cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1556-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1556-Control-DLPFC/1556-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 3762 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 5675e01877) cellbender:remove-background: 2024-06-06 15:12:34 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/1556-Control-DLPFC.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: 31494 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 6684 cellbender:remove-background: Prior on counts for empty droplets is 69 cellbender:remove-background: Excluding 11571 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19923 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 34 cellbender:remove-background: Using 3762 probable cell barcodes, plus an additional 16238 barcodes, and 22210 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 68 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpx0r1_oo4 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: 4776.0213 cellbender:remove-background: [epoch 002] average training loss: 3524.8227 (13.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 32 epochs cellbender:remove-background: [epoch 003] average training loss: 2998.5988 cellbender:remove-background: [epoch 004] average training loss: 2723.6063 cellbender:remove-background: [epoch 005] average training loss: 2664.0519 cellbender:remove-background: [epoch 005] average test loss: 2756.0081 cellbender:remove-background: [epoch 006] average training loss: 2643.1222 cellbender:remove-background: [epoch 007] average training loss: 2610.4215 cellbender:remove-background: [epoch 008] average training loss: 2580.1309 cellbender:remove-background: [epoch 009] average training loss: 2561.2438 cellbender:remove-background: [epoch 010] average training loss: 2493.7842 cellbender:remove-background: [epoch 010] average test loss: 2518.0807 cellbender:remove-background: [epoch 011] average training loss: 2455.3349 cellbender:remove-background: [epoch 012] average training loss: 2440.0180 cellbender:remove-background: [epoch 013] average training loss: 2420.1513 cellbender:remove-background: [epoch 014] average training loss: 2420.7872 cellbender:remove-background: [epoch 015] average training loss: 2398.1338 cellbender:remove-background: [epoch 015] average test loss: 2447.4160 cellbender:remove-background: [epoch 016] average training loss: 2383.3628 cellbender:remove-background: [epoch 017] average training loss: 2388.6097 cellbender:remove-background: [epoch 018] average training loss: 2378.5254 cellbender:remove-background: [epoch 019] average training loss: 2370.6551 cellbender:remove-background: [epoch 020] average training loss: 2355.7833 cellbender:remove-background: [epoch 020] average test loss: 2391.6586 cellbender:remove-background: [epoch 021] average training loss: 2348.5702 cellbender:remove-background: [epoch 022] average training loss: 2328.5208 cellbender:remove-background: [epoch 023] average training loss: 2321.1970 cellbender:remove-background: [epoch 024] average training loss: 2309.6268 cellbender:remove-background: [epoch 025] average training loss: 2303.0892 cellbender:remove-background: [epoch 025] average test loss: 2323.9641 cellbender:remove-background: [epoch 026] average training loss: 2292.7730 cellbender:remove-background: [epoch 027] average training loss: 2288.7114 cellbender:remove-background: [epoch 028] average training loss: 2283.4869 cellbender:remove-background: [epoch 029] average training loss: 2282.0989 cellbender:remove-background: [epoch 030] average training loss: 2277.2571 cellbender:remove-background: [epoch 030] average test loss: 2299.3983 cellbender:remove-background: [epoch 031] average training loss: 2274.7364 cellbender:remove-background: [epoch 032] average training loss: 2273.3642 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/1556-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 033] average training loss: 2274.7506 cellbender:remove-background: [epoch 034] average training loss: 2270.6269 cellbender:remove-background: [epoch 035] average training loss: 2270.6231 cellbender:remove-background: [epoch 035] average test loss: 2286.7005 cellbender:remove-background: [epoch 036] average training loss: 2267.9734 cellbender:remove-background: [epoch 037] average training loss: 2266.5960 cellbender:remove-background: [epoch 038] average training loss: 2268.4095 cellbender:remove-background: [epoch 039] average training loss: 2267.4404 cellbender:remove-background: [epoch 040] average training loss: 2265.2326 cellbender:remove-background: [epoch 040] average test loss: 2289.4408 cellbender:remove-background: [epoch 041] average training loss: 2267.5024 cellbender:remove-background: [epoch 042] average training loss: 2263.9498 cellbender:remove-background: [epoch 043] average training loss: 2264.1810 cellbender:remove-background: [epoch 044] average training loss: 2263.0661 cellbender:remove-background: [epoch 045] average training loss: 2263.9946 cellbender:remove-background: [epoch 045] average test loss: 2307.6339 cellbender:remove-background: [epoch 046] average training loss: 2266.0366 cellbender:remove-background: [epoch 047] average training loss: 2262.9962 cellbender:remove-background: [epoch 048] average training loss: 2267.3045 cellbender:remove-background: [epoch 049] average training loss: 2266.2853 cellbender:remove-background: [epoch 050] average training loss: 2267.1363 cellbender:remove-background: [epoch 050] average test loss: 2288.9207 cellbender:remove-background: [epoch 051] average training loss: 2272.5477 cellbender:remove-background: [epoch 052] average training loss: 2269.0914 cellbender:remove-background: [epoch 053] average training loss: 2268.9063 cellbender:remove-background: [epoch 054] average training loss: 2272.2628 cellbender:remove-background: [epoch 055] average training loss: 2274.2634 cellbender:remove-background: [epoch 055] average test loss: 2283.5853 cellbender:remove-background: [epoch 056] average training loss: 2273.7395 cellbender:remove-background: [epoch 057] average training loss: 2278.4215 cellbender:remove-background: [epoch 058] average training loss: 2278.3712 cellbender:remove-background: [epoch 059] average training loss: 2280.4518 cellbender:remove-background: [epoch 060] average training loss: 2287.6554 cellbender:remove-background: [epoch 060] average test loss: 2321.9540 cellbender:remove-background: [epoch 061] average training loss: 2281.1860 cellbender:remove-background: [epoch 062] average training loss: 2281.3503 cellbender:remove-background: [epoch 063] average training loss: 2281.4710 cellbender:remove-background: [epoch 064] average training loss: 2276.4486 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/1556-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 065] average training loss: 2284.5202 cellbender:remove-background: [epoch 065] average test loss: 2323.6008 cellbender:remove-background: [epoch 066] average training loss: 2283.1979 cellbender:remove-background: [epoch 067] average training loss: 2280.7395 cellbender:remove-background: [epoch 068] average training loss: 2284.1291 cellbender:remove-background: [epoch 069] average training loss: 2280.4664 cellbender:remove-background: [epoch 070] average training loss: 2280.9121 cellbender:remove-background: [epoch 070] average test loss: 2336.4344 cellbender:remove-background: [epoch 071] average training loss: 2282.7503 cellbender:remove-background: [epoch 072] average training loss: 2289.0614 cellbender:remove-background: [epoch 073] average training loss: 2283.9574 cellbender:remove-background: [epoch 074] average training loss: 2297.3984 cellbender:remove-background: [epoch 075] average training loss: 2292.3871 cellbender:remove-background: [epoch 075] average test loss: 2330.3117 cellbender:remove-background: [epoch 076] average training loss: 2297.4120 cellbender:remove-background: [epoch 077] average training loss: 2296.2861 cellbender:remove-background: [epoch 078] average training loss: 2314.4320 cellbender:remove-background: [epoch 079] average training loss: 2299.7166 cellbender:remove-background: [epoch 080] average training loss: 2308.3312 cellbender:remove-background: [epoch 080] average test loss: 2337.2344 cellbender:remove-background: [epoch 081] average training loss: 2302.0237 cellbender:remove-background: [epoch 082] average training loss: 2299.0606 cellbender:remove-background: [epoch 083] average training loss: 2298.5245 cellbender:remove-background: [epoch 084] average training loss: 2303.7268 cellbender:remove-background: [epoch 085] average training loss: 2290.8055 cellbender:remove-background: [epoch 085] average test loss: 2359.2080 cellbender:remove-background: [epoch 086] average training loss: 2295.9670 cellbender:remove-background: [epoch 087] average training loss: 2302.9889 cellbender:remove-background: [epoch 088] average training loss: 2295.8185 cellbender:remove-background: [epoch 089] average training loss: 2298.5286 cellbender:remove-background: [epoch 090] average training loss: 2293.6315 cellbender:remove-background: [epoch 090] average test loss: 2376.7373 cellbender:remove-background: [epoch 091] average training loss: 2294.5899 cellbender:remove-background: [epoch 092] average training loss: 2296.3159 cellbender:remove-background: [epoch 093] average training loss: 2285.9135 cellbender:remove-background: [epoch 094] average training loss: 2295.9745 cellbender:remove-background: [epoch 095] average training loss: 2294.5084 cellbender:remove-background: [epoch 095] average test loss: 2352.9839 cellbender:remove-background: [epoch 096] average training loss: 2293.8629 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/1556-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 097] average training loss: 2292.5391 cellbender:remove-background: [epoch 098] average training loss: 2292.8780 cellbender:remove-background: [epoch 099] average training loss: 2288.5785 cellbender:remove-background: [epoch 100] average training loss: 2288.5166 cellbender:remove-background: [epoch 100] average test loss: 2358.9706 cellbender:remove-background: [epoch 101] average training loss: 2287.2732 cellbender:remove-background: [epoch 102] average training loss: 2291.0773 cellbender:remove-background: [epoch 103] average training loss: 2293.5073 cellbender:remove-background: [epoch 104] average training loss: 2289.3011 cellbender:remove-background: [epoch 105] average training loss: 2293.6018 cellbender:remove-background: [epoch 105] average test loss: 2371.4221 cellbender:remove-background: [epoch 106] average training loss: 2291.5062 cellbender:remove-background: [epoch 107] average training loss: 2291.7669 cellbender:remove-background: [epoch 108] average training loss: 2291.6214 cellbender:remove-background: [epoch 109] average training loss: 2291.6213 cellbender:remove-background: [epoch 110] average training loss: 2292.2386 cellbender:remove-background: [epoch 110] average test loss: 2362.2055 cellbender:remove-background: [epoch 111] average training loss: 2290.7006 cellbender:remove-background: [epoch 112] average training loss: 2293.2390 cellbender:remove-background: [epoch 113] average training loss: 2287.5174 cellbender:remove-background: [epoch 114] average training loss: 2284.2639 cellbender:remove-background: [epoch 115] average training loss: 2289.1188 cellbender:remove-background: [epoch 115] average test loss: 2358.7257 cellbender:remove-background: [epoch 116] average training loss: 2285.2045 cellbender:remove-background: [epoch 117] average training loss: 2285.8823 cellbender:remove-background: [epoch 118] average training loss: 2280.9075 cellbender:remove-background: [epoch 119] average training loss: 2286.0681 cellbender:remove-background: [epoch 120] average training loss: 2282.4557 cellbender:remove-background: [epoch 120] average test loss: 2380.7935 cellbender:remove-background: [epoch 121] average training loss: 2281.2645 cellbender:remove-background: [epoch 122] average training loss: 2284.6012 cellbender:remove-background: [epoch 123] average training loss: 2285.2824 cellbender:remove-background: [epoch 124] average training loss: 2283.0551 cellbender:remove-background: [epoch 125] average training loss: 2283.0873 cellbender:remove-background: [epoch 125] average test loss: 2369.4663 cellbender:remove-background: [epoch 126] average training loss: 2280.5990 cellbender:remove-background: [epoch 127] average training loss: 2281.7937 cellbender:remove-background: [epoch 128] average training loss: 2281.2455 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/1556-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 129] average training loss: 2283.9028 cellbender:remove-background: [epoch 130] average training loss: 2282.5464 cellbender:remove-background: [epoch 130] average test loss: 2358.7280 cellbender:remove-background: [epoch 131] average training loss: 2277.7816 cellbender:remove-background: [epoch 132] average training loss: 2280.6167 cellbender:remove-background: [epoch 133] average training loss: 2279.6666 cellbender:remove-background: [epoch 134] average training loss: 2281.5362 cellbender:remove-background: [epoch 135] average training loss: 2283.9821 cellbender:remove-background: [epoch 135] average test loss: 2356.3043 cellbender:remove-background: [epoch 136] average training loss: 2282.8833 cellbender:remove-background: [epoch 137] average training loss: 2286.3715 cellbender:remove-background: [epoch 138] average training loss: 2283.4706 cellbender:remove-background: [epoch 139] average training loss: 2278.6578 cellbender:remove-background: [epoch 140] average training loss: 2283.9725 cellbender:remove-background: [epoch 140] average test loss: 2369.4697 cellbender:remove-background: [epoch 141] average training loss: 2281.5115 cellbender:remove-background: [epoch 142] average training loss: 2280.9053 cellbender:remove-background: [epoch 143] average training loss: 2279.9026 cellbender:remove-background: [epoch 144] average training loss: 2282.8650 cellbender:remove-background: [epoch 145] average training loss: 2280.9900 cellbender:remove-background: [epoch 145] average test loss: 2364.1429 cellbender:remove-background: [epoch 146] average training loss: 2278.4731 cellbender:remove-background: [epoch 147] average training loss: 2283.8634 cellbender:remove-background: [epoch 148] average training loss: 2279.2138 cellbender:remove-background: [epoch 149] average training loss: 2280.8257 cellbender:remove-background: [epoch 150] average training loss: 2283.2873 cellbender:remove-background: [epoch 150] average test loss: 2372.6120 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/1556-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:52:45 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpj07bsl20 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpj07bsl20 /tmp/tmpj07bsl20/5675e01877_random.pyro /tmp/tmpj07bsl20/5675e01877_random.cuda /tmp/tmpj07bsl20/5675e01877_model.torch /tmp/tmpj07bsl20/5675e01877_optim.torch /tmp/tmpj07bsl20/5675e01877_optim.pyro /tmp/tmpj07bsl20/5675e01877_params.pyro /tmp/tmpj07bsl20/5675e01877_train.loaderstate /tmp/tmpj07bsl20/5675e01877_test.loaderstate /tmp/tmpj07bsl20/5675e01877_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 (1/62) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/62) cellbender:remove-background: Working on chunk (3/62) cellbender:remove-background: Working on chunk (4/62) cellbender:remove-background: Working on chunk (5/62) cellbender:remove-background: Working on chunk (6/62) cellbender:remove-background: Working on chunk (7/62) cellbender:remove-background: Working on chunk (8/62) cellbender:remove-background: Working on chunk (9/62) cellbender:remove-background: Working on chunk (10/62) cellbender:remove-background: Working on chunk (11/62) cellbender:remove-background: Working on chunk (12/62) cellbender:remove-background: Working on chunk (13/62) cellbender:remove-background: Working on chunk (14/62) cellbender:remove-background: Working on chunk (15/62) cellbender:remove-background: Working on chunk (16/62) cellbender:remove-background: Working on chunk (17/62) cellbender:remove-background: Working on chunk (18/62) cellbender:remove-background: Working on chunk (19/62) cellbender:remove-background: Working on chunk (20/62) cellbender:remove-background: Working on chunk (21/62) cellbender:remove-background: Working on chunk (22/62) cellbender:remove-background: Working on chunk (23/62) cellbender:remove-background: Working on chunk (24/62) cellbender:remove-background: Working on chunk (25/62) cellbender:remove-background: Working on chunk (26/62) cellbender:remove-background: Working on chunk (27/62) cellbender:remove-background: Working on chunk (28/62) cellbender:remove-background: Working on chunk (29/62) cellbender:remove-background: Working on chunk (30/62) cellbender:remove-background: Working on chunk (31/62) cellbender:remove-background: Working on chunk (32/62) cellbender:remove-background: Working on chunk (33/62) cellbender:remove-background: Working on chunk (34/62) cellbender:remove-background: Working on chunk (35/62) cellbender:remove-background: Working on chunk (36/62) cellbender:remove-background: Working on chunk (37/62) cellbender:remove-background: Working on chunk (38/62) cellbender:remove-background: Working on chunk (39/62) cellbender:remove-background: Working on chunk (40/62) cellbender:remove-background: Working on chunk (41/62) cellbender:remove-background: Working on chunk (42/62) cellbender:remove-background: Working on chunk (43/62) cellbender:remove-background: Working on chunk (44/62) cellbender:remove-background: Working on chunk (45/62) cellbender:remove-background: Working on chunk (46/62) cellbender:remove-background: Working on chunk (47/62) cellbender:remove-background: Working on chunk (48/62) cellbender:remove-background: Working on chunk (49/62) cellbender:remove-background: Working on chunk (50/62) cellbender:remove-background: Working on chunk (51/62) cellbender:remove-background: Working on chunk (52/62) cellbender:remove-background: Working on chunk (53/62) cellbender:remove-background: Working on chunk (54/62) cellbender:remove-background: Working on chunk (55/62) cellbender:remove-background: Working on chunk (56/62) cellbender:remove-background: Working on chunk (57/62) cellbender:remove-background: Working on chunk (58/62) cellbender:remove-background: Working on chunk (59/62) cellbender:remove-background: Working on chunk (60/62) cellbender:remove-background: Working on chunk (61/62) cellbender:remove-background: Working on chunk (62/62) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1556-Control-DLPFC/1556-Control-DLPFC.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/1556-Control-DLPFC/1556-Control-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:58:32 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1556-Control-DLPFC/1556-Control-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1556-Control-DLPFC/1556-Control-DLPFC.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: [1.51 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 16:09:35 Total MCKP estimation time = 628.34 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/1556-Control-DLPFC/1556-Control-DLPFC.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/1556-Control-DLPFC/1556-Control-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1556-Control-DLPFC/1556-Control-DLPFC.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/1556-Control-DLPFC/1556-Control-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:10:00