cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2927-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-dACC/2927-Control-dACC.cellbender.output.h5 --cuda --expected-cells 20000 --total-droplets-included 21000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 98a20959d5) cellbender:remove-background: 2024-06-06 15:26:07 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/2927-Control-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: 31812 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1153 cellbender:remove-background: Prior on counts for empty droplets is 279 cellbender:remove-background: Excluding 6754 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 25058 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 139 cellbender:remove-background: Using 20000 probable cell barcodes, plus an additional 1000 barcodes, and 4148 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 268 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpg3na1jdh 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: 5227.9262 cellbender:remove-background: [epoch 002] average training loss: 4376.2769 (15.0 seconds per epoch) cellbender:remove-background: Will checkpoint every 28 epochs cellbender:remove-background: [epoch 003] average training loss: 3807.6133 cellbender:remove-background: [epoch 004] average training loss: 3471.1081 cellbender:remove-background: [epoch 005] average training loss: 3357.0929 cellbender:remove-background: [epoch 005] average test loss: 3348.4361 cellbender:remove-background: [epoch 006] average training loss: 3289.5617 cellbender:remove-background: [epoch 007] average training loss: 3274.4628 cellbender:remove-background: [epoch 008] average training loss: 3247.8625 cellbender:remove-background: [epoch 009] average training loss: 3241.7899 cellbender:remove-background: [epoch 010] average training loss: 3239.3962 cellbender:remove-background: [epoch 010] average test loss: 3240.1432 cellbender:remove-background: [epoch 011] average training loss: 3231.9403 cellbender:remove-background: [epoch 012] average training loss: 3222.1544 cellbender:remove-background: [epoch 013] average training loss: 3236.1351 cellbender:remove-background: [epoch 014] average training loss: 3217.4798 cellbender:remove-background: [epoch 015] average training loss: 3216.4457 cellbender:remove-background: [epoch 015] average test loss: 3230.6794 cellbender:remove-background: [epoch 016] average training loss: 3221.6188 cellbender:remove-background: [epoch 017] average training loss: 3219.6949 cellbender:remove-background: [epoch 018] average training loss: 3209.5690 cellbender:remove-background: [epoch 019] average training loss: 3205.7785 cellbender:remove-background: [epoch 020] average training loss: 3200.7828 cellbender:remove-background: [epoch 020] average test loss: 3225.4428 cellbender:remove-background: [epoch 021] average training loss: 3188.8757 cellbender:remove-background: [epoch 022] average training loss: 3172.5477 cellbender:remove-background: [epoch 023] average training loss: 3161.1148 cellbender:remove-background: [epoch 024] average training loss: 3158.0924 cellbender:remove-background: [epoch 025] average training loss: 3153.3505 cellbender:remove-background: [epoch 025] average test loss: 3182.7958 cellbender:remove-background: [epoch 026] average training loss: 3151.7143 cellbender:remove-background: [epoch 027] average training loss: 3146.4084 cellbender:remove-background: [epoch 028] average training loss: 3144.3020 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 029] average training loss: 3143.6143 cellbender:remove-background: [epoch 030] average training loss: 3140.0001 cellbender:remove-background: [epoch 030] average test loss: 3145.3724 cellbender:remove-background: [epoch 031] average training loss: 3136.9217 cellbender:remove-background: [epoch 032] average training loss: 3137.1630 cellbender:remove-background: [epoch 033] average training loss: 3136.0009 cellbender:remove-background: [epoch 034] average training loss: 3132.7790 cellbender:remove-background: [epoch 035] average training loss: 3131.9659 cellbender:remove-background: [epoch 035] average test loss: 3146.9439 cellbender:remove-background: [epoch 036] average training loss: 3131.9887 cellbender:remove-background: [epoch 037] average training loss: 3134.1390 cellbender:remove-background: [epoch 038] average training loss: 3129.8514 cellbender:remove-background: [epoch 039] average training loss: 3132.7104 cellbender:remove-background: [epoch 040] average training loss: 3127.0173 cellbender:remove-background: [epoch 040] average test loss: 3141.3975 cellbender:remove-background: [epoch 041] average training loss: 3127.1925 cellbender:remove-background: [epoch 042] average training loss: 3123.8522 cellbender:remove-background: [epoch 043] average training loss: 3126.5057 cellbender:remove-background: [epoch 044] average training loss: 3121.9259 cellbender:remove-background: [epoch 045] average training loss: 3119.4466 cellbender:remove-background: [epoch 045] average test loss: 3135.1550 cellbender:remove-background: [epoch 046] average training loss: 3120.5171 cellbender:remove-background: [epoch 047] average training loss: 3119.8680 cellbender:remove-background: [epoch 048] average training loss: 3119.8983 cellbender:remove-background: [epoch 049] average training loss: 3117.2336 cellbender:remove-background: [epoch 050] average training loss: 3113.5921 cellbender:remove-background: [epoch 050] average test loss: 3121.6471 cellbender:remove-background: [epoch 051] average training loss: 3112.2040 cellbender:remove-background: [epoch 052] average training loss: 3112.8546 cellbender:remove-background: [epoch 053] average training loss: 3111.6997 cellbender:remove-background: [epoch 054] average training loss: 3111.4557 cellbender:remove-background: [epoch 055] average training loss: 3114.9703 cellbender:remove-background: [epoch 055] average test loss: 3124.1594 cellbender:remove-background: [epoch 056] average training loss: 3116.0445 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 057] average training loss: 3112.8479 cellbender:remove-background: [epoch 058] average training loss: 3116.7187 cellbender:remove-background: [epoch 059] average training loss: 3115.6820 cellbender:remove-background: [epoch 060] average training loss: 3112.1718 cellbender:remove-background: [epoch 060] average test loss: 3126.3444 cellbender:remove-background: [epoch 061] average training loss: 3111.7147 cellbender:remove-background: [epoch 062] average training loss: 3112.4650 cellbender:remove-background: [epoch 063] average training loss: 3114.6332 cellbender:remove-background: [epoch 064] average training loss: 3114.0366 cellbender:remove-background: [epoch 065] average training loss: 3114.2074 cellbender:remove-background: [epoch 065] average test loss: 3119.4410 cellbender:remove-background: [epoch 066] average training loss: 3115.4966 cellbender:remove-background: [epoch 067] average training loss: 3118.2597 cellbender:remove-background: [epoch 068] average training loss: 3113.4311 cellbender:remove-background: [epoch 069] average training loss: 3114.7011 cellbender:remove-background: [epoch 070] average training loss: 3116.2015 cellbender:remove-background: [epoch 070] average test loss: 3143.2514 cellbender:remove-background: [epoch 071] average training loss: 3115.1733 cellbender:remove-background: [epoch 072] average training loss: 3117.1499 cellbender:remove-background: [epoch 073] average training loss: 3114.7752 cellbender:remove-background: [epoch 074] average training loss: 3119.1439 cellbender:remove-background: [epoch 075] average training loss: 3115.3884 cellbender:remove-background: [epoch 075] average test loss: 3138.2348 cellbender:remove-background: [epoch 076] average training loss: 3113.7129 cellbender:remove-background: [epoch 077] average training loss: 3117.2217 cellbender:remove-background: [epoch 078] average training loss: 3116.2262 cellbender:remove-background: [epoch 079] average training loss: 3116.9986 cellbender:remove-background: [epoch 080] average training loss: 3117.2982 cellbender:remove-background: [epoch 080] average test loss: 3124.3688 cellbender:remove-background: [epoch 081] average training loss: 3115.4315 cellbender:remove-background: [epoch 082] average training loss: 3115.0365 cellbender:remove-background: [epoch 083] average training loss: 3113.1144 cellbender:remove-background: [epoch 084] average training loss: 3115.4645 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 085] average training loss: 3115.6926 cellbender:remove-background: [epoch 085] average test loss: 3130.7854 cellbender:remove-background: [epoch 086] average training loss: 3116.0487 cellbender:remove-background: [epoch 087] average training loss: 3117.1156 cellbender:remove-background: [epoch 088] average training loss: 3114.4863 cellbender:remove-background: [epoch 089] average training loss: 3113.5132 cellbender:remove-background: [epoch 090] average training loss: 3112.2484 cellbender:remove-background: [epoch 090] average test loss: 3136.5021 cellbender:remove-background: [epoch 091] average training loss: 3113.8535 cellbender:remove-background: [epoch 092] average training loss: 3115.3487 cellbender:remove-background: [epoch 093] average training loss: 3119.3433 cellbender:remove-background: [epoch 094] average training loss: 3113.0260 cellbender:remove-background: [epoch 095] average training loss: 3114.6694 cellbender:remove-background: [epoch 095] average test loss: 3124.9289 cellbender:remove-background: [epoch 096] average training loss: 3112.3615 cellbender:remove-background: [epoch 097] average training loss: 3113.8379 cellbender:remove-background: [epoch 098] average training loss: 3116.5067 cellbender:remove-background: [epoch 099] average training loss: 3110.7538 cellbender:remove-background: [epoch 100] average training loss: 3110.8428 cellbender:remove-background: [epoch 100] average test loss: 3138.8806 cellbender:remove-background: [epoch 101] average training loss: 3110.6639 cellbender:remove-background: [epoch 102] average training loss: 3113.1186 cellbender:remove-background: [epoch 103] average training loss: 3110.5696 cellbender:remove-background: [epoch 104] average training loss: 3109.7184 cellbender:remove-background: [epoch 105] average training loss: 3110.9903 cellbender:remove-background: [epoch 105] average test loss: 3131.5318 cellbender:remove-background: [epoch 106] average training loss: 3111.6143 cellbender:remove-background: [epoch 107] average training loss: 3107.3537 cellbender:remove-background: [epoch 108] average training loss: 3112.5605 cellbender:remove-background: [epoch 109] average training loss: 3111.8113 cellbender:remove-background: [epoch 110] average training loss: 3110.0579 cellbender:remove-background: [epoch 110] average test loss: 3127.7853 cellbender:remove-background: [epoch 111] average training loss: 3111.6551 cellbender:remove-background: [epoch 112] average training loss: 3111.4757 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 113] average training loss: 3109.3738 cellbender:remove-background: [epoch 114] average training loss: 3108.0458 cellbender:remove-background: [epoch 115] average training loss: 3106.7610 cellbender:remove-background: [epoch 115] average test loss: 3125.8785 cellbender:remove-background: [epoch 116] average training loss: 3110.6446 cellbender:remove-background: [epoch 117] average training loss: 3111.4286 cellbender:remove-background: [epoch 118] average training loss: 3111.4908 cellbender:remove-background: [epoch 119] average training loss: 3109.8447 cellbender:remove-background: [epoch 120] average training loss: 3110.7900 cellbender:remove-background: [epoch 120] average test loss: 3133.0365 cellbender:remove-background: [epoch 121] average training loss: 3108.4855 cellbender:remove-background: [epoch 122] average training loss: 3110.7691 cellbender:remove-background: [epoch 123] average training loss: 3107.8476 cellbender:remove-background: [epoch 124] average training loss: 3111.2407 cellbender:remove-background: [epoch 125] average training loss: 3105.7958 cellbender:remove-background: [epoch 125] average test loss: 3130.6566 cellbender:remove-background: [epoch 126] average training loss: 3107.1010 cellbender:remove-background: [epoch 127] average training loss: 3107.3011 cellbender:remove-background: [epoch 128] average training loss: 3107.2267 cellbender:remove-background: [epoch 129] average training loss: 3108.2275 cellbender:remove-background: [epoch 130] average training loss: 3108.3026 cellbender:remove-background: [epoch 130] average test loss: 3131.8594 cellbender:remove-background: [epoch 131] average training loss: 3107.8447 cellbender:remove-background: [epoch 132] average training loss: 3109.0816 cellbender:remove-background: [epoch 133] average training loss: 3106.7252 cellbender:remove-background: [epoch 134] average training loss: 3105.4438 cellbender:remove-background: [epoch 135] average training loss: 3110.4692 cellbender:remove-background: [epoch 135] average test loss: 3133.9816 cellbender:remove-background: [epoch 136] average training loss: 3107.3064 cellbender:remove-background: [epoch 137] average training loss: 3108.2782 cellbender:remove-background: [epoch 138] average training loss: 3107.3093 cellbender:remove-background: [epoch 139] average training loss: 3105.5587 cellbender:remove-background: [epoch 140] average training loss: 3106.5554 cellbender:remove-background: [epoch 140] average test loss: 3133.9796 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 141] average training loss: 3107.0705 cellbender:remove-background: [epoch 142] average training loss: 3108.0583 cellbender:remove-background: [epoch 143] average training loss: 3107.3294 cellbender:remove-background: [epoch 144] average training loss: 3108.4922 cellbender:remove-background: [epoch 145] average training loss: 3105.8833 cellbender:remove-background: [epoch 145] average test loss: 3130.5077 cellbender:remove-background: [epoch 146] average training loss: 3105.5360 cellbender:remove-background: [epoch 147] average training loss: 3107.4227 cellbender:remove-background: [epoch 148] average training loss: 3106.7925 cellbender:remove-background: [epoch 149] average training loss: 3105.8591 cellbender:remove-background: [epoch 150] average training loss: 3106.3367 cellbender:remove-background: [epoch 150] average test loss: 3133.2294 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/2927-Control-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:13:14 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpe9hib1jy cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpe9hib1jy /tmp/tmpe9hib1jy/98a20959d5_random.pyro /tmp/tmpe9hib1jy/98a20959d5_random.cuda /tmp/tmpe9hib1jy/98a20959d5_model.torch /tmp/tmpe9hib1jy/98a20959d5_optim.torch /tmp/tmpe9hib1jy/98a20959d5_optim.pyro /tmp/tmpe9hib1jy/98a20959d5_params.pyro /tmp/tmpe9hib1jy/98a20959d5_train.loaderstate /tmp/tmpe9hib1jy/98a20959d5_test.loaderstate /tmp/tmpe9hib1jy/98a20959d5_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 (1/142) cellbender:remove-background: [0.07 mins per chunk] cellbender:remove-background: Working on chunk (2/142) cellbender:remove-background: Working on chunk (3/142) cellbender:remove-background: Working on chunk (4/142) cellbender:remove-background: Working on chunk (5/142) cellbender:remove-background: Working on chunk (6/142) cellbender:remove-background: Working on chunk (7/142) cellbender:remove-background: Working on chunk (8/142) cellbender:remove-background: Working on chunk (9/142) cellbender:remove-background: Working on chunk (10/142) cellbender:remove-background: Working on chunk (11/142) cellbender:remove-background: Working on chunk (12/142) cellbender:remove-background: Working on chunk (13/142) cellbender:remove-background: Working on chunk (14/142) cellbender:remove-background: Working on chunk (15/142) cellbender:remove-background: Working on chunk (16/142) cellbender:remove-background: Working on chunk (17/142) cellbender:remove-background: Working on chunk 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cellbender:remove-background: Working on chunk (125/142) cellbender:remove-background: Working on chunk (126/142) cellbender:remove-background: Working on chunk (127/142) cellbender:remove-background: Working on chunk (128/142) cellbender:remove-background: Working on chunk (129/142) cellbender:remove-background: Working on chunk (130/142) cellbender:remove-background: Working on chunk (131/142) cellbender:remove-background: Working on chunk (132/142) cellbender:remove-background: Working on chunk (133/142) cellbender:remove-background: Working on chunk (134/142) cellbender:remove-background: Working on chunk (135/142) cellbender:remove-background: Working on chunk (136/142) cellbender:remove-background: Working on chunk (137/142) cellbender:remove-background: Working on chunk (138/142) cellbender:remove-background: Working on chunk (139/142) cellbender:remove-background: Working on chunk (140/142) cellbender:remove-background: Working on chunk (141/142) cellbender:remove-background: Working on chunk (142/142) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-dACC/2927-Control-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/2927-Control-dACC/2927-Control-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:24:52 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-dACC/2927-Control-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-dACC/2927-Control-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: [2.20 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 16:40:48 Total MCKP estimation time = 907.03 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/2927-Control-dACC/2927-Control-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/2927-Control-dACC/2927-Control-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/2927-Control-dACC/2927-Control-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/2927-Control-dACC/2927-Control-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:41:18