cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1527-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-Hippocampus/1527-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 6309 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 28bc396047) cellbender:remove-background: 2024-06-06 15:25:28 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/1527-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: 31644 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3296 cellbender:remove-background: Prior on counts for empty droplets is 47 cellbender:remove-background: Excluding 11917 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19727 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 23 cellbender:remove-background: Using 6309 probable cell barcodes, plus an additional 13691 barcodes, and 38882 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 46 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp9htt7kcr 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: 4701.8455 cellbender:remove-background: [epoch 002] average training loss: 3745.9085 (5.7 seconds per epoch) cellbender:remove-background: Will checkpoint every 74 epochs cellbender:remove-background: [epoch 003] average training loss: 3232.9264 cellbender:remove-background: [epoch 004] average training loss: 2882.1192 cellbender:remove-background: [epoch 005] average training loss: 2754.5515 cellbender:remove-background: [epoch 005] average test loss: 2770.3435 cellbender:remove-background: [epoch 006] average training loss: 2705.4208 cellbender:remove-background: [epoch 007] average training loss: 2648.7251 cellbender:remove-background: [epoch 008] average training loss: 2629.5989 cellbender:remove-background: [epoch 009] average training loss: 2629.2768 cellbender:remove-background: [epoch 010] average training loss: 2580.6088 cellbender:remove-background: [epoch 010] average test loss: 2577.5447 cellbender:remove-background: [epoch 011] average training loss: 2556.6939 cellbender:remove-background: [epoch 012] average training loss: 2452.2072 cellbender:remove-background: [epoch 013] average training loss: 2402.0873 cellbender:remove-background: [epoch 014] average training loss: 2403.7927 cellbender:remove-background: [epoch 015] average training loss: 2359.0051 cellbender:remove-background: [epoch 015] average test loss: 2339.6606 cellbender:remove-background: [epoch 016] average training loss: 2304.2805 cellbender:remove-background: [epoch 017] average training loss: 2298.7476 cellbender:remove-background: [epoch 018] average training loss: 2275.8925 cellbender:remove-background: [epoch 019] average training loss: 2256.4776 cellbender:remove-background: [epoch 020] average training loss: 2233.3506 cellbender:remove-background: [epoch 020] average test loss: 2251.6713 cellbender:remove-background: [epoch 021] average training loss: 2224.7562 cellbender:remove-background: [epoch 022] average training loss: 2220.0364 cellbender:remove-background: [epoch 023] average training loss: 2212.0729 cellbender:remove-background: [epoch 024] average training loss: 2196.5151 cellbender:remove-background: [epoch 025] average training loss: 2190.3426 cellbender:remove-background: [epoch 025] average test loss: 2176.9965 cellbender:remove-background: [epoch 026] average training loss: 2174.7558 cellbender:remove-background: [epoch 027] average training loss: 2167.3721 cellbender:remove-background: [epoch 028] average training loss: 2162.8567 cellbender:remove-background: [epoch 029] average training loss: 2154.4210 cellbender:remove-background: [epoch 030] average training loss: 2148.2140 cellbender:remove-background: [epoch 030] average test loss: 2147.4580 cellbender:remove-background: [epoch 031] average training loss: 2146.3371 cellbender:remove-background: [epoch 032] average training loss: 2141.6307 cellbender:remove-background: [epoch 033] average training loss: 2140.5888 cellbender:remove-background: [epoch 034] average training loss: 2141.1085 cellbender:remove-background: [epoch 035] average training loss: 2141.3304 cellbender:remove-background: [epoch 035] average test loss: 2145.3966 cellbender:remove-background: [epoch 036] average training loss: 2141.3885 cellbender:remove-background: [epoch 037] average training loss: 2141.8633 cellbender:remove-background: [epoch 038] average training loss: 2149.2561 cellbender:remove-background: [epoch 039] average training loss: 2157.7832 cellbender:remove-background: [epoch 040] average training loss: 2155.8273 cellbender:remove-background: [epoch 040] average test loss: 2130.8934 cellbender:remove-background: [epoch 041] average training loss: 2164.9226 cellbender:remove-background: [epoch 042] average training loss: 2173.6572 cellbender:remove-background: [epoch 043] average training loss: 2172.6387 cellbender:remove-background: [epoch 044] average training loss: 2183.1280 cellbender:remove-background: [epoch 045] average training loss: 2160.7164 cellbender:remove-background: [epoch 045] average test loss: 2134.7150 cellbender:remove-background: [epoch 046] average training loss: 2183.9469 cellbender:remove-background: [epoch 047] average training loss: 2184.1608 cellbender:remove-background: [epoch 048] average training loss: 2180.3470 cellbender:remove-background: [epoch 049] average training loss: 2184.0433 cellbender:remove-background: [epoch 050] average training loss: 2187.0877 cellbender:remove-background: [epoch 050] average test loss: 2154.1150 cellbender:remove-background: [epoch 051] average training loss: 2216.6635 cellbender:remove-background: [epoch 052] average training loss: 2167.5836 cellbender:remove-background: [epoch 053] average training loss: 2191.1359 cellbender:remove-background: [epoch 054] average training loss: 2193.2751 cellbender:remove-background: [epoch 055] average training loss: 2203.4662 cellbender:remove-background: [epoch 055] average test loss: 2171.3923 cellbender:remove-background: [epoch 056] average training loss: 2212.9764 cellbender:remove-background: [epoch 057] average training loss: 2187.9167 cellbender:remove-background: [epoch 058] average training loss: 2202.5880 cellbender:remove-background: [epoch 059] average training loss: 2230.9254 cellbender:remove-background: [epoch 060] average training loss: 2206.4723 cellbender:remove-background: [epoch 060] average test loss: 2231.1596 cellbender:remove-background: [epoch 061] average training loss: 2218.0171 cellbender:remove-background: [epoch 062] average training loss: 2234.7435 cellbender:remove-background: [epoch 063] average training loss: 2213.0533 cellbender:remove-background: [epoch 064] average training loss: 2224.1059 cellbender:remove-background: [epoch 065] average training loss: 2216.1271 cellbender:remove-background: [epoch 065] average test loss: 2310.8963 cellbender:remove-background: [epoch 066] average training loss: 2253.3689 cellbender:remove-background: [epoch 067] average training loss: 2263.1160 cellbender:remove-background: [epoch 068] average training loss: 2217.6546 cellbender:remove-background: [epoch 069] average training loss: 2224.2170 cellbender:remove-background: [epoch 070] average training loss: 2221.7303 cellbender:remove-background: [epoch 070] average test loss: 2286.4022 cellbender:remove-background: [epoch 071] average training loss: 2231.6592 cellbender:remove-background: [epoch 072] average training loss: 2256.0298 cellbender:remove-background: [epoch 073] average training loss: 2245.9475 cellbender:remove-background: [epoch 074] average training loss: 2242.7592 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/1527-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 075] average training loss: 2259.7794 cellbender:remove-background: [epoch 075] average test loss: 2258.5856 cellbender:remove-background: [epoch 076] average training loss: 2262.1491 cellbender:remove-background: [epoch 077] average training loss: 2217.1113 cellbender:remove-background: [epoch 078] average training loss: 2251.2737 cellbender:remove-background: [epoch 079] average training loss: 2234.9894 cellbender:remove-background: [epoch 080] average training loss: 2289.2394 cellbender:remove-background: [epoch 080] average test loss: 2260.5448 cellbender:remove-background: [epoch 081] average training loss: 2265.6524 cellbender:remove-background: [epoch 082] average training loss: 2255.0306 cellbender:remove-background: [epoch 083] average training loss: 2260.6838 cellbender:remove-background: [epoch 084] average training loss: 2278.8962 cellbender:remove-background: [epoch 085] average training loss: 2247.0740 cellbender:remove-background: [epoch 085] average test loss: 2236.1060 cellbender:remove-background: [epoch 086] average training loss: 2251.2817 cellbender:remove-background: [epoch 087] average training loss: 2244.0230 cellbender:remove-background: [epoch 088] average training loss: 2242.6617 cellbender:remove-background: [epoch 089] average training loss: 2265.2324 cellbender:remove-background: [epoch 090] average training loss: 2261.4170 cellbender:remove-background: [epoch 090] average test loss: 2317.9064 cellbender:remove-background: [epoch 091] average training loss: 2278.1156 cellbender:remove-background: [epoch 092] average training loss: 2256.8403 cellbender:remove-background: [epoch 093] average training loss: 2262.7352 cellbender:remove-background: [epoch 094] average training loss: 2266.6199 cellbender:remove-background: [epoch 095] average training loss: 2267.8202 cellbender:remove-background: [epoch 095] average test loss: 2255.3969 cellbender:remove-background: [epoch 096] average training loss: 2272.5140 cellbender:remove-background: [epoch 097] average training loss: 2251.4785 cellbender:remove-background: [epoch 098] average training loss: 2276.3121 cellbender:remove-background: [epoch 099] average training loss: 2251.0167 cellbender:remove-background: [epoch 100] average training loss: 2258.2087 cellbender:remove-background: [epoch 100] average test loss: 2366.3659 cellbender:remove-background: [epoch 101] average training loss: 2249.9433 cellbender:remove-background: [epoch 102] average training loss: 2247.6018 cellbender:remove-background: [epoch 103] average training loss: 2261.4990 cellbender:remove-background: [epoch 104] average training loss: 2276.3817 cellbender:remove-background: [epoch 105] average training loss: 2286.0516 cellbender:remove-background: [epoch 105] average test loss: 2234.8871 cellbender:remove-background: [epoch 106] average training loss: 2248.3248 cellbender:remove-background: [epoch 107] average training loss: 2273.0764 cellbender:remove-background: [epoch 108] average training loss: 2268.6864 cellbender:remove-background: [epoch 109] average training loss: 2244.5611 cellbender:remove-background: [epoch 110] average training loss: 2229.5773 cellbender:remove-background: [epoch 110] average test loss: 2298.2722 cellbender:remove-background: [epoch 111] average training loss: 2247.5363 cellbender:remove-background: [epoch 112] average training loss: 2251.8418 cellbender:remove-background: [epoch 113] average training loss: 2266.9538 cellbender:remove-background: [epoch 114] average training loss: 2258.8120 cellbender:remove-background: [epoch 115] average training loss: 2282.1073 cellbender:remove-background: [epoch 115] average test loss: 2326.7830 cellbender:remove-background: [epoch 116] average training loss: 2264.0407 cellbender:remove-background: [epoch 117] average training loss: 2284.4795 cellbender:remove-background: [epoch 118] average training loss: 2253.0248 cellbender:remove-background: [epoch 119] average training loss: 2255.4900 cellbender:remove-background: [epoch 120] average training loss: 2271.9898 cellbender:remove-background: [epoch 120] average test loss: 2280.7609 cellbender:remove-background: [epoch 121] average training loss: 2255.8990 cellbender:remove-background: [epoch 122] average training loss: 2245.5148 cellbender:remove-background: [epoch 123] average training loss: 2251.3743 cellbender:remove-background: [epoch 124] average training loss: 2255.0216 cellbender:remove-background: [epoch 125] average training loss: 2281.5430 cellbender:remove-background: [epoch 125] average test loss: 2357.9147 cellbender:remove-background: [epoch 126] average training loss: 2264.4866 cellbender:remove-background: [epoch 127] average training loss: 2295.3566 cellbender:remove-background: [epoch 128] average training loss: 2262.3188 cellbender:remove-background: [epoch 129] average training loss: 2247.5643 cellbender:remove-background: [epoch 130] average training loss: 2246.2773 cellbender:remove-background: [epoch 130] average test loss: 2305.8032 cellbender:remove-background: [epoch 131] average training loss: 2263.3621 cellbender:remove-background: [epoch 132] average training loss: 2282.5402 cellbender:remove-background: [epoch 133] average training loss: 2257.1416 cellbender:remove-background: [epoch 134] average training loss: 2241.6298 cellbender:remove-background: [epoch 135] average training loss: 2281.2957 cellbender:remove-background: [epoch 135] average test loss: 2366.5441 cellbender:remove-background: [epoch 136] average training loss: 2240.9986 cellbender:remove-background: [epoch 137] average training loss: 2249.2692 cellbender:remove-background: [epoch 138] average training loss: 2251.2347 cellbender:remove-background: [epoch 139] average training loss: 2234.4081 cellbender:remove-background: [epoch 140] average training loss: 2238.5366 cellbender:remove-background: [epoch 140] average test loss: 2289.5343 cellbender:remove-background: [epoch 141] average training loss: 2259.5152 cellbender:remove-background: [epoch 142] average training loss: 2244.7771 cellbender:remove-background: [epoch 143] average training loss: 2268.4975 cellbender:remove-background: [epoch 144] average training loss: 2251.5085 cellbender:remove-background: [epoch 145] average training loss: 2249.0260 cellbender:remove-background: [epoch 145] average test loss: 2330.8838 cellbender:remove-background: [epoch 146] average training loss: 2270.6994 cellbender:remove-background: [epoch 147] average training loss: 2264.2137 cellbender:remove-background: [epoch 148] average training loss: 2260.6010 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/1527-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 149] average training loss: 2235.2193 cellbender:remove-background: [epoch 150] average training loss: 2258.0202 cellbender:remove-background: [epoch 150] average test loss: 2306.7689 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/1527-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:42:31 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzikboka0 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpzikboka0 /tmp/tmpzikboka0/28bc396047_random.pyro /tmp/tmpzikboka0/28bc396047_random.cuda /tmp/tmpzikboka0/28bc396047_model.torch /tmp/tmpzikboka0/28bc396047_optim.torch /tmp/tmpzikboka0/28bc396047_optim.pyro /tmp/tmpzikboka0/28bc396047_params.pyro /tmp/tmpzikboka0/28bc396047_train.loaderstate /tmp/tmpzikboka0/28bc396047_test.loaderstate /tmp/tmpzikboka0/28bc396047_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 (1/74) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/74) cellbender:remove-background: Working on chunk (3/74) cellbender:remove-background: Working on chunk (4/74) cellbender:remove-background: Working on chunk (5/74) cellbender:remove-background: Working on chunk (6/74) cellbender:remove-background: Working on chunk (7/74) cellbender:remove-background: Working on chunk (8/74) cellbender:remove-background: Working on chunk (9/74) cellbender:remove-background: Working on chunk (10/74) cellbender:remove-background: Working on chunk (11/74) cellbender:remove-background: Working on chunk (12/74) cellbender:remove-background: Working on chunk (13/74) cellbender:remove-background: Working on chunk (14/74) cellbender:remove-background: Working on chunk (15/74) cellbender:remove-background: Working on chunk (16/74) cellbender:remove-background: Working on chunk (17/74) cellbender:remove-background: Working on chunk (18/74) cellbender:remove-background: Working on chunk (19/74) cellbender:remove-background: Working on chunk (20/74) cellbender:remove-background: Working on chunk (21/74) cellbender:remove-background: Working on chunk (22/74) cellbender:remove-background: Working on chunk (23/74) cellbender:remove-background: Working on chunk (24/74) cellbender:remove-background: Working on chunk (25/74) cellbender:remove-background: Working on chunk (26/74) cellbender:remove-background: Working on chunk (27/74) cellbender:remove-background: Working on chunk (28/74) cellbender:remove-background: Working on chunk (29/74) cellbender:remove-background: Working on chunk (30/74) cellbender:remove-background: Working on chunk (31/74) cellbender:remove-background: Working on chunk (32/74) cellbender:remove-background: Working on chunk (33/74) cellbender:remove-background: Working on chunk (34/74) cellbender:remove-background: Working on chunk (35/74) cellbender:remove-background: Working on chunk (36/74) cellbender:remove-background: Working on chunk (37/74) cellbender:remove-background: Working on chunk (38/74) cellbender:remove-background: Working on chunk (39/74) cellbender:remove-background: Working on chunk (40/74) cellbender:remove-background: Working on chunk (41/74) cellbender:remove-background: Working on chunk (42/74) cellbender:remove-background: Working on chunk (43/74) cellbender:remove-background: Working on chunk (44/74) cellbender:remove-background: Working on chunk (45/74) cellbender:remove-background: Working on chunk (46/74) cellbender:remove-background: Working on chunk (47/74) cellbender:remove-background: Working on chunk (48/74) cellbender:remove-background: Working on chunk (49/74) cellbender:remove-background: Working on chunk (50/74) cellbender:remove-background: Working on chunk (51/74) cellbender:remove-background: Working on chunk (52/74) cellbender:remove-background: Working on chunk (53/74) cellbender:remove-background: Working on chunk (54/74) cellbender:remove-background: Working on chunk (55/74) cellbender:remove-background: Working on chunk (56/74) cellbender:remove-background: Working on chunk (57/74) cellbender:remove-background: Working on chunk (58/74) cellbender:remove-background: Working on chunk (59/74) cellbender:remove-background: Working on chunk (60/74) cellbender:remove-background: Working on chunk (61/74) cellbender:remove-background: Working on chunk (62/74) cellbender:remove-background: Working on chunk (63/74) cellbender:remove-background: Working on chunk (64/74) cellbender:remove-background: Working on chunk (65/74) cellbender:remove-background: Working on chunk (66/74) cellbender:remove-background: Working on chunk (67/74) cellbender:remove-background: Working on chunk (68/74) cellbender:remove-background: Working on chunk (69/74) cellbender:remove-background: Working on chunk (70/74) cellbender:remove-background: Working on chunk (71/74) cellbender:remove-background: Working on chunk (72/74) cellbender:remove-background: Working on chunk (73/74) cellbender:remove-background: Working on chunk (74/74) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-Hippocampus/1527-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/1527-Schizophrenia-Hippocampus/1527-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:45:55 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-Hippocampus/1527-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/1527-Schizophrenia-Hippocampus/1527-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: [0.87 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 15:52:17 Total MCKP estimation time = 365.41 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/1527-Schizophrenia-Hippocampus/1527-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/1527-Schizophrenia-Hippocampus/1527-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/1527-Schizophrenia-Hippocampus/1527-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/1527-Schizophrenia-Hippocampus/1527-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:52:31