cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1672-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-DLPFC/1672-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 5160 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 6d84627c57) cellbender:remove-background: 2024-06-06 15:41:58 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-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: 31650 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 4405 cellbender:remove-background: Prior on counts for empty droplets is 57 cellbender:remove-background: Excluding 12601 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19049 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 28 cellbender:remove-background: Using 5160 probable cell barcodes, plus an additional 14840 barcodes, and 37791 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 56 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpqucz5vpx 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: 4293.9552 cellbender:remove-background: [epoch 002] average training loss: 3318.6501 (5.8 seconds per epoch) cellbender:remove-background: Will checkpoint every 73 epochs cellbender:remove-background: [epoch 003] average training loss: 2863.5345 cellbender:remove-background: [epoch 004] average training loss: 2611.1317 cellbender:remove-background: [epoch 005] average training loss: 2531.9702 cellbender:remove-background: [epoch 005] average test loss: 2566.8027 cellbender:remove-background: [epoch 006] average training loss: 2510.5557 cellbender:remove-background: [epoch 007] average training loss: 2481.7343 cellbender:remove-background: [epoch 008] average training loss: 2462.2948 cellbender:remove-background: [epoch 009] average training loss: 2455.8433 cellbender:remove-background: [epoch 010] average training loss: 2387.3006 cellbender:remove-background: [epoch 010] average test loss: 2406.9044 cellbender:remove-background: [epoch 011] average training loss: 2323.4969 cellbender:remove-background: [epoch 012] average training loss: 2306.5267 cellbender:remove-background: [epoch 013] average training loss: 2281.5376 cellbender:remove-background: [epoch 014] average training loss: 2292.5809 cellbender:remove-background: [epoch 015] average training loss: 2266.5825 cellbender:remove-background: [epoch 015] average test loss: 2258.3318 cellbender:remove-background: [epoch 016] average training loss: 2257.8119 cellbender:remove-background: [epoch 017] average training loss: 2262.0695 cellbender:remove-background: [epoch 018] average training loss: 2253.2071 cellbender:remove-background: [epoch 019] average training loss: 2243.1443 cellbender:remove-background: [epoch 020] average training loss: 2232.7640 cellbender:remove-background: [epoch 020] average test loss: 2236.0837 cellbender:remove-background: [epoch 021] average training loss: 2230.7922 cellbender:remove-background: [epoch 022] average training loss: 2231.7444 cellbender:remove-background: [epoch 023] average training loss: 2231.6866 cellbender:remove-background: [epoch 024] average training loss: 2225.4897 cellbender:remove-background: [epoch 025] average training loss: 2224.8413 cellbender:remove-background: [epoch 025] average test loss: 2204.7392 cellbender:remove-background: [epoch 026] average training loss: 2217.9577 cellbender:remove-background: [epoch 027] average training loss: 2218.8576 cellbender:remove-background: [epoch 028] average training loss: 2215.9979 cellbender:remove-background: [epoch 029] average training loss: 2213.0375 cellbender:remove-background: [epoch 030] average training loss: 2206.1830 cellbender:remove-background: [epoch 030] average test loss: 2193.7192 cellbender:remove-background: [epoch 031] average training loss: 2203.9963 cellbender:remove-background: [epoch 032] average training loss: 2190.4400 cellbender:remove-background: [epoch 033] average training loss: 2181.9436 cellbender:remove-background: [epoch 034] average training loss: 2179.8190 cellbender:remove-background: [epoch 035] average training loss: 2173.3643 cellbender:remove-background: [epoch 035] average test loss: 2156.7230 cellbender:remove-background: [epoch 036] average training loss: 2169.8342 cellbender:remove-background: [epoch 037] average training loss: 2167.9619 cellbender:remove-background: [epoch 038] average training loss: 2167.7795 cellbender:remove-background: [epoch 039] average training loss: 2167.2165 cellbender:remove-background: [epoch 040] average training loss: 2175.4731 cellbender:remove-background: [epoch 040] average test loss: 2169.1914 cellbender:remove-background: [epoch 041] average training loss: 2169.4442 cellbender:remove-background: [epoch 042] average training loss: 2169.3574 cellbender:remove-background: [epoch 043] average training loss: 2168.6665 cellbender:remove-background: [epoch 044] average training loss: 2162.5220 cellbender:remove-background: [epoch 045] average training loss: 2169.2452 cellbender:remove-background: [epoch 045] average test loss: 2167.1045 cellbender:remove-background: [epoch 046] average training loss: 2166.8384 cellbender:remove-background: [epoch 047] average training loss: 2165.3644 cellbender:remove-background: [epoch 048] average training loss: 2167.4873 cellbender:remove-background: [epoch 049] average training loss: 2165.4129 cellbender:remove-background: [epoch 050] average training loss: 2164.8357 cellbender:remove-background: [epoch 050] average test loss: 2148.2641 cellbender:remove-background: [epoch 051] average training loss: 2165.7292 cellbender:remove-background: [epoch 052] average training loss: 2164.1054 cellbender:remove-background: [epoch 053] average training loss: 2164.4135 cellbender:remove-background: [epoch 054] average training loss: 2163.8017 cellbender:remove-background: [epoch 055] average training loss: 2162.8835 cellbender:remove-background: [epoch 055] average test loss: 2164.0655 cellbender:remove-background: [epoch 056] average training loss: 2159.4187 cellbender:remove-background: [epoch 057] average training loss: 2158.6614 cellbender:remove-background: [epoch 058] average training loss: 2155.3498 cellbender:remove-background: [epoch 059] average training loss: 2156.4055 cellbender:remove-background: [epoch 060] average training loss: 2158.4643 cellbender:remove-background: [epoch 060] average test loss: 2151.1937 cellbender:remove-background: [epoch 061] average training loss: 2159.6981 cellbender:remove-background: [epoch 062] average training loss: 2156.0905 cellbender:remove-background: [epoch 063] average training loss: 2154.7284 cellbender:remove-background: [epoch 064] average training loss: 2154.3189 cellbender:remove-background: [epoch 065] average training loss: 2151.0271 cellbender:remove-background: [epoch 065] average test loss: 2157.1917 cellbender:remove-background: [epoch 066] average training loss: 2154.7706 cellbender:remove-background: [epoch 067] average training loss: 2148.5511 cellbender:remove-background: [epoch 068] average training loss: 2148.9437 cellbender:remove-background: [epoch 069] average training loss: 2147.7131 cellbender:remove-background: [epoch 070] average training loss: 2147.1185 cellbender:remove-background: [epoch 070] average test loss: 2152.1264 cellbender:remove-background: [epoch 071] average training loss: 2147.9748 cellbender:remove-background: [epoch 072] average training loss: 2150.3243 cellbender:remove-background: [epoch 073] average training loss: 2147.9774 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 074] average training loss: 2145.0023 cellbender:remove-background: [epoch 075] average training loss: 2142.6754 cellbender:remove-background: [epoch 075] average test loss: 2164.9634 cellbender:remove-background: [epoch 076] average training loss: 2146.3826 cellbender:remove-background: [epoch 077] average training loss: 2143.9361 cellbender:remove-background: [epoch 078] average training loss: 2140.5531 cellbender:remove-background: [epoch 079] average training loss: 2143.9325 cellbender:remove-background: [epoch 080] average training loss: 2142.7840 cellbender:remove-background: [epoch 080] average test loss: 2168.8645 cellbender:remove-background: [epoch 081] average training loss: 2145.4503 cellbender:remove-background: [epoch 082] average training loss: 2143.4815 cellbender:remove-background: [epoch 083] average training loss: 2142.7567 cellbender:remove-background: [epoch 084] average training loss: 2140.0117 cellbender:remove-background: [epoch 085] average training loss: 2142.0469 cellbender:remove-background: [epoch 085] average test loss: 2151.0546 cellbender:remove-background: [epoch 086] average training loss: 2140.5620 cellbender:remove-background: [epoch 087] average training loss: 2138.4201 cellbender:remove-background: [epoch 088] average training loss: 2138.6889 cellbender:remove-background: [epoch 089] average training loss: 2137.7057 cellbender:remove-background: [epoch 090] average training loss: 2145.8552 cellbender:remove-background: [epoch 090] average test loss: 2144.4250 cellbender:remove-background: [epoch 091] average training loss: 2136.3825 cellbender:remove-background: [epoch 092] average training loss: 2138.9912 cellbender:remove-background: [epoch 093] average training loss: 2138.1931 cellbender:remove-background: [epoch 094] average training loss: 2133.4291 cellbender:remove-background: [epoch 095] average training loss: 2134.7654 cellbender:remove-background: [epoch 095] average test loss: 2146.6906 cellbender:remove-background: [epoch 096] average training loss: 2133.6282 cellbender:remove-background: [epoch 097] average training loss: 2136.3420 cellbender:remove-background: [epoch 098] average training loss: 2139.0436 cellbender:remove-background: [epoch 099] average training loss: 2129.8357 cellbender:remove-background: [epoch 100] average training loss: 2130.1747 cellbender:remove-background: [epoch 100] average test loss: 2149.6315 cellbender:remove-background: [epoch 101] average training loss: 2128.3520 cellbender:remove-background: [epoch 102] average training loss: 2128.5473 cellbender:remove-background: [epoch 103] average training loss: 2127.5266 cellbender:remove-background: [epoch 104] average training loss: 2127.5347 cellbender:remove-background: [epoch 105] average training loss: 2125.7606 cellbender:remove-background: [epoch 105] average test loss: 2159.2561 cellbender:remove-background: [epoch 106] average training loss: 2126.4976 cellbender:remove-background: [epoch 107] average training loss: 2127.8035 cellbender:remove-background: [epoch 108] average training loss: 2126.4097 cellbender:remove-background: [epoch 109] average training loss: 2126.4451 cellbender:remove-background: [epoch 110] average training loss: 2124.6331 cellbender:remove-background: [epoch 110] average test loss: 2148.5578 cellbender:remove-background: [epoch 111] average training loss: 2126.6202 cellbender:remove-background: [epoch 112] average training loss: 2124.6782 cellbender:remove-background: [epoch 113] average training loss: 2125.6467 cellbender:remove-background: [epoch 114] average training loss: 2124.5993 cellbender:remove-background: [epoch 115] average training loss: 2122.4991 cellbender:remove-background: [epoch 115] average test loss: 2136.0319 cellbender:remove-background: [epoch 116] average training loss: 2120.0203 cellbender:remove-background: [epoch 117] average training loss: 2124.4560 cellbender:remove-background: [epoch 118] average training loss: 2122.9864 cellbender:remove-background: [epoch 119] average training loss: 2124.1404 cellbender:remove-background: [epoch 120] average training loss: 2123.0731 cellbender:remove-background: [epoch 120] average test loss: 2139.4556 cellbender:remove-background: [epoch 121] average training loss: 2119.0868 cellbender:remove-background: [epoch 122] average training loss: 2121.3894 cellbender:remove-background: [epoch 123] average training loss: 2121.9895 cellbender:remove-background: [epoch 124] average training loss: 2120.4569 cellbender:remove-background: [epoch 125] average training loss: 2119.4162 cellbender:remove-background: [epoch 125] average test loss: 2139.0267 cellbender:remove-background: [epoch 126] average training loss: 2120.1794 cellbender:remove-background: [epoch 127] average training loss: 2119.6292 cellbender:remove-background: [epoch 128] average training loss: 2119.1338 cellbender:remove-background: [epoch 129] average training loss: 2121.4076 cellbender:remove-background: [epoch 130] average training loss: 2117.6327 cellbender:remove-background: [epoch 130] average test loss: 2134.0874 cellbender:remove-background: [epoch 131] average training loss: 2121.3859 cellbender:remove-background: [epoch 132] average training loss: 2120.4706 cellbender:remove-background: [epoch 133] average training loss: 2123.8758 cellbender:remove-background: [epoch 134] average training loss: 2120.9724 cellbender:remove-background: [epoch 135] average training loss: 2118.7046 cellbender:remove-background: [epoch 135] average test loss: 2142.0659 cellbender:remove-background: [epoch 136] average training loss: 2117.9291 cellbender:remove-background: [epoch 137] average training loss: 2116.8466 cellbender:remove-background: [epoch 138] average training loss: 2118.4442 cellbender:remove-background: [epoch 139] average training loss: 2119.6316 cellbender:remove-background: [epoch 140] average training loss: 2116.9335 cellbender:remove-background: [epoch 140] average test loss: 2134.1788 cellbender:remove-background: [epoch 141] average training loss: 2117.8941 cellbender:remove-background: [epoch 142] average training loss: 2118.0782 cellbender:remove-background: [epoch 143] average training loss: 2117.5376 cellbender:remove-background: [epoch 144] average training loss: 2118.0454 cellbender:remove-background: [epoch 145] average training loss: 2117.6832 cellbender:remove-background: [epoch 145] average test loss: 2134.0349 cellbender:remove-background: [epoch 146] average training loss: 2117.8866 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 147] average training loss: 2117.3791 cellbender:remove-background: [epoch 148] average training loss: 2117.4903 cellbender:remove-background: [epoch 149] average training loss: 2117.0165 cellbender:remove-background: [epoch 150] average training loss: 2117.9956 cellbender:remove-background: [epoch 150] average test loss: 2136.4935 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-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:58:54 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpxclio2ed cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpxclio2ed /tmp/tmpxclio2ed/6d84627c57_random.pyro /tmp/tmpxclio2ed/6d84627c57_random.cuda /tmp/tmpxclio2ed/6d84627c57_model.torch /tmp/tmpxclio2ed/6d84627c57_optim.torch /tmp/tmpxclio2ed/6d84627c57_optim.pyro /tmp/tmpxclio2ed/6d84627c57_params.pyro /tmp/tmpxclio2ed/6d84627c57_train.loaderstate /tmp/tmpxclio2ed/6d84627c57_test.loaderstate /tmp/tmpxclio2ed/6d84627c57_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 (1/44) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/44) cellbender:remove-background: Working on chunk (3/44) cellbender:remove-background: Working on chunk (4/44) cellbender:remove-background: Working on chunk (5/44) cellbender:remove-background: Working on chunk (6/44) cellbender:remove-background: Working on chunk (7/44) cellbender:remove-background: Working on chunk (8/44) cellbender:remove-background: Working on chunk (9/44) cellbender:remove-background: Working on chunk (10/44) cellbender:remove-background: Working on chunk (11/44) cellbender:remove-background: Working on chunk (12/44) cellbender:remove-background: Working on chunk (13/44) cellbender:remove-background: Working on chunk (14/44) cellbender:remove-background: Working on chunk (15/44) cellbender:remove-background: Working on chunk (16/44) cellbender:remove-background: Working on chunk (17/44) cellbender:remove-background: Working on chunk (18/44) cellbender:remove-background: Working on chunk (19/44) cellbender:remove-background: Working on chunk (20/44) cellbender:remove-background: Working on chunk (21/44) cellbender:remove-background: Working on chunk (22/44) cellbender:remove-background: Working on chunk (23/44) cellbender:remove-background: Working on chunk (24/44) cellbender:remove-background: Working on chunk (25/44) cellbender:remove-background: Working on chunk (26/44) cellbender:remove-background: Working on chunk (27/44) cellbender:remove-background: Working on chunk (28/44) cellbender:remove-background: Working on chunk (29/44) cellbender:remove-background: Working on chunk (30/44) cellbender:remove-background: Working on chunk (31/44) cellbender:remove-background: Working on chunk (32/44) cellbender:remove-background: Working on chunk (33/44) cellbender:remove-background: Working on chunk (34/44) cellbender:remove-background: Working on chunk (35/44) cellbender:remove-background: Working on chunk (36/44) cellbender:remove-background: Working on chunk (37/44) cellbender:remove-background: Working on chunk (38/44) cellbender:remove-background: Working on chunk (39/44) cellbender:remove-background: Working on chunk (40/44) cellbender:remove-background: Working on chunk (41/44) cellbender:remove-background: Working on chunk (42/44) cellbender:remove-background: Working on chunk (43/44) cellbender:remove-background: Working on chunk (44/44) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-DLPFC/1672-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/1672-Schizophrenia-DLPFC/1672-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:01:55 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-DLPFC/1672-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/1672-Schizophrenia-DLPFC/1672-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: [1.37 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 16:11:53 Total MCKP estimation time = 576.25 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-DLPFC/1672-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/1672-Schizophrenia-DLPFC/1672-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/1672-Schizophrenia-DLPFC/1672-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/1672-Schizophrenia-DLPFC/1672-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:12:11