cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1320-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 4763 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 0c64186f1b) cellbender:remove-background: 2024-06-06 14:54:02 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/1320-Schizophrenia-DLPFC.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: 31961 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3638 cellbender:remove-background: Prior on counts for empty droplets is 77 cellbender:remove-background: Excluding 9946 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22015 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 38 cellbender:remove-background: Using 4763 probable cell barcodes, plus an additional 15237 barcodes, and 61335 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 77 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpi36n629n 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: 4709.9712 cellbender:remove-background: [epoch 002] average training loss: 3618.0867 (14.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 30 epochs cellbender:remove-background: [epoch 003] average training loss: 3061.4111 cellbender:remove-background: [epoch 004] average training loss: 2692.2674 cellbender:remove-background: [epoch 005] average training loss: 2578.2193 cellbender:remove-background: [epoch 005] average test loss: 2747.5313 cellbender:remove-background: [epoch 006] average training loss: 2561.3658 cellbender:remove-background: [epoch 007] average training loss: 2507.2732 cellbender:remove-background: [epoch 008] average training loss: 2474.7885 cellbender:remove-background: [epoch 009] average training loss: 2449.4004 cellbender:remove-background: [epoch 010] average training loss: 2381.8699 cellbender:remove-background: [epoch 010] average test loss: 2424.6022 cellbender:remove-background: [epoch 011] average training loss: 2299.2311 cellbender:remove-background: [epoch 012] average training loss: 2261.7122 cellbender:remove-background: [epoch 013] average training loss: 2238.4163 cellbender:remove-background: [epoch 014] average training loss: 2251.8417 cellbender:remove-background: [epoch 015] average training loss: 2217.7025 cellbender:remove-background: [epoch 015] average test loss: 2280.1611 cellbender:remove-background: [epoch 016] average training loss: 2203.6872 cellbender:remove-background: [epoch 017] average training loss: 2210.1694 cellbender:remove-background: [epoch 018] average training loss: 2199.2004 cellbender:remove-background: [epoch 019] average training loss: 2182.4215 cellbender:remove-background: [epoch 020] average training loss: 2163.1128 cellbender:remove-background: [epoch 020] average test loss: 2213.8795 cellbender:remove-background: [epoch 021] average training loss: 2147.7988 cellbender:remove-background: [epoch 022] average training loss: 2130.9196 cellbender:remove-background: [epoch 023] average training loss: 2121.6847 cellbender:remove-background: [epoch 024] average training loss: 2110.5076 cellbender:remove-background: [epoch 025] average training loss: 2105.6504 cellbender:remove-background: [epoch 025] average test loss: 2136.9980 cellbender:remove-background: [epoch 026] average training loss: 2096.7048 cellbender:remove-background: [epoch 027] average training loss: 2098.2631 cellbender:remove-background: [epoch 028] average training loss: 2105.3414 cellbender:remove-background: [epoch 029] average training loss: 2099.0259 cellbender:remove-background: [epoch 030] average training loss: 2095.8523 cellbender:remove-background: [epoch 030] average test loss: 2128.7967 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/1320-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 031] average training loss: 2098.6472 cellbender:remove-background: [epoch 032] average training loss: 2098.1818 cellbender:remove-background: [epoch 033] average training loss: 2091.4329 cellbender:remove-background: [epoch 034] average training loss: 2096.8950 cellbender:remove-background: [epoch 035] average training loss: 2087.3873 cellbender:remove-background: [epoch 035] average test loss: 2114.9171 cellbender:remove-background: [epoch 036] average training loss: 2090.3437 cellbender:remove-background: [epoch 037] average training loss: 2091.1940 cellbender:remove-background: [epoch 038] average training loss: 2097.1672 cellbender:remove-background: [epoch 039] average training loss: 2101.6178 cellbender:remove-background: [epoch 040] average training loss: 2116.0480 cellbender:remove-background: [epoch 040] average test loss: 2168.5267 cellbender:remove-background: [epoch 041] average training loss: 2111.8859 cellbender:remove-background: [epoch 042] average training loss: 2102.2295 cellbender:remove-background: [epoch 043] average training loss: 2095.0718 cellbender:remove-background: [epoch 044] average training loss: 2093.5349 cellbender:remove-background: [epoch 045] average training loss: 2099.3342 cellbender:remove-background: [epoch 045] average test loss: 2115.2718 cellbender:remove-background: [epoch 046] average training loss: 2111.2468 cellbender:remove-background: [epoch 047] average training loss: 2112.3408 cellbender:remove-background: [epoch 048] average training loss: 2125.5952 cellbender:remove-background: [epoch 049] average training loss: 2105.4564 cellbender:remove-background: [epoch 050] average training loss: 2113.5368 cellbender:remove-background: [epoch 050] average test loss: 2202.2260 cellbender:remove-background: [epoch 051] average training loss: 2131.8281 cellbender:remove-background: [epoch 052] average training loss: 2107.2982 cellbender:remove-background: [epoch 053] average training loss: 2126.5865 cellbender:remove-background: [epoch 054] average training loss: 2128.1457 cellbender:remove-background: [epoch 055] average training loss: 2123.1696 cellbender:remove-background: [epoch 055] average test loss: 2156.6114 cellbender:remove-background: [epoch 056] average training loss: 2124.2315 cellbender:remove-background: [epoch 057] average training loss: 2137.4980 cellbender:remove-background: [epoch 058] average training loss: 2124.9571 cellbender:remove-background: [epoch 059] average training loss: 2136.7776 cellbender:remove-background: [epoch 060] average training loss: 2122.4446 cellbender:remove-background: [epoch 060] average test loss: 2177.0027 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/1320-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 061] average training loss: 2130.1738 cellbender:remove-background: [epoch 062] average training loss: 2125.9441 cellbender:remove-background: [epoch 063] average training loss: 2137.2672 cellbender:remove-background: [epoch 064] average training loss: 2121.9872 cellbender:remove-background: [epoch 065] average training loss: 2115.6884 cellbender:remove-background: [epoch 065] average test loss: 2200.0326 cellbender:remove-background: [epoch 066] average training loss: 2125.8456 cellbender:remove-background: [epoch 067] average training loss: 2124.1888 cellbender:remove-background: [epoch 068] average training loss: 2136.0081 cellbender:remove-background: [epoch 069] average training loss: 2120.4229 cellbender:remove-background: [epoch 070] average training loss: 2133.3985 cellbender:remove-background: [epoch 070] average test loss: 2149.5989 cellbender:remove-background: [epoch 071] average training loss: 2131.9649 cellbender:remove-background: [epoch 072] average training loss: 2133.3240 cellbender:remove-background: [epoch 073] average training loss: 2139.1111 cellbender:remove-background: [epoch 074] average training loss: 2122.6279 cellbender:remove-background: [epoch 075] average training loss: 2121.7454 cellbender:remove-background: [epoch 075] average test loss: 2194.2884 cellbender:remove-background: [epoch 076] average training loss: 2129.4379 cellbender:remove-background: [epoch 077] average training loss: 2126.1353 cellbender:remove-background: [epoch 078] average training loss: 2119.7136 cellbender:remove-background: [epoch 079] average training loss: 2117.5447 cellbender:remove-background: [epoch 080] average training loss: 2124.4855 cellbender:remove-background: [epoch 080] average test loss: 2144.7822 cellbender:remove-background: [epoch 081] average training loss: 2104.2282 cellbender:remove-background: [epoch 082] average training loss: 2120.2701 cellbender:remove-background: [epoch 083] average training loss: 2116.5536 cellbender:remove-background: [epoch 084] average training loss: 2125.1422 cellbender:remove-background: [epoch 085] average training loss: 2106.4961 cellbender:remove-background: [epoch 085] average test loss: 2209.3957 cellbender:remove-background: [epoch 086] average training loss: 2117.7588 cellbender:remove-background: [epoch 087] average training loss: 2121.5022 cellbender:remove-background: [epoch 088] average training loss: 2121.5514 cellbender:remove-background: [epoch 089] average training loss: 2119.7568 cellbender:remove-background: [epoch 090] average training loss: 2109.5011 cellbender:remove-background: [epoch 090] average test loss: 2194.9533 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/1320-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 091] average training loss: 2112.2980 cellbender:remove-background: [epoch 092] average training loss: 2109.3439 cellbender:remove-background: [epoch 093] average training loss: 2125.3798 cellbender:remove-background: [epoch 094] average training loss: 2120.6945 cellbender:remove-background: [epoch 095] average training loss: 2118.4914 cellbender:remove-background: [epoch 095] average test loss: 2171.4189 cellbender:remove-background: [epoch 096] average training loss: 2119.4808 cellbender:remove-background: [epoch 097] average training loss: 2098.9090 cellbender:remove-background: [epoch 098] average training loss: 2116.8661 cellbender:remove-background: [epoch 099] average training loss: 2102.7176 cellbender:remove-background: [epoch 100] average training loss: 2100.8642 cellbender:remove-background: [epoch 100] average test loss: 2195.7691 cellbender:remove-background: [epoch 101] average training loss: 2109.0945 cellbender:remove-background: [epoch 102] average training loss: 2103.9661 cellbender:remove-background: [epoch 103] average training loss: 2107.6470 cellbender:remove-background: [epoch 104] average training loss: 2102.8820 cellbender:remove-background: [epoch 105] average training loss: 2108.2892 cellbender:remove-background: [epoch 105] average test loss: 2171.9494 cellbender:remove-background: [epoch 106] average training loss: 2119.9582 cellbender:remove-background: [epoch 107] average training loss: 2100.8609 cellbender:remove-background: [epoch 108] average training loss: 2097.4769 cellbender:remove-background: [epoch 109] average training loss: 2105.7373 cellbender:remove-background: [epoch 110] average training loss: 2104.7414 cellbender:remove-background: [epoch 110] average test loss: 2178.6043 cellbender:remove-background: [epoch 111] average training loss: 2110.7786 cellbender:remove-background: [epoch 112] average training loss: 2103.4277 cellbender:remove-background: [epoch 113] average training loss: 2100.3112 cellbender:remove-background: [epoch 114] average training loss: 2102.8781 cellbender:remove-background: [epoch 115] average training loss: 2102.3188 cellbender:remove-background: [epoch 115] average test loss: 2190.6262 cellbender:remove-background: [epoch 116] average training loss: 2102.3607 cellbender:remove-background: [epoch 117] average training loss: 2106.3109 cellbender:remove-background: [epoch 118] average training loss: 2095.0565 cellbender:remove-background: [epoch 119] average training loss: 2115.8092 cellbender:remove-background: [epoch 120] average training loss: 2109.1375 cellbender:remove-background: [epoch 120] average test loss: 2188.6333 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/1320-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 121] average training loss: 2095.5607 cellbender:remove-background: [epoch 122] average training loss: 2097.8440 cellbender:remove-background: [epoch 123] average training loss: 2104.8813 cellbender:remove-background: [epoch 124] average training loss: 2098.5865 cellbender:remove-background: [epoch 125] average training loss: 2099.2690 cellbender:remove-background: [epoch 125] average test loss: 2171.5834 cellbender:remove-background: [epoch 126] average training loss: 2096.7110 cellbender:remove-background: [epoch 127] average training loss: 2102.3811 cellbender:remove-background: [epoch 128] average training loss: 2102.6363 cellbender:remove-background: [epoch 129] average training loss: 2093.5015 cellbender:remove-background: [epoch 130] average training loss: 2103.0424 cellbender:remove-background: [epoch 130] average test loss: 2188.7018 cellbender:remove-background: [epoch 131] average training loss: 2100.7600 cellbender:remove-background: [epoch 132] average training loss: 2103.8929 cellbender:remove-background: [epoch 133] average training loss: 2099.6863 cellbender:remove-background: [epoch 134] average training loss: 2093.1164 cellbender:remove-background: [epoch 135] average training loss: 2097.6965 cellbender:remove-background: [epoch 135] average test loss: 2176.2007 cellbender:remove-background: [epoch 136] average training loss: 2094.8679 cellbender:remove-background: [epoch 137] average training loss: 2096.1998 cellbender:remove-background: [epoch 138] average training loss: 2097.5524 cellbender:remove-background: [epoch 139] average training loss: 2098.7136 cellbender:remove-background: [epoch 140] average training loss: 2098.5646 cellbender:remove-background: [epoch 140] average test loss: 2173.0158 cellbender:remove-background: [epoch 141] average training loss: 2089.8876 cellbender:remove-background: [epoch 142] average training loss: 2095.6157 cellbender:remove-background: [epoch 143] average training loss: 2086.1470 cellbender:remove-background: [epoch 144] average training loss: 2096.3968 cellbender:remove-background: [epoch 145] average training loss: 2095.3008 cellbender:remove-background: [epoch 145] average test loss: 2190.9816 cellbender:remove-background: [epoch 146] average training loss: 2096.8244 cellbender:remove-background: [epoch 147] average training loss: 2094.8827 cellbender:remove-background: [epoch 148] average training loss: 2092.3793 cellbender:remove-background: [epoch 149] average training loss: 2093.5109 cellbender:remove-background: [epoch 150] average training loss: 2101.1080 cellbender:remove-background: [epoch 150] average test loss: 2174.1981 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/1320-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:36:01 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpo5r9hsff cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpo5r9hsff /tmp/tmpo5r9hsff/0c64186f1b_random.pyro /tmp/tmpo5r9hsff/0c64186f1b_random.cuda /tmp/tmpo5r9hsff/0c64186f1b_model.torch /tmp/tmpo5r9hsff/0c64186f1b_optim.torch /tmp/tmpo5r9hsff/0c64186f1b_optim.pyro /tmp/tmpo5r9hsff/0c64186f1b_params.pyro /tmp/tmpo5r9hsff/0c64186f1b_train.loaderstate /tmp/tmpo5r9hsff/0c64186f1b_test.loaderstate /tmp/tmpo5r9hsff/0c64186f1b_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 (1/46) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/46) cellbender:remove-background: Working on chunk (3/46) cellbender:remove-background: Working on chunk (4/46) cellbender:remove-background: Working on chunk (5/46) cellbender:remove-background: Working on chunk (6/46) cellbender:remove-background: Working on chunk (7/46) cellbender:remove-background: Working on chunk (8/46) cellbender:remove-background: Working on chunk (9/46) cellbender:remove-background: Working on chunk (10/46) cellbender:remove-background: Working on chunk (11/46) cellbender:remove-background: Working on chunk (12/46) cellbender:remove-background: Working on chunk (13/46) cellbender:remove-background: Working on chunk (14/46) cellbender:remove-background: Working on chunk (15/46) cellbender:remove-background: Working on chunk (16/46) cellbender:remove-background: Working on chunk (17/46) cellbender:remove-background: Working on chunk (18/46) cellbender:remove-background: Working on chunk (19/46) cellbender:remove-background: Working on chunk (20/46) cellbender:remove-background: Working on chunk (21/46) cellbender:remove-background: Working on chunk (22/46) cellbender:remove-background: Working on chunk (23/46) cellbender:remove-background: Working on chunk (24/46) cellbender:remove-background: Working on chunk (25/46) cellbender:remove-background: Working on chunk (26/46) cellbender:remove-background: Working on chunk (27/46) cellbender:remove-background: Working on chunk (28/46) cellbender:remove-background: Working on chunk (29/46) cellbender:remove-background: Working on chunk (30/46) cellbender:remove-background: Working on chunk (31/46) cellbender:remove-background: Working on chunk (32/46) cellbender:remove-background: Working on chunk (33/46) cellbender:remove-background: Working on chunk (34/46) cellbender:remove-background: Working on chunk (35/46) cellbender:remove-background: Working on chunk (36/46) cellbender:remove-background: Working on chunk (37/46) cellbender:remove-background: Working on chunk (38/46) cellbender:remove-background: Working on chunk (39/46) cellbender:remove-background: Working on chunk (40/46) cellbender:remove-background: Working on chunk (41/46) cellbender:remove-background: Working on chunk (42/46) cellbender:remove-background: Working on chunk (43/46) cellbender:remove-background: Working on chunk (44/46) cellbender:remove-background: Working on chunk (45/46) cellbender:remove-background: Working on chunk (46/46) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.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/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:40:58 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.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: [1.31 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 15:50:31 Total MCKP estimation time = 544.66 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/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.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/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.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/1320-Schizophrenia-DLPFC/1320-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:50:53