cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1676-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-dACC/1676-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 6437 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 71a1ccb2d2) cellbender:remove-background: 2024-06-06 14:54:14 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/1676-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: 32407 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 7069 cellbender:remove-background: Prior on counts for empty droplets is 65 cellbender:remove-background: Excluding 11279 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21128 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 32 cellbender:remove-background: Using 6437 probable cell barcodes, plus an additional 13563 barcodes, and 51023 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 64 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpmi3wx9ax 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: 6711.3383 cellbender:remove-background: [epoch 002] average training loss: 5075.1910 (4.9 seconds per epoch) cellbender:remove-background: Will checkpoint every 86 epochs cellbender:remove-background: [epoch 003] average training loss: 4273.5406 cellbender:remove-background: [epoch 004] average training loss: 3796.6134 cellbender:remove-background: [epoch 005] average training loss: 3703.0641 cellbender:remove-background: [epoch 005] average test loss: 3722.2932 cellbender:remove-background: [epoch 006] average training loss: 3679.3936 cellbender:remove-background: [epoch 007] average training loss: 3617.1924 cellbender:remove-background: [epoch 008] average training loss: 3577.3139 cellbender:remove-background: [epoch 009] average training loss: 3579.2482 cellbender:remove-background: [epoch 010] average training loss: 3521.2904 cellbender:remove-background: [epoch 010] average test loss: 3471.1001 cellbender:remove-background: [epoch 011] average training loss: 3469.3420 cellbender:remove-background: [epoch 012] average training loss: 3329.5790 cellbender:remove-background: [epoch 013] average training loss: 3279.9154 cellbender:remove-background: [epoch 014] average training loss: 3296.4548 cellbender:remove-background: [epoch 015] average training loss: 3255.3652 cellbender:remove-background: [epoch 015] average test loss: 3243.0253 cellbender:remove-background: [epoch 016] average training loss: 3238.9568 cellbender:remove-background: [epoch 017] average training loss: 3246.5960 cellbender:remove-background: [epoch 018] average training loss: 3233.0426 cellbender:remove-background: [epoch 019] average training loss: 3207.5842 cellbender:remove-background: [epoch 020] average training loss: 3151.7259 cellbender:remove-background: [epoch 020] average test loss: 3148.8412 cellbender:remove-background: [epoch 021] average training loss: 3128.0074 cellbender:remove-background: [epoch 022] average training loss: 3116.4855 cellbender:remove-background: [epoch 023] average training loss: 3098.9678 cellbender:remove-background: [epoch 024] average training loss: 3061.3573 cellbender:remove-background: [epoch 025] average training loss: 3042.9674 cellbender:remove-background: [epoch 025] average test loss: 2995.7418 cellbender:remove-background: [epoch 026] average training loss: 3020.6147 cellbender:remove-background: [epoch 027] average training loss: 3010.9276 cellbender:remove-background: [epoch 028] average training loss: 3007.2340 cellbender:remove-background: [epoch 029] average training loss: 2996.6582 cellbender:remove-background: [epoch 030] average training loss: 2991.2802 cellbender:remove-background: [epoch 030] average test loss: 2957.7968 cellbender:remove-background: [epoch 031] average training loss: 2987.5712 cellbender:remove-background: [epoch 032] average training loss: 2985.9498 cellbender:remove-background: [epoch 033] average training loss: 2981.0007 cellbender:remove-background: [epoch 034] average training loss: 2978.7890 cellbender:remove-background: [epoch 035] average training loss: 2976.5437 cellbender:remove-background: [epoch 035] average test loss: 2934.0755 cellbender:remove-background: [epoch 036] average training loss: 2975.2608 cellbender:remove-background: [epoch 037] average training loss: 2973.2051 cellbender:remove-background: [epoch 038] average training loss: 2974.9613 cellbender:remove-background: [epoch 039] average training loss: 2975.5935 cellbender:remove-background: [epoch 040] average training loss: 2986.1269 cellbender:remove-background: [epoch 040] average test loss: 2948.1586 cellbender:remove-background: [epoch 041] average training loss: 2976.0470 cellbender:remove-background: [epoch 042] average training loss: 2972.2991 cellbender:remove-background: [epoch 043] average training loss: 2972.0785 cellbender:remove-background: [epoch 044] average training loss: 2977.2608 cellbender:remove-background: [epoch 045] average training loss: 2970.2800 cellbender:remove-background: [epoch 045] average test loss: 2922.2149 cellbender:remove-background: [epoch 046] average training loss: 2971.8178 cellbender:remove-background: [epoch 047] average training loss: 2970.1101 cellbender:remove-background: [epoch 048] average training loss: 2970.1291 cellbender:remove-background: [epoch 049] average training loss: 2971.8875 cellbender:remove-background: [epoch 050] average training loss: 2966.5032 cellbender:remove-background: [epoch 050] average test loss: 2929.0067 cellbender:remove-background: [epoch 051] average training loss: 2971.3869 cellbender:remove-background: [epoch 052] average training loss: 2972.7068 cellbender:remove-background: [epoch 053] average training loss: 2958.9639 cellbender:remove-background: [epoch 054] average training loss: 2984.6308 cellbender:remove-background: [epoch 055] average training loss: 2960.1218 cellbender:remove-background: [epoch 055] average test loss: 2922.8941 cellbender:remove-background: [epoch 056] average training loss: 2955.2960 cellbender:remove-background: [epoch 057] average training loss: 2955.4432 cellbender:remove-background: [epoch 058] average training loss: 2950.9458 cellbender:remove-background: [epoch 059] average training loss: 2949.3637 cellbender:remove-background: [epoch 060] average training loss: 2948.9815 cellbender:remove-background: [epoch 060] average test loss: 2910.9138 cellbender:remove-background: [epoch 061] average training loss: 2948.5085 cellbender:remove-background: [epoch 062] average training loss: 2949.2532 cellbender:remove-background: [epoch 063] average training loss: 2953.9762 cellbender:remove-background: [epoch 064] average training loss: 2945.5511 cellbender:remove-background: [epoch 065] average training loss: 2945.6329 cellbender:remove-background: [epoch 065] average test loss: 2923.8290 cellbender:remove-background: [epoch 066] average training loss: 2944.7843 cellbender:remove-background: [epoch 067] average training loss: 2943.6926 cellbender:remove-background: [epoch 068] average training loss: 2939.2137 cellbender:remove-background: [epoch 069] average training loss: 2946.1615 cellbender:remove-background: [epoch 070] average training loss: 2942.5427 cellbender:remove-background: [epoch 070] average test loss: 2915.3344 cellbender:remove-background: [epoch 071] average training loss: 2939.5975 cellbender:remove-background: [epoch 072] average training loss: 2942.4245 cellbender:remove-background: [epoch 073] average training loss: 2943.2715 cellbender:remove-background: [epoch 074] average training loss: 2940.8418 cellbender:remove-background: [epoch 075] average training loss: 2940.4707 cellbender:remove-background: [epoch 075] average test loss: 2920.1411 cellbender:remove-background: [epoch 076] average training loss: 2942.4591 cellbender:remove-background: [epoch 077] average training loss: 2941.9581 cellbender:remove-background: [epoch 078] average training loss: 2944.7478 cellbender:remove-background: [epoch 079] average training loss: 2937.1833 cellbender:remove-background: [epoch 080] average training loss: 2937.2069 cellbender:remove-background: [epoch 080] average test loss: 2937.2457 cellbender:remove-background: [epoch 081] average training loss: 2936.3516 cellbender:remove-background: [epoch 082] average training loss: 2937.3164 cellbender:remove-background: [epoch 083] average training loss: 2936.9599 cellbender:remove-background: [epoch 084] average training loss: 2937.5660 cellbender:remove-background: [epoch 085] average training loss: 2934.1251 cellbender:remove-background: [epoch 085] average test loss: 2917.1041 cellbender:remove-background: [epoch 086] average training loss: 2932.3151 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/1676-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 087] average training loss: 2933.5912 cellbender:remove-background: [epoch 088] average training loss: 2934.2970 cellbender:remove-background: [epoch 089] average training loss: 2933.5819 cellbender:remove-background: [epoch 090] average training loss: 2932.4225 cellbender:remove-background: [epoch 090] average test loss: 2920.1466 cellbender:remove-background: [epoch 091] average training loss: 2934.0424 cellbender:remove-background: [epoch 092] average training loss: 2933.4469 cellbender:remove-background: [epoch 093] average training loss: 2933.0699 cellbender:remove-background: [epoch 094] average training loss: 2938.1853 cellbender:remove-background: [epoch 095] average training loss: 2934.0422 cellbender:remove-background: [epoch 095] average test loss: 2914.0919 cellbender:remove-background: [epoch 096] average training loss: 2933.7889 cellbender:remove-background: [epoch 097] average training loss: 2931.8414 cellbender:remove-background: [epoch 098] average training loss: 2930.8699 cellbender:remove-background: [epoch 099] average training loss: 2929.4230 cellbender:remove-background: [epoch 100] average training loss: 2933.1288 cellbender:remove-background: [epoch 100] average test loss: 2919.4057 cellbender:remove-background: [epoch 101] average training loss: 2928.5627 cellbender:remove-background: [epoch 102] average training loss: 2928.1718 cellbender:remove-background: [epoch 103] average training loss: 2928.2161 cellbender:remove-background: [epoch 104] average training loss: 2930.5406 cellbender:remove-background: [epoch 105] average training loss: 2929.5576 cellbender:remove-background: [epoch 105] average test loss: 2909.1979 cellbender:remove-background: [epoch 106] average training loss: 2925.6834 cellbender:remove-background: [epoch 107] average training loss: 2928.1377 cellbender:remove-background: [epoch 108] average training loss: 2924.9197 cellbender:remove-background: [epoch 109] average training loss: 2929.8960 cellbender:remove-background: [epoch 110] average training loss: 2924.0889 cellbender:remove-background: [epoch 110] average test loss: 2917.8363 cellbender:remove-background: [epoch 111] average training loss: 2925.4125 cellbender:remove-background: [epoch 112] average training loss: 2930.5717 cellbender:remove-background: [epoch 113] average training loss: 2926.7110 cellbender:remove-background: [epoch 114] average training loss: 2923.3722 cellbender:remove-background: [epoch 115] average training loss: 2929.0927 cellbender:remove-background: [epoch 115] average test loss: 2914.1243 cellbender:remove-background: [epoch 116] average training loss: 2926.3419 cellbender:remove-background: [epoch 117] average training loss: 2932.1136 cellbender:remove-background: [epoch 118] average training loss: 2925.0387 cellbender:remove-background: [epoch 119] average training loss: 2925.8506 cellbender:remove-background: [epoch 120] average training loss: 2923.8007 cellbender:remove-background: [epoch 120] average test loss: 2913.7131 cellbender:remove-background: [epoch 121] average training loss: 2922.5117 cellbender:remove-background: [epoch 122] average training loss: 2921.0734 cellbender:remove-background: [epoch 123] average training loss: 2922.8162 cellbender:remove-background: [epoch 124] average training loss: 2919.9082 cellbender:remove-background: [epoch 125] average training loss: 2921.1486 cellbender:remove-background: [epoch 125] average test loss: 2914.8632 cellbender:remove-background: [epoch 126] average training loss: 2932.3379 cellbender:remove-background: [epoch 127] average training loss: 2922.9718 cellbender:remove-background: [epoch 128] average training loss: 2919.6485 cellbender:remove-background: [epoch 129] average training loss: 2924.4756 cellbender:remove-background: [epoch 130] average training loss: 2925.5272 cellbender:remove-background: [epoch 130] average test loss: 2911.4665 cellbender:remove-background: [epoch 131] average training loss: 2922.1251 cellbender:remove-background: [epoch 132] average training loss: 2919.3181 cellbender:remove-background: [epoch 133] average training loss: 2920.6892 cellbender:remove-background: [epoch 134] average training loss: 2923.2115 cellbender:remove-background: [epoch 135] average training loss: 2917.3298 cellbender:remove-background: [epoch 135] average test loss: 2912.0091 cellbender:remove-background: [epoch 136] average training loss: 2918.5085 cellbender:remove-background: [epoch 137] average training loss: 2921.7248 cellbender:remove-background: [epoch 138] average training loss: 2917.3148 cellbender:remove-background: [epoch 139] average training loss: 2917.8949 cellbender:remove-background: [epoch 140] average training loss: 2918.3490 cellbender:remove-background: [epoch 140] average test loss: 2909.1497 cellbender:remove-background: [epoch 141] average training loss: 2921.0742 cellbender:remove-background: [epoch 142] average training loss: 2919.0611 cellbender:remove-background: [epoch 143] average training loss: 2919.1139 cellbender:remove-background: [epoch 144] average training loss: 2919.9457 cellbender:remove-background: [epoch 145] average training loss: 2918.2689 cellbender:remove-background: [epoch 145] average test loss: 2910.0371 cellbender:remove-background: [epoch 146] average training loss: 2921.2531 cellbender:remove-background: [epoch 147] average training loss: 2917.4698 cellbender:remove-background: [epoch 148] average training loss: 2920.9754 cellbender:remove-background: [epoch 149] average training loss: 2917.1358 cellbender:remove-background: [epoch 150] average training loss: 2918.8019 cellbender:remove-background: [epoch 150] average test loss: 2913.2668 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/1676-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:08:55 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp84n2izi5 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp84n2izi5 /tmp/tmp84n2izi5/71a1ccb2d2_random.pyro /tmp/tmp84n2izi5/71a1ccb2d2_random.cuda /tmp/tmp84n2izi5/71a1ccb2d2_model.torch /tmp/tmp84n2izi5/71a1ccb2d2_optim.torch /tmp/tmp84n2izi5/71a1ccb2d2_optim.pyro /tmp/tmp84n2izi5/71a1ccb2d2_params.pyro /tmp/tmp84n2izi5/71a1ccb2d2_train.loaderstate /tmp/tmp84n2izi5/71a1ccb2d2_test.loaderstate /tmp/tmp84n2izi5/71a1ccb2d2_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 (1/54) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/54) cellbender:remove-background: Working on chunk (3/54) cellbender:remove-background: Working on chunk (4/54) cellbender:remove-background: Working on chunk (5/54) cellbender:remove-background: Working on chunk (6/54) cellbender:remove-background: Working on chunk (7/54) cellbender:remove-background: Working on chunk (8/54) cellbender:remove-background: Working on chunk (9/54) cellbender:remove-background: Working on chunk (10/54) cellbender:remove-background: Working on chunk (11/54) cellbender:remove-background: Working on chunk (12/54) cellbender:remove-background: Working on chunk (13/54) cellbender:remove-background: Working on chunk (14/54) cellbender:remove-background: Working on chunk (15/54) cellbender:remove-background: Working on chunk (16/54) cellbender:remove-background: Working on chunk (17/54) cellbender:remove-background: Working on chunk (18/54) cellbender:remove-background: Working on chunk (19/54) cellbender:remove-background: Working on chunk (20/54) cellbender:remove-background: Working on chunk (21/54) cellbender:remove-background: Working on chunk (22/54) cellbender:remove-background: Working on chunk (23/54) cellbender:remove-background: Working on chunk (24/54) cellbender:remove-background: Working on chunk (25/54) cellbender:remove-background: Working on chunk (26/54) cellbender:remove-background: Working on chunk (27/54) cellbender:remove-background: Working on chunk (28/54) cellbender:remove-background: Working on chunk (29/54) cellbender:remove-background: Working on chunk (30/54) cellbender:remove-background: Working on chunk (31/54) cellbender:remove-background: Working on chunk (32/54) cellbender:remove-background: Working on chunk (33/54) cellbender:remove-background: Working on chunk (34/54) cellbender:remove-background: Working on chunk (35/54) cellbender:remove-background: Working on chunk (36/54) cellbender:remove-background: Working on chunk (37/54) cellbender:remove-background: Working on chunk (38/54) cellbender:remove-background: Working on chunk (39/54) cellbender:remove-background: Working on chunk (40/54) cellbender:remove-background: Working on chunk (41/54) cellbender:remove-background: Working on chunk (42/54) cellbender:remove-background: Working on chunk (43/54) cellbender:remove-background: Working on chunk (44/54) cellbender:remove-background: Working on chunk (45/54) cellbender:remove-background: Working on chunk (46/54) cellbender:remove-background: Working on chunk (47/54) cellbender:remove-background: Working on chunk (48/54) cellbender:remove-background: Working on chunk (49/54) cellbender:remove-background: Working on chunk (50/54) cellbender:remove-background: Working on chunk (51/54) cellbender:remove-background: Working on chunk (52/54) cellbender:remove-background: Working on chunk (53/54) cellbender:remove-background: Working on chunk (54/54) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-dACC/1676-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/1676-Schizophrenia-dACC/1676-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:12:07 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-dACC/1676-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/1676-Schizophrenia-dACC/1676-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: [1.40 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 15:22:49 Total MCKP estimation time = 592.87 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/1676-Schizophrenia-dACC/1676-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/1676-Schizophrenia-dACC/1676-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/1676-Schizophrenia-dACC/1676-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/1676-Schizophrenia-dACC/1676-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:23:08