background: [epoch 138] average training loss: 3237.9690 cellbender:remove-background: [epoch 139] average training loss: 3234.2461 cellbender:remove-background: [epoch 140] average training loss: 3234.4755 cellbender:remove-background: [epoch 140] average test loss: 3288.8100 cellbender:remove-background: [epoch 141] average training loss: 3231.8173 cellbender:remove-background: [epoch 142] average training loss: 3236.6765 cellbender:remove-background: [epoch 143] average training loss: 3234.0849 cellbender:remove-background: [epoch 144] average training loss: 3235.8916 cellbender:remove-background: [epoch 145] average training loss: 3234.6861 cellbender:remove-background: [epoch 145] average test loss: 3295.6805 cellbender:remove-background: [epoch 146] average training loss: 3235.6711 cellbender:remove-background: [epoch 147] average training loss: 3231.9118 cellbender:remove-background: [epoch 148] average training loss: 3233.7387 cellbender:remove-background: [epoch 149] average training loss: 3232.7459 cellbender:remove-background: [epoch 150] average training loss: 3233.6425 cellbender:remove-background: [epoch 150] average test loss: 3292.1289 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/2686-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:30:37 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpk01g15o1 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpk01g15o1 /tmp/tmpk01g15o1/dcf5d7f844_random.pyro /tmp/tmpk01g15o1/dcf5d7f844_random.cuda /tmp/tmpk01g15o1/dcf5d7f844_model.torch /tmp/tmpk01g15o1/dcf5d7f844_optim.torch /tmp/tmpk01g15o1/dcf5d7f844_optim.pyro /tmp/tmpk01g15o1/dcf5d7f844_params.pyro /tmp/tmpk01g15o1/dcf5d7f844_train.loaderstate /tmp/tmpk01g15o1/dcf5d7f844_test.loaderstate /tmp/tmpk01g15o1/dcf5d7f844_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 (1/91) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/91) cellbender:remove-background: Working on chunk (3/91) cellbender:remove-background: Working on chunk (4/91) cellbender:remove-background: Working on chunk (5/91) cellbender:remove-background: Working on chunk (6/91) cellbender:remove-background: Working on chunk (7/91) cellbender:remove-background: Working on chunk (8/91) cellbender:remove-background: Working on chunk (9/91) cellbender:remove-background: Working on chunk (10/91) cellbender:remove-background: Working on chunk (11/91) cellbender:remove-background: Working on chunk (12/91) cellbender:remove-background: Working on chunk (13/91) cellbender:remove-background: Working on chunk (14/91) cellbender:remove-background: Working on chunk (15/91) cellbender:remove-background: Working on chunk (16/91) cellbender:remove-background: Working on chunk (17/91) cellbender:remove-background: Working on chunk (18/91) cellbender:remove-background: Working on chunk (19/91) cellbender:remove-background: Working on chunk (20/91) cellbender:remove-background: Working on chunk (21/91) cellbender:remove-background: Working on chunk (22/91) cellbender:remove-background: Working on chunk (23/91) cellbender:remove-background: Working on chunk (24/91) cellbender:remove-background: Working on chunk (25/91) cellbender:remove-background: Working on chunk (26/91) cellbender:remove-background: Working on chunk (27/91) cellbender:remove-background: Working on chunk (28/91) cellbender:remove-background: Working on chunk (29/91) cellbender:remove-background: Working on chunk (30/91) cellbender:remove-background: Working on chunk (31/91) cellbender:remove-background: Working on chunk (32/91) cellbender:remove-background: Working on chunk (33/91) cellbender:remove-background: Working on chunk (34/91) cellbender:remove-background: Working on chunk (35/91) cellbender:remove-background: Working on chunk (36/91) cellbender:remove-background: Working on chunk (37/91) cellbender:remove-background: Working on chunk (38/91) cellbender:remove-background: Working on chunk (39/91) cellbender:remove-background: Working on chunk (40/91) cellbender:remove-background: Working on chunk (41/91) cellbender:remove-background: Working on chunk (42/91) cellbender:remove-background: Working on chunk (43/91) cellbender:remove-background: Working on chunk (44/91) cellbender:remove-background: Working on chunk (45/91) cellbender:remove-background: Working on chunk (46/91) cellbender:remove-background: Working on chunk (47/91) cellbender:remove-background: Working on chunk (48/91) cellbender:remove-background: Working on chunk (49/91) cellbender:remove-background: Working on chunk (50/91) cellbender:remove-background: Working on chunk (51/91) cellbender:remove-background: Working on chunk (52/91) cellbender:remove-background: Working on chunk (53/91) cellbender:remove-background: Working on chunk (54/91) cellbender:remove-background: Working on chunk (55/91) cellbender:remove-background: Working on chunk (56/91) cellbender:remove-background: Working on chunk (57/91) cellbender:remove-background: Working on chunk (58/91) cellbender:remove-background: Working on chunk (59/91) cellbender:remove-background: Working on chunk (60/91) cellbender:remove-background: Working on chunk (61/91) cellbender:remove-background: Working on chunk (62/91) cellbender:remove-background: Working on chunk (63/91) cellbender:remove-background: Working on chunk (64/91) cellbender:remove-background: Working on chunk (65/91) cellbender:remove-background: Working on chunk (66/91) cellbender:remove-background: Working on chunk (67/91) cellbender:remove-background: Working on chunk (68/91) cellbender:remove-background: Working on chunk (69/91) cellbender:remove-background: Working on chunk (70/91) cellbender:remove-background: Working on chunk (71/91) cellbender:remove-background: Working on chunk (72/91) cellbender:remove-background: Working on chunk (73/91) cellbender:remove-background: Working on chunk (74/91) cellbender:remove-background: Working on chunk (75/91) cellbender:remove-background: Working on chunk (76/91) cellbender:remove-background: Working on chunk (77/91) cellbender:remove-background: Working on chunk (78/91) cellbender:remove-background: Working on chunk (79/91) cellbender:remove-background: Working on chunk (80/91) cellbender:remove-background: Working on chunk (81/91) cellbender:remove-background: Working on chunk (82/91) cellbender:remove-background: Working on chunk (83/91) cellbender:remove-background: Working on chunk (84/91) cellbender:remove-background: Working on chunk (85/91) cellbender:remove-background: Working on chunk (86/91) cellbender:remove-background: Working on chunk (87/91) cellbender:remove-background: Working on chunk (88/91) cellbender:remove-background: Working on chunk (89/91) cellbender:remove-background: Working on chunk (90/91) cellbender:remove-background: Working on chunk (91/91) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-Hippocampus/2686-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/2686-Bipolar-Hippocampus/2686-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:38:43 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-Hippocampus/2686-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/2686-Bipolar-Hippocampus/2686-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: [2.24 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 16:55:12 Total MCKP estimation time = 936.24 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/2686-Bipolar-Hippocampus/2686-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/2686-Bipolar-Hippocampus/2686-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/2686-Bipolar-Hippocampus/2686-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/2686-Bipolar-Hippocampus/2686-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:55:45