cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1436-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-Hippocampus/1436-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 4389 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 87479e879e) cellbender:remove-background: 2024-06-06 15:31:45 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-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: 32300 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 8659 cellbender:remove-background: Prior on counts for empty droplets is 50 cellbender:remove-background: Excluding 12410 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19890 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 25 cellbender:remove-background: Using 4389 probable cell barcodes, plus an additional 15611 barcodes, and 50245 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 49 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpl4hpepnz 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: 7044.6391 cellbender:remove-background: [epoch 002] average training loss: 4515.7280 (4.7 seconds per epoch) cellbender:remove-background: Will checkpoint every 90 epochs cellbender:remove-background: [epoch 003] average training loss: 3593.2856 cellbender:remove-background: [epoch 004] average training loss: 3187.0585 cellbender:remove-background: [epoch 005] average training loss: 3111.4916 cellbender:remove-background: [epoch 005] average test loss: 3345.0991 cellbender:remove-background: [epoch 006] average training loss: 3100.5795 cellbender:remove-background: [epoch 007] average training loss: 3030.2626 cellbender:remove-background: [epoch 008] average training loss: 2981.2874 cellbender:remove-background: [epoch 009] average training loss: 2961.3721 cellbender:remove-background: [epoch 010] average training loss: 2847.6728 cellbender:remove-background: [epoch 010] average test loss: 2828.1226 cellbender:remove-background: [epoch 011] average training loss: 2786.3549 cellbender:remove-background: [epoch 012] average training loss: 2725.1742 cellbender:remove-background: [epoch 013] average training loss: 2651.3987 cellbender:remove-background: [epoch 014] average training loss: 2620.5674 cellbender:remove-background: [epoch 015] average training loss: 2583.6661 cellbender:remove-background: [epoch 015] average test loss: 2625.7367 cellbender:remove-background: [epoch 016] average training loss: 2567.9902 cellbender:remove-background: [epoch 017] average training loss: 2567.7539 cellbender:remove-background: [epoch 018] average training loss: 2536.1021 cellbender:remove-background: [epoch 019] average training loss: 2507.9565 cellbender:remove-background: [epoch 020] average training loss: 2486.4739 cellbender:remove-background: [epoch 020] average test loss: 2572.9653 cellbender:remove-background: [epoch 021] average training loss: 2475.0985 cellbender:remove-background: [epoch 022] average training loss: 2470.2660 cellbender:remove-background: [epoch 023] average training loss: 2464.6004 cellbender:remove-background: [epoch 024] average training loss: 2450.7146 cellbender:remove-background: [epoch 025] average training loss: 2441.9068 cellbender:remove-background: [epoch 025] average test loss: 2481.9179 cellbender:remove-background: [epoch 026] average training loss: 2431.9997 cellbender:remove-background: [epoch 027] average training loss: 2427.1646 cellbender:remove-background: [epoch 028] average training loss: 2422.0856 cellbender:remove-background: [epoch 029] average training loss: 2415.2254 cellbender:remove-background: [epoch 030] average training loss: 2413.1552 cellbender:remove-background: [epoch 030] average test loss: 2433.0545 cellbender:remove-background: [epoch 031] average training loss: 2411.3113 cellbender:remove-background: [epoch 032] average training loss: 2406.9490 cellbender:remove-background: [epoch 033] average training loss: 2401.6872 cellbender:remove-background: [epoch 034] average training loss: 2402.5344 cellbender:remove-background: [epoch 035] average training loss: 2410.0175 cellbender:remove-background: [epoch 035] average test loss: 2479.9979 cellbender:remove-background: [epoch 036] average training loss: 2399.8049 cellbender:remove-background: [epoch 037] average training loss: 2394.0167 cellbender:remove-background: [epoch 038] average training loss: 2394.3859 cellbender:remove-background: [epoch 039] average training loss: 2397.1090 cellbender:remove-background: [epoch 040] average training loss: 2390.2247 cellbender:remove-background: [epoch 040] average test loss: 2414.3854 cellbender:remove-background: [epoch 041] average training loss: 2397.0280 cellbender:remove-background: [epoch 042] average training loss: 2388.8197 cellbender:remove-background: [epoch 043] average training loss: 2392.9041 cellbender:remove-background: [epoch 044] average training loss: 2401.3687 cellbender:remove-background: [epoch 045] average training loss: 2388.0243 cellbender:remove-background: [epoch 045] average test loss: 2398.4256 cellbender:remove-background: [epoch 046] average training loss: 2388.2126 cellbender:remove-background: [epoch 047] average training loss: 2387.8792 cellbender:remove-background: [epoch 048] average training loss: 2387.6562 cellbender:remove-background: [epoch 049] average training loss: 2384.1966 cellbender:remove-background: [epoch 050] average training loss: 2384.3181 cellbender:remove-background: [epoch 050] average test loss: 2404.0485 cellbender:remove-background: [epoch 051] average training loss: 2384.5869 cellbender:remove-background: [epoch 052] average training loss: 2382.1900 cellbender:remove-background: [epoch 053] average training loss: 2385.2403 cellbender:remove-background: [epoch 054] average training loss: 2383.7476 cellbender:remove-background: [epoch 055] average training loss: 2382.7256 cellbender:remove-background: [epoch 055] average test loss: 2388.2564 cellbender:remove-background: [epoch 056] average training loss: 2386.5640 cellbender:remove-background: [epoch 057] average training loss: 2383.7472 cellbender:remove-background: [epoch 058] average training loss: 2386.8988 cellbender:remove-background: [epoch 059] average training loss: 2385.3642 cellbender:remove-background: [epoch 060] average training loss: 2387.4025 cellbender:remove-background: [epoch 060] average test loss: 2408.4527 cellbender:remove-background: [epoch 061] average training loss: 2389.1589 cellbender:remove-background: [epoch 062] average training loss: 2391.2793 cellbender:remove-background: [epoch 063] average training loss: 2388.0765 cellbender:remove-background: [epoch 064] average training loss: 2390.0222 cellbender:remove-background: [epoch 065] average training loss: 2394.1136 cellbender:remove-background: [epoch 065] average test loss: 2423.2597 cellbender:remove-background: [epoch 066] average training loss: 2395.8459 cellbender:remove-background: [epoch 067] average training loss: 2399.9583 cellbender:remove-background: [epoch 068] average training loss: 2394.9491 cellbender:remove-background: [epoch 069] average training loss: 2412.6908 cellbender:remove-background: [epoch 070] average training loss: 2394.3835 cellbender:remove-background: [epoch 070] average test loss: 2408.1477 cellbender:remove-background: [epoch 071] average training loss: 2393.1993 cellbender:remove-background: [epoch 072] average training loss: 2395.4233 cellbender:remove-background: [epoch 073] average training loss: 2401.7009 cellbender:remove-background: [epoch 074] average training loss: 2393.9491 cellbender:remove-background: [epoch 075] average training loss: 2397.8816 cellbender:remove-background: [epoch 075] average test loss: 2434.3734 cellbender:remove-background: [epoch 076] average training loss: 2404.6169 cellbender:remove-background: [epoch 077] average training loss: 2400.4234 cellbender:remove-background: [epoch 078] average training loss: 2406.3413 cellbender:remove-background: [epoch 079] average training loss: 2404.3751 cellbender:remove-background: [epoch 080] average training loss: 2398.2855 cellbender:remove-background: [epoch 080] average test loss: 2440.8353 cellbender:remove-background: [epoch 081] average training loss: 2399.7201 cellbender:remove-background: [epoch 082] average training loss: 2399.5149 cellbender:remove-background: [epoch 083] average training loss: 2401.4581 cellbender:remove-background: [epoch 084] average training loss: 2438.0807 cellbender:remove-background: [epoch 085] average training loss: 2405.4409 cellbender:remove-background: [epoch 085] average test loss: 2478.6736 cellbender:remove-background: [epoch 086] average training loss: 2412.7916 cellbender:remove-background: [epoch 087] average training loss: 2404.8034 cellbender:remove-background: [epoch 088] average training loss: 2426.9471 cellbender:remove-background: [epoch 089] average training loss: 2418.0209 cellbender:remove-background: [epoch 090] average training loss: 2394.9223 cellbender:remove-background: [epoch 090] average test loss: 2451.1745 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-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 091] average training loss: 2400.0957 cellbender:remove-background: [epoch 092] average training loss: 2406.6611 cellbender:remove-background: [epoch 093] average training loss: 2397.3380 cellbender:remove-background: [epoch 094] average training loss: 2408.5622 cellbender:remove-background: [epoch 095] average training loss: 2456.5281 cellbender:remove-background: [epoch 095] average test loss: 2439.4733 cellbender:remove-background: [epoch 096] average training loss: 2414.2524 cellbender:remove-background: [epoch 097] average training loss: 2420.5641 cellbender:remove-background: [epoch 098] average training loss: 2406.7609 cellbender:remove-background: [epoch 099] average training loss: 2424.5727 cellbender:remove-background: [epoch 100] average training loss: 2405.7877 cellbender:remove-background: [epoch 100] average test loss: 2427.1781 cellbender:remove-background: [epoch 101] average training loss: 2408.6856 cellbender:remove-background: [epoch 102] average training loss: 2409.5232 cellbender:remove-background: [epoch 103] average training loss: 2400.9169 cellbender:remove-background: [epoch 104] average training loss: 2405.3594 cellbender:remove-background: [epoch 105] average training loss: 2414.9448 cellbender:remove-background: [epoch 105] average test loss: 2450.7438 cellbender:remove-background: [epoch 106] average training loss: 2400.7355 cellbender:remove-background: [epoch 107] average training loss: 2405.5703 cellbender:remove-background: [epoch 108] average training loss: 2411.2299 cellbender:remove-background: [epoch 109] average training loss: 2417.6123 cellbender:remove-background: [epoch 110] average training loss: 2399.5380 cellbender:remove-background: [epoch 110] average test loss: 2449.8295 cellbender:remove-background: [epoch 111] average training loss: 2419.9271 cellbender:remove-background: [epoch 112] average training loss: 2400.3194 cellbender:remove-background: [epoch 113] average training loss: 2399.7324 cellbender:remove-background: [epoch 114] average training loss: 2402.0675 cellbender:remove-background: [epoch 115] average training loss: 2415.2874 cellbender:remove-background: [epoch 115] average test loss: 2426.4489 cellbender:remove-background: [epoch 116] average training loss: 2402.6805 cellbender:remove-background: [epoch 117] average training loss: 2399.4035 cellbender:remove-background: [epoch 118] average training loss: 2400.2478 cellbender:remove-background: [epoch 119] average training loss: 2397.4983 cellbender:remove-background: [epoch 120] average training loss: 2396.2891 cellbender:remove-background: [epoch 120] average test loss: 2468.7022 cellbender:remove-background: [epoch 121] average training loss: 2393.3647 cellbender:remove-background: [epoch 122] average training loss: 2395.4412 cellbender:remove-background: [epoch 123] average training loss: 2408.3313 cellbender:remove-background: [epoch 124] average training loss: 2394.8973 cellbender:remove-background: [epoch 125] average training loss: 2398.0089 cellbender:remove-background: [epoch 125] average test loss: 2485.2262 cellbender:remove-background: [epoch 126] average training loss: 2394.0663 cellbender:remove-background: [epoch 127] average training loss: 2396.5443 cellbender:remove-background: [epoch 128] average training loss: 2399.1502 cellbender:remove-background: [epoch 129] average training loss: 2399.3364 cellbender:remove-background: [epoch 130] average training loss: 2395.5145 cellbender:remove-background: [epoch 130] average test loss: 2448.1863 cellbender:remove-background: [epoch 131] average training loss: 2404.9374 cellbender:remove-background: [epoch 132] average training loss: 2398.5679 cellbender:remove-background: [epoch 133] average training loss: 2392.4387 cellbender:remove-background: [epoch 134] average training loss: 2394.9522 cellbender:remove-background: [epoch 135] average training loss: 2393.7737 cellbender:remove-background: [epoch 135] average test loss: 2435.2354 cellbender:remove-background: [epoch 136] average training loss: 2393.6291 cellbender:remove-background: [epoch 137] average training loss: 2389.7311 cellbender:remove-background: [epoch 138] average training loss: 2393.8318 cellbender:remove-background: [epoch 139] average training loss: 2394.0344 cellbender:remove-background: [epoch 140] average training loss: 2393.2938 cellbender:remove-background: [epoch 140] average test loss: 2447.5903 cellbender:remove-background: [epoch 141] average training loss: 2391.4891 cellbender:remove-background: [epoch 142] average training loss: 2393.2094 cellbender:remove-background: [epoch 143] average training loss: 2392.4051 cellbender:remove-background: [epoch 144] average training loss: 2395.8344 cellbender:remove-background: [epoch 145] average training loss: 2391.6326 cellbender:remove-background: [epoch 145] average test loss: 2446.7031 cellbender:remove-background: [epoch 146] average training loss: 2396.3731 cellbender:remove-background: [epoch 147] average training loss: 2395.5017 cellbender:remove-background: [epoch 148] average training loss: 2395.7545 cellbender:remove-background: [epoch 149] average training loss: 2392.2360 cellbender:remove-background: [epoch 150] average training loss: 2398.2438 cellbender:remove-background: [epoch 150] average test loss: 2445.0940 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-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:45:38 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_1bf37pr cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_1bf37pr /tmp/tmp_1bf37pr/87479e879e_random.pyro /tmp/tmp_1bf37pr/87479e879e_random.cuda /tmp/tmp_1bf37pr/87479e879e_model.torch /tmp/tmp_1bf37pr/87479e879e_optim.torch /tmp/tmp_1bf37pr/87479e879e_optim.pyro /tmp/tmp_1bf37pr/87479e879e_params.pyro /tmp/tmp_1bf37pr/87479e879e_train.loaderstate /tmp/tmp_1bf37pr/87479e879e_test.loaderstate /tmp/tmp_1bf37pr/87479e879e_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 (1/46) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/46) cellbender:remove-background: Working on chunk (3/46) cellbender:remove-background: Working on chunk (4/46) cellbender:remove-background: Working on chunk (5/46) cellbender:remove-background: Working on chunk (6/46) cellbender:remove-background: Working on chunk (7/46) cellbender:remove-background: Working on chunk (8/46) cellbender:remove-background: Working on chunk (9/46) cellbender:remove-background: Working on chunk (10/46) cellbender:remove-background: Working on chunk (11/46) cellbender:remove-background: Working on chunk (12/46) cellbender:remove-background: Working on chunk (13/46) cellbender:remove-background: Working on chunk (14/46) cellbender:remove-background: Working on chunk (15/46) cellbender:remove-background: Working on chunk (16/46) cellbender:remove-background: Working on chunk (17/46) cellbender:remove-background: Working on chunk (18/46) cellbender:remove-background: Working on chunk (19/46) cellbender:remove-background: Working on chunk (20/46) cellbender:remove-background: Working on chunk (21/46) cellbender:remove-background: Working on chunk (22/46) cellbender:remove-background: Working on chunk (23/46) cellbender:remove-background: Working on chunk (24/46) cellbender:remove-background: Working on chunk (25/46) cellbender:remove-background: Working on chunk (26/46) cellbender:remove-background: Working on chunk (27/46) cellbender:remove-background: Working on chunk (28/46) cellbender:remove-background: Working on chunk (29/46) cellbender:remove-background: Working on chunk (30/46) cellbender:remove-background: Working on chunk (31/46) cellbender:remove-background: Working on chunk (32/46) cellbender:remove-background: Working on chunk (33/46) cellbender:remove-background: Working on chunk (34/46) cellbender:remove-background: Working on chunk (35/46) cellbender:remove-background: Working on chunk (36/46) cellbender:remove-background: Working on chunk (37/46) cellbender:remove-background: Working on chunk (38/46) cellbender:remove-background: Working on chunk (39/46) cellbender:remove-background: Working on chunk (40/46) cellbender:remove-background: Working on chunk (41/46) cellbender:remove-background: Working on chunk (42/46) cellbender:remove-background: Working on chunk (43/46) cellbender:remove-background: Working on chunk (44/46) cellbender:remove-background: Working on chunk (45/46) cellbender:remove-background: Working on chunk (46/46) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-Hippocampus/1436-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/1436-Schizophrenia-Hippocampus/1436-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:48:19 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-Hippocampus/1436-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/1436-Schizophrenia-Hippocampus/1436-Schizophrenia-Hippocampus.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.02 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 15:55:49 Total MCKP estimation time = 429.95 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-Hippocampus/1436-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/1436-Schizophrenia-Hippocampus/1436-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/1436-Schizophrenia-Hippocampus/1436-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/1436-Schizophrenia-Hippocampus/1436-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:56:04