cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1317-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-dACC/1317-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 7885 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 945da75a69) cellbender:remove-background: 2024-06-06 15:37:03 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/1317-Bipolar-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: 30694 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 315 cellbender:remove-background: Prior on counts for empty droplets is 37 cellbender:remove-background: Excluding 5071 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 25623 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 18 cellbender:remove-background: Using 7885 probable cell barcodes, plus an additional 12115 barcodes, and 39670 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 36 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmppdofstzn 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: 1514.5670 cellbender:remove-background: [epoch 002] average training loss: 1266.2550 (6.0 seconds per epoch) cellbender:remove-background: Will checkpoint every 71 epochs cellbender:remove-background: [epoch 003] average training loss: 1142.9050 cellbender:remove-background: [epoch 004] average training loss: 1045.8693 cellbender:remove-background: [epoch 005] average training loss: 1010.1111 cellbender:remove-background: [epoch 005] average test loss: 1134.8132 cellbender:remove-background: [epoch 006] average training loss: 980.0658 cellbender:remove-background: [epoch 007] average training loss: 952.9198 cellbender:remove-background: [epoch 008] average training loss: 941.5642 cellbender:remove-background: [epoch 009] average training loss: 945.1131 cellbender:remove-background: [epoch 010] average training loss: 932.6547 cellbender:remove-background: [epoch 010] average test loss: 976.6039 cellbender:remove-background: [epoch 011] average training loss: 940.0324 cellbender:remove-background: [epoch 012] average training loss: 934.5453 cellbender:remove-background: [epoch 013] average training loss: 924.0570 cellbender:remove-background: [epoch 014] average training loss: 916.8523 cellbender:remove-background: [epoch 015] average training loss: 904.9744 cellbender:remove-background: [epoch 015] average test loss: 941.4164 cellbender:remove-background: [epoch 016] average training loss: 896.3569 cellbender:remove-background: [epoch 017] average training loss: 889.3069 cellbender:remove-background: [epoch 018] average training loss: 886.3628 cellbender:remove-background: [epoch 019] average training loss: 878.2013 cellbender:remove-background: [epoch 020] average training loss: 872.3678 cellbender:remove-background: [epoch 020] average test loss: 909.7247 cellbender:remove-background: [epoch 021] average training loss: 862.2448 cellbender:remove-background: [epoch 022] average training loss: 858.9186 cellbender:remove-background: [epoch 023] average training loss: 856.6627 cellbender:remove-background: [epoch 024] average training loss: 855.5960 cellbender:remove-background: [epoch 025] average training loss: 853.9366 cellbender:remove-background: [epoch 025] average test loss: 891.0164 cellbender:remove-background: [epoch 026] average training loss: 852.9745 cellbender:remove-background: [epoch 027] average training loss: 854.8722 cellbender:remove-background: [epoch 028] average training loss: 854.0967 cellbender:remove-background: [epoch 029] average training loss: 852.0381 cellbender:remove-background: [epoch 030] average training loss: 852.2578 cellbender:remove-background: [epoch 030] average test loss: 884.7256 cellbender:remove-background: [epoch 031] average training loss: 853.3620 cellbender:remove-background: [epoch 032] average training loss: 853.3916 cellbender:remove-background: [epoch 033] average training loss: 853.4136 cellbender:remove-background: [epoch 034] average training loss: 852.4785 cellbender:remove-background: [epoch 035] average training loss: 854.6032 cellbender:remove-background: [epoch 035] average test loss: 906.1327 cellbender:remove-background: [epoch 036] average training loss: 853.3226 cellbender:remove-background: [epoch 037] average training loss: 852.7169 cellbender:remove-background: [epoch 038] average training loss: 852.7530 cellbender:remove-background: [epoch 039] average training loss: 852.1263 cellbender:remove-background: [epoch 040] average training loss: 853.0959 cellbender:remove-background: [epoch 040] average test loss: 903.0808 cellbender:remove-background: [epoch 041] average training loss: 852.5884 cellbender:remove-background: [epoch 042] average training loss: 851.7756 cellbender:remove-background: [epoch 043] average training loss: 850.7951 cellbender:remove-background: [epoch 044] average training loss: 850.4524 cellbender:remove-background: [epoch 045] average training loss: 850.5164 cellbender:remove-background: [epoch 045] average test loss: 886.2286 cellbender:remove-background: [epoch 046] average training loss: 849.0218 cellbender:remove-background: [epoch 047] average training loss: 851.8517 cellbender:remove-background: [epoch 048] average training loss: 849.4662 cellbender:remove-background: [epoch 049] average training loss: 848.7476 cellbender:remove-background: [epoch 050] average training loss: 847.9002 cellbender:remove-background: [epoch 050] average test loss: 874.3243 cellbender:remove-background: [epoch 051] average training loss: 849.0225 cellbender:remove-background: [epoch 052] average training loss: 846.9907 cellbender:remove-background: [epoch 053] average training loss: 844.9374 cellbender:remove-background: [epoch 054] average training loss: 845.3085 cellbender:remove-background: [epoch 055] average training loss: 845.0035 cellbender:remove-background: [epoch 055] average test loss: 880.6772 cellbender:remove-background: [epoch 056] average training loss: 843.7923 cellbender:remove-background: [epoch 057] average training loss: 843.8935 cellbender:remove-background: [epoch 058] average training loss: 844.9090 cellbender:remove-background: [epoch 059] average training loss: 842.9416 cellbender:remove-background: [epoch 060] average training loss: 843.0478 cellbender:remove-background: [epoch 060] average test loss: 873.6540 cellbender:remove-background: [epoch 061] average training loss: 843.0623 cellbender:remove-background: [epoch 062] average training loss: 842.0307 cellbender:remove-background: [epoch 063] average training loss: 842.0076 cellbender:remove-background: [epoch 064] average training loss: 842.7515 cellbender:remove-background: [epoch 065] average training loss: 842.5704 cellbender:remove-background: [epoch 065] average test loss: 878.8696 cellbender:remove-background: [epoch 066] average training loss: 841.0286 cellbender:remove-background: [epoch 067] average training loss: 841.3685 cellbender:remove-background: [epoch 068] average training loss: 840.7866 cellbender:remove-background: [epoch 069] average training loss: 838.6421 cellbender:remove-background: [epoch 070] average training loss: 838.5558 cellbender:remove-background: [epoch 070] average test loss: 872.9579 cellbender:remove-background: [epoch 071] average training loss: 838.2500 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/1317-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 072] average training loss: 838.3515 cellbender:remove-background: [epoch 073] average training loss: 839.4530 cellbender:remove-background: [epoch 074] average training loss: 838.2633 cellbender:remove-background: [epoch 075] average training loss: 837.0842 cellbender:remove-background: [epoch 075] average test loss: 878.3397 cellbender:remove-background: [epoch 076] average training loss: 836.1183 cellbender:remove-background: [epoch 077] average training loss: 836.5260 cellbender:remove-background: [epoch 078] average training loss: 837.7130 cellbender:remove-background: [epoch 079] average training loss: 836.6445 cellbender:remove-background: [epoch 080] average training loss: 835.4896 cellbender:remove-background: [epoch 080] average test loss: 878.1160 cellbender:remove-background: [epoch 081] average training loss: 834.7800 cellbender:remove-background: [epoch 082] average training loss: 834.7301 cellbender:remove-background: [epoch 083] average training loss: 834.4141 cellbender:remove-background: [epoch 084] average training loss: 833.5639 cellbender:remove-background: [epoch 085] average training loss: 835.4207 cellbender:remove-background: [epoch 085] average test loss: 873.6910 cellbender:remove-background: [epoch 086] average training loss: 833.1226 cellbender:remove-background: [epoch 087] average training loss: 832.9384 cellbender:remove-background: [epoch 088] average training loss: 834.1009 cellbender:remove-background: [epoch 089] average training loss: 834.5942 cellbender:remove-background: [epoch 090] average training loss: 832.3434 cellbender:remove-background: [epoch 090] average test loss: 874.1423 cellbender:remove-background: [epoch 091] average training loss: 832.1469 cellbender:remove-background: [epoch 092] average training loss: 832.9233 cellbender:remove-background: [epoch 093] average training loss: 833.0201 cellbender:remove-background: [epoch 094] average training loss: 832.5103 cellbender:remove-background: [epoch 095] average training loss: 831.3657 cellbender:remove-background: [epoch 095] average test loss: 875.5761 cellbender:remove-background: [epoch 096] average training loss: 830.4798 cellbender:remove-background: [epoch 097] average training loss: 830.5090 cellbender:remove-background: [epoch 098] average training loss: 832.5399 cellbender:remove-background: [epoch 099] average training loss: 832.4782 cellbender:remove-background: [epoch 100] average training loss: 829.7938 cellbender:remove-background: [epoch 100] average test loss: 873.9169 cellbender:remove-background: [epoch 101] average training loss: 830.5221 cellbender:remove-background: [epoch 102] average training loss: 830.0882 cellbender:remove-background: [epoch 103] average training loss: 829.7350 cellbender:remove-background: [epoch 104] average training loss: 829.5368 cellbender:remove-background: [epoch 105] average training loss: 829.0765 cellbender:remove-background: [epoch 105] average test loss: 874.8059 cellbender:remove-background: [epoch 106] average training loss: 830.8156 cellbender:remove-background: [epoch 107] average training loss: 829.2447 cellbender:remove-background: [epoch 108] average training loss: 826.9480 cellbender:remove-background: [epoch 109] average training loss: 828.8032 cellbender:remove-background: [epoch 110] average training loss: 828.4896 cellbender:remove-background: [epoch 110] average test loss: 876.8410 cellbender:remove-background: [epoch 111] average training loss: 828.5008 cellbender:remove-background: [epoch 112] average training loss: 826.8338 cellbender:remove-background: [epoch 113] average training loss: 828.2191 cellbender:remove-background: [epoch 114] average training loss: 828.3541 cellbender:remove-background: [epoch 115] average training loss: 825.2454 cellbender:remove-background: [epoch 115] average test loss: 875.1071 cellbender:remove-background: [epoch 116] average training loss: 830.7048 cellbender:remove-background: [epoch 117] average training loss: 826.8083 cellbender:remove-background: [epoch 118] average training loss: 827.3107 cellbender:remove-background: [epoch 119] average training loss: 827.3099 cellbender:remove-background: [epoch 120] average training loss: 825.6638 cellbender:remove-background: [epoch 120] average test loss: 872.2858 cellbender:remove-background: [epoch 121] average training loss: 828.7474 cellbender:remove-background: [epoch 122] average training loss: 825.0229 cellbender:remove-background: [epoch 123] average training loss: 826.8593 cellbender:remove-background: [epoch 124] average training loss: 825.1501 cellbender:remove-background: [epoch 125] average training loss: 826.2275 cellbender:remove-background: [epoch 125] average test loss: 868.1728 cellbender:remove-background: [epoch 126] average training loss: 824.2568 cellbender:remove-background: [epoch 127] average training loss: 825.3358 cellbender:remove-background: [epoch 128] average training loss: 825.7381 cellbender:remove-background: [epoch 129] average training loss: 824.1630 cellbender:remove-background: [epoch 130] average training loss: 823.5571 cellbender:remove-background: [epoch 130] average test loss: 876.1931 cellbender:remove-background: [epoch 131] average training loss: 824.5045 cellbender:remove-background: [epoch 132] average training loss: 824.9257 cellbender:remove-background: [epoch 133] average training loss: 823.4571 cellbender:remove-background: [epoch 134] average training loss: 823.8961 cellbender:remove-background: [epoch 135] average training loss: 825.2402 cellbender:remove-background: [epoch 135] average test loss: 873.3248 cellbender:remove-background: [epoch 136] average training loss: 824.6727 cellbender:remove-background: [epoch 137] average training loss: 825.9245 cellbender:remove-background: [epoch 138] average training loss: 823.9991 cellbender:remove-background: [epoch 139] average training loss: 823.8636 cellbender:remove-background: [epoch 140] average training loss: 824.8347 cellbender:remove-background: [epoch 140] average test loss: 874.6238 cellbender:remove-background: [epoch 141] average training loss: 823.6554 cellbender:remove-background: [epoch 142] average training loss: 823.7921 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/1317-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 143] average training loss: 824.7037 cellbender:remove-background: [epoch 144] average training loss: 825.1914 cellbender:remove-background: [epoch 145] average training loss: 824.7247 cellbender:remove-background: [epoch 145] average test loss: 877.8652 cellbender:remove-background: [epoch 146] average training loss: 824.1694 cellbender:remove-background: [epoch 147] average training loss: 823.3674 cellbender:remove-background: [epoch 148] average training loss: 823.2047 cellbender:remove-background: [epoch 149] average training loss: 823.4764 cellbender:remove-background: [epoch 150] average training loss: 823.5543 cellbender:remove-background: [epoch 150] average test loss: 876.9170 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/1317-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:56:41 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpwlhyhfel cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpwlhyhfel /tmp/tmpwlhyhfel/945da75a69_random.pyro /tmp/tmpwlhyhfel/945da75a69_random.cuda /tmp/tmpwlhyhfel/945da75a69_model.torch /tmp/tmpwlhyhfel/945da75a69_optim.torch /tmp/tmpwlhyhfel/945da75a69_optim.pyro /tmp/tmpwlhyhfel/945da75a69_params.pyro /tmp/tmpwlhyhfel/945da75a69_train.loaderstate /tmp/tmpwlhyhfel/945da75a69_test.loaderstate /tmp/tmpwlhyhfel/945da75a69_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 (1/56) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/56) cellbender:remove-background: Working on chunk (3/56) cellbender:remove-background: Working on chunk (4/56) cellbender:remove-background: Working on chunk (5/56) cellbender:remove-background: Working on chunk (6/56) cellbender:remove-background: Working on chunk (7/56) cellbender:remove-background: Working on chunk (8/56) cellbender:remove-background: Working on chunk (9/56) cellbender:remove-background: Working on chunk (10/56) cellbender:remove-background: Working on chunk (11/56) cellbender:remove-background: Working on chunk (12/56) cellbender:remove-background: Working on chunk (13/56) cellbender:remove-background: Working on chunk (14/56) cellbender:remove-background: Working on chunk (15/56) cellbender:remove-background: Working on chunk (16/56) cellbender:remove-background: Working on chunk (17/56) cellbender:remove-background: Working on chunk (18/56) cellbender:remove-background: Working on chunk (19/56) cellbender:remove-background: Working on chunk (20/56) cellbender:remove-background: Working on chunk (21/56) cellbender:remove-background: Working on chunk (22/56) cellbender:remove-background: Working on chunk (23/56) cellbender:remove-background: Working on chunk (24/56) cellbender:remove-background: Working on chunk (25/56) cellbender:remove-background: Working on chunk (26/56) cellbender:remove-background: Working on chunk (27/56) cellbender:remove-background: Working on chunk (28/56) cellbender:remove-background: Working on chunk (29/56) cellbender:remove-background: Working on chunk (30/56) cellbender:remove-background: Working on chunk (31/56) cellbender:remove-background: Working on chunk (32/56) cellbender:remove-background: Working on chunk (33/56) cellbender:remove-background: Working on chunk (34/56) cellbender:remove-background: Working on chunk (35/56) cellbender:remove-background: Working on chunk (36/56) cellbender:remove-background: Working on chunk (37/56) cellbender:remove-background: Working on chunk (38/56) cellbender:remove-background: Working on chunk (39/56) cellbender:remove-background: Working on chunk (40/56) cellbender:remove-background: Working on chunk (41/56) cellbender:remove-background: Working on chunk (42/56) cellbender:remove-background: Working on chunk (43/56) cellbender:remove-background: Working on chunk (44/56) cellbender:remove-background: Working on chunk (45/56) cellbender:remove-background: Working on chunk (46/56) cellbender:remove-background: Working on chunk (47/56) cellbender:remove-background: Working on chunk (48/56) cellbender:remove-background: Working on chunk (49/56) cellbender:remove-background: Working on chunk (50/56) cellbender:remove-background: Working on chunk (51/56) cellbender:remove-background: Working on chunk (52/56) cellbender:remove-background: Working on chunk (53/56) cellbender:remove-background: Working on chunk (54/56) cellbender:remove-background: Working on chunk (55/56) cellbender:remove-background: Working on chunk (56/56) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-dACC/1317-Bipolar-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/1317-Bipolar-dACC/1317-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:00:06 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-dACC/1317-Bipolar-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-dACC/1317-Bipolar-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: [0.40 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 16:03:03 Total MCKP estimation time = 169.17 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/1317-Bipolar-dACC/1317-Bipolar-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/1317-Bipolar-dACC/1317-Bipolar-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/1317-Bipolar-dACC/1317-Bipolar-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/1317-Bipolar-dACC/1317-Bipolar-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:03:13