cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2337-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 8640 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 5596b9b5ea) cellbender:remove-background: 2024-06-06 15:20:32 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/2337-Schizophrenia-dACC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 31954 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1703 cellbender:remove-background: Prior on counts for empty droplets is 95 cellbender:remove-background: Excluding 6105 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 25849 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 47 cellbender:remove-background: Using 8640 probable cell barcodes, plus an additional 11360 barcodes, and 48513 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 94 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp142c7nrn 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: 4464.5110 cellbender:remove-background: [epoch 002] average training loss: 3621.9272 (7.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 59 epochs cellbender:remove-background: [epoch 003] average training loss: 3108.6341 cellbender:remove-background: [epoch 004] average training loss: 2806.6035 cellbender:remove-background: [epoch 005] average training loss: 2699.8286 cellbender:remove-background: [epoch 005] average test loss: 2735.3198 cellbender:remove-background: [epoch 006] average training loss: 2662.6862 cellbender:remove-background: [epoch 007] average training loss: 2623.4850 cellbender:remove-background: [epoch 008] average training loss: 2605.2930 cellbender:remove-background: [epoch 009] average training loss: 2598.4902 cellbender:remove-background: [epoch 010] average training loss: 2576.4152 cellbender:remove-background: [epoch 010] average test loss: 2542.3869 cellbender:remove-background: [epoch 011] average training loss: 2534.0343 cellbender:remove-background: [epoch 012] average training loss: 2480.1319 cellbender:remove-background: [epoch 013] average training loss: 2458.6445 cellbender:remove-background: [epoch 014] average training loss: 2462.3259 cellbender:remove-background: [epoch 015] average training loss: 2445.7584 cellbender:remove-background: [epoch 015] average test loss: 2443.4696 cellbender:remove-background: [epoch 016] average training loss: 2436.4735 cellbender:remove-background: [epoch 017] average training loss: 2438.5804 cellbender:remove-background: [epoch 018] average training loss: 2433.2562 cellbender:remove-background: [epoch 019] average training loss: 2423.3177 cellbender:remove-background: [epoch 020] average training loss: 2408.0807 cellbender:remove-background: [epoch 020] average test loss: 2420.9637 cellbender:remove-background: [epoch 021] average training loss: 2408.0671 cellbender:remove-background: [epoch 022] average training loss: 2405.8056 cellbender:remove-background: [epoch 023] average training loss: 2399.9182 cellbender:remove-background: [epoch 024] average training loss: 2380.2846 cellbender:remove-background: [epoch 025] average training loss: 2364.0425 cellbender:remove-background: [epoch 025] average test loss: 2344.5149 cellbender:remove-background: [epoch 026] average training loss: 2344.3576 cellbender:remove-background: [epoch 027] average training loss: 2335.7624 cellbender:remove-background: [epoch 028] average training loss: 2332.4284 cellbender:remove-background: [epoch 029] average training loss: 2327.0792 cellbender:remove-background: [epoch 030] average training loss: 2323.8936 cellbender:remove-background: [epoch 030] average test loss: 2302.2080 cellbender:remove-background: [epoch 031] average training loss: 2317.9884 cellbender:remove-background: [epoch 032] average training loss: 2316.9869 cellbender:remove-background: [epoch 033] average training loss: 2317.3596 cellbender:remove-background: [epoch 034] average training loss: 2314.5655 cellbender:remove-background: [epoch 035] average training loss: 2311.8490 cellbender:remove-background: [epoch 035] average test loss: 2293.2230 cellbender:remove-background: [epoch 036] average training loss: 2310.5769 cellbender:remove-background: [epoch 037] average training loss: 2308.3782 cellbender:remove-background: [epoch 038] average training loss: 2307.2865 cellbender:remove-background: [epoch 039] average training loss: 2305.5338 cellbender:remove-background: [epoch 040] average training loss: 2303.7957 cellbender:remove-background: [epoch 040] average test loss: 2280.4090 cellbender:remove-background: [epoch 041] average training loss: 2302.1859 cellbender:remove-background: [epoch 042] average training loss: 2299.0445 cellbender:remove-background: [epoch 043] average training loss: 2300.5641 cellbender:remove-background: [epoch 044] average training loss: 2298.3388 cellbender:remove-background: [epoch 045] average training loss: 2297.4327 cellbender:remove-background: [epoch 045] average test loss: 2286.2916 cellbender:remove-background: [epoch 046] average training loss: 2296.4497 cellbender:remove-background: [epoch 047] average training loss: 2294.6794 cellbender:remove-background: [epoch 048] average training loss: 2292.2832 cellbender:remove-background: [epoch 049] average training loss: 2292.9451 cellbender:remove-background: [epoch 050] average training loss: 2292.4771 cellbender:remove-background: [epoch 050] average test loss: 2292.6396 cellbender:remove-background: [epoch 051] average training loss: 2290.6040 cellbender:remove-background: [epoch 052] average training loss: 2291.5170 cellbender:remove-background: [epoch 053] average training loss: 2289.5544 cellbender:remove-background: [epoch 054] average training loss: 2288.2390 cellbender:remove-background: [epoch 055] average training loss: 2287.2959 cellbender:remove-background: [epoch 055] average test loss: 2266.4701 cellbender:remove-background: [epoch 056] average training loss: 2285.5991 cellbender:remove-background: [epoch 057] average training loss: 2284.7166 cellbender:remove-background: [epoch 058] average training loss: 2288.3170 cellbender:remove-background: [epoch 059] average training loss: 2290.1289 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/2337-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 060] average training loss: 2287.6344 cellbender:remove-background: [epoch 060] average test loss: 2283.2095 cellbender:remove-background: [epoch 061] average training loss: 2288.9783 cellbender:remove-background: [epoch 062] average training loss: 2287.0938 cellbender:remove-background: [epoch 063] average training loss: 2287.4000 cellbender:remove-background: [epoch 064] average training loss: 2288.5253 cellbender:remove-background: [epoch 065] average training loss: 2285.6322 cellbender:remove-background: [epoch 065] average test loss: 2287.7658 cellbender:remove-background: [epoch 066] average training loss: 2287.5633 cellbender:remove-background: [epoch 067] average training loss: 2284.8846 cellbender:remove-background: [epoch 068] average training loss: 2286.2619 cellbender:remove-background: [epoch 069] average training loss: 2284.4711 cellbender:remove-background: [epoch 070] average training loss: 2288.0463 cellbender:remove-background: [epoch 070] average test loss: 2289.4420 cellbender:remove-background: [epoch 071] average training loss: 2287.1145 cellbender:remove-background: [epoch 072] average training loss: 2284.2579 cellbender:remove-background: [epoch 073] average training loss: 2287.3390 cellbender:remove-background: [epoch 074] average training loss: 2286.0039 cellbender:remove-background: [epoch 075] average training loss: 2286.2565 cellbender:remove-background: [epoch 075] average test loss: 2287.4092 cellbender:remove-background: [epoch 076] average training loss: 2285.0539 cellbender:remove-background: [epoch 077] average training loss: 2282.1024 cellbender:remove-background: [epoch 078] average training loss: 2283.9001 cellbender:remove-background: [epoch 079] average training loss: 2282.7361 cellbender:remove-background: [epoch 080] average training loss: 2283.7154 cellbender:remove-background: [epoch 080] average test loss: 2276.7130 cellbender:remove-background: [epoch 081] average training loss: 2283.3237 cellbender:remove-background: [epoch 082] average training loss: 2288.1966 cellbender:remove-background: [epoch 083] average training loss: 2288.5254 cellbender:remove-background: [epoch 084] average training loss: 2287.6404 cellbender:remove-background: [epoch 085] average training loss: 2286.3252 cellbender:remove-background: [epoch 085] average test loss: 2283.9522 cellbender:remove-background: [epoch 086] average training loss: 2283.7521 cellbender:remove-background: [epoch 087] average training loss: 2286.2062 cellbender:remove-background: [epoch 088] average training loss: 2288.1253 cellbender:remove-background: [epoch 089] average training loss: 2287.1820 cellbender:remove-background: [epoch 090] average training loss: 2282.7389 cellbender:remove-background: [epoch 090] average test loss: 2291.2463 cellbender:remove-background: [epoch 091] average training loss: 2286.6116 cellbender:remove-background: [epoch 092] average training loss: 2286.3417 cellbender:remove-background: [epoch 093] average training loss: 2286.1268 cellbender:remove-background: [epoch 094] average training loss: 2287.1215 cellbender:remove-background: [epoch 095] average training loss: 2287.6105 cellbender:remove-background: [epoch 095] average test loss: 2292.9443 cellbender:remove-background: [epoch 096] average training loss: 2283.2854 cellbender:remove-background: [epoch 097] average training loss: 2287.0316 cellbender:remove-background: [epoch 098] average training loss: 2284.2777 cellbender:remove-background: [epoch 099] average training loss: 2286.5117 cellbender:remove-background: [epoch 100] average training loss: 2286.7835 cellbender:remove-background: [epoch 100] average test loss: 2302.0316 cellbender:remove-background: [epoch 101] average training loss: 2284.4895 cellbender:remove-background: [epoch 102] average training loss: 2283.9096 cellbender:remove-background: [epoch 103] average training loss: 2283.9932 cellbender:remove-background: [epoch 104] average training loss: 2283.0136 cellbender:remove-background: [epoch 105] average training loss: 2283.6077 cellbender:remove-background: [epoch 105] average test loss: 2306.3167 cellbender:remove-background: [epoch 106] average training loss: 2279.8425 cellbender:remove-background: [epoch 107] average training loss: 2283.9608 cellbender:remove-background: [epoch 108] average training loss: 2282.2925 cellbender:remove-background: [epoch 109] average training loss: 2282.5831 cellbender:remove-background: [epoch 110] average training loss: 2283.1895 cellbender:remove-background: [epoch 110] average test loss: 2299.0232 cellbender:remove-background: [epoch 111] average training loss: 2281.8604 cellbender:remove-background: [epoch 112] average training loss: 2286.2260 cellbender:remove-background: [epoch 113] average training loss: 2283.0753 cellbender:remove-background: [epoch 114] average training loss: 2281.3749 cellbender:remove-background: [epoch 115] average training loss: 2284.5120 cellbender:remove-background: [epoch 115] average test loss: 2300.0121 cellbender:remove-background: [epoch 116] average training loss: 2281.7678 cellbender:remove-background: [epoch 117] average training loss: 2285.1675 cellbender:remove-background: [epoch 118] average training loss: 2278.1007 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/2337-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 119] average training loss: 2283.7048 cellbender:remove-background: [epoch 120] average training loss: 2282.1401 cellbender:remove-background: [epoch 120] average test loss: 2292.8573 cellbender:remove-background: [epoch 121] average training loss: 2279.8506 cellbender:remove-background: [epoch 122] average training loss: 2282.5846 cellbender:remove-background: [epoch 123] average training loss: 2280.1739 cellbender:remove-background: [epoch 124] average training loss: 2282.3894 cellbender:remove-background: [epoch 125] average training loss: 2279.3683 cellbender:remove-background: [epoch 125] average test loss: 2306.7473 cellbender:remove-background: [epoch 126] average training loss: 2280.7887 cellbender:remove-background: [epoch 127] average training loss: 2278.8215 cellbender:remove-background: [epoch 128] average training loss: 2279.6773 cellbender:remove-background: [epoch 129] average training loss: 2283.7744 cellbender:remove-background: [epoch 130] average training loss: 2281.1104 cellbender:remove-background: [epoch 130] average test loss: 2304.3991 cellbender:remove-background: [epoch 131] average training loss: 2279.5845 cellbender:remove-background: [epoch 132] average training loss: 2282.3100 cellbender:remove-background: [epoch 133] average training loss: 2278.1913 cellbender:remove-background: [epoch 134] average training loss: 2281.9276 cellbender:remove-background: [epoch 135] average training loss: 2281.5731 cellbender:remove-background: [epoch 135] average test loss: 2318.5065 cellbender:remove-background: [epoch 136] average training loss: 2282.3388 cellbender:remove-background: [epoch 137] average training loss: 2281.6327 cellbender:remove-background: [epoch 138] average training loss: 2279.5894 cellbender:remove-background: [epoch 139] average training loss: 2281.9701 cellbender:remove-background: [epoch 140] average training loss: 2281.6823 cellbender:remove-background: [epoch 140] average test loss: 2304.9490 cellbender:remove-background: [epoch 141] average training loss: 2280.7064 cellbender:remove-background: [epoch 142] average training loss: 2279.7639 cellbender:remove-background: [epoch 143] average training loss: 2281.6561 cellbender:remove-background: [epoch 144] average training loss: 2279.0656 cellbender:remove-background: [epoch 145] average training loss: 2280.4783 cellbender:remove-background: [epoch 145] average test loss: 2305.5436 cellbender:remove-background: [epoch 146] average training loss: 2279.9490 cellbender:remove-background: [epoch 147] average training loss: 2279.8140 cellbender:remove-background: [epoch 148] average training loss: 2279.8161 cellbender:remove-background: [epoch 149] average training loss: 2278.7829 cellbender:remove-background: [epoch 150] average training loss: 2279.3456 cellbender:remove-background: [epoch 150] average test loss: 2306.8656 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/2337-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:42:00 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpytqi8trk cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpytqi8trk /tmp/tmpytqi8trk/5596b9b5ea_random.pyro /tmp/tmpytqi8trk/5596b9b5ea_random.cuda /tmp/tmpytqi8trk/5596b9b5ea_model.torch /tmp/tmpytqi8trk/5596b9b5ea_optim.torch /tmp/tmpytqi8trk/5596b9b5ea_optim.pyro /tmp/tmpytqi8trk/5596b9b5ea_params.pyro /tmp/tmpytqi8trk/5596b9b5ea_train.loaderstate /tmp/tmpytqi8trk/5596b9b5ea_test.loaderstate /tmp/tmpytqi8trk/5596b9b5ea_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 (1/63) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/63) cellbender:remove-background: Working on chunk (3/63) cellbender:remove-background: Working on chunk (4/63) cellbender:remove-background: Working on chunk (5/63) cellbender:remove-background: Working on chunk (6/63) cellbender:remove-background: Working on chunk (7/63) cellbender:remove-background: Working on chunk (8/63) cellbender:remove-background: Working on chunk (9/63) cellbender:remove-background: Working on chunk (10/63) cellbender:remove-background: Working on chunk (11/63) cellbender:remove-background: Working on chunk (12/63) cellbender:remove-background: Working on chunk (13/63) cellbender:remove-background: Working on chunk (14/63) cellbender:remove-background: Working on chunk (15/63) cellbender:remove-background: Working on chunk (16/63) cellbender:remove-background: Working on chunk (17/63) cellbender:remove-background: Working on chunk (18/63) cellbender:remove-background: Working on chunk (19/63) cellbender:remove-background: Working on chunk (20/63) cellbender:remove-background: Working on chunk (21/63) cellbender:remove-background: Working on chunk (22/63) cellbender:remove-background: Working on chunk (23/63) cellbender:remove-background: Working on chunk (24/63) cellbender:remove-background: Working on chunk (25/63) cellbender:remove-background: Working on chunk (26/63) cellbender:remove-background: Working on chunk (27/63) cellbender:remove-background: Working on chunk (28/63) cellbender:remove-background: Working on chunk (29/63) cellbender:remove-background: Working on chunk (30/63) cellbender:remove-background: Working on chunk (31/63) cellbender:remove-background: Working on chunk (32/63) cellbender:remove-background: Working on chunk (33/63) cellbender:remove-background: Working on chunk (34/63) cellbender:remove-background: Working on chunk (35/63) cellbender:remove-background: Working on chunk (36/63) cellbender:remove-background: Working on chunk (37/63) cellbender:remove-background: Working on chunk (38/63) cellbender:remove-background: Working on chunk (39/63) cellbender:remove-background: Working on chunk (40/63) cellbender:remove-background: Working on chunk (41/63) cellbender:remove-background: Working on chunk (42/63) cellbender:remove-background: Working on chunk (43/63) cellbender:remove-background: Working on chunk (44/63) cellbender:remove-background: Working on chunk (45/63) cellbender:remove-background: Working on chunk (46/63) cellbender:remove-background: Working on chunk (47/63) cellbender:remove-background: Working on chunk (48/63) cellbender:remove-background: Working on chunk (49/63) cellbender:remove-background: Working on chunk (50/63) cellbender:remove-background: Working on chunk (51/63) cellbender:remove-background: Working on chunk (52/63) cellbender:remove-background: Working on chunk (53/63) cellbender:remove-background: Working on chunk (54/63) cellbender:remove-background: Working on chunk (55/63) cellbender:remove-background: Working on chunk (56/63) cellbender:remove-background: Working on chunk (57/63) cellbender:remove-background: Working on chunk (58/63) cellbender:remove-background: Working on chunk (59/63) cellbender:remove-background: Working on chunk (60/63) cellbender:remove-background: Working on chunk (61/63) cellbender:remove-background: Working on chunk (62/63) cellbender:remove-background: Working on chunk (63/63) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:46:06 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.03 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 15:53:37 Total MCKP estimation time = 431.75 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/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-dACC/2337-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:53:51