cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2337-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 4792 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 0f4939823a) cellbender:remove-background: 2024-06-06 15:26:03 cellbender:remove-background: Running remove-background cellbender:remove-background: Loading data from /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2337-Schizophrenia-Hippocampus.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: 31836 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3784 cellbender:remove-background: Prior on counts for empty droplets is 87 cellbender:remove-background: Excluding 10535 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21301 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 43 cellbender:remove-background: Using 4792 probable cell barcodes, plus an additional 15208 barcodes, and 39098 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 86 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpk5q7xtwn 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: 4640.6865 cellbender:remove-background: [epoch 002] average training loss: 3580.8148 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 67 epochs cellbender:remove-background: [epoch 003] average training loss: 3057.1145 cellbender:remove-background: [epoch 004] average training loss: 2701.7079 cellbender:remove-background: [epoch 005] average training loss: 2587.1517 cellbender:remove-background: [epoch 005] average test loss: 2808.2349 cellbender:remove-background: [epoch 006] average training loss: 2546.5129 cellbender:remove-background: [epoch 007] average training loss: 2503.8425 cellbender:remove-background: [epoch 008] average training loss: 2479.0950 cellbender:remove-background: [epoch 009] average training loss: 2462.6670 cellbender:remove-background: [epoch 010] average training loss: 2397.8336 cellbender:remove-background: [epoch 010] average test loss: 2412.1650 cellbender:remove-background: [epoch 011] average training loss: 2371.9907 cellbender:remove-background: [epoch 012] average training loss: 2349.7526 cellbender:remove-background: [epoch 013] average training loss: 2333.8283 cellbender:remove-background: [epoch 014] average training loss: 2343.1221 cellbender:remove-background: [epoch 015] average training loss: 2321.8503 cellbender:remove-background: [epoch 015] average test loss: 2347.7422 cellbender:remove-background: [epoch 016] average training loss: 2305.3575 cellbender:remove-background: [epoch 017] average training loss: 2318.1505 cellbender:remove-background: [epoch 018] average training loss: 2307.0368 cellbender:remove-background: [epoch 019] average training loss: 2296.8597 cellbender:remove-background: [epoch 020] average training loss: 2276.5818 cellbender:remove-background: [epoch 020] average test loss: 2340.5022 cellbender:remove-background: [epoch 021] average training loss: 2271.0827 cellbender:remove-background: [epoch 022] average training loss: 2274.9650 cellbender:remove-background: [epoch 023] average training loss: 2270.7428 cellbender:remove-background: [epoch 024] average training loss: 2252.8374 cellbender:remove-background: [epoch 025] average training loss: 2235.0284 cellbender:remove-background: [epoch 025] average test loss: 2266.0737 cellbender:remove-background: [epoch 026] average training loss: 2216.2488 cellbender:remove-background: [epoch 027] average training loss: 2211.0839 cellbender:remove-background: [epoch 028] average training loss: 2206.0192 cellbender:remove-background: [epoch 029] average training loss: 2195.7071 cellbender:remove-background: [epoch 030] average training loss: 2186.8694 cellbender:remove-background: [epoch 030] average test loss: 2224.2269 cellbender:remove-background: [epoch 031] average training loss: 2180.9115 cellbender:remove-background: [epoch 032] average training loss: 2175.4008 cellbender:remove-background: [epoch 033] average training loss: 2177.4368 cellbender:remove-background: [epoch 034] average training loss: 2172.3777 cellbender:remove-background: [epoch 035] average training loss: 2175.0981 cellbender:remove-background: [epoch 035] average test loss: 2222.0752 cellbender:remove-background: [epoch 036] average training loss: 2171.7781 cellbender:remove-background: [epoch 037] average training loss: 2181.8416 cellbender:remove-background: [epoch 038] average training loss: 2183.7085 cellbender:remove-background: [epoch 039] average training loss: 2193.8728 cellbender:remove-background: [epoch 040] average training loss: 2192.7476 cellbender:remove-background: [epoch 040] average test loss: 2228.0977 cellbender:remove-background: [epoch 041] average training loss: 2206.7663 cellbender:remove-background: [epoch 042] average training loss: 2192.5037 cellbender:remove-background: [epoch 043] average training loss: 2203.8415 cellbender:remove-background: [epoch 044] average training loss: 2207.1533 cellbender:remove-background: [epoch 045] average training loss: 2226.8179 cellbender:remove-background: [epoch 045] average test loss: 2271.3197 cellbender:remove-background: [epoch 046] average training loss: 2233.0095 cellbender:remove-background: [epoch 047] average training loss: 2233.2901 cellbender:remove-background: [epoch 048] average training loss: 2217.9810 cellbender:remove-background: [epoch 049] average training loss: 2208.1078 cellbender:remove-background: [epoch 050] average training loss: 2234.3486 cellbender:remove-background: [epoch 050] average test loss: 2241.5785 cellbender:remove-background: [epoch 051] average training loss: 2204.3241 cellbender:remove-background: [epoch 052] average training loss: 2232.6225 cellbender:remove-background: [epoch 053] average training loss: 2216.4798 cellbender:remove-background: [epoch 054] average training loss: 2211.6507 cellbender:remove-background: [epoch 055] average training loss: 2213.7214 cellbender:remove-background: [epoch 055] average test loss: 2239.3556 cellbender:remove-background: [epoch 056] average training loss: 2227.3080 cellbender:remove-background: [epoch 057] average training loss: 2204.9081 cellbender:remove-background: [epoch 058] average training loss: 2216.6631 cellbender:remove-background: [epoch 059] average training loss: 2221.1151 cellbender:remove-background: [epoch 060] average training loss: 2215.2539 cellbender:remove-background: [epoch 060] average test loss: 2271.6012 cellbender:remove-background: [epoch 061] average training loss: 2228.6355 cellbender:remove-background: [epoch 062] average training loss: 2222.8552 cellbender:remove-background: [epoch 063] average training loss: 2234.4251 cellbender:remove-background: [epoch 064] average training loss: 2224.2260 cellbender:remove-background: [epoch 065] average training loss: 2256.7305 cellbender:remove-background: [epoch 065] average test loss: 2256.9812 cellbender:remove-background: [epoch 066] average training loss: 2230.9134 cellbender:remove-background: [epoch 067] average training loss: 2242.9962 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/2337-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 068] average training loss: 2227.1436 cellbender:remove-background: [epoch 069] average training loss: 2212.8856 cellbender:remove-background: [epoch 070] average training loss: 2230.5283 cellbender:remove-background: [epoch 070] average test loss: 2276.0159 cellbender:remove-background: [epoch 071] average training loss: 2220.2643 cellbender:remove-background: [epoch 072] average training loss: 2228.0198 cellbender:remove-background: [epoch 073] average training loss: 2238.4355 cellbender:remove-background: [epoch 074] average training loss: 2211.6523 cellbender:remove-background: [epoch 075] average training loss: 2231.7179 cellbender:remove-background: [epoch 075] average test loss: 2276.2982 cellbender:remove-background: [epoch 076] average training loss: 2221.9130 cellbender:remove-background: [epoch 077] average training loss: 2235.1991 cellbender:remove-background: [epoch 078] average training loss: 2225.5622 cellbender:remove-background: [epoch 079] average training loss: 2252.4669 cellbender:remove-background: [epoch 080] average training loss: 2230.8011 cellbender:remove-background: [epoch 080] average test loss: 2284.6621 cellbender:remove-background: [epoch 081] average training loss: 2248.0355 cellbender:remove-background: [epoch 082] average training loss: 2249.8701 cellbender:remove-background: [epoch 083] average training loss: 2222.3557 cellbender:remove-background: [epoch 084] average training loss: 2241.1123 cellbender:remove-background: [epoch 085] average training loss: 2238.8382 cellbender:remove-background: [epoch 085] average test loss: 2348.1724 cellbender:remove-background: [epoch 086] average training loss: 2261.7986 cellbender:remove-background: [epoch 087] average training loss: 2249.2494 cellbender:remove-background: [epoch 088] average training loss: 2239.7623 cellbender:remove-background: [epoch 089] average training loss: 2248.7153 cellbender:remove-background: [epoch 090] average training loss: 2237.3240 cellbender:remove-background: [epoch 090] average test loss: 2300.4093 cellbender:remove-background: [epoch 091] average training loss: 2250.1845 cellbender:remove-background: [epoch 092] average training loss: 2250.0419 cellbender:remove-background: [epoch 093] average training loss: 2238.2435 cellbender:remove-background: [epoch 094] average training loss: 2246.8393 cellbender:remove-background: [epoch 095] average training loss: 2233.7638 cellbender:remove-background: [epoch 095] average test loss: 2301.2305 cellbender:remove-background: [epoch 096] average training loss: 2268.2435 cellbender:remove-background: [epoch 097] average training loss: 2239.2108 cellbender:remove-background: [epoch 098] average training loss: 2239.3914 cellbender:remove-background: [epoch 099] average training loss: 2242.3242 cellbender:remove-background: [epoch 100] average training loss: 2233.9010 cellbender:remove-background: [epoch 100] average test loss: 2334.3278 cellbender:remove-background: [epoch 101] average training loss: 2248.8187 cellbender:remove-background: [epoch 102] average training loss: 2233.3716 cellbender:remove-background: [epoch 103] average training loss: 2230.2285 cellbender:remove-background: [epoch 104] average training loss: 2230.4914 cellbender:remove-background: [epoch 105] average training loss: 2247.8076 cellbender:remove-background: [epoch 105] average test loss: 2331.2336 cellbender:remove-background: [epoch 106] average training loss: 2238.5120 cellbender:remove-background: [epoch 107] average training loss: 2227.4692 cellbender:remove-background: [epoch 108] average training loss: 2229.2949 cellbender:remove-background: [epoch 109] average training loss: 2241.3321 cellbender:remove-background: [epoch 110] average training loss: 2220.0298 cellbender:remove-background: [epoch 110] average test loss: 2352.0393 cellbender:remove-background: [epoch 111] average training loss: 2239.9125 cellbender:remove-background: [epoch 112] average training loss: 2218.4319 cellbender:remove-background: [epoch 113] average training loss: 2242.7416 cellbender:remove-background: [epoch 114] average training loss: 2217.7419 cellbender:remove-background: [epoch 115] average training loss: 2220.4710 cellbender:remove-background: [epoch 115] average test loss: 2344.6510 cellbender:remove-background: [epoch 116] average training loss: 2234.3550 cellbender:remove-background: [epoch 117] average training loss: 2211.9823 cellbender:remove-background: [epoch 118] average training loss: 2221.9736 cellbender:remove-background: [epoch 119] average training loss: 2232.1252 cellbender:remove-background: [epoch 120] average training loss: 2206.5503 cellbender:remove-background: [epoch 120] average test loss: 2288.1864 cellbender:remove-background: [epoch 121] average training loss: 2234.8675 cellbender:remove-background: [epoch 122] average training loss: 2216.4503 cellbender:remove-background: [epoch 123] average training loss: 2213.0528 cellbender:remove-background: [epoch 124] average training loss: 2222.1249 cellbender:remove-background: [epoch 125] average training loss: 2237.3699 cellbender:remove-background: [epoch 125] average test loss: 2273.1773 cellbender:remove-background: [epoch 126] average training loss: 2224.8759 cellbender:remove-background: [epoch 127] average training loss: 2219.8769 cellbender:remove-background: [epoch 128] average training loss: 2226.1430 cellbender:remove-background: [epoch 129] average training loss: 2218.7780 cellbender:remove-background: [epoch 130] average training loss: 2235.6222 cellbender:remove-background: [epoch 130] average test loss: 2293.2602 cellbender:remove-background: [epoch 131] average training loss: 2219.9294 cellbender:remove-background: [epoch 132] average training loss: 2225.5562 cellbender:remove-background: [epoch 133] average training loss: 2219.4124 cellbender:remove-background: [epoch 134] average training loss: 2211.3646 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/2337-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 135] average training loss: 2218.0357 cellbender:remove-background: [epoch 135] average test loss: 2323.3843 cellbender:remove-background: [epoch 136] average training loss: 2227.0842 cellbender:remove-background: [epoch 137] average training loss: 2224.7740 cellbender:remove-background: [epoch 138] average training loss: 2206.7362 cellbender:remove-background: [epoch 139] average training loss: 2226.5782 cellbender:remove-background: [epoch 140] average training loss: 2204.8320 cellbender:remove-background: [epoch 140] average test loss: 2297.9451 cellbender:remove-background: [epoch 141] average training loss: 2214.1791 cellbender:remove-background: [epoch 142] average training loss: 2224.7462 cellbender:remove-background: [epoch 143] average training loss: 2222.8273 cellbender:remove-background: [epoch 144] average training loss: 2214.3355 cellbender:remove-background: [epoch 145] average training loss: 2212.1079 cellbender:remove-background: [epoch 145] average test loss: 2312.6013 cellbender:remove-background: [epoch 146] average training loss: 2227.2554 cellbender:remove-background: [epoch 147] average training loss: 2218.8569 cellbender:remove-background: [epoch 148] average training loss: 2219.9781 cellbender:remove-background: [epoch 149] average training loss: 2215.7607 cellbender:remove-background: [epoch 150] average training loss: 2223.0977 cellbender:remove-background: [epoch 150] average test loss: 2314.1782 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/2337-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:45:26 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmph8tb89wp cellbender:remove-background: Successfully unpacked tarball to /tmp/tmph8tb89wp /tmp/tmph8tb89wp/0f4939823a_random.pyro /tmp/tmph8tb89wp/0f4939823a_random.cuda /tmp/tmph8tb89wp/0f4939823a_model.torch /tmp/tmph8tb89wp/0f4939823a_optim.torch /tmp/tmph8tb89wp/0f4939823a_optim.pyro /tmp/tmph8tb89wp/0f4939823a_params.pyro /tmp/tmph8tb89wp/0f4939823a_train.loaderstate /tmp/tmph8tb89wp/0f4939823a_test.loaderstate /tmp/tmph8tb89wp/0f4939823a_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 (1/55) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/55) cellbender:remove-background: Working on chunk (3/55) cellbender:remove-background: Working on chunk (4/55) cellbender:remove-background: Working on chunk (5/55) cellbender:remove-background: Working on chunk (6/55) cellbender:remove-background: Working on chunk (7/55) cellbender:remove-background: Working on chunk (8/55) cellbender:remove-background: Working on chunk (9/55) cellbender:remove-background: Working on chunk (10/55) cellbender:remove-background: Working on chunk (11/55) cellbender:remove-background: Working on chunk (12/55) cellbender:remove-background: Working on chunk (13/55) cellbender:remove-background: Working on chunk (14/55) cellbender:remove-background: Working on chunk (15/55) cellbender:remove-background: Working on chunk (16/55) cellbender:remove-background: Working on chunk (17/55) cellbender:remove-background: Working on chunk (18/55) cellbender:remove-background: Working on chunk (19/55) cellbender:remove-background: Working on chunk (20/55) cellbender:remove-background: Working on chunk (21/55) cellbender:remove-background: Working on chunk (22/55) cellbender:remove-background: Working on chunk (23/55) cellbender:remove-background: Working on chunk (24/55) cellbender:remove-background: Working on chunk (25/55) cellbender:remove-background: Working on chunk (26/55) cellbender:remove-background: Working on chunk (27/55) cellbender:remove-background: Working on chunk (28/55) cellbender:remove-background: Working on chunk (29/55) cellbender:remove-background: Working on chunk (30/55) cellbender:remove-background: Working on chunk (31/55) cellbender:remove-background: Working on chunk (32/55) cellbender:remove-background: Working on chunk (33/55) cellbender:remove-background: Working on chunk (34/55) cellbender:remove-background: Working on chunk (35/55) cellbender:remove-background: Working on chunk (36/55) cellbender:remove-background: Working on chunk (37/55) cellbender:remove-background: Working on chunk (38/55) cellbender:remove-background: Working on chunk (39/55) cellbender:remove-background: Working on chunk (40/55) cellbender:remove-background: Working on chunk (41/55) cellbender:remove-background: Working on chunk (42/55) cellbender:remove-background: Working on chunk (43/55) cellbender:remove-background: Working on chunk (44/55) cellbender:remove-background: Working on chunk (45/55) cellbender:remove-background: Working on chunk (46/55) cellbender:remove-background: Working on chunk (47/55) cellbender:remove-background: Working on chunk (48/55) cellbender:remove-background: Working on chunk (49/55) cellbender:remove-background: Working on chunk (50/55) cellbender:remove-background: Working on chunk (51/55) cellbender:remove-background: Working on chunk (52/55) cellbender:remove-background: Working on chunk (53/55) cellbender:remove-background: Working on chunk (54/55) cellbender:remove-background: Working on chunk (55/55) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.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/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:49:11 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.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: [1.34 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 15:58:58 Total MCKP estimation time = 565.73 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/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.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/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.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/2337-Schizophrenia-Hippocampus/2337-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:59:14