cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1436-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-DLPFC/1436-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 7945 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 00386d6b8d) cellbender:remove-background: 2024-06-06 15:42:51 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/1436-Schizophrenia-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: 31547 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2661 cellbender:remove-background: Prior on counts for empty droplets is 59 cellbender:remove-background: Excluding 8213 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23334 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 29 cellbender:remove-background: Using 7945 probable cell barcodes, plus an additional 12055 barcodes, and 45985 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 58 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp3ya292wc 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: 4991.4573 cellbender:remove-background: [epoch 002] average training loss: 3885.3616 (5.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 75 epochs cellbender:remove-background: [epoch 003] average training loss: 3344.6888 cellbender:remove-background: [epoch 004] average training loss: 3022.2207 cellbender:remove-background: [epoch 005] average training loss: 2932.0299 cellbender:remove-background: [epoch 005] average test loss: 3050.1273 cellbender:remove-background: [epoch 006] average training loss: 2890.8858 cellbender:remove-background: [epoch 007] average training loss: 2858.7448 cellbender:remove-background: [epoch 008] average training loss: 2823.7665 cellbender:remove-background: [epoch 009] average training loss: 2810.2986 cellbender:remove-background: [epoch 010] average training loss: 2689.7808 cellbender:remove-background: [epoch 010] average test loss: 2759.9820 cellbender:remove-background: [epoch 011] average training loss: 2603.3178 cellbender:remove-background: [epoch 012] average training loss: 2580.4464 cellbender:remove-background: [epoch 013] average training loss: 2558.5458 cellbender:remove-background: [epoch 014] average training loss: 2558.7406 cellbender:remove-background: [epoch 015] average training loss: 2532.6042 cellbender:remove-background: [epoch 015] average test loss: 2559.0343 cellbender:remove-background: [epoch 016] average training loss: 2519.7578 cellbender:remove-background: [epoch 017] average training loss: 2521.9857 cellbender:remove-background: [epoch 018] average training loss: 2516.4391 cellbender:remove-background: [epoch 019] average training loss: 2506.4465 cellbender:remove-background: [epoch 020] average training loss: 2493.3697 cellbender:remove-background: [epoch 020] average test loss: 2534.8585 cellbender:remove-background: [epoch 021] average training loss: 2493.1173 cellbender:remove-background: [epoch 022] average training loss: 2492.7050 cellbender:remove-background: [epoch 023] average training loss: 2489.6872 cellbender:remove-background: [epoch 024] average training loss: 2484.9594 cellbender:remove-background: [epoch 025] average training loss: 2485.2621 cellbender:remove-background: [epoch 025] average test loss: 2494.3078 cellbender:remove-background: [epoch 026] average training loss: 2473.9967 cellbender:remove-background: [epoch 027] average training loss: 2469.9415 cellbender:remove-background: [epoch 028] average training loss: 2464.8660 cellbender:remove-background: [epoch 029] average training loss: 2454.0297 cellbender:remove-background: [epoch 030] average training loss: 2441.2500 cellbender:remove-background: [epoch 030] average test loss: 2461.2191 cellbender:remove-background: [epoch 031] average training loss: 2433.2736 cellbender:remove-background: [epoch 032] average training loss: 2424.6601 cellbender:remove-background: [epoch 033] average training loss: 2420.1924 cellbender:remove-background: [epoch 034] average training loss: 2414.8402 cellbender:remove-background: [epoch 035] average training loss: 2412.1898 cellbender:remove-background: [epoch 035] average test loss: 2425.6775 cellbender:remove-background: [epoch 036] average training loss: 2412.4000 cellbender:remove-background: [epoch 037] average training loss: 2410.7857 cellbender:remove-background: [epoch 038] average training loss: 2408.2521 cellbender:remove-background: [epoch 039] average training loss: 2411.6408 cellbender:remove-background: [epoch 040] average training loss: 2411.2028 cellbender:remove-background: [epoch 040] average test loss: 2431.5249 cellbender:remove-background: [epoch 041] average training loss: 2415.5762 cellbender:remove-background: [epoch 042] average training loss: 2412.4247 cellbender:remove-background: [epoch 043] average training loss: 2404.4867 cellbender:remove-background: [epoch 044] average training loss: 2409.3494 cellbender:remove-background: [epoch 045] average training loss: 2407.9388 cellbender:remove-background: [epoch 045] average test loss: 2426.8168 cellbender:remove-background: [epoch 046] average training loss: 2403.5000 cellbender:remove-background: [epoch 047] average training loss: 2410.0039 cellbender:remove-background: [epoch 048] average training loss: 2403.0487 cellbender:remove-background: [epoch 049] average training loss: 2402.9480 cellbender:remove-background: [epoch 050] average training loss: 2402.7868 cellbender:remove-background: [epoch 050] average test loss: 2416.8117 cellbender:remove-background: [epoch 051] average training loss: 2402.4440 cellbender:remove-background: [epoch 052] average training loss: 2403.8623 cellbender:remove-background: [epoch 053] average training loss: 2400.3772 cellbender:remove-background: [epoch 054] average training loss: 2397.0165 cellbender:remove-background: [epoch 055] average training loss: 2398.1746 cellbender:remove-background: [epoch 055] average test loss: 2424.0205 cellbender:remove-background: [epoch 056] average training loss: 2397.6173 cellbender:remove-background: [epoch 057] average training loss: 2397.5064 cellbender:remove-background: [epoch 058] average training loss: 2396.5843 cellbender:remove-background: [epoch 059] average training loss: 2394.8540 cellbender:remove-background: [epoch 060] average training loss: 2395.2480 cellbender:remove-background: [epoch 060] average test loss: 2411.9349 cellbender:remove-background: [epoch 061] average training loss: 2393.0374 cellbender:remove-background: [epoch 062] average training loss: 2393.3348 cellbender:remove-background: [epoch 063] average training loss: 2394.4391 cellbender:remove-background: [epoch 064] average training loss: 2392.5571 cellbender:remove-background: [epoch 065] average training loss: 2391.9176 cellbender:remove-background: [epoch 065] average test loss: 2432.2538 cellbender:remove-background: [epoch 066] average training loss: 2392.4463 cellbender:remove-background: [epoch 067] average training loss: 2393.8851 cellbender:remove-background: [epoch 068] average training loss: 2393.4693 cellbender:remove-background: [epoch 069] average training loss: 2393.5226 cellbender:remove-background: [epoch 070] average training loss: 2392.4769 cellbender:remove-background: [epoch 070] average test loss: 2426.1224 cellbender:remove-background: [epoch 071] average training loss: 2391.3825 cellbender:remove-background: [epoch 072] average training loss: 2391.7617 cellbender:remove-background: [epoch 073] average training loss: 2388.8015 cellbender:remove-background: [epoch 074] average training loss: 2392.6975 cellbender:remove-background: [epoch 075] average training loss: 2390.8239 cellbender:remove-background: [epoch 075] average test loss: 2420.0850 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/1436-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 076] average training loss: 2393.1930 cellbender:remove-background: [epoch 077] average training loss: 2392.4242 cellbender:remove-background: [epoch 078] average training loss: 2388.9811 cellbender:remove-background: [epoch 079] average training loss: 2391.7242 cellbender:remove-background: [epoch 080] average training loss: 2394.7621 cellbender:remove-background: [epoch 080] average test loss: 2434.4307 cellbender:remove-background: [epoch 081] average training loss: 2392.9517 cellbender:remove-background: [epoch 082] average training loss: 2394.7105 cellbender:remove-background: [epoch 083] average training loss: 2394.1877 cellbender:remove-background: [epoch 084] average training loss: 2391.8262 cellbender:remove-background: [epoch 085] average training loss: 2392.4388 cellbender:remove-background: [epoch 085] average test loss: 2447.6520 cellbender:remove-background: [epoch 086] average training loss: 2393.7001 cellbender:remove-background: [epoch 087] average training loss: 2388.9450 cellbender:remove-background: [epoch 088] average training loss: 2389.8370 cellbender:remove-background: [epoch 089] average training loss: 2388.3362 cellbender:remove-background: [epoch 090] average training loss: 2389.0747 cellbender:remove-background: [epoch 090] average test loss: 2430.7489 cellbender:remove-background: [epoch 091] average training loss: 2387.2957 cellbender:remove-background: [epoch 092] average training loss: 2386.1238 cellbender:remove-background: [epoch 093] average training loss: 2386.0743 cellbender:remove-background: [epoch 094] average training loss: 2386.6641 cellbender:remove-background: [epoch 095] average training loss: 2384.8316 cellbender:remove-background: [epoch 095] average test loss: 2420.2257 cellbender:remove-background: [epoch 096] average training loss: 2384.8293 cellbender:remove-background: [epoch 097] average training loss: 2383.8779 cellbender:remove-background: [epoch 098] average training loss: 2384.8858 cellbender:remove-background: [epoch 099] average training loss: 2383.9193 cellbender:remove-background: [epoch 100] average training loss: 2381.9244 cellbender:remove-background: [epoch 100] average test loss: 2436.4272 cellbender:remove-background: [epoch 101] average training loss: 2385.4720 cellbender:remove-background: [epoch 102] average training loss: 2381.9743 cellbender:remove-background: [epoch 103] average training loss: 2380.7972 cellbender:remove-background: [epoch 104] average training loss: 2384.9417 cellbender:remove-background: [epoch 105] average training loss: 2382.1582 cellbender:remove-background: [epoch 105] average test loss: 2418.6017 cellbender:remove-background: [epoch 106] average training loss: 2381.7880 cellbender:remove-background: [epoch 107] average training loss: 2379.9318 cellbender:remove-background: [epoch 108] average training loss: 2380.6115 cellbender:remove-background: [epoch 109] average training loss: 2380.9763 cellbender:remove-background: [epoch 110] average training loss: 2379.9511 cellbender:remove-background: [epoch 110] average test loss: 2420.8335 cellbender:remove-background: [epoch 111] average training loss: 2381.6352 cellbender:remove-background: [epoch 112] average training loss: 2378.4059 cellbender:remove-background: [epoch 113] average training loss: 2380.1771 cellbender:remove-background: [epoch 114] average training loss: 2378.7565 cellbender:remove-background: [epoch 115] average training loss: 2377.4587 cellbender:remove-background: [epoch 115] average test loss: 2421.1001 cellbender:remove-background: [epoch 116] average training loss: 2378.7329 cellbender:remove-background: [epoch 117] average training loss: 2378.3279 cellbender:remove-background: [epoch 118] average training loss: 2375.9433 cellbender:remove-background: [epoch 119] average training loss: 2375.9527 cellbender:remove-background: [epoch 120] average training loss: 2376.0787 cellbender:remove-background: [epoch 120] average test loss: 2409.4427 cellbender:remove-background: [epoch 121] average training loss: 2374.0549 cellbender:remove-background: [epoch 122] average training loss: 2377.2751 cellbender:remove-background: [epoch 123] average training loss: 2375.9966 cellbender:remove-background: [epoch 124] average training loss: 2377.7170 cellbender:remove-background: [epoch 125] average training loss: 2374.7161 cellbender:remove-background: [epoch 125] average test loss: 2413.5986 cellbender:remove-background: [epoch 126] average training loss: 2376.0087 cellbender:remove-background: [epoch 127] average training loss: 2374.6357 cellbender:remove-background: [epoch 128] average training loss: 2377.4118 cellbender:remove-background: [epoch 129] average training loss: 2374.5567 cellbender:remove-background: [epoch 130] average training loss: 2375.9008 cellbender:remove-background: [epoch 130] average test loss: 2413.8720 cellbender:remove-background: [epoch 131] average training loss: 2373.1272 cellbender:remove-background: [epoch 132] average training loss: 2376.0379 cellbender:remove-background: [epoch 133] average training loss: 2375.9347 cellbender:remove-background: [epoch 134] average training loss: 2374.6617 cellbender:remove-background: [epoch 135] average training loss: 2374.7778 cellbender:remove-background: [epoch 135] average test loss: 2410.9726 cellbender:remove-background: [epoch 136] average training loss: 2373.9203 cellbender:remove-background: [epoch 137] average training loss: 2374.5028 cellbender:remove-background: [epoch 138] average training loss: 2374.9946 cellbender:remove-background: [epoch 139] average training loss: 2373.9299 cellbender:remove-background: [epoch 140] average training loss: 2375.4160 cellbender:remove-background: [epoch 140] average test loss: 2414.7619 cellbender:remove-background: [epoch 141] average training loss: 2374.2082 cellbender:remove-background: [epoch 142] average training loss: 2375.0384 cellbender:remove-background: [epoch 143] average training loss: 2372.8978 cellbender:remove-background: [epoch 144] average training loss: 2374.2350 cellbender:remove-background: [epoch 145] average training loss: 2374.2890 cellbender:remove-background: [epoch 145] average test loss: 2412.2505 cellbender:remove-background: [epoch 146] average training loss: 2374.1791 cellbender:remove-background: [epoch 147] average training loss: 2374.3880 cellbender:remove-background: [epoch 148] average training loss: 2373.9006 cellbender:remove-background: [epoch 149] average training loss: 2373.1886 cellbender:remove-background: [epoch 150] average training loss: 2373.5983 cellbender:remove-background: [epoch 150] average test loss: 2412.2134 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/1436-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:59:49 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpgck4ctvj cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpgck4ctvj /tmp/tmpgck4ctvj/00386d6b8d_random.pyro /tmp/tmpgck4ctvj/00386d6b8d_random.cuda /tmp/tmpgck4ctvj/00386d6b8d_model.torch /tmp/tmpgck4ctvj/00386d6b8d_optim.torch /tmp/tmpgck4ctvj/00386d6b8d_optim.pyro /tmp/tmpgck4ctvj/00386d6b8d_params.pyro /tmp/tmpgck4ctvj/00386d6b8d_train.loaderstate /tmp/tmpgck4ctvj/00386d6b8d_test.loaderstate /tmp/tmpgck4ctvj/00386d6b8d_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 (1/72) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/72) cellbender:remove-background: Working on chunk (3/72) cellbender:remove-background: Working on chunk (4/72) cellbender:remove-background: Working on chunk (5/72) cellbender:remove-background: Working on chunk (6/72) cellbender:remove-background: Working on chunk (7/72) cellbender:remove-background: Working on chunk (8/72) cellbender:remove-background: Working on chunk (9/72) cellbender:remove-background: Working on chunk (10/72) cellbender:remove-background: Working on chunk (11/72) cellbender:remove-background: Working on chunk (12/72) cellbender:remove-background: Working on chunk (13/72) cellbender:remove-background: Working on chunk (14/72) cellbender:remove-background: Working on chunk (15/72) cellbender:remove-background: Working on chunk (16/72) cellbender:remove-background: Working on chunk (17/72) cellbender:remove-background: Working on chunk (18/72) cellbender:remove-background: Working on chunk (19/72) cellbender:remove-background: Working on chunk (20/72) cellbender:remove-background: Working on chunk (21/72) cellbender:remove-background: Working on chunk (22/72) cellbender:remove-background: Working on chunk (23/72) cellbender:remove-background: Working on chunk (24/72) cellbender:remove-background: Working on chunk (25/72) cellbender:remove-background: Working on chunk (26/72) cellbender:remove-background: Working on chunk (27/72) cellbender:remove-background: Working on chunk (28/72) cellbender:remove-background: Working on chunk (29/72) cellbender:remove-background: Working on chunk (30/72) cellbender:remove-background: Working on chunk (31/72) cellbender:remove-background: Working on chunk (32/72) cellbender:remove-background: Working on chunk (33/72) cellbender:remove-background: Working on chunk (34/72) cellbender:remove-background: Working on chunk (35/72) cellbender:remove-background: Working on chunk (36/72) cellbender:remove-background: Working on chunk (37/72) cellbender:remove-background: Working on chunk (38/72) cellbender:remove-background: Working on chunk (39/72) cellbender:remove-background: Working on chunk (40/72) cellbender:remove-background: Working on chunk (41/72) cellbender:remove-background: Working on chunk (42/72) cellbender:remove-background: Working on chunk (43/72) cellbender:remove-background: Working on chunk (44/72) cellbender:remove-background: Working on chunk (45/72) cellbender:remove-background: Working on chunk (46/72) cellbender:remove-background: Working on chunk (47/72) cellbender:remove-background: Working on chunk (48/72) cellbender:remove-background: Working on chunk (49/72) cellbender:remove-background: Working on chunk (50/72) cellbender:remove-background: Working on chunk (51/72) cellbender:remove-background: Working on chunk (52/72) cellbender:remove-background: Working on chunk (53/72) cellbender:remove-background: Working on chunk (54/72) cellbender:remove-background: Working on chunk (55/72) cellbender:remove-background: Working on chunk (56/72) cellbender:remove-background: Working on chunk (57/72) cellbender:remove-background: Working on chunk (58/72) cellbender:remove-background: Working on chunk (59/72) cellbender:remove-background: Working on chunk (60/72) cellbender:remove-background: Working on chunk (61/72) cellbender:remove-background: Working on chunk (62/72) cellbender:remove-background: Working on chunk (63/72) cellbender:remove-background: Working on chunk (64/72) cellbender:remove-background: Working on chunk (65/72) cellbender:remove-background: Working on chunk (66/72) cellbender:remove-background: Working on chunk (67/72) cellbender:remove-background: Working on chunk (68/72) cellbender:remove-background: Working on chunk (69/72) cellbender:remove-background: Working on chunk (70/72) cellbender:remove-background: Working on chunk (71/72) cellbender:remove-background: Working on chunk (72/72) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-DLPFC/1436-Schizophrenia-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/1436-Schizophrenia-DLPFC/1436-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:03:48 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-DLPFC/1436-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-DLPFC/1436-Schizophrenia-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: [1.36 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 16:13:47 Total MCKP estimation time = 574.85 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/1436-Schizophrenia-DLPFC/1436-Schizophrenia-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/1436-Schizophrenia-DLPFC/1436-Schizophrenia-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/1436-Schizophrenia-DLPFC/1436-Schizophrenia-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/1436-Schizophrenia-DLPFC/1436-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:14:04