cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2337-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-DLPFC/2337-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 5599 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash fe560588dc) cellbender:remove-background: 2024-06-06 15:25:23 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-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: 31585 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2073 cellbender:remove-background: Prior on counts for empty droplets is 77 cellbender:remove-background: Excluding 9840 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21745 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 38 cellbender:remove-background: Using 5599 probable cell barcodes, plus an additional 14401 barcodes, and 42900 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/tmpwaroc9nw 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: 3561.0444 cellbender:remove-background: [epoch 002] average training loss: 2856.5061 (6.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 68 epochs cellbender:remove-background: [epoch 003] average training loss: 2501.9209 cellbender:remove-background: [epoch 004] average training loss: 2277.7006 cellbender:remove-background: [epoch 005] average training loss: 2205.7472 cellbender:remove-background: [epoch 005] average test loss: 2398.3535 cellbender:remove-background: [epoch 006] average training loss: 2184.6594 cellbender:remove-background: [epoch 007] average training loss: 2155.0022 cellbender:remove-background: [epoch 008] average training loss: 2131.6842 cellbender:remove-background: [epoch 009] average training loss: 2113.8360 cellbender:remove-background: [epoch 010] average training loss: 2050.7289 cellbender:remove-background: [epoch 010] average test loss: 2049.0869 cellbender:remove-background: [epoch 011] average training loss: 2010.1842 cellbender:remove-background: [epoch 012] average training loss: 2002.6689 cellbender:remove-background: [epoch 013] average training loss: 1990.5468 cellbender:remove-background: [epoch 014] average training loss: 1988.9211 cellbender:remove-background: [epoch 015] average training loss: 1973.3187 cellbender:remove-background: [epoch 015] average test loss: 2035.7112 cellbender:remove-background: [epoch 016] average training loss: 1966.0078 cellbender:remove-background: [epoch 017] average training loss: 1968.8075 cellbender:remove-background: [epoch 018] average training loss: 1964.2413 cellbender:remove-background: [epoch 019] average training loss: 1959.3455 cellbender:remove-background: [epoch 020] average training loss: 1951.2090 cellbender:remove-background: [epoch 020] average test loss: 2016.2411 cellbender:remove-background: [epoch 021] average training loss: 1950.3472 cellbender:remove-background: [epoch 022] average training loss: 1950.0627 cellbender:remove-background: [epoch 023] average training loss: 1947.8267 cellbender:remove-background: [epoch 024] average training loss: 1944.1598 cellbender:remove-background: [epoch 025] average training loss: 1944.5671 cellbender:remove-background: [epoch 025] average test loss: 1989.1302 cellbender:remove-background: [epoch 026] average training loss: 1940.1908 cellbender:remove-background: [epoch 027] average training loss: 1939.3065 cellbender:remove-background: [epoch 028] average training loss: 1939.8184 cellbender:remove-background: [epoch 029] average training loss: 1937.0472 cellbender:remove-background: [epoch 030] average training loss: 1934.9003 cellbender:remove-background: [epoch 030] average test loss: 1976.2835 cellbender:remove-background: [epoch 031] average training loss: 1932.7813 cellbender:remove-background: [epoch 032] average training loss: 1930.4161 cellbender:remove-background: [epoch 033] average training loss: 1928.5699 cellbender:remove-background: [epoch 034] average training loss: 1929.3628 cellbender:remove-background: [epoch 035] average training loss: 1927.4946 cellbender:remove-background: [epoch 035] average test loss: 1967.9284 cellbender:remove-background: [epoch 036] average training loss: 1927.3663 cellbender:remove-background: [epoch 037] average training loss: 1924.7282 cellbender:remove-background: [epoch 038] average training loss: 1923.4886 cellbender:remove-background: [epoch 039] average training loss: 1922.7593 cellbender:remove-background: [epoch 040] average training loss: 1919.7830 cellbender:remove-background: [epoch 040] average test loss: 1966.1030 cellbender:remove-background: [epoch 041] average training loss: 1917.6913 cellbender:remove-background: [epoch 042] average training loss: 1926.4062 cellbender:remove-background: [epoch 043] average training loss: 1913.7961 cellbender:remove-background: [epoch 044] average training loss: 1916.0402 cellbender:remove-background: [epoch 045] average training loss: 1910.9568 cellbender:remove-background: [epoch 045] average test loss: 1950.9981 cellbender:remove-background: [epoch 046] average training loss: 1912.7474 cellbender:remove-background: [epoch 047] average training loss: 1907.2000 cellbender:remove-background: [epoch 048] average training loss: 1901.5099 cellbender:remove-background: [epoch 049] average training loss: 1905.7187 cellbender:remove-background: [epoch 050] average training loss: 1904.3888 cellbender:remove-background: [epoch 050] average test loss: 1947.3920 cellbender:remove-background: [epoch 051] average training loss: 1901.2070 cellbender:remove-background: [epoch 052] average training loss: 1907.2585 cellbender:remove-background: [epoch 053] average training loss: 1901.7155 cellbender:remove-background: [epoch 054] average training loss: 1900.3738 cellbender:remove-background: [epoch 055] average training loss: 1895.2833 cellbender:remove-background: [epoch 055] average test loss: 1942.8897 cellbender:remove-background: [epoch 056] average training loss: 1894.8705 cellbender:remove-background: [epoch 057] average training loss: 1891.1820 cellbender:remove-background: [epoch 058] average training loss: 1898.5970 cellbender:remove-background: [epoch 059] average training loss: 1901.4089 cellbender:remove-background: [epoch 060] average training loss: 1897.8312 cellbender:remove-background: [epoch 060] average test loss: 1942.9707 cellbender:remove-background: [epoch 061] average training loss: 1890.6602 cellbender:remove-background: [epoch 062] average training loss: 1886.7795 cellbender:remove-background: [epoch 063] average training loss: 1888.2233 cellbender:remove-background: [epoch 064] average training loss: 1891.7754 cellbender:remove-background: [epoch 065] average training loss: 1890.1670 cellbender:remove-background: [epoch 065] average test loss: 1940.7667 cellbender:remove-background: [epoch 066] average training loss: 1891.5794 cellbender:remove-background: [epoch 067] average training loss: 1892.2877 cellbender:remove-background: [epoch 068] average training loss: 1891.8456 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 069] average training loss: 1893.0662 cellbender:remove-background: [epoch 070] average training loss: 1889.5498 cellbender:remove-background: [epoch 070] average test loss: 1954.7093 cellbender:remove-background: [epoch 071] average training loss: 1891.8680 cellbender:remove-background: [epoch 072] average training loss: 1892.7307 cellbender:remove-background: [epoch 073] average training loss: 1890.3196 cellbender:remove-background: [epoch 074] average training loss: 1892.2687 cellbender:remove-background: [epoch 075] average training loss: 1888.6676 cellbender:remove-background: [epoch 075] average test loss: 1944.7714 cellbender:remove-background: [epoch 076] average training loss: 1893.5478 cellbender:remove-background: [epoch 077] average training loss: 1889.0494 cellbender:remove-background: [epoch 078] average training loss: 1890.6426 cellbender:remove-background: [epoch 079] average training loss: 1893.7597 cellbender:remove-background: [epoch 080] average training loss: 1893.3586 cellbender:remove-background: [epoch 080] average test loss: 1963.8053 cellbender:remove-background: [epoch 081] average training loss: 1896.0189 cellbender:remove-background: [epoch 082] average training loss: 1894.9556 cellbender:remove-background: [epoch 083] average training loss: 1894.4113 cellbender:remove-background: [epoch 084] average training loss: 1894.6232 cellbender:remove-background: [epoch 085] average training loss: 1894.1212 cellbender:remove-background: [epoch 085] average test loss: 1954.9528 cellbender:remove-background: [epoch 086] average training loss: 1897.4801 cellbender:remove-background: [epoch 087] average training loss: 1892.1968 cellbender:remove-background: [epoch 088] average training loss: 1896.4658 cellbender:remove-background: [epoch 089] average training loss: 1892.8029 cellbender:remove-background: [epoch 090] average training loss: 1893.7421 cellbender:remove-background: [epoch 090] average test loss: 1964.3632 cellbender:remove-background: [epoch 091] average training loss: 1896.4776 cellbender:remove-background: [epoch 092] average training loss: 1894.9663 cellbender:remove-background: [epoch 093] average training loss: 1902.3421 cellbender:remove-background: [epoch 094] average training loss: 1893.8654 cellbender:remove-background: [epoch 095] average training loss: 1893.8094 cellbender:remove-background: [epoch 095] average test loss: 1959.2503 cellbender:remove-background: [epoch 096] average training loss: 1893.9362 cellbender:remove-background: [epoch 097] average training loss: 1895.8320 cellbender:remove-background: [epoch 098] average training loss: 1895.6787 cellbender:remove-background: [epoch 099] average training loss: 1895.2373 cellbender:remove-background: [epoch 100] average training loss: 1893.0982 cellbender:remove-background: [epoch 100] average test loss: 1975.0331 cellbender:remove-background: [epoch 101] average training loss: 1894.9677 cellbender:remove-background: [epoch 102] average training loss: 1892.5647 cellbender:remove-background: [epoch 103] average training loss: 1893.8514 cellbender:remove-background: [epoch 104] average training loss: 1894.2769 cellbender:remove-background: [epoch 105] average training loss: 1893.7882 cellbender:remove-background: [epoch 105] average test loss: 1963.7494 cellbender:remove-background: [epoch 106] average training loss: 1895.9140 cellbender:remove-background: [epoch 107] average training loss: 1894.3341 cellbender:remove-background: [epoch 108] average training loss: 1895.7071 cellbender:remove-background: [epoch 109] average training loss: 1892.5066 cellbender:remove-background: [epoch 110] average training loss: 1896.2800 cellbender:remove-background: [epoch 110] average test loss: 1970.7681 cellbender:remove-background: [epoch 111] average training loss: 1894.1316 cellbender:remove-background: [epoch 112] average training loss: 1894.7303 cellbender:remove-background: [epoch 113] average training loss: 1892.8486 cellbender:remove-background: [epoch 114] average training loss: 1895.0531 cellbender:remove-background: [epoch 115] average training loss: 1892.3167 cellbender:remove-background: [epoch 115] average test loss: 1979.3553 cellbender:remove-background: [epoch 116] average training loss: 1895.8589 cellbender:remove-background: [epoch 117] average training loss: 1894.6942 cellbender:remove-background: [epoch 118] average training loss: 1895.8195 cellbender:remove-background: [epoch 119] average training loss: 1893.3824 cellbender:remove-background: [epoch 120] average training loss: 1892.7109 cellbender:remove-background: [epoch 120] average test loss: 1975.0511 cellbender:remove-background: [epoch 121] average training loss: 1895.7604 cellbender:remove-background: [epoch 122] average training loss: 1891.6110 cellbender:remove-background: [epoch 123] average training loss: 1892.9969 cellbender:remove-background: [epoch 124] average training loss: 1890.9874 cellbender:remove-background: [epoch 125] average training loss: 1893.2313 cellbender:remove-background: [epoch 125] average test loss: 1962.6478 cellbender:remove-background: [epoch 126] average training loss: 1887.4845 cellbender:remove-background: [epoch 127] average training loss: 1892.7312 cellbender:remove-background: [epoch 128] average training loss: 1891.3149 cellbender:remove-background: [epoch 129] average training loss: 1892.0276 cellbender:remove-background: [epoch 130] average training loss: 1890.0908 cellbender:remove-background: [epoch 130] average test loss: 1970.0463 cellbender:remove-background: [epoch 131] average training loss: 1891.2049 cellbender:remove-background: [epoch 132] average training loss: 1891.0545 cellbender:remove-background: [epoch 133] average training loss: 1888.3343 cellbender:remove-background: [epoch 134] average training loss: 1893.0431 cellbender:remove-background: [epoch 135] average training loss: 1892.4260 cellbender:remove-background: [epoch 135] average test loss: 1972.4827 cellbender:remove-background: [epoch 136] average training loss: 1892.3795 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 137] average training loss: 1890.8777 cellbender:remove-background: [epoch 138] average training loss: 1893.4414 cellbender:remove-background: [epoch 139] average training loss: 1889.2083 cellbender:remove-background: [epoch 140] average training loss: 1889.5867 cellbender:remove-background: [epoch 140] average test loss: 1965.5086 cellbender:remove-background: [epoch 141] average training loss: 1890.6581 cellbender:remove-background: [epoch 142] average training loss: 1893.2798 cellbender:remove-background: [epoch 143] average training loss: 1888.2522 cellbender:remove-background: [epoch 144] average training loss: 1891.3310 cellbender:remove-background: [epoch 145] average training loss: 1890.3707 cellbender:remove-background: [epoch 145] average test loss: 1965.4097 cellbender:remove-background: [epoch 146] average training loss: 1889.4598 cellbender:remove-background: [epoch 147] average training loss: 1889.8197 cellbender:remove-background: [epoch 148] average training loss: 1890.6360 cellbender:remove-background: [epoch 149] average training loss: 1890.7520 cellbender:remove-background: [epoch 150] average training loss: 1890.7244 cellbender:remove-background: [epoch 150] average test loss: 1965.1086 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-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:44:50 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpgf3jl3r0 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpgf3jl3r0 /tmp/tmpgf3jl3r0/fe560588dc_random.pyro /tmp/tmpgf3jl3r0/fe560588dc_random.cuda /tmp/tmpgf3jl3r0/fe560588dc_model.torch /tmp/tmpgf3jl3r0/fe560588dc_optim.torch /tmp/tmpgf3jl3r0/fe560588dc_optim.pyro /tmp/tmpgf3jl3r0/fe560588dc_params.pyro /tmp/tmpgf3jl3r0/fe560588dc_train.loaderstate /tmp/tmpgf3jl3r0/fe560588dc_test.loaderstate /tmp/tmpgf3jl3r0/fe560588dc_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 (1/53) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/53) cellbender:remove-background: Working on chunk (3/53) cellbender:remove-background: Working on chunk (4/53) cellbender:remove-background: Working on chunk (5/53) cellbender:remove-background: Working on chunk (6/53) cellbender:remove-background: Working on chunk (7/53) cellbender:remove-background: Working on chunk (8/53) cellbender:remove-background: Working on chunk (9/53) cellbender:remove-background: Working on chunk (10/53) cellbender:remove-background: Working on chunk (11/53) cellbender:remove-background: Working on chunk (12/53) cellbender:remove-background: Working on chunk (13/53) cellbender:remove-background: Working on chunk (14/53) cellbender:remove-background: Working on chunk (15/53) cellbender:remove-background: Working on chunk (16/53) cellbender:remove-background: Working on chunk (17/53) cellbender:remove-background: Working on chunk (18/53) cellbender:remove-background: Working on chunk (19/53) cellbender:remove-background: Working on chunk (20/53) cellbender:remove-background: Working on chunk (21/53) cellbender:remove-background: Working on chunk (22/53) cellbender:remove-background: Working on chunk (23/53) cellbender:remove-background: Working on chunk (24/53) cellbender:remove-background: Working on chunk (25/53) cellbender:remove-background: Working on chunk (26/53) cellbender:remove-background: Working on chunk (27/53) cellbender:remove-background: Working on chunk (28/53) cellbender:remove-background: Working on chunk (29/53) cellbender:remove-background: Working on chunk (30/53) cellbender:remove-background: Working on chunk (31/53) cellbender:remove-background: Working on chunk (32/53) cellbender:remove-background: Working on chunk (33/53) cellbender:remove-background: Working on chunk (34/53) cellbender:remove-background: Working on chunk (35/53) cellbender:remove-background: Working on chunk (36/53) cellbender:remove-background: Working on chunk (37/53) cellbender:remove-background: Working on chunk (38/53) cellbender:remove-background: Working on chunk (39/53) cellbender:remove-background: Working on chunk (40/53) cellbender:remove-background: Working on chunk (41/53) cellbender:remove-background: Working on chunk (42/53) cellbender:remove-background: Working on chunk (43/53) cellbender:remove-background: Working on chunk (44/53) cellbender:remove-background: Working on chunk (45/53) cellbender:remove-background: Working on chunk (46/53) cellbender:remove-background: Working on chunk (47/53) cellbender:remove-background: Working on chunk (48/53) cellbender:remove-background: Working on chunk (49/53) cellbender:remove-background: Working on chunk (50/53) cellbender:remove-background: Working on chunk (51/53) cellbender:remove-background: Working on chunk (52/53) cellbender:remove-background: Working on chunk (53/53) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-DLPFC/2337-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/2337-Schizophrenia-DLPFC/2337-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:48:21 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2337-Schizophrenia-DLPFC/2337-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/2337-Schizophrenia-DLPFC/2337-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: [1.12 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 15:56:27 Total MCKP estimation time = 467.86 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-DLPFC/2337-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/2337-Schizophrenia-DLPFC/2337-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/2337-Schizophrenia-DLPFC/2337-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/2337-Schizophrenia-DLPFC/2337-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:56:42