cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2781-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output.h5 --cuda --expected-cells 7582 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 247d10eeab) cellbender:remove-background: 2024-06-06 14:52:31 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/2781-Control-dACC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 32025 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3755 cellbender:remove-background: Prior on counts for empty droplets is 98 cellbender:remove-background: Excluding 6938 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 25087 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 49 cellbender:remove-background: Using 7582 probable cell barcodes, plus an additional 12418 barcodes, and 39986 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 96 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpx16zf5cm 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: 6000.9373 cellbender:remove-background: [epoch 002] average training loss: 4703.1383 (6.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 69 epochs cellbender:remove-background: [epoch 003] average training loss: 3988.6614 cellbender:remove-background: [epoch 004] average training loss: 3568.0118 cellbender:remove-background: [epoch 005] average training loss: 3461.6012 cellbender:remove-background: [epoch 005] average test loss: 3651.9404 cellbender:remove-background: [epoch 006] average training loss: 3415.3204 cellbender:remove-background: [epoch 007] average training loss: 3371.7629 cellbender:remove-background: [epoch 008] average training loss: 3322.9412 cellbender:remove-background: [epoch 009] average training loss: 3306.5900 cellbender:remove-background: [epoch 010] average training loss: 3179.9988 cellbender:remove-background: [epoch 010] average test loss: 3285.2469 cellbender:remove-background: [epoch 011] average training loss: 3090.2523 cellbender:remove-background: [epoch 012] average training loss: 3057.7503 cellbender:remove-background: [epoch 013] average training loss: 3029.8347 cellbender:remove-background: [epoch 014] average training loss: 3028.4594 cellbender:remove-background: [epoch 015] average training loss: 2992.4350 cellbender:remove-background: [epoch 015] average test loss: 3066.0364 cellbender:remove-background: [epoch 016] average training loss: 2976.9320 cellbender:remove-background: [epoch 017] average training loss: 2986.8112 cellbender:remove-background: [epoch 018] average training loss: 2975.7204 cellbender:remove-background: [epoch 019] average training loss: 2961.0017 cellbender:remove-background: [epoch 020] average training loss: 2946.1701 cellbender:remove-background: [epoch 020] average test loss: 2994.1551 cellbender:remove-background: [epoch 021] average training loss: 2939.0972 cellbender:remove-background: [epoch 022] average training loss: 2936.0095 cellbender:remove-background: [epoch 023] average training loss: 2928.3216 cellbender:remove-background: [epoch 024] average training loss: 2902.3298 cellbender:remove-background: [epoch 025] average training loss: 2889.8201 cellbender:remove-background: [epoch 025] average test loss: 2899.5361 cellbender:remove-background: [epoch 026] average training loss: 2864.1787 cellbender:remove-background: [epoch 027] average training loss: 2853.2760 cellbender:remove-background: [epoch 028] average training loss: 2845.4957 cellbender:remove-background: [epoch 029] average training loss: 2833.1497 cellbender:remove-background: [epoch 030] average training loss: 2826.8653 cellbender:remove-background: [epoch 030] average test loss: 2839.8788 cellbender:remove-background: [epoch 031] average training loss: 2820.0029 cellbender:remove-background: [epoch 032] average training loss: 2813.2176 cellbender:remove-background: [epoch 033] average training loss: 2811.2237 cellbender:remove-background: [epoch 034] average training loss: 2806.4136 cellbender:remove-background: [epoch 035] average training loss: 2803.0700 cellbender:remove-background: [epoch 035] average test loss: 2804.5058 cellbender:remove-background: [epoch 036] average training loss: 2799.0852 cellbender:remove-background: [epoch 037] average training loss: 2798.0624 cellbender:remove-background: [epoch 038] average training loss: 2797.3223 cellbender:remove-background: [epoch 039] average training loss: 2796.3818 cellbender:remove-background: [epoch 040] average training loss: 2793.6438 cellbender:remove-background: [epoch 040] average test loss: 2808.3769 cellbender:remove-background: [epoch 041] average training loss: 2793.3479 cellbender:remove-background: [epoch 042] average training loss: 2793.9541 cellbender:remove-background: [epoch 043] average training loss: 2792.8561 cellbender:remove-background: [epoch 044] average training loss: 2797.7084 cellbender:remove-background: [epoch 045] average training loss: 2794.6090 cellbender:remove-background: [epoch 045] average test loss: 2798.6803 cellbender:remove-background: [epoch 046] average training loss: 2793.7561 cellbender:remove-background: [epoch 047] average training loss: 2797.3700 cellbender:remove-background: [epoch 048] average training loss: 2796.4888 cellbender:remove-background: [epoch 049] average training loss: 2799.9525 cellbender:remove-background: [epoch 050] average training loss: 2798.3571 cellbender:remove-background: [epoch 050] average test loss: 2828.2481 cellbender:remove-background: [epoch 051] average training loss: 2800.7135 cellbender:remove-background: [epoch 052] average training loss: 2803.3190 cellbender:remove-background: [epoch 053] average training loss: 2806.7020 cellbender:remove-background: [epoch 054] average training loss: 2806.5250 cellbender:remove-background: [epoch 055] average training loss: 2801.4585 cellbender:remove-background: [epoch 055] average test loss: 2840.5814 cellbender:remove-background: [epoch 056] average training loss: 2803.4519 cellbender:remove-background: [epoch 057] average training loss: 2806.9119 cellbender:remove-background: [epoch 058] average training loss: 2810.4891 cellbender:remove-background: [epoch 059] average training loss: 2806.0223 cellbender:remove-background: [epoch 060] average training loss: 2805.5875 cellbender:remove-background: [epoch 060] average test loss: 2880.8940 cellbender:remove-background: [epoch 061] average training loss: 2809.2796 cellbender:remove-background: [epoch 062] average training loss: 2804.8628 cellbender:remove-background: [epoch 063] average training loss: 2807.5935 cellbender:remove-background: [epoch 064] average training loss: 2807.0839 cellbender:remove-background: [epoch 065] average training loss: 2805.2864 cellbender:remove-background: [epoch 065] average test loss: 2838.4508 cellbender:remove-background: [epoch 066] average training loss: 2804.4353 cellbender:remove-background: [epoch 067] average training loss: 2800.3797 cellbender:remove-background: [epoch 068] average training loss: 2805.9195 cellbender:remove-background: [epoch 069] average training loss: 2800.0708 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/2781-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 070] average training loss: 2808.6765 cellbender:remove-background: [epoch 070] average test loss: 2837.2514 cellbender:remove-background: [epoch 071] average training loss: 2803.2266 cellbender:remove-background: [epoch 072] average training loss: 2801.3745 cellbender:remove-background: [epoch 073] average training loss: 2803.6874 cellbender:remove-background: [epoch 074] average training loss: 2801.9017 cellbender:remove-background: [epoch 075] average training loss: 2798.8378 cellbender:remove-background: [epoch 075] average test loss: 2825.6972 cellbender:remove-background: [epoch 076] average training loss: 2797.1638 cellbender:remove-background: [epoch 077] average training loss: 2796.5924 cellbender:remove-background: [epoch 078] average training loss: 2803.8505 cellbender:remove-background: [epoch 079] average training loss: 2799.4862 cellbender:remove-background: [epoch 080] average training loss: 2803.1458 cellbender:remove-background: [epoch 080] average test loss: 2826.3703 cellbender:remove-background: [epoch 081] average training loss: 2796.7087 cellbender:remove-background: [epoch 082] average training loss: 2799.3669 cellbender:remove-background: [epoch 083] average training loss: 2802.0880 cellbender:remove-background: [epoch 084] average training loss: 2799.1660 cellbender:remove-background: [epoch 085] average training loss: 2795.6443 cellbender:remove-background: [epoch 085] average test loss: 2846.8697 cellbender:remove-background: [epoch 086] average training loss: 2798.4442 cellbender:remove-background: [epoch 087] average training loss: 2800.6772 cellbender:remove-background: [epoch 088] average training loss: 2796.3626 cellbender:remove-background: [epoch 089] average training loss: 2797.7031 cellbender:remove-background: [epoch 090] average training loss: 2797.4516 cellbender:remove-background: [epoch 090] average test loss: 2846.1426 cellbender:remove-background: [epoch 091] average training loss: 2798.1351 cellbender:remove-background: [epoch 092] average training loss: 2800.1106 cellbender:remove-background: [epoch 093] average training loss: 2801.0575 cellbender:remove-background: [epoch 094] average training loss: 2798.0808 cellbender:remove-background: [epoch 095] average training loss: 2797.5416 cellbender:remove-background: [epoch 095] average test loss: 2845.0208 cellbender:remove-background: [epoch 096] average training loss: 2803.5686 cellbender:remove-background: [epoch 097] average training loss: 2797.7880 cellbender:remove-background: [epoch 098] average training loss: 2798.6989 cellbender:remove-background: [epoch 099] average training loss: 2795.1444 cellbender:remove-background: [epoch 100] average training loss: 2796.7795 cellbender:remove-background: [epoch 100] average test loss: 2851.2169 cellbender:remove-background: [epoch 101] average training loss: 2797.3989 cellbender:remove-background: [epoch 102] average training loss: 2800.1295 cellbender:remove-background: [epoch 103] average training loss: 2795.6474 cellbender:remove-background: [epoch 104] average training loss: 2794.8380 cellbender:remove-background: [epoch 105] average training loss: 2795.9614 cellbender:remove-background: [epoch 105] average test loss: 2832.0091 cellbender:remove-background: [epoch 106] average training loss: 2795.1674 cellbender:remove-background: [epoch 107] average training loss: 2793.2919 cellbender:remove-background: [epoch 108] average training loss: 2796.6133 cellbender:remove-background: [epoch 109] average training loss: 2798.4678 cellbender:remove-background: [epoch 110] average training loss: 2794.9120 cellbender:remove-background: [epoch 110] average test loss: 2848.5689 cellbender:remove-background: [epoch 111] average training loss: 2796.7855 cellbender:remove-background: [epoch 112] average training loss: 2794.3364 cellbender:remove-background: [epoch 113] average training loss: 2795.9183 cellbender:remove-background: [epoch 114] average training loss: 2795.6488 cellbender:remove-background: [epoch 115] average training loss: 2794.7961 cellbender:remove-background: [epoch 115] average test loss: 2835.6582 cellbender:remove-background: [epoch 116] average training loss: 2794.7851 cellbender:remove-background: [epoch 117] average training loss: 2794.3191 cellbender:remove-background: [epoch 118] average training loss: 2792.8127 cellbender:remove-background: [epoch 119] average training loss: 2790.8026 cellbender:remove-background: [epoch 120] average training loss: 2795.7878 cellbender:remove-background: [epoch 120] average test loss: 2843.4587 cellbender:remove-background: [epoch 121] average training loss: 2793.2484 cellbender:remove-background: [epoch 122] average training loss: 2794.5613 cellbender:remove-background: [epoch 123] average training loss: 2790.2259 cellbender:remove-background: [epoch 124] average training loss: 2795.5133 cellbender:remove-background: [epoch 125] average training loss: 2794.5211 cellbender:remove-background: [epoch 125] average test loss: 2844.8235 cellbender:remove-background: [epoch 126] average training loss: 2792.3198 cellbender:remove-background: [epoch 127] average training loss: 2792.2069 cellbender:remove-background: [epoch 128] average training loss: 2795.3316 cellbender:remove-background: [epoch 129] average training loss: 2795.5278 cellbender:remove-background: [epoch 130] average training loss: 2790.3142 cellbender:remove-background: [epoch 130] average test loss: 2847.8000 cellbender:remove-background: [epoch 131] average training loss: 2790.9605 cellbender:remove-background: [epoch 132] average training loss: 2793.6010 cellbender:remove-background: [epoch 133] average training loss: 2789.7637 cellbender:remove-background: [epoch 134] average training loss: 2798.4179 cellbender:remove-background: [epoch 135] average training loss: 2793.0936 cellbender:remove-background: [epoch 135] average test loss: 2838.6367 cellbender:remove-background: [epoch 136] average training loss: 2793.3410 cellbender:remove-background: [epoch 137] average training loss: 2794.3776 cellbender:remove-background: [epoch 138] average training loss: 2793.1600 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/2781-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 139] average training loss: 2794.3288 cellbender:remove-background: [epoch 140] average training loss: 2792.1016 cellbender:remove-background: [epoch 140] average test loss: 2839.8336 cellbender:remove-background: [epoch 141] average training loss: 2793.1436 cellbender:remove-background: [epoch 142] average training loss: 2794.6988 cellbender:remove-background: [epoch 143] average training loss: 2793.0052 cellbender:remove-background: [epoch 144] average training loss: 2792.5435 cellbender:remove-background: [epoch 145] average training loss: 2791.8822 cellbender:remove-background: [epoch 145] average test loss: 2839.9572 cellbender:remove-background: [epoch 146] average training loss: 2794.3330 cellbender:remove-background: [epoch 147] average training loss: 2791.8900 cellbender:remove-background: [epoch 148] average training loss: 2792.2112 cellbender:remove-background: [epoch 149] average training loss: 2790.2011 cellbender:remove-background: [epoch 150] average training loss: 2790.9885 cellbender:remove-background: [epoch 150] average test loss: 2835.8941 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/2781-Control-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:12:46 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpm8nrz5n7 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpm8nrz5n7 /tmp/tmpm8nrz5n7/247d10eeab_random.pyro /tmp/tmpm8nrz5n7/247d10eeab_random.cuda /tmp/tmpm8nrz5n7/247d10eeab_model.torch /tmp/tmpm8nrz5n7/247d10eeab_optim.torch /tmp/tmpm8nrz5n7/247d10eeab_optim.pyro /tmp/tmpm8nrz5n7/247d10eeab_params.pyro /tmp/tmpm8nrz5n7/247d10eeab_train.loaderstate /tmp/tmpm8nrz5n7/247d10eeab_test.loaderstate /tmp/tmpm8nrz5n7/247d10eeab_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 (1/82) cellbender:remove-background: [0.05 mins per chunk] cellbender:remove-background: Working on chunk (2/82) cellbender:remove-background: Working on chunk (3/82) cellbender:remove-background: Working on chunk (4/82) cellbender:remove-background: Working on chunk (5/82) cellbender:remove-background: Working on chunk (6/82) cellbender:remove-background: Working on chunk (7/82) cellbender:remove-background: Working on chunk (8/82) cellbender:remove-background: Working on chunk (9/82) cellbender:remove-background: Working on chunk (10/82) cellbender:remove-background: Working on chunk (11/82) cellbender:remove-background: Working on chunk (12/82) cellbender:remove-background: Working on chunk (13/82) cellbender:remove-background: Working on chunk (14/82) cellbender:remove-background: Working on chunk (15/82) cellbender:remove-background: Working on chunk (16/82) cellbender:remove-background: Working on chunk (17/82) cellbender:remove-background: Working on chunk (18/82) cellbender:remove-background: Working on chunk (19/82) cellbender:remove-background: Working on chunk (20/82) cellbender:remove-background: Working on chunk (21/82) cellbender:remove-background: Working on chunk (22/82) cellbender:remove-background: Working on chunk (23/82) cellbender:remove-background: Working on chunk (24/82) cellbender:remove-background: Working on chunk (25/82) cellbender:remove-background: Working on chunk (26/82) cellbender:remove-background: Working on chunk (27/82) cellbender:remove-background: Working on chunk (28/82) cellbender:remove-background: Working on chunk (29/82) cellbender:remove-background: Working on chunk (30/82) cellbender:remove-background: Working on chunk (31/82) cellbender:remove-background: Working on chunk (32/82) cellbender:remove-background: Working on chunk (33/82) cellbender:remove-background: Working on chunk (34/82) cellbender:remove-background: Working on chunk (35/82) cellbender:remove-background: Working on chunk (36/82) cellbender:remove-background: Working on chunk (37/82) cellbender:remove-background: Working on chunk (38/82) cellbender:remove-background: Working on chunk (39/82) cellbender:remove-background: Working on chunk (40/82) cellbender:remove-background: Working on chunk (41/82) cellbender:remove-background: Working on chunk (42/82) cellbender:remove-background: Working on chunk (43/82) cellbender:remove-background: Working on chunk (44/82) cellbender:remove-background: Working on chunk (45/82) cellbender:remove-background: Working on chunk (46/82) cellbender:remove-background: Working on chunk (47/82) cellbender:remove-background: Working on chunk (48/82) cellbender:remove-background: Working on chunk (49/82) cellbender:remove-background: Working on chunk (50/82) cellbender:remove-background: Working on chunk (51/82) cellbender:remove-background: Working on chunk (52/82) cellbender:remove-background: Working on chunk (53/82) cellbender:remove-background: Working on chunk (54/82) cellbender:remove-background: Working on chunk (55/82) cellbender:remove-background: Working on chunk (56/82) cellbender:remove-background: Working on chunk (57/82) cellbender:remove-background: Working on chunk (58/82) cellbender:remove-background: Working on chunk (59/82) cellbender:remove-background: Working on chunk (60/82) cellbender:remove-background: Working on chunk (61/82) cellbender:remove-background: Working on chunk (62/82) cellbender:remove-background: Working on chunk (63/82) cellbender:remove-background: Working on chunk (64/82) cellbender:remove-background: Working on chunk (65/82) cellbender:remove-background: Working on chunk (66/82) cellbender:remove-background: Working on chunk (67/82) cellbender:remove-background: Working on chunk (68/82) cellbender:remove-background: Working on chunk (69/82) cellbender:remove-background: Working on chunk (70/82) cellbender:remove-background: Working on chunk (71/82) cellbender:remove-background: Working on chunk (72/82) cellbender:remove-background: Working on chunk (73/82) cellbender:remove-background: Working on chunk (74/82) cellbender:remove-background: Working on chunk (75/82) cellbender:remove-background: Working on chunk (76/82) cellbender:remove-background: Working on chunk (77/82) cellbender:remove-background: Working on chunk (78/82) cellbender:remove-background: Working on chunk (79/82) cellbender:remove-background: Working on chunk (80/82) cellbender:remove-background: Working on chunk (81/82) cellbender:remove-background: Working on chunk (82/82) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:18:34 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.85 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 15:32:13 Total MCKP estimation time = 786.32 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/2781-Control-dACC/2781-Control-dACC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-dACC/2781-Control-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:32:51