cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1672-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-dACC/1672-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 2289 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 17cf6a3602) cellbender:remove-background: 2024-06-06 15:12:35 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/1672-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: 32181 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 15875 cellbender:remove-background: Prior on counts for empty droplets is 170 cellbender:remove-background: Excluding 10873 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21308 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 85 cellbender:remove-background: Using 2289 probable cell barcodes, plus an additional 17711 barcodes, and 15555 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 167 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpsth1bbhf 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: 5317.7718 cellbender:remove-background: [epoch 002] average training loss: 4259.4197 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 67 epochs cellbender:remove-background: [epoch 003] average training loss: 3755.9179 cellbender:remove-background: [epoch 004] average training loss: 3406.6717 cellbender:remove-background: [epoch 005] average training loss: 3301.5701 cellbender:remove-background: [epoch 005] average test loss: 3484.0272 cellbender:remove-background: [epoch 006] average training loss: 3249.5728 cellbender:remove-background: [epoch 007] average training loss: 3198.1973 cellbender:remove-background: [epoch 008] average training loss: 3160.1189 cellbender:remove-background: [epoch 009] average training loss: 3149.0296 cellbender:remove-background: [epoch 010] average training loss: 3096.1233 cellbender:remove-background: [epoch 010] average test loss: 3097.3417 cellbender:remove-background: [epoch 011] average training loss: 3075.1223 cellbender:remove-background: [epoch 012] average training loss: 3050.4188 cellbender:remove-background: [epoch 013] average training loss: 3026.0653 cellbender:remove-background: [epoch 014] average training loss: 3031.6353 cellbender:remove-background: [epoch 015] average training loss: 3008.4003 cellbender:remove-background: [epoch 015] average test loss: 3029.7303 cellbender:remove-background: [epoch 016] average training loss: 2998.3610 cellbender:remove-background: [epoch 017] average training loss: 3000.5709 cellbender:remove-background: [epoch 018] average training loss: 2991.2155 cellbender:remove-background: [epoch 019] average training loss: 2982.2642 cellbender:remove-background: [epoch 020] average training loss: 2958.6925 cellbender:remove-background: [epoch 020] average test loss: 3038.4604 cellbender:remove-background: [epoch 021] average training loss: 2957.6861 cellbender:remove-background: [epoch 022] average training loss: 2952.6128 cellbender:remove-background: [epoch 023] average training loss: 2930.8643 cellbender:remove-background: [epoch 024] average training loss: 2904.3396 cellbender:remove-background: [epoch 025] average training loss: 2898.0544 cellbender:remove-background: [epoch 025] average test loss: 2904.1790 cellbender:remove-background: [epoch 026] average training loss: 2883.6695 cellbender:remove-background: [epoch 027] average training loss: 2898.0499 cellbender:remove-background: [epoch 028] average training loss: 2901.8193 cellbender:remove-background: [epoch 029] average training loss: 2885.5304 cellbender:remove-background: [epoch 030] average training loss: 2880.8722 cellbender:remove-background: [epoch 030] average test loss: 2924.2067 cellbender:remove-background: [epoch 031] average training loss: 2871.9939 cellbender:remove-background: [epoch 032] average training loss: 2864.7796 cellbender:remove-background: [epoch 033] average training loss: 2870.4167 cellbender:remove-background: [epoch 034] average training loss: 2870.3504 cellbender:remove-background: [epoch 035] average training loss: 2863.0917 cellbender:remove-background: [epoch 035] average test loss: 2873.4358 cellbender:remove-background: [epoch 036] average training loss: 2869.1926 cellbender:remove-background: [epoch 037] average training loss: 2867.3876 cellbender:remove-background: [epoch 038] average training loss: 2865.7766 cellbender:remove-background: [epoch 039] average training loss: 2874.6469 cellbender:remove-background: [epoch 040] average training loss: 2874.0247 cellbender:remove-background: [epoch 040] average test loss: 2887.6666 cellbender:remove-background: [epoch 041] average training loss: 2865.0115 cellbender:remove-background: [epoch 042] average training loss: 2870.0254 cellbender:remove-background: [epoch 043] average training loss: 2869.6451 cellbender:remove-background: [epoch 044] average training loss: 2874.1985 cellbender:remove-background: [epoch 045] average training loss: 2879.2803 cellbender:remove-background: [epoch 045] average test loss: 2917.2395 cellbender:remove-background: [epoch 046] average training loss: 2880.6077 cellbender:remove-background: [epoch 047] average training loss: 2889.6174 cellbender:remove-background: [epoch 048] average training loss: 2911.6690 cellbender:remove-background: [epoch 049] average training loss: 2889.9275 cellbender:remove-background: [epoch 050] average training loss: 2919.9459 cellbender:remove-background: [epoch 050] average test loss: 2943.2997 cellbender:remove-background: [epoch 051] average training loss: 2926.7287 cellbender:remove-background: [epoch 052] average training loss: 2903.6775 cellbender:remove-background: [epoch 053] average training loss: 2904.2737 cellbender:remove-background: [epoch 054] average training loss: 2937.8127 cellbender:remove-background: [epoch 055] average training loss: 2922.5930 cellbender:remove-background: [epoch 055] average test loss: 2917.3350 cellbender:remove-background: [epoch 056] average training loss: 2922.1370 cellbender:remove-background: [epoch 057] average training loss: 2937.5210 cellbender:remove-background: [epoch 058] average training loss: 2911.1279 cellbender:remove-background: [epoch 059] average training loss: 2909.1811 cellbender:remove-background: [epoch 060] average training loss: 2919.0734 cellbender:remove-background: [epoch 060] average test loss: 3007.7706 cellbender:remove-background: [epoch 061] average training loss: 2944.9435 cellbender:remove-background: [epoch 062] average training loss: 2981.4674 cellbender:remove-background: [epoch 063] average training loss: 2992.0058 cellbender:remove-background: [epoch 064] average training loss: 2980.5303 cellbender:remove-background: [epoch 065] average training loss: 2964.8092 cellbender:remove-background: [epoch 065] average test loss: 2985.4867 cellbender:remove-background: [epoch 066] average training loss: 2999.8260 cellbender:remove-background: [epoch 067] average training loss: 2979.2833 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/1672-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 068] average training loss: 3014.4670 cellbender:remove-background: [epoch 069] average training loss: 2971.3824 cellbender:remove-background: [epoch 070] average training loss: 2989.7870 cellbender:remove-background: [epoch 070] average test loss: 2963.0327 cellbender:remove-background: [epoch 071] average training loss: 3005.6244 cellbender:remove-background: [epoch 072] average training loss: 3010.1767 cellbender:remove-background: [epoch 073] average training loss: 3054.3976 cellbender:remove-background: [epoch 074] average training loss: 3050.2347 cellbender:remove-background: [epoch 075] average training loss: 3023.5587 cellbender:remove-background: [epoch 075] average test loss: 3099.2378 cellbender:remove-background: [epoch 076] average training loss: 3076.1201 cellbender:remove-background: [epoch 077] average training loss: 3036.1959 cellbender:remove-background: [epoch 078] average training loss: 3120.9095 cellbender:remove-background: [epoch 079] average training loss: 3070.9838 cellbender:remove-background: [epoch 080] average training loss: 3101.6779 cellbender:remove-background: [epoch 080] average test loss: 3218.3842 cellbender:remove-background: [epoch 081] average training loss: 3095.5885 cellbender:remove-background: [epoch 082] average training loss: 3062.5602 cellbender:remove-background: [epoch 083] average training loss: 3220.6742 cellbender:remove-background: [epoch 084] average training loss: 3122.9050 cellbender:remove-background: [epoch 085] average training loss: 3117.2243 cellbender:remove-background: [epoch 085] average test loss: 3197.4840 cellbender:remove-background: [epoch 086] average training loss: 3066.5402 cellbender:remove-background: [epoch 087] average training loss: 3152.7699 cellbender:remove-background: [epoch 088] average training loss: 3090.8417 cellbender:remove-background: [epoch 089] average training loss: 3080.4639 cellbender:remove-background: [epoch 090] average training loss: 3220.3352 cellbender:remove-background: [epoch 090] average test loss: 3233.9160 cellbender:remove-background: [epoch 091] average training loss: 3100.7043 cellbender:remove-background: [epoch 092] average training loss: 3139.7256 cellbender:remove-background: [epoch 093] average training loss: 3103.0033 cellbender:remove-background: [epoch 094] average training loss: 3155.1256 cellbender:remove-background: [epoch 095] average training loss: 3129.5532 cellbender:remove-background: [epoch 095] average test loss: 3139.4473 cellbender:remove-background: [epoch 096] average training loss: 3181.5810 cellbender:remove-background: [epoch 097] average training loss: 3151.2556 cellbender:remove-background: [epoch 098] average training loss: 3167.5002 cellbender:remove-background: [epoch 099] average training loss: 3134.1050 cellbender:remove-background: [epoch 100] average training loss: 3111.5364 cellbender:remove-background: [epoch 100] average test loss: 3181.6159 cellbender:remove-background: [epoch 101] average training loss: 3148.9017 cellbender:remove-background: [epoch 102] average training loss: 3200.3268 cellbender:remove-background: [epoch 103] average training loss: 3184.2600 cellbender:remove-background: [epoch 104] average training loss: 3097.5791 cellbender:remove-background: [epoch 105] average training loss: 3102.7144 cellbender:remove-background: [epoch 105] average test loss: 3109.2294 cellbender:remove-background: [epoch 106] average training loss: 3146.6083 cellbender:remove-background: [epoch 107] average training loss: 3203.6982 cellbender:remove-background: [epoch 108] average training loss: 3184.4122 cellbender:remove-background: [epoch 109] average training loss: 3142.1510 cellbender:remove-background: [epoch 110] average training loss: 3166.9618 cellbender:remove-background: [epoch 110] average test loss: 3370.3669 cellbender:remove-background: [epoch 111] average training loss: 3160.1420 cellbender:remove-background: [epoch 112] average training loss: 3121.7155 cellbender:remove-background: [epoch 113] average training loss: 3261.4641 cellbender:remove-background: [epoch 114] average training loss: 3218.9428 cellbender:remove-background: [epoch 115] average training loss: 3194.4450 cellbender:remove-background: [epoch 115] average test loss: 3234.6706 cellbender:remove-background: [epoch 116] average training loss: 3212.5818 cellbender:remove-background: [epoch 117] average training loss: 3140.5486 cellbender:remove-background: [epoch 118] average training loss: 3189.4200 cellbender:remove-background: [epoch 119] average training loss: 3153.6842 cellbender:remove-background: [epoch 120] average training loss: 3189.7282 cellbender:remove-background: [epoch 120] average test loss: 3277.1980 cellbender:remove-background: [epoch 121] average training loss: 3138.3314 cellbender:remove-background: [epoch 122] average training loss: 3262.7893 cellbender:remove-background: [epoch 123] average training loss: 3145.0122 cellbender:remove-background: [epoch 124] average training loss: 3188.4298 cellbender:remove-background: [epoch 125] average training loss: 3164.6481 cellbender:remove-background: [epoch 125] average test loss: 3256.1638 cellbender:remove-background: [epoch 126] average training loss: 3156.0175 cellbender:remove-background: [epoch 127] average training loss: 3217.4749 cellbender:remove-background: [epoch 128] average training loss: 3218.9138 cellbender:remove-background: [epoch 129] average training loss: 3133.7623 cellbender:remove-background: [epoch 130] average training loss: 3192.6308 cellbender:remove-background: [epoch 130] average test loss: 3198.5866 cellbender:remove-background: [epoch 131] average training loss: 3228.4499 cellbender:remove-background: [epoch 132] average training loss: 3140.9601 cellbender:remove-background: [epoch 133] average training loss: 3116.2741 cellbender:remove-background: [epoch 134] average training loss: 3172.0390 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/1672-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 135] average training loss: 3133.0717 cellbender:remove-background: [epoch 135] average test loss: 3204.8504 cellbender:remove-background: [epoch 136] average training loss: 3174.9468 cellbender:remove-background: [epoch 137] average training loss: 3195.2083 cellbender:remove-background: [epoch 138] average training loss: 3131.8359 cellbender:remove-background: [epoch 139] average training loss: 3213.7307 cellbender:remove-background: [epoch 140] average training loss: 3135.5656 cellbender:remove-background: [epoch 140] average test loss: 3219.5039 cellbender:remove-background: [epoch 141] average training loss: 3203.1412 cellbender:remove-background: [epoch 142] average training loss: 3221.8287 cellbender:remove-background: [epoch 143] average training loss: 3217.1967 cellbender:remove-background: [epoch 144] average training loss: 3170.5675 cellbender:remove-background: [epoch 145] average training loss: 3247.2573 cellbender:remove-background: [epoch 145] average test loss: 3175.1017 cellbender:remove-background: [epoch 146] average training loss: 3201.6765 cellbender:remove-background: [epoch 147] average training loss: 3208.3176 cellbender:remove-background: [epoch 148] average training loss: 3165.4648 cellbender:remove-background: [epoch 149] average training loss: 3175.9415 cellbender:remove-background: [epoch 150] average training loss: 3174.4635 cellbender:remove-background: [epoch 150] average test loss: 3301.5120 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/1672-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:32:06 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp4b3joday cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp4b3joday /tmp/tmp4b3joday/17cf6a3602_random.pyro /tmp/tmp4b3joday/17cf6a3602_random.cuda /tmp/tmp4b3joday/17cf6a3602_model.torch /tmp/tmp4b3joday/17cf6a3602_optim.torch /tmp/tmp4b3joday/17cf6a3602_optim.pyro /tmp/tmp4b3joday/17cf6a3602_params.pyro /tmp/tmp4b3joday/17cf6a3602_train.loaderstate /tmp/tmp4b3joday/17cf6a3602_test.loaderstate /tmp/tmp4b3joday/17cf6a3602_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 (1/60) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/60) cellbender:remove-background: Working on chunk (3/60) cellbender:remove-background: Working on chunk (4/60) cellbender:remove-background: Working on chunk (5/60) cellbender:remove-background: Working on chunk (6/60) cellbender:remove-background: Working on chunk (7/60) cellbender:remove-background: Working on chunk (8/60) cellbender:remove-background: Working on chunk (9/60) cellbender:remove-background: Working on chunk (10/60) cellbender:remove-background: Working on chunk (11/60) cellbender:remove-background: Working on chunk (12/60) cellbender:remove-background: Working on chunk (13/60) cellbender:remove-background: Working on chunk (14/60) cellbender:remove-background: Working on chunk (15/60) cellbender:remove-background: Working on chunk (16/60) cellbender:remove-background: Working on chunk (17/60) cellbender:remove-background: Working on chunk (18/60) cellbender:remove-background: Working on chunk (19/60) cellbender:remove-background: Working on chunk (20/60) cellbender:remove-background: Working on chunk (21/60) cellbender:remove-background: Working on chunk (22/60) cellbender:remove-background: Working on chunk (23/60) cellbender:remove-background: Working on chunk (24/60) cellbender:remove-background: Working on chunk (25/60) cellbender:remove-background: Working on chunk (26/60) cellbender:remove-background: Working on chunk (27/60) cellbender:remove-background: Working on chunk (28/60) cellbender:remove-background: Working on chunk (29/60) cellbender:remove-background: Working on chunk (30/60) cellbender:remove-background: Working on chunk (31/60) cellbender:remove-background: Working on chunk (32/60) cellbender:remove-background: Working on chunk (33/60) cellbender:remove-background: Working on chunk (34/60) cellbender:remove-background: Working on chunk (35/60) cellbender:remove-background: Working on chunk (36/60) cellbender:remove-background: Working on chunk (37/60) cellbender:remove-background: Working on chunk (38/60) cellbender:remove-background: Working on chunk (39/60) cellbender:remove-background: Working on chunk (40/60) cellbender:remove-background: Working on chunk (41/60) cellbender:remove-background: Working on chunk (42/60) cellbender:remove-background: Working on chunk (43/60) cellbender:remove-background: Working on chunk (44/60) cellbender:remove-background: Working on chunk (45/60) cellbender:remove-background: Working on chunk (46/60) cellbender:remove-background: Working on chunk (47/60) cellbender:remove-background: Working on chunk (48/60) cellbender:remove-background: Working on chunk (49/60) cellbender:remove-background: Working on chunk (50/60) cellbender:remove-background: Working on chunk (51/60) cellbender:remove-background: Working on chunk (52/60) cellbender:remove-background: Working on chunk (53/60) cellbender:remove-background: Working on chunk (54/60) cellbender:remove-background: Working on chunk (55/60) cellbender:remove-background: Working on chunk (56/60) cellbender:remove-background: Working on chunk (57/60) cellbender:remove-background: Working on chunk (58/60) cellbender:remove-background: Working on chunk (59/60) cellbender:remove-background: Working on chunk (60/60) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-dACC/1672-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/1672-Schizophrenia-dACC/1672-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:36:13 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-dACC/1672-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/1672-Schizophrenia-dACC/1672-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: [1.68 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 15:48:28 Total MCKP estimation time = 707.52 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/1672-Schizophrenia-dACC/1672-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/1672-Schizophrenia-dACC/1672-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/1672-Schizophrenia-dACC/1672-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/1672-Schizophrenia-dACC/1672-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:48:46