cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2797-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-dACC/2797-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 6314 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 8751780443) cellbender:remove-background: 2024-06-06 15:12:38 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/2797-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: 31779 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3026 cellbender:remove-background: Prior on counts for empty droplets is 126 cellbender:remove-background: Excluding 8065 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23714 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 63 cellbender:remove-background: Using 6314 probable cell barcodes, plus an additional 13686 barcodes, and 49313 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 125 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmph9ooofy2 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: 4486.7240 cellbender:remove-background: [epoch 002] average training loss: 3633.0346 (7.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 56 epochs cellbender:remove-background: [epoch 003] average training loss: 3182.4339 cellbender:remove-background: [epoch 004] average training loss: 2873.9068 cellbender:remove-background: [epoch 005] average training loss: 2787.7028 cellbender:remove-background: [epoch 005] average test loss: 2854.5580 cellbender:remove-background: [epoch 006] average training loss: 2752.1727 cellbender:remove-background: [epoch 007] average training loss: 2719.8757 cellbender:remove-background: [epoch 008] average training loss: 2693.6546 cellbender:remove-background: [epoch 009] average training loss: 2682.5186 cellbender:remove-background: [epoch 010] average training loss: 2650.2540 cellbender:remove-background: [epoch 010] average test loss: 2623.9719 cellbender:remove-background: [epoch 011] average training loss: 2603.5804 cellbender:remove-background: [epoch 012] average training loss: 2567.8972 cellbender:remove-background: [epoch 013] average training loss: 2548.1741 cellbender:remove-background: [epoch 014] average training loss: 2550.7239 cellbender:remove-background: [epoch 015] average training loss: 2536.3416 cellbender:remove-background: [epoch 015] average test loss: 2546.9630 cellbender:remove-background: [epoch 016] average training loss: 2525.8788 cellbender:remove-background: [epoch 017] average training loss: 2534.7710 cellbender:remove-background: [epoch 018] average training loss: 2519.3364 cellbender:remove-background: [epoch 019] average training loss: 2511.2115 cellbender:remove-background: [epoch 020] average training loss: 2494.5397 cellbender:remove-background: [epoch 020] average test loss: 2511.9197 cellbender:remove-background: [epoch 021] average training loss: 2495.3515 cellbender:remove-background: [epoch 022] average training loss: 2490.7742 cellbender:remove-background: [epoch 023] average training loss: 2476.1885 cellbender:remove-background: [epoch 024] average training loss: 2452.1207 cellbender:remove-background: [epoch 025] average training loss: 2441.6803 cellbender:remove-background: [epoch 025] average test loss: 2431.3862 cellbender:remove-background: [epoch 026] average training loss: 2429.0542 cellbender:remove-background: [epoch 027] average training loss: 2424.9446 cellbender:remove-background: [epoch 028] average training loss: 2422.4031 cellbender:remove-background: [epoch 029] average training loss: 2415.3087 cellbender:remove-background: [epoch 030] average training loss: 2410.5217 cellbender:remove-background: [epoch 030] average test loss: 2404.3227 cellbender:remove-background: [epoch 031] average training loss: 2406.2082 cellbender:remove-background: [epoch 032] average training loss: 2402.4941 cellbender:remove-background: [epoch 033] average training loss: 2401.9943 cellbender:remove-background: [epoch 034] average training loss: 2398.9524 cellbender:remove-background: [epoch 035] average training loss: 2397.0354 cellbender:remove-background: [epoch 035] average test loss: 2398.0495 cellbender:remove-background: [epoch 036] average training loss: 2394.7722 cellbender:remove-background: [epoch 037] average training loss: 2393.2866 cellbender:remove-background: [epoch 038] average training loss: 2397.9483 cellbender:remove-background: [epoch 039] average training loss: 2393.9194 cellbender:remove-background: [epoch 040] average training loss: 2399.9360 cellbender:remove-background: [epoch 040] average test loss: 2411.0955 cellbender:remove-background: [epoch 041] average training loss: 2399.5339 cellbender:remove-background: [epoch 042] average training loss: 2396.9973 cellbender:remove-background: [epoch 043] average training loss: 2401.5026 cellbender:remove-background: [epoch 044] average training loss: 2398.9970 cellbender:remove-background: [epoch 045] average training loss: 2400.5349 cellbender:remove-background: [epoch 045] average test loss: 2428.3725 cellbender:remove-background: [epoch 046] average training loss: 2394.6244 cellbender:remove-background: [epoch 047] average training loss: 2402.0971 cellbender:remove-background: [epoch 048] average training loss: 2411.0577 cellbender:remove-background: [epoch 049] average training loss: 2406.7531 cellbender:remove-background: [epoch 050] average training loss: 2408.8167 cellbender:remove-background: [epoch 050] average test loss: 2388.5075 cellbender:remove-background: [epoch 051] average training loss: 2401.0822 cellbender:remove-background: [epoch 052] average training loss: 2419.5004 cellbender:remove-background: [epoch 053] average training loss: 2407.1078 cellbender:remove-background: [epoch 054] average training loss: 2438.2522 cellbender:remove-background: [epoch 055] average training loss: 2420.4715 cellbender:remove-background: [epoch 055] average test loss: 2394.5212 cellbender:remove-background: [epoch 056] average training loss: 2416.0025 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/2797-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 057] average training loss: 2407.7496 cellbender:remove-background: [epoch 058] average training loss: 2404.9407 cellbender:remove-background: [epoch 059] average training loss: 2407.0489 cellbender:remove-background: [epoch 060] average training loss: 2415.3996 cellbender:remove-background: [epoch 060] average test loss: 2383.4152 cellbender:remove-background: [epoch 061] average training loss: 2412.8346 cellbender:remove-background: [epoch 062] average training loss: 2415.9227 cellbender:remove-background: [epoch 063] average training loss: 2411.7785 cellbender:remove-background: [epoch 064] average training loss: 2416.9750 cellbender:remove-background: [epoch 065] average training loss: 2415.9655 cellbender:remove-background: [epoch 065] average test loss: 2454.4486 cellbender:remove-background: [epoch 066] average training loss: 2411.8142 cellbender:remove-background: [epoch 067] average training loss: 2405.9183 cellbender:remove-background: [epoch 068] average training loss: 2410.6847 cellbender:remove-background: [epoch 069] average training loss: 2407.9698 cellbender:remove-background: [epoch 070] average training loss: 2407.3642 cellbender:remove-background: [epoch 070] average test loss: 2430.1739 cellbender:remove-background: [epoch 071] average training loss: 2404.2759 cellbender:remove-background: [epoch 072] average training loss: 2407.1600 cellbender:remove-background: [epoch 073] average training loss: 2410.6228 cellbender:remove-background: [epoch 074] average training loss: 2402.5562 cellbender:remove-background: [epoch 075] average training loss: 2405.7964 cellbender:remove-background: [epoch 075] average test loss: 2395.5651 cellbender:remove-background: [epoch 076] average training loss: 2400.8333 cellbender:remove-background: [epoch 077] average training loss: 2395.1300 cellbender:remove-background: [epoch 078] average training loss: 2397.7662 cellbender:remove-background: [epoch 079] average training loss: 2390.3167 cellbender:remove-background: [epoch 080] average training loss: 2394.4283 cellbender:remove-background: [epoch 080] average test loss: 2415.5927 cellbender:remove-background: [epoch 081] average training loss: 2397.0064 cellbender:remove-background: [epoch 082] average training loss: 2399.0785 cellbender:remove-background: [epoch 083] average training loss: 2398.7723 cellbender:remove-background: [epoch 084] average training loss: 2394.3435 cellbender:remove-background: [epoch 085] average training loss: 2395.3695 cellbender:remove-background: [epoch 085] average test loss: 2410.7988 cellbender:remove-background: [epoch 086] average training loss: 2391.7673 cellbender:remove-background: [epoch 087] average training loss: 2397.4333 cellbender:remove-background: [epoch 088] average training loss: 2388.6629 cellbender:remove-background: [epoch 089] average training loss: 2391.3233 cellbender:remove-background: [epoch 090] average training loss: 2390.1171 cellbender:remove-background: [epoch 090] average test loss: 2394.1231 cellbender:remove-background: [epoch 091] average training loss: 2393.8741 cellbender:remove-background: [epoch 092] average training loss: 2389.4410 cellbender:remove-background: [epoch 093] average training loss: 2388.3544 cellbender:remove-background: [epoch 094] average training loss: 2379.8798 cellbender:remove-background: [epoch 095] average training loss: 2388.4192 cellbender:remove-background: [epoch 095] average test loss: 2407.3791 cellbender:remove-background: [epoch 096] average training loss: 2383.5013 cellbender:remove-background: [epoch 097] average training loss: 2388.7776 cellbender:remove-background: [epoch 098] average training loss: 2385.2385 cellbender:remove-background: [epoch 099] average training loss: 2384.7749 cellbender:remove-background: [epoch 100] average training loss: 2383.1262 cellbender:remove-background: [epoch 100] average test loss: 2411.5256 cellbender:remove-background: [epoch 101] average training loss: 2381.7702 cellbender:remove-background: [epoch 102] average training loss: 2384.8821 cellbender:remove-background: [epoch 103] average training loss: 2379.4819 cellbender:remove-background: [epoch 104] average training loss: 2377.0122 cellbender:remove-background: [epoch 105] average training loss: 2385.2771 cellbender:remove-background: [epoch 105] average test loss: 2400.6532 cellbender:remove-background: [epoch 106] average training loss: 2377.3159 cellbender:remove-background: [epoch 107] average training loss: 2382.9056 cellbender:remove-background: [epoch 108] average training loss: 2376.8925 cellbender:remove-background: [epoch 109] average training loss: 2372.5194 cellbender:remove-background: [epoch 110] average training loss: 2375.8296 cellbender:remove-background: [epoch 110] average test loss: 2394.2340 cellbender:remove-background: [epoch 111] average training loss: 2378.6538 cellbender:remove-background: [epoch 112] average training loss: 2376.2491 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/2797-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 113] average training loss: 2373.4819 cellbender:remove-background: [epoch 114] average training loss: 2367.8197 cellbender:remove-background: [epoch 115] average training loss: 2375.4317 cellbender:remove-background: [epoch 115] average test loss: 2395.9276 cellbender:remove-background: [epoch 116] average training loss: 2369.8869 cellbender:remove-background: [epoch 117] average training loss: 2371.9772 cellbender:remove-background: [epoch 118] average training loss: 2373.2680 cellbender:remove-background: [epoch 119] average training loss: 2365.1212 cellbender:remove-background: [epoch 120] average training loss: 2374.6180 cellbender:remove-background: [epoch 120] average test loss: 2392.8512 cellbender:remove-background: [epoch 121] average training loss: 2369.5046 cellbender:remove-background: [epoch 122] average training loss: 2371.9778 cellbender:remove-background: [epoch 123] average training loss: 2368.0880 cellbender:remove-background: [epoch 124] average training loss: 2379.9115 cellbender:remove-background: [epoch 125] average training loss: 2364.2975 cellbender:remove-background: [epoch 125] average test loss: 2415.6454 cellbender:remove-background: [epoch 126] average training loss: 2368.2560 cellbender:remove-background: [epoch 127] average training loss: 2370.0782 cellbender:remove-background: [epoch 128] average training loss: 2373.0700 cellbender:remove-background: [epoch 129] average training loss: 2373.1557 cellbender:remove-background: [epoch 130] average training loss: 2369.8832 cellbender:remove-background: [epoch 130] average test loss: 2403.4096 cellbender:remove-background: [epoch 131] average training loss: 2370.1958 cellbender:remove-background: [epoch 132] average training loss: 2367.7990 cellbender:remove-background: [epoch 133] average training loss: 2365.0892 cellbender:remove-background: [epoch 134] average training loss: 2365.4909 cellbender:remove-background: [epoch 135] average training loss: 2368.9194 cellbender:remove-background: [epoch 135] average test loss: 2422.9072 cellbender:remove-background: [epoch 136] average training loss: 2367.9241 cellbender:remove-background: [epoch 137] average training loss: 2368.5831 cellbender:remove-background: [epoch 138] average training loss: 2366.7416 cellbender:remove-background: [epoch 139] average training loss: 2366.8403 cellbender:remove-background: [epoch 140] average training loss: 2364.5291 cellbender:remove-background: [epoch 140] average test loss: 2405.4448 cellbender:remove-background: [epoch 141] average training loss: 2364.6246 cellbender:remove-background: [epoch 142] average training loss: 2367.8366 cellbender:remove-background: [epoch 143] average training loss: 2365.7351 cellbender:remove-background: [epoch 144] average training loss: 2365.7770 cellbender:remove-background: [epoch 145] average training loss: 2367.9784 cellbender:remove-background: [epoch 145] average test loss: 2408.7182 cellbender:remove-background: [epoch 146] average training loss: 2367.2419 cellbender:remove-background: [epoch 147] average training loss: 2367.1193 cellbender:remove-background: [epoch 148] average training loss: 2365.2020 cellbender:remove-background: [epoch 149] average training loss: 2366.2202 cellbender:remove-background: [epoch 150] average training loss: 2366.6441 cellbender:remove-background: [epoch 150] average test loss: 2408.7843 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/2797-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:35:47 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp7m39p5wg cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp7m39p5wg /tmp/tmp7m39p5wg/8751780443_random.pyro /tmp/tmp7m39p5wg/8751780443_random.cuda /tmp/tmp7m39p5wg/8751780443_model.torch /tmp/tmp7m39p5wg/8751780443_optim.torch /tmp/tmp7m39p5wg/8751780443_optim.pyro /tmp/tmp7m39p5wg/8751780443_params.pyro /tmp/tmp7m39p5wg/8751780443_train.loaderstate /tmp/tmp7m39p5wg/8751780443_test.loaderstate /tmp/tmp7m39p5wg/8751780443_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 (1/51) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/51) cellbender:remove-background: Working on chunk (3/51) cellbender:remove-background: Working on chunk (4/51) cellbender:remove-background: Working on chunk (5/51) cellbender:remove-background: Working on chunk (6/51) cellbender:remove-background: Working on chunk (7/51) cellbender:remove-background: Working on chunk (8/51) cellbender:remove-background: Working on chunk (9/51) cellbender:remove-background: Working on chunk (10/51) cellbender:remove-background: Working on chunk (11/51) cellbender:remove-background: Working on chunk (12/51) cellbender:remove-background: Working on chunk (13/51) cellbender:remove-background: Working on chunk (14/51) cellbender:remove-background: Working on chunk (15/51) cellbender:remove-background: Working on chunk (16/51) cellbender:remove-background: Working on chunk (17/51) cellbender:remove-background: Working on chunk (18/51) cellbender:remove-background: Working on chunk (19/51) cellbender:remove-background: Working on chunk (20/51) cellbender:remove-background: Working on chunk (21/51) cellbender:remove-background: Working on chunk (22/51) cellbender:remove-background: Working on chunk (23/51) cellbender:remove-background: Working on chunk (24/51) cellbender:remove-background: Working on chunk (25/51) cellbender:remove-background: Working on chunk (26/51) cellbender:remove-background: Working on chunk (27/51) cellbender:remove-background: Working on chunk (28/51) cellbender:remove-background: Working on chunk (29/51) cellbender:remove-background: Working on chunk (30/51) cellbender:remove-background: Working on chunk (31/51) cellbender:remove-background: Working on chunk (32/51) cellbender:remove-background: Working on chunk (33/51) cellbender:remove-background: Working on chunk (34/51) cellbender:remove-background: Working on chunk (35/51) cellbender:remove-background: Working on chunk (36/51) cellbender:remove-background: Working on chunk (37/51) cellbender:remove-background: Working on chunk (38/51) cellbender:remove-background: Working on chunk (39/51) cellbender:remove-background: Working on chunk (40/51) cellbender:remove-background: Working on chunk (41/51) cellbender:remove-background: Working on chunk (42/51) cellbender:remove-background: Working on chunk (43/51) cellbender:remove-background: Working on chunk (44/51) cellbender:remove-background: Working on chunk (45/51) cellbender:remove-background: Working on chunk (46/51) cellbender:remove-background: Working on chunk (47/51) cellbender:remove-background: Working on chunk (48/51) cellbender:remove-background: Working on chunk (49/51) cellbender:remove-background: Working on chunk (50/51) cellbender:remove-background: Working on chunk (51/51) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-dACC/2797-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/2797-Schizophrenia-dACC/2797-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:39:47 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-dACC/2797-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/2797-Schizophrenia-dACC/2797-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: [1.47 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 15:50:23 Total MCKP estimation time = 614.38 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/2797-Schizophrenia-dACC/2797-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/2797-Schizophrenia-dACC/2797-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/2797-Schizophrenia-dACC/2797-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/2797-Schizophrenia-dACC/2797-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:50:40