cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1414-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1414-Bipolar-dACC/1414-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 12123 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash fe949ecf35) cellbender:remove-background: 2024-06-06 14:52:01 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/1414-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: 30903 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1552 cellbender:remove-background: Prior on counts for empty droplets is 64 cellbender:remove-background: Excluding 9001 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21902 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 32 cellbender:remove-background: Using 12123 probable cell barcodes, plus an additional 7877 barcodes, and 8182 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 62 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpl6z9oby_ 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: 4285.0236 cellbender:remove-background: [epoch 002] average training loss: 3545.5885 (14.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 30 epochs cellbender:remove-background: [epoch 003] average training loss: 3097.5038 cellbender:remove-background: [epoch 004] average training loss: 2827.3105 cellbender:remove-background: [epoch 005] average training loss: 2714.0103 cellbender:remove-background: [epoch 005] average test loss: 2705.5237 cellbender:remove-background: [epoch 006] average training loss: 2679.6386 cellbender:remove-background: [epoch 007] average training loss: 2657.7838 cellbender:remove-background: [epoch 008] average training loss: 2641.4536 cellbender:remove-background: [epoch 009] average training loss: 2638.4828 cellbender:remove-background: [epoch 010] average training loss: 2620.0879 cellbender:remove-background: [epoch 010] average test loss: 2644.9801 cellbender:remove-background: [epoch 011] average training loss: 2621.1841 cellbender:remove-background: [epoch 012] average training loss: 2615.1450 cellbender:remove-background: [epoch 013] average training loss: 2580.4912 cellbender:remove-background: [epoch 014] average training loss: 2469.1069 cellbender:remove-background: [epoch 015] average training loss: 2436.8969 cellbender:remove-background: [epoch 015] average test loss: 2464.9361 cellbender:remove-background: [epoch 016] average training loss: 2421.1252 cellbender:remove-background: [epoch 017] average training loss: 2416.0764 cellbender:remove-background: [epoch 018] average training loss: 2404.5414 cellbender:remove-background: [epoch 019] average training loss: 2394.9111 cellbender:remove-background: [epoch 020] average training loss: 2382.4320 cellbender:remove-background: [epoch 020] average test loss: 2395.2338 cellbender:remove-background: [epoch 021] average training loss: 2375.9088 cellbender:remove-background: [epoch 022] average training loss: 2368.0709 cellbender:remove-background: [epoch 023] average training loss: 2361.5957 cellbender:remove-background: [epoch 024] average training loss: 2352.9324 cellbender:remove-background: [epoch 025] average training loss: 2347.0840 cellbender:remove-background: [epoch 025] average test loss: 2350.0478 cellbender:remove-background: [epoch 026] average training loss: 2341.6236 cellbender:remove-background: [epoch 027] average training loss: 2337.8510 cellbender:remove-background: [epoch 028] average training loss: 2335.1833 cellbender:remove-background: [epoch 029] average training loss: 2335.4240 cellbender:remove-background: [epoch 030] average training loss: 2334.4954 cellbender:remove-background: [epoch 030] average test loss: 2339.3327 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/1414-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 031] average training loss: 2332.1898 cellbender:remove-background: [epoch 032] average training loss: 2329.6694 cellbender:remove-background: [epoch 033] average training loss: 2327.2051 cellbender:remove-background: [epoch 034] average training loss: 2327.6953 cellbender:remove-background: [epoch 035] average training loss: 2326.3271 cellbender:remove-background: [epoch 035] average test loss: 2330.5268 cellbender:remove-background: [epoch 036] average training loss: 2324.6771 cellbender:remove-background: [epoch 037] average training loss: 2323.7465 cellbender:remove-background: [epoch 038] average training loss: 2322.6854 cellbender:remove-background: [epoch 039] average training loss: 2322.1385 cellbender:remove-background: [epoch 040] average training loss: 2320.7320 cellbender:remove-background: [epoch 040] average test loss: 2319.6702 cellbender:remove-background: [epoch 041] average training loss: 2319.3166 cellbender:remove-background: [epoch 042] average training loss: 2318.0192 cellbender:remove-background: [epoch 043] average training loss: 2313.3533 cellbender:remove-background: [epoch 044] average training loss: 2312.8253 cellbender:remove-background: [epoch 045] average training loss: 2310.5999 cellbender:remove-background: [epoch 045] average test loss: 2313.4214 cellbender:remove-background: [epoch 046] average training loss: 2309.6966 cellbender:remove-background: [epoch 047] average training loss: 2307.7405 cellbender:remove-background: [epoch 048] average training loss: 2307.4163 cellbender:remove-background: [epoch 049] average training loss: 2307.8431 cellbender:remove-background: [epoch 050] average training loss: 2306.9089 cellbender:remove-background: [epoch 050] average test loss: 2306.3603 cellbender:remove-background: [epoch 051] average training loss: 2304.0114 cellbender:remove-background: [epoch 052] average training loss: 2301.7675 cellbender:remove-background: [epoch 053] average training loss: 2299.6080 cellbender:remove-background: [epoch 054] average training loss: 2301.8648 cellbender:remove-background: [epoch 055] average training loss: 2299.2567 cellbender:remove-background: [epoch 055] average test loss: 2305.9088 cellbender:remove-background: [epoch 056] average training loss: 2298.9828 cellbender:remove-background: [epoch 057] average training loss: 2300.4068 cellbender:remove-background: [epoch 058] average training loss: 2298.9060 cellbender:remove-background: [epoch 059] average training loss: 2302.6757 cellbender:remove-background: [epoch 060] average training loss: 2299.9767 cellbender:remove-background: [epoch 060] average test loss: 2301.7756 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/1414-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 061] average training loss: 2303.5428 cellbender:remove-background: [epoch 062] average training loss: 2307.2772 cellbender:remove-background: [epoch 063] average training loss: 2301.5979 cellbender:remove-background: [epoch 064] average training loss: 2309.7855 cellbender:remove-background: [epoch 065] average training loss: 2310.7405 cellbender:remove-background: [epoch 065] average test loss: 2351.1094 cellbender:remove-background: [epoch 066] average training loss: 2321.4668 cellbender:remove-background: [epoch 067] average training loss: 2311.5411 cellbender:remove-background: [epoch 068] average training loss: 2323.5075 cellbender:remove-background: [epoch 069] average training loss: 2312.3021 cellbender:remove-background: [epoch 070] average training loss: 2320.5920 cellbender:remove-background: [epoch 070] average test loss: 2308.8544 cellbender:remove-background: [epoch 071] average training loss: 2309.1810 cellbender:remove-background: [epoch 072] average training loss: 2317.4517 cellbender:remove-background: [epoch 073] average training loss: 2315.6557 cellbender:remove-background: [epoch 074] average training loss: 2306.7047 cellbender:remove-background: [epoch 075] average training loss: 2316.6508 cellbender:remove-background: [epoch 075] average test loss: 2296.2166 cellbender:remove-background: [epoch 076] average training loss: 2316.7024 cellbender:remove-background: [epoch 077] average training loss: 2307.2218 cellbender:remove-background: [epoch 078] average training loss: 2306.1588 cellbender:remove-background: [epoch 079] average training loss: 2312.9506 cellbender:remove-background: [epoch 080] average training loss: 2322.8686 cellbender:remove-background: [epoch 080] average test loss: 2339.0820 cellbender:remove-background: [epoch 081] average training loss: 2304.4376 cellbender:remove-background: [epoch 082] average training loss: 2302.5654 cellbender:remove-background: [epoch 083] average training loss: 2302.7657 cellbender:remove-background: [epoch 084] average training loss: 2304.6370 cellbender:remove-background: [epoch 085] average training loss: 2306.2678 cellbender:remove-background: [epoch 085] average test loss: 2308.5521 cellbender:remove-background: [epoch 086] average training loss: 2320.1220 cellbender:remove-background: [epoch 087] average training loss: 2295.1342 cellbender:remove-background: [epoch 088] average training loss: 2311.2707 cellbender:remove-background: [epoch 089] average training loss: 2299.6962 cellbender:remove-background: [epoch 090] average training loss: 2308.5529 cellbender:remove-background: [epoch 090] average test loss: 2311.4681 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/1414-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 091] average training loss: 2300.6169 cellbender:remove-background: [epoch 092] average training loss: 2298.7018 cellbender:remove-background: [epoch 093] average training loss: 2296.2791 cellbender:remove-background: [epoch 094] average training loss: 2305.1066 cellbender:remove-background: [epoch 095] average training loss: 2294.7534 cellbender:remove-background: [epoch 095] average test loss: 2321.5256 cellbender:remove-background: [epoch 096] average training loss: 2290.0023 cellbender:remove-background: [epoch 097] average training loss: 2297.9921 cellbender:remove-background: [epoch 098] average training loss: 2291.4841 cellbender:remove-background: [epoch 099] average training loss: 2313.9805 cellbender:remove-background: [epoch 100] average training loss: 2298.3299 cellbender:remove-background: [epoch 100] average test loss: 2328.4232 cellbender:remove-background: [epoch 101] average training loss: 2295.7305 cellbender:remove-background: [epoch 102] average training loss: 2288.5440 cellbender:remove-background: [epoch 103] average training loss: 2297.8161 cellbender:remove-background: [epoch 104] average training loss: 2290.6407 cellbender:remove-background: [epoch 105] average training loss: 2289.1170 cellbender:remove-background: [epoch 105] average test loss: 2312.9505 cellbender:remove-background: [epoch 106] average training loss: 2288.0787 cellbender:remove-background: [epoch 107] average training loss: 2292.4681 cellbender:remove-background: [epoch 108] average training loss: 2291.2532 cellbender:remove-background: [epoch 109] average training loss: 2290.5178 cellbender:remove-background: [epoch 110] average training loss: 2287.6095 cellbender:remove-background: [epoch 110] average test loss: 2321.5503 cellbender:remove-background: [epoch 111] average training loss: 2289.2337 cellbender:remove-background: [epoch 112] average training loss: 2290.4943 cellbender:remove-background: [epoch 113] average training loss: 2296.9983 cellbender:remove-background: [epoch 114] average training loss: 2287.6174 cellbender:remove-background: [epoch 115] average training loss: 2289.1241 cellbender:remove-background: [epoch 115] average test loss: 2314.8596 cellbender:remove-background: [epoch 116] average training loss: 2289.7052 cellbender:remove-background: [epoch 117] average training loss: 2291.1265 cellbender:remove-background: [epoch 118] average training loss: 2290.0713 cellbender:remove-background: [epoch 119] average training loss: 2291.9053 cellbender:remove-background: [epoch 120] average training loss: 2292.5418 cellbender:remove-background: [epoch 120] average test loss: 2322.0101 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/1414-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 121] average training loss: 2294.1214 cellbender:remove-background: [epoch 122] average training loss: 2289.6140 cellbender:remove-background: [epoch 123] average training loss: 2289.0449 cellbender:remove-background: [epoch 124] average training loss: 2287.4194 cellbender:remove-background: [epoch 125] average training loss: 2285.5822 cellbender:remove-background: [epoch 125] average test loss: 2308.4190 cellbender:remove-background: [epoch 126] average training loss: 2283.2462 cellbender:remove-background: [epoch 127] average training loss: 2287.7631 cellbender:remove-background: [epoch 128] average training loss: 2281.9791 cellbender:remove-background: [epoch 129] average training loss: 2292.0087 cellbender:remove-background: [epoch 130] average training loss: 2281.7549 cellbender:remove-background: [epoch 130] average test loss: 2316.3574 cellbender:remove-background: [epoch 131] average training loss: 2289.7148 cellbender:remove-background: [epoch 132] average training loss: 2281.4512 cellbender:remove-background: [epoch 133] average training loss: 2282.7982 cellbender:remove-background: [epoch 134] average training loss: 2286.4889 cellbender:remove-background: [epoch 135] average training loss: 2282.7080 cellbender:remove-background: [epoch 135] average test loss: 2302.2202 cellbender:remove-background: [epoch 136] average training loss: 2289.8280 cellbender:remove-background: [epoch 137] average training loss: 2292.8167 cellbender:remove-background: [epoch 138] average training loss: 2287.7036 cellbender:remove-background: [epoch 139] average training loss: 2284.6849 cellbender:remove-background: [epoch 140] average training loss: 2282.4168 cellbender:remove-background: [epoch 140] average test loss: 2323.5323 cellbender:remove-background: [epoch 141] average training loss: 2285.1706 cellbender:remove-background: [epoch 142] average training loss: 2283.2091 cellbender:remove-background: [epoch 143] average training loss: 2281.1635 cellbender:remove-background: [epoch 144] average training loss: 2284.6651 cellbender:remove-background: [epoch 145] average training loss: 2288.3519 cellbender:remove-background: [epoch 145] average test loss: 2320.3511 cellbender:remove-background: [epoch 146] average training loss: 2286.8888 cellbender:remove-background: [epoch 147] average training loss: 2283.5992 cellbender:remove-background: [epoch 148] average training loss: 2284.5338 cellbender:remove-background: [epoch 149] average training loss: 2279.0234 cellbender:remove-background: [epoch 150] average training loss: 2279.6355 cellbender:remove-background: [epoch 150] average test loss: 2310.5162 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/1414-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:33:41 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpfaqy110i cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpfaqy110i /tmp/tmpfaqy110i/fe949ecf35_random.pyro /tmp/tmpfaqy110i/fe949ecf35_random.cuda /tmp/tmpfaqy110i/fe949ecf35_model.torch /tmp/tmpfaqy110i/fe949ecf35_optim.torch /tmp/tmpfaqy110i/fe949ecf35_optim.pyro /tmp/tmpfaqy110i/fe949ecf35_params.pyro /tmp/tmpfaqy110i/fe949ecf35_train.loaderstate /tmp/tmpfaqy110i/fe949ecf35_test.loaderstate /tmp/tmpfaqy110i/fe949ecf35_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 (1/109) cellbender:remove-background: [0.07 mins per chunk] cellbender:remove-background: Working on chunk (2/109) cellbender:remove-background: Working on chunk (3/109) cellbender:remove-background: Working on chunk (4/109) cellbender:remove-background: Working on chunk (5/109) cellbender:remove-background: Working on chunk (6/109) cellbender:remove-background: Working on chunk (7/109) cellbender:remove-background: Working on chunk (8/109) cellbender:remove-background: Working on chunk (9/109) cellbender:remove-background: Working on chunk (10/109) cellbender:remove-background: Working on chunk (11/109) cellbender:remove-background: Working on chunk (12/109) cellbender:remove-background: Working on chunk (13/109) cellbender:remove-background: Working on chunk (14/109) cellbender:remove-background: Working on chunk (15/109) cellbender:remove-background: Working on chunk (16/109) cellbender:remove-background: Working on chunk (17/109) cellbender:remove-background: Working on chunk 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(89/109) cellbender:remove-background: Working on chunk (90/109) cellbender:remove-background: Working on chunk (91/109) cellbender:remove-background: Working on chunk (92/109) cellbender:remove-background: Working on chunk (93/109) cellbender:remove-background: Working on chunk (94/109) cellbender:remove-background: Working on chunk (95/109) cellbender:remove-background: Working on chunk (96/109) cellbender:remove-background: Working on chunk (97/109) cellbender:remove-background: Working on chunk (98/109) cellbender:remove-background: Working on chunk (99/109) cellbender:remove-background: Working on chunk (100/109) cellbender:remove-background: Working on chunk (101/109) cellbender:remove-background: Working on chunk (102/109) cellbender:remove-background: Working on chunk (103/109) cellbender:remove-background: Working on chunk (104/109) cellbender:remove-background: Working on chunk (105/109) cellbender:remove-background: Working on chunk (106/109) cellbender:remove-background: Working on chunk (107/109) cellbender:remove-background: Working on chunk (108/109) cellbender:remove-background: Working on chunk (109/109) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1414-Bipolar-dACC/1414-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/1414-Bipolar-dACC/1414-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:42:31 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1414-Bipolar-dACC/1414-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/1414-Bipolar-dACC/1414-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: [1.69 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 15:54:45 Total MCKP estimation time = 697.07 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/1414-Bipolar-dACC/1414-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/1414-Bipolar-dACC/1414-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/1414-Bipolar-dACC/1414-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/1414-Bipolar-dACC/1414-Bipolar-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:55:10