cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2291-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 5183 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash aaa2e2ca11) cellbender:remove-background: 2024-06-06 15:15:02 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/2291-Schizophrenia-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: 31110 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3457 cellbender:remove-background: Prior on counts for empty droplets is 113 cellbender:remove-background: Excluding 9887 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21223 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 56 cellbender:remove-background: Using 5183 probable cell barcodes, plus an additional 14817 barcodes, and 27755 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 112 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpwr_l2nkw 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: 3789.6802 cellbender:remove-background: [epoch 002] average training loss: 3095.9181 (5.7 seconds per epoch) cellbender:remove-background: Will checkpoint every 75 epochs cellbender:remove-background: [epoch 003] average training loss: 2718.7743 cellbender:remove-background: [epoch 004] average training loss: 2456.0752 cellbender:remove-background: [epoch 005] average training loss: 2394.5854 cellbender:remove-background: [epoch 005] average test loss: 2401.5257 cellbender:remove-background: [epoch 006] average training loss: 2377.4665 cellbender:remove-background: [epoch 007] average training loss: 2343.0690 cellbender:remove-background: [epoch 008] average training loss: 2326.5407 cellbender:remove-background: [epoch 009] average training loss: 2326.0353 cellbender:remove-background: [epoch 010] average training loss: 2296.6508 cellbender:remove-background: [epoch 010] average test loss: 2266.2061 cellbender:remove-background: [epoch 011] average training loss: 2293.3129 cellbender:remove-background: [epoch 012] average training loss: 2277.4499 cellbender:remove-background: [epoch 013] average training loss: 2225.1883 cellbender:remove-background: [epoch 014] average training loss: 2213.3448 cellbender:remove-background: [epoch 015] average training loss: 2178.4895 cellbender:remove-background: [epoch 015] average test loss: 2162.5062 cellbender:remove-background: [epoch 016] average training loss: 2114.0942 cellbender:remove-background: [epoch 017] average training loss: 2100.0750 cellbender:remove-background: [epoch 018] average training loss: 2077.4006 cellbender:remove-background: [epoch 019] average training loss: 2062.0809 cellbender:remove-background: [epoch 020] average training loss: 2043.5369 cellbender:remove-background: [epoch 020] average test loss: 2057.8623 cellbender:remove-background: [epoch 021] average training loss: 2038.5145 cellbender:remove-background: [epoch 022] average training loss: 2040.0886 cellbender:remove-background: [epoch 023] average training loss: 2037.6833 cellbender:remove-background: [epoch 024] average training loss: 2032.4022 cellbender:remove-background: [epoch 025] average training loss: 2032.8517 cellbender:remove-background: [epoch 025] average test loss: 2050.9297 cellbender:remove-background: [epoch 026] average training loss: 2028.1012 cellbender:remove-background: [epoch 027] average training loss: 2025.4663 cellbender:remove-background: [epoch 028] average training loss: 2032.4413 cellbender:remove-background: [epoch 029] average training loss: 2032.5347 cellbender:remove-background: [epoch 030] average training loss: 2032.0164 cellbender:remove-background: [epoch 030] average test loss: 1998.7855 cellbender:remove-background: [epoch 031] average training loss: 2031.5050 cellbender:remove-background: [epoch 032] average training loss: 2024.0906 cellbender:remove-background: [epoch 033] average training loss: 2034.3703 cellbender:remove-background: [epoch 034] average training loss: 2035.2622 cellbender:remove-background: [epoch 035] average training loss: 2031.7606 cellbender:remove-background: [epoch 035] average test loss: 2025.1761 cellbender:remove-background: [epoch 036] average training loss: 2035.5511 cellbender:remove-background: [epoch 037] average training loss: 2038.6555 cellbender:remove-background: [epoch 038] average training loss: 2042.8327 cellbender:remove-background: [epoch 039] average training loss: 2047.6140 cellbender:remove-background: [epoch 040] average training loss: 2053.4143 cellbender:remove-background: [epoch 040] average test loss: 2064.2655 cellbender:remove-background: [epoch 041] average training loss: 2054.1894 cellbender:remove-background: [epoch 042] average training loss: 2059.6608 cellbender:remove-background: [epoch 043] average training loss: 2063.3305 cellbender:remove-background: [epoch 044] average training loss: 2078.4680 cellbender:remove-background: [epoch 045] average training loss: 2099.8598 cellbender:remove-background: [epoch 045] average test loss: 2125.6826 cellbender:remove-background: [epoch 046] average training loss: 2094.9293 cellbender:remove-background: [epoch 047] average training loss: 2090.1307 cellbender:remove-background: [epoch 048] average training loss: 2098.7953 cellbender:remove-background: [epoch 049] average training loss: 2104.3505 cellbender:remove-background: [epoch 050] average training loss: 2108.3086 cellbender:remove-background: [epoch 050] average test loss: 2098.8861 cellbender:remove-background: [epoch 051] average training loss: 2105.8957 cellbender:remove-background: [epoch 052] average training loss: 2117.0017 cellbender:remove-background: [epoch 053] average training loss: 2110.0845 cellbender:remove-background: [epoch 054] average training loss: 2102.8338 cellbender:remove-background: [epoch 055] average training loss: 2124.6407 cellbender:remove-background: [epoch 055] average test loss: 2219.8810 cellbender:remove-background: [epoch 056] average training loss: 2133.8313 cellbender:remove-background: [epoch 057] average training loss: 2130.1984 cellbender:remove-background: [epoch 058] average training loss: 2110.0763 cellbender:remove-background: [epoch 059] average training loss: 2127.8615 cellbender:remove-background: [epoch 060] average training loss: 2113.4303 cellbender:remove-background: [epoch 060] average test loss: 2137.7596 cellbender:remove-background: [epoch 061] average training loss: 2135.0732 cellbender:remove-background: [epoch 062] average training loss: 2121.9964 cellbender:remove-background: [epoch 063] average training loss: 2137.4612 cellbender:remove-background: [epoch 064] average training loss: 2136.4333 cellbender:remove-background: [epoch 065] average training loss: 2116.5283 cellbender:remove-background: [epoch 065] average test loss: 2164.7247 cellbender:remove-background: [epoch 066] average training loss: 2114.8371 cellbender:remove-background: [epoch 067] average training loss: 2126.3890 cellbender:remove-background: [epoch 068] average training loss: 2110.0857 cellbender:remove-background: [epoch 069] average training loss: 2119.9305 cellbender:remove-background: [epoch 070] average training loss: 2119.4741 cellbender:remove-background: [epoch 070] average test loss: 2123.9226 cellbender:remove-background: [epoch 071] average training loss: 2108.6894 cellbender:remove-background: [epoch 072] average training loss: 2122.6107 cellbender:remove-background: [epoch 073] average training loss: 2125.4803 cellbender:remove-background: [epoch 074] average training loss: 2117.0035 cellbender:remove-background: [epoch 075] average training loss: 2116.8423 cellbender:remove-background: [epoch 075] average test loss: 2136.8631 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/2291-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 076] average training loss: 2109.4183 cellbender:remove-background: [epoch 077] average training loss: 2121.9762 cellbender:remove-background: [epoch 078] average training loss: 2110.1154 cellbender:remove-background: [epoch 079] average training loss: 2125.1620 cellbender:remove-background: [epoch 080] average training loss: 2115.2811 cellbender:remove-background: [epoch 080] average test loss: 2156.4095 cellbender:remove-background: [epoch 081] average training loss: 2124.9943 cellbender:remove-background: [epoch 082] average training loss: 2112.8471 cellbender:remove-background: [epoch 083] average training loss: 2104.0771 cellbender:remove-background: [epoch 084] average training loss: 2132.7679 cellbender:remove-background: [epoch 085] average training loss: 2134.8335 cellbender:remove-background: [epoch 085] average test loss: 2157.9825 cellbender:remove-background: [epoch 086] average training loss: 2129.2012 cellbender:remove-background: [epoch 087] average training loss: 2132.7270 cellbender:remove-background: [epoch 088] average training loss: 2121.9848 cellbender:remove-background: [epoch 089] average training loss: 2124.4320 cellbender:remove-background: [epoch 090] average training loss: 2114.4158 cellbender:remove-background: [epoch 090] average test loss: 2172.7405 cellbender:remove-background: [epoch 091] average training loss: 2100.3787 cellbender:remove-background: [epoch 092] average training loss: 2108.8949 cellbender:remove-background: [epoch 093] average training loss: 2105.3735 cellbender:remove-background: [epoch 094] average training loss: 2111.3470 cellbender:remove-background: [epoch 095] average training loss: 2107.8527 cellbender:remove-background: [epoch 095] average test loss: 2175.4591 cellbender:remove-background: [epoch 096] average training loss: 2116.8741 cellbender:remove-background: [epoch 097] average training loss: 2105.9585 cellbender:remove-background: [epoch 098] average training loss: 2103.6191 cellbender:remove-background: [epoch 099] average training loss: 2102.6661 cellbender:remove-background: [epoch 100] average training loss: 2108.4685 cellbender:remove-background: [epoch 100] average test loss: 2181.9499 cellbender:remove-background: [epoch 101] average training loss: 2107.2119 cellbender:remove-background: [epoch 102] average training loss: 2100.4758 cellbender:remove-background: [epoch 103] average training loss: 2105.5600 cellbender:remove-background: [epoch 104] average training loss: 2109.0680 cellbender:remove-background: [epoch 105] average training loss: 2105.7500 cellbender:remove-background: [epoch 105] average test loss: 2148.9933 cellbender:remove-background: [epoch 106] average training loss: 2091.3513 cellbender:remove-background: [epoch 107] average training loss: 2108.9336 cellbender:remove-background: [epoch 108] average training loss: 2094.1619 cellbender:remove-background: [epoch 109] average training loss: 2093.3856 cellbender:remove-background: [epoch 110] average training loss: 2095.3623 cellbender:remove-background: [epoch 110] average test loss: 2160.5618 cellbender:remove-background: [epoch 111] average training loss: 2088.5491 cellbender:remove-background: [epoch 112] average training loss: 2091.0791 cellbender:remove-background: [epoch 113] average training loss: 2096.4951 cellbender:remove-background: [epoch 114] average training loss: 2092.3362 cellbender:remove-background: [epoch 115] average training loss: 2088.0577 cellbender:remove-background: [epoch 115] average test loss: 2150.0327 cellbender:remove-background: [epoch 116] average training loss: 2092.9728 cellbender:remove-background: [epoch 117] average training loss: 2095.7820 cellbender:remove-background: [epoch 118] average training loss: 2090.6176 cellbender:remove-background: [epoch 119] average training loss: 2097.5995 cellbender:remove-background: [epoch 120] average training loss: 2098.9437 cellbender:remove-background: [epoch 120] average test loss: 2162.1523 cellbender:remove-background: [epoch 121] average training loss: 2097.0277 cellbender:remove-background: [epoch 122] average training loss: 2094.8863 cellbender:remove-background: [epoch 123] average training loss: 2100.6316 cellbender:remove-background: [epoch 124] average training loss: 2112.8466 cellbender:remove-background: [epoch 125] average training loss: 2090.3848 cellbender:remove-background: [epoch 125] average test loss: 2158.5272 cellbender:remove-background: [epoch 126] average training loss: 2086.0853 cellbender:remove-background: [epoch 127] average training loss: 2090.5829 cellbender:remove-background: [epoch 128] average training loss: 2096.4331 cellbender:remove-background: [epoch 129] average training loss: 2098.2313 cellbender:remove-background: [epoch 130] average training loss: 2088.3700 cellbender:remove-background: [epoch 130] average test loss: 2165.8032 cellbender:remove-background: [epoch 131] average training loss: 2094.0999 cellbender:remove-background: [epoch 132] average training loss: 2094.5210 cellbender:remove-background: [epoch 133] average training loss: 2098.9930 cellbender:remove-background: [epoch 134] average training loss: 2098.0449 cellbender:remove-background: [epoch 135] average training loss: 2091.2302 cellbender:remove-background: [epoch 135] average test loss: 2156.3021 cellbender:remove-background: [epoch 136] average training loss: 2093.3853 cellbender:remove-background: [epoch 137] average training loss: 2095.9529 cellbender:remove-background: [epoch 138] average training loss: 2089.0088 cellbender:remove-background: [epoch 139] average training loss: 2104.1979 cellbender:remove-background: [epoch 140] average training loss: 2094.6897 cellbender:remove-background: [epoch 140] average test loss: 2167.3360 cellbender:remove-background: [epoch 141] average training loss: 2096.8297 cellbender:remove-background: [epoch 142] average training loss: 2087.8206 cellbender:remove-background: [epoch 143] average training loss: 2088.5218 cellbender:remove-background: [epoch 144] average training loss: 2090.7109 cellbender:remove-background: [epoch 145] average training loss: 2091.0598 cellbender:remove-background: [epoch 145] average test loss: 2168.6431 cellbender:remove-background: [epoch 146] average training loss: 2090.8812 cellbender:remove-background: [epoch 147] average training loss: 2090.7740 cellbender:remove-background: [epoch 148] average training loss: 2089.3567 cellbender:remove-background: [epoch 149] average training loss: 2094.3728 cellbender:remove-background: [epoch 150] average training loss: 2092.6397 cellbender:remove-background: [epoch 150] average test loss: 2191.2625 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/2291-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:31:54 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpdo5gns8l cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpdo5gns8l /tmp/tmpdo5gns8l/aaa2e2ca11_random.pyro /tmp/tmpdo5gns8l/aaa2e2ca11_random.cuda /tmp/tmpdo5gns8l/aaa2e2ca11_model.torch /tmp/tmpdo5gns8l/aaa2e2ca11_optim.torch /tmp/tmpdo5gns8l/aaa2e2ca11_optim.pyro /tmp/tmpdo5gns8l/aaa2e2ca11_params.pyro /tmp/tmpdo5gns8l/aaa2e2ca11_train.loaderstate /tmp/tmpdo5gns8l/aaa2e2ca11_test.loaderstate /tmp/tmpdo5gns8l/aaa2e2ca11_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 (1/83) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/83) cellbender:remove-background: Working on chunk (3/83) cellbender:remove-background: Working on chunk (4/83) cellbender:remove-background: Working on chunk (5/83) cellbender:remove-background: Working on chunk (6/83) cellbender:remove-background: Working on chunk (7/83) cellbender:remove-background: Working on chunk (8/83) cellbender:remove-background: Working on chunk (9/83) cellbender:remove-background: Working on chunk (10/83) cellbender:remove-background: Working on chunk (11/83) cellbender:remove-background: Working on chunk (12/83) cellbender:remove-background: Working on chunk (13/83) cellbender:remove-background: Working on chunk (14/83) cellbender:remove-background: Working on chunk (15/83) cellbender:remove-background: Working on chunk (16/83) cellbender:remove-background: Working on chunk (17/83) cellbender:remove-background: Working on chunk (18/83) cellbender:remove-background: Working on chunk (19/83) cellbender:remove-background: Working on chunk (20/83) cellbender:remove-background: Working on chunk (21/83) cellbender:remove-background: Working on chunk (22/83) cellbender:remove-background: Working on chunk (23/83) cellbender:remove-background: Working on chunk (24/83) cellbender:remove-background: Working on chunk (25/83) cellbender:remove-background: Working on chunk (26/83) cellbender:remove-background: Working on chunk (27/83) cellbender:remove-background: Working on chunk (28/83) cellbender:remove-background: Working on chunk (29/83) cellbender:remove-background: Working on chunk (30/83) cellbender:remove-background: Working on chunk (31/83) cellbender:remove-background: Working on chunk (32/83) cellbender:remove-background: Working on chunk (33/83) cellbender:remove-background: Working on chunk (34/83) cellbender:remove-background: Working on chunk (35/83) cellbender:remove-background: Working on chunk (36/83) cellbender:remove-background: Working on chunk (37/83) cellbender:remove-background: Working on chunk (38/83) cellbender:remove-background: Working on chunk (39/83) cellbender:remove-background: Working on chunk (40/83) cellbender:remove-background: Working on chunk (41/83) cellbender:remove-background: Working on chunk (42/83) cellbender:remove-background: Working on chunk (43/83) cellbender:remove-background: Working on chunk (44/83) cellbender:remove-background: Working on chunk (45/83) cellbender:remove-background: Working on chunk (46/83) cellbender:remove-background: Working on chunk (47/83) cellbender:remove-background: Working on chunk (48/83) cellbender:remove-background: Working on chunk (49/83) cellbender:remove-background: Working on chunk (50/83) cellbender:remove-background: Working on chunk (51/83) cellbender:remove-background: Working on chunk (52/83) cellbender:remove-background: Working on chunk (53/83) cellbender:remove-background: Working on chunk (54/83) cellbender:remove-background: Working on chunk (55/83) cellbender:remove-background: Working on chunk (56/83) cellbender:remove-background: Working on chunk (57/83) cellbender:remove-background: Working on chunk (58/83) cellbender:remove-background: Working on chunk (59/83) cellbender:remove-background: Working on chunk (60/83) cellbender:remove-background: Working on chunk (61/83) cellbender:remove-background: Working on chunk (62/83) cellbender:remove-background: Working on chunk (63/83) cellbender:remove-background: Working on chunk (64/83) cellbender:remove-background: Working on chunk (65/83) cellbender:remove-background: Working on chunk (66/83) cellbender:remove-background: Working on chunk (67/83) cellbender:remove-background: Working on chunk (68/83) cellbender:remove-background: Working on chunk (69/83) cellbender:remove-background: Working on chunk (70/83) cellbender:remove-background: Working on chunk (71/83) cellbender:remove-background: Working on chunk (72/83) cellbender:remove-background: Working on chunk (73/83) cellbender:remove-background: Working on chunk (74/83) cellbender:remove-background: Working on chunk (75/83) cellbender:remove-background: Working on chunk (76/83) cellbender:remove-background: Working on chunk (77/83) cellbender:remove-background: Working on chunk (78/83) cellbender:remove-background: Working on chunk (79/83) cellbender:remove-background: Working on chunk (80/83) cellbender:remove-background: Working on chunk (81/83) cellbender:remove-background: Working on chunk (82/83) cellbender:remove-background: Working on chunk (83/83) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-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/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:35:56 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-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: [1.20 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 15:44:35 Total MCKP estimation time = 498.73 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/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-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/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-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/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-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/2291-Schizophrenia-Hippocampus/2291-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:44:50