cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2083-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-Hippocampus/2083-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 9648 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 3c3b924bd1) cellbender:remove-background: 2024-06-06 14:48:48 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/2083-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: 32327 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2955 cellbender:remove-background: Prior on counts for empty droplets is 86 cellbender:remove-background: Excluding 7402 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24925 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 43 cellbender:remove-background: Using 9648 probable cell barcodes, plus an additional 10352 barcodes, and 36055 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 85 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpe0_xegzt 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: 6024.6777 cellbender:remove-background: [epoch 002] average training loss: 4853.3712 (5.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 76 epochs cellbender:remove-background: [epoch 003] average training loss: 4258.0178 cellbender:remove-background: [epoch 004] average training loss: 3910.4220 cellbender:remove-background: [epoch 005] average training loss: 3833.8568 cellbender:remove-background: [epoch 005] average test loss: 3842.3523 cellbender:remove-background: [epoch 006] average training loss: 3797.5941 cellbender:remove-background: [epoch 007] average training loss: 3737.8154 cellbender:remove-background: [epoch 008] average training loss: 3716.2615 cellbender:remove-background: [epoch 009] average training loss: 3700.7129 cellbender:remove-background: [epoch 010] average training loss: 3641.4555 cellbender:remove-background: [epoch 010] average test loss: 3652.6847 cellbender:remove-background: [epoch 011] average training loss: 3540.7865 cellbender:remove-background: [epoch 012] average training loss: 3467.4380 cellbender:remove-background: [epoch 013] average training loss: 3431.0593 cellbender:remove-background: [epoch 014] average training loss: 3442.3522 cellbender:remove-background: [epoch 015] average training loss: 3385.2858 cellbender:remove-background: [epoch 015] average test loss: 3338.0331 cellbender:remove-background: [epoch 016] average training loss: 3294.7266 cellbender:remove-background: [epoch 017] average training loss: 3265.4593 cellbender:remove-background: [epoch 018] average training loss: 3230.3424 cellbender:remove-background: [epoch 019] average training loss: 3204.6245 cellbender:remove-background: [epoch 020] average training loss: 3166.9425 cellbender:remove-background: [epoch 020] average test loss: 3159.9413 cellbender:remove-background: [epoch 021] average training loss: 3150.2428 cellbender:remove-background: [epoch 022] average training loss: 3135.9808 cellbender:remove-background: [epoch 023] average training loss: 3122.3374 cellbender:remove-background: [epoch 024] average training loss: 3104.7411 cellbender:remove-background: [epoch 025] average training loss: 3092.1576 cellbender:remove-background: [epoch 025] average test loss: 3075.5800 cellbender:remove-background: [epoch 026] average training loss: 3075.9398 cellbender:remove-background: [epoch 027] average training loss: 3068.1452 cellbender:remove-background: [epoch 028] average training loss: 3061.2371 cellbender:remove-background: [epoch 029] average training loss: 3049.8124 cellbender:remove-background: [epoch 030] average training loss: 3042.3484 cellbender:remove-background: [epoch 030] average test loss: 3014.8420 cellbender:remove-background: [epoch 031] average training loss: 3037.3693 cellbender:remove-background: [epoch 032] average training loss: 3034.7713 cellbender:remove-background: [epoch 033] average training loss: 3032.2525 cellbender:remove-background: [epoch 034] average training loss: 3028.1620 cellbender:remove-background: [epoch 035] average training loss: 3028.1237 cellbender:remove-background: [epoch 035] average test loss: 3009.3332 cellbender:remove-background: [epoch 036] average training loss: 3025.3252 cellbender:remove-background: [epoch 037] average training loss: 3022.8814 cellbender:remove-background: [epoch 038] average training loss: 3021.1884 cellbender:remove-background: [epoch 039] average training loss: 3020.1479 cellbender:remove-background: [epoch 040] average training loss: 3020.4769 cellbender:remove-background: [epoch 040] average test loss: 3005.1223 cellbender:remove-background: [epoch 041] average training loss: 3018.9562 cellbender:remove-background: [epoch 042] average training loss: 3019.3549 cellbender:remove-background: [epoch 043] average training loss: 3018.8113 cellbender:remove-background: [epoch 044] average training loss: 3020.7619 cellbender:remove-background: [epoch 045] average training loss: 3018.2901 cellbender:remove-background: [epoch 045] average test loss: 2995.8185 cellbender:remove-background: [epoch 046] average training loss: 3020.6864 cellbender:remove-background: [epoch 047] average training loss: 3020.2647 cellbender:remove-background: [epoch 048] average training loss: 3019.6074 cellbender:remove-background: [epoch 049] average training loss: 3019.0031 cellbender:remove-background: [epoch 050] average training loss: 3022.3465 cellbender:remove-background: [epoch 050] average test loss: 3001.2091 cellbender:remove-background: [epoch 051] average training loss: 3021.5779 cellbender:remove-background: [epoch 052] average training loss: 3018.0101 cellbender:remove-background: [epoch 053] average training loss: 3020.3957 cellbender:remove-background: [epoch 054] average training loss: 3023.5285 cellbender:remove-background: [epoch 055] average training loss: 3018.7173 cellbender:remove-background: [epoch 055] average test loss: 3016.9129 cellbender:remove-background: [epoch 056] average training loss: 3016.5046 cellbender:remove-background: [epoch 057] average training loss: 3018.7709 cellbender:remove-background: [epoch 058] average training loss: 3020.9697 cellbender:remove-background: [epoch 059] average training loss: 3018.8375 cellbender:remove-background: [epoch 060] average training loss: 3016.9166 cellbender:remove-background: [epoch 060] average test loss: 3014.7730 cellbender:remove-background: [epoch 061] average training loss: 3020.4637 cellbender:remove-background: [epoch 062] average training loss: 3018.6869 cellbender:remove-background: [epoch 063] average training loss: 3022.7027 cellbender:remove-background: [epoch 064] average training loss: 3019.5331 cellbender:remove-background: [epoch 065] average training loss: 3025.8951 cellbender:remove-background: [epoch 065] average test loss: 3034.4825 cellbender:remove-background: [epoch 066] average training loss: 3024.1016 cellbender:remove-background: [epoch 067] average training loss: 3022.5001 cellbender:remove-background: [epoch 068] average training loss: 3022.3944 cellbender:remove-background: [epoch 069] average training loss: 3024.1559 cellbender:remove-background: [epoch 070] average training loss: 3021.4223 cellbender:remove-background: [epoch 070] average test loss: 3032.3807 cellbender:remove-background: [epoch 071] average training loss: 3022.6234 cellbender:remove-background: [epoch 072] average training loss: 3018.5029 cellbender:remove-background: [epoch 073] average training loss: 3028.0940 cellbender:remove-background: [epoch 074] average training loss: 3024.0441 cellbender:remove-background: [epoch 075] average training loss: 3019.4438 cellbender:remove-background: [epoch 075] average test loss: 3046.3600 cellbender:remove-background: [epoch 076] average training loss: 3019.4056 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/2083-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 077] average training loss: 3016.8917 cellbender:remove-background: [epoch 078] average training loss: 3019.2208 cellbender:remove-background: [epoch 079] average training loss: 3015.8947 cellbender:remove-background: [epoch 080] average training loss: 3016.5409 cellbender:remove-background: [epoch 080] average test loss: 3041.6634 cellbender:remove-background: [epoch 081] average training loss: 3016.3781 cellbender:remove-background: [epoch 082] average training loss: 3015.6436 cellbender:remove-background: [epoch 083] average training loss: 3017.5582 cellbender:remove-background: [epoch 084] average training loss: 3018.1635 cellbender:remove-background: [epoch 085] average training loss: 3018.9401 cellbender:remove-background: [epoch 085] average test loss: 3038.4681 cellbender:remove-background: [epoch 086] average training loss: 3019.6969 cellbender:remove-background: [epoch 087] average training loss: 3021.6855 cellbender:remove-background: [epoch 088] average training loss: 3017.6951 cellbender:remove-background: [epoch 089] average training loss: 3015.6536 cellbender:remove-background: [epoch 090] average training loss: 3015.9599 cellbender:remove-background: [epoch 090] average test loss: 3008.0997 cellbender:remove-background: [epoch 091] average training loss: 3012.4573 cellbender:remove-background: [epoch 092] average training loss: 3015.1155 cellbender:remove-background: [epoch 093] average training loss: 3017.5299 cellbender:remove-background: [epoch 094] average training loss: 3017.6661 cellbender:remove-background: [epoch 095] average training loss: 3015.6075 cellbender:remove-background: [epoch 095] average test loss: 3027.6149 cellbender:remove-background: [epoch 096] average training loss: 3014.2885 cellbender:remove-background: [epoch 097] average training loss: 3016.7300 cellbender:remove-background: [epoch 098] average training loss: 3014.7157 cellbender:remove-background: [epoch 099] average training loss: 3016.7079 cellbender:remove-background: [epoch 100] average training loss: 3013.8420 cellbender:remove-background: [epoch 100] average test loss: 3029.5771 cellbender:remove-background: [epoch 101] average training loss: 3013.4327 cellbender:remove-background: [epoch 102] average training loss: 3017.0128 cellbender:remove-background: [epoch 103] average training loss: 3012.5290 cellbender:remove-background: [epoch 104] average training loss: 3015.1291 cellbender:remove-background: [epoch 105] average training loss: 3013.0736 cellbender:remove-background: [epoch 105] average test loss: 3030.5090 cellbender:remove-background: [epoch 106] average training loss: 3016.1267 cellbender:remove-background: [epoch 107] average training loss: 3015.2286 cellbender:remove-background: [epoch 108] average training loss: 3015.9563 cellbender:remove-background: [epoch 109] average training loss: 3010.3770 cellbender:remove-background: [epoch 110] average training loss: 3016.0898 cellbender:remove-background: [epoch 110] average test loss: 3027.6549 cellbender:remove-background: [epoch 111] average training loss: 3011.3771 cellbender:remove-background: [epoch 112] average training loss: 3011.9827 cellbender:remove-background: [epoch 113] average training loss: 3012.5804 cellbender:remove-background: [epoch 114] average training loss: 3010.5346 cellbender:remove-background: [epoch 115] average training loss: 3010.3963 cellbender:remove-background: [epoch 115] average test loss: 3022.9577 cellbender:remove-background: [epoch 116] average training loss: 3008.8433 cellbender:remove-background: [epoch 117] average training loss: 3011.1647 cellbender:remove-background: [epoch 118] average training loss: 3008.3358 cellbender:remove-background: [epoch 119] average training loss: 3009.3587 cellbender:remove-background: [epoch 120] average training loss: 3006.4987 cellbender:remove-background: [epoch 120] average test loss: 3031.8337 cellbender:remove-background: [epoch 121] average training loss: 3014.8232 cellbender:remove-background: [epoch 122] average training loss: 3010.2979 cellbender:remove-background: [epoch 123] average training loss: 3011.2761 cellbender:remove-background: [epoch 124] average training loss: 3010.4064 cellbender:remove-background: [epoch 125] average training loss: 3007.2847 cellbender:remove-background: [epoch 125] average test loss: 3027.7619 cellbender:remove-background: [epoch 126] average training loss: 3011.0856 cellbender:remove-background: [epoch 127] average training loss: 3006.8573 cellbender:remove-background: [epoch 128] average training loss: 3011.5600 cellbender:remove-background: [epoch 129] average training loss: 3004.4078 cellbender:remove-background: [epoch 130] average training loss: 3006.0344 cellbender:remove-background: [epoch 130] average test loss: 3017.2923 cellbender:remove-background: [epoch 131] average training loss: 3007.8075 cellbender:remove-background: [epoch 132] average training loss: 3006.7818 cellbender:remove-background: [epoch 133] average training loss: 3010.2040 cellbender:remove-background: [epoch 134] average training loss: 3009.0011 cellbender:remove-background: [epoch 135] average training loss: 3009.2180 cellbender:remove-background: [epoch 135] average test loss: 3028.4638 cellbender:remove-background: [epoch 136] average training loss: 3005.4373 cellbender:remove-background: [epoch 137] average training loss: 3008.5112 cellbender:remove-background: [epoch 138] average training loss: 3007.6158 cellbender:remove-background: [epoch 139] average training loss: 3006.8778 cellbender:remove-background: [epoch 140] average training loss: 3006.6791 cellbender:remove-background: [epoch 140] average test loss: 3029.2812 cellbender:remove-background: [epoch 141] average training loss: 3006.2656 cellbender:remove-background: [epoch 142] average training loss: 3008.2863 cellbender:remove-background: [epoch 143] average training loss: 3007.0105 cellbender:remove-background: [epoch 144] average training loss: 3008.6255 cellbender:remove-background: [epoch 145] average training loss: 3009.0530 cellbender:remove-background: [epoch 145] average test loss: 3025.4110 cellbender:remove-background: [epoch 146] average training loss: 3009.5242 cellbender:remove-background: [epoch 147] average training loss: 3008.6659 cellbender:remove-background: [epoch 148] average training loss: 3006.1360 cellbender:remove-background: [epoch 149] average training loss: 3006.9007 cellbender:remove-background: [epoch 150] average training loss: 3005.0476 cellbender:remove-background: [epoch 150] average test loss: 3025.1015 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/2083-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:05:25 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpkd4tf1jr cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpkd4tf1jr /tmp/tmpkd4tf1jr/3c3b924bd1_random.pyro /tmp/tmpkd4tf1jr/3c3b924bd1_random.cuda /tmp/tmpkd4tf1jr/3c3b924bd1_model.torch /tmp/tmpkd4tf1jr/3c3b924bd1_optim.torch /tmp/tmpkd4tf1jr/3c3b924bd1_optim.pyro /tmp/tmpkd4tf1jr/3c3b924bd1_params.pyro /tmp/tmpkd4tf1jr/3c3b924bd1_train.loaderstate /tmp/tmpkd4tf1jr/3c3b924bd1_test.loaderstate /tmp/tmpkd4tf1jr/3c3b924bd1_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 (1/86) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/86) cellbender:remove-background: Working on chunk (3/86) cellbender:remove-background: Working on chunk (4/86) cellbender:remove-background: Working on chunk (5/86) cellbender:remove-background: Working on chunk (6/86) cellbender:remove-background: Working on chunk (7/86) cellbender:remove-background: Working on chunk (8/86) cellbender:remove-background: Working on chunk (9/86) cellbender:remove-background: Working on chunk (10/86) cellbender:remove-background: Working on chunk (11/86) cellbender:remove-background: Working on chunk (12/86) cellbender:remove-background: Working on chunk (13/86) cellbender:remove-background: Working on chunk (14/86) cellbender:remove-background: Working on chunk (15/86) cellbender:remove-background: Working on chunk (16/86) cellbender:remove-background: Working on chunk (17/86) cellbender:remove-background: Working on chunk (18/86) cellbender:remove-background: Working on chunk (19/86) cellbender:remove-background: Working on chunk (20/86) cellbender:remove-background: Working on chunk (21/86) cellbender:remove-background: Working on chunk (22/86) cellbender:remove-background: Working on chunk (23/86) cellbender:remove-background: Working on chunk (24/86) cellbender:remove-background: Working on chunk (25/86) cellbender:remove-background: Working on chunk (26/86) cellbender:remove-background: Working on chunk (27/86) cellbender:remove-background: Working on chunk (28/86) cellbender:remove-background: Working on chunk (29/86) cellbender:remove-background: Working on chunk (30/86) cellbender:remove-background: Working on chunk (31/86) cellbender:remove-background: Working on chunk (32/86) cellbender:remove-background: Working on chunk (33/86) cellbender:remove-background: Working on chunk (34/86) cellbender:remove-background: Working on chunk (35/86) cellbender:remove-background: Working on chunk (36/86) cellbender:remove-background: Working on chunk (37/86) cellbender:remove-background: Working on chunk (38/86) cellbender:remove-background: Working on chunk (39/86) cellbender:remove-background: Working on chunk (40/86) cellbender:remove-background: Working on chunk (41/86) cellbender:remove-background: Working on chunk (42/86) cellbender:remove-background: Working on chunk (43/86) cellbender:remove-background: Working on chunk (44/86) cellbender:remove-background: Working on chunk (45/86) cellbender:remove-background: Working on chunk (46/86) cellbender:remove-background: Working on chunk (47/86) cellbender:remove-background: Working on chunk (48/86) cellbender:remove-background: Working on chunk (49/86) cellbender:remove-background: Working on chunk (50/86) cellbender:remove-background: Working on chunk (51/86) cellbender:remove-background: Working on chunk (52/86) cellbender:remove-background: Working on chunk (53/86) cellbender:remove-background: Working on chunk (54/86) cellbender:remove-background: Working on chunk (55/86) cellbender:remove-background: Working on chunk (56/86) cellbender:remove-background: Working on chunk (57/86) cellbender:remove-background: Working on chunk (58/86) cellbender:remove-background: Working on chunk (59/86) cellbender:remove-background: Working on chunk (60/86) cellbender:remove-background: Working on chunk (61/86) cellbender:remove-background: Working on chunk (62/86) cellbender:remove-background: Working on chunk (63/86) cellbender:remove-background: Working on chunk (64/86) cellbender:remove-background: Working on chunk (65/86) cellbender:remove-background: Working on chunk (66/86) cellbender:remove-background: Working on chunk (67/86) cellbender:remove-background: Working on chunk (68/86) cellbender:remove-background: Working on chunk (69/86) cellbender:remove-background: Working on chunk (70/86) cellbender:remove-background: Working on chunk (71/86) cellbender:remove-background: Working on chunk (72/86) cellbender:remove-background: Working on chunk (73/86) cellbender:remove-background: Working on chunk (74/86) cellbender:remove-background: Working on chunk (75/86) cellbender:remove-background: Working on chunk (76/86) cellbender:remove-background: Working on chunk (77/86) cellbender:remove-background: Working on chunk (78/86) cellbender:remove-background: Working on chunk (79/86) cellbender:remove-background: Working on chunk (80/86) cellbender:remove-background: Working on chunk (81/86) cellbender:remove-background: Working on chunk (82/86) cellbender:remove-background: Working on chunk (83/86) cellbender:remove-background: Working on chunk (84/86) cellbender:remove-background: Working on chunk (85/86) cellbender:remove-background: Working on chunk (86/86) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-Hippocampus/2083-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/2083-Bipolar-Hippocampus/2083-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:10:04 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-Hippocampus/2083-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/2083-Bipolar-Hippocampus/2083-Bipolar-Hippocampus.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.54 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 15:21:18 Total MCKP estimation time = 648.69 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/2083-Bipolar-Hippocampus/2083-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/2083-Bipolar-Hippocampus/2083-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/2083-Bipolar-Hippocampus/2083-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/2083-Bipolar-Hippocampus/2083-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:21:36