cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2275-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 13428 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash dc53e14360) cellbender:remove-background: 2024-06-06 14:48:30 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/2275-Bipolar-dACC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 30503 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 786 cellbender:remove-background: Prior on counts for empty droplets is 75 cellbender:remove-background: Excluding 7277 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23226 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 37 cellbender:remove-background: Using 13428 probable cell barcodes, plus an additional 6572 barcodes, and 19800 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 74 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp3xyvj650 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: 3648.8499 cellbender:remove-background: [epoch 002] average training loss: 2999.7346 (13.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 33 epochs cellbender:remove-background: [epoch 003] average training loss: 2645.4840 cellbender:remove-background: [epoch 004] average training loss: 2413.9214 cellbender:remove-background: [epoch 005] average training loss: 2331.9513 cellbender:remove-background: [epoch 005] average test loss: 2310.9286 cellbender:remove-background: [epoch 006] average training loss: 2302.9171 cellbender:remove-background: [epoch 007] average training loss: 2275.6538 cellbender:remove-background: [epoch 008] average training loss: 2261.6995 cellbender:remove-background: [epoch 009] average training loss: 2259.1290 cellbender:remove-background: [epoch 010] average training loss: 2244.9836 cellbender:remove-background: [epoch 010] average test loss: 2232.6423 cellbender:remove-background: [epoch 011] average training loss: 2234.8057 cellbender:remove-background: [epoch 012] average training loss: 2226.8188 cellbender:remove-background: [epoch 013] average training loss: 2172.5334 cellbender:remove-background: [epoch 014] average training loss: 2152.4873 cellbender:remove-background: [epoch 015] average training loss: 2139.1789 cellbender:remove-background: [epoch 015] average test loss: 2140.3095 cellbender:remove-background: [epoch 016] average training loss: 2133.9901 cellbender:remove-background: [epoch 017] average training loss: 2136.6804 cellbender:remove-background: [epoch 018] average training loss: 2131.2928 cellbender:remove-background: [epoch 019] average training loss: 2125.2101 cellbender:remove-background: [epoch 020] average training loss: 2114.1160 cellbender:remove-background: [epoch 020] average test loss: 2116.6430 cellbender:remove-background: [epoch 021] average training loss: 2112.1042 cellbender:remove-background: [epoch 022] average training loss: 2108.0289 cellbender:remove-background: [epoch 023] average training loss: 2104.7939 cellbender:remove-background: [epoch 024] average training loss: 2098.1365 cellbender:remove-background: [epoch 025] average training loss: 2097.1703 cellbender:remove-background: [epoch 025] average test loss: 2087.2533 cellbender:remove-background: [epoch 026] average training loss: 2088.8893 cellbender:remove-background: [epoch 027] average training loss: 2084.9777 cellbender:remove-background: [epoch 028] average training loss: 2078.7851 cellbender:remove-background: [epoch 029] average training loss: 2073.6483 cellbender:remove-background: [epoch 030] average training loss: 2070.1886 cellbender:remove-background: [epoch 030] average test loss: 2056.0450 cellbender:remove-background: [epoch 031] average training loss: 2069.3167 cellbender:remove-background: [epoch 032] average training loss: 2066.1026 cellbender:remove-background: [epoch 033] average training loss: 2066.0375 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/2275-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 034] average training loss: 2062.9913 cellbender:remove-background: [epoch 035] average training loss: 2060.5683 cellbender:remove-background: [epoch 035] average test loss: 2046.2638 cellbender:remove-background: [epoch 036] average training loss: 2057.2691 cellbender:remove-background: [epoch 037] average training loss: 2055.6947 cellbender:remove-background: [epoch 038] average training loss: 2053.4185 cellbender:remove-background: [epoch 039] average training loss: 2052.6128 cellbender:remove-background: [epoch 040] average training loss: 2051.1887 cellbender:remove-background: [epoch 040] average test loss: 2035.1927 cellbender:remove-background: [epoch 041] average training loss: 2049.5943 cellbender:remove-background: [epoch 042] average training loss: 2048.8496 cellbender:remove-background: [epoch 043] average training loss: 2046.2385 cellbender:remove-background: [epoch 044] average training loss: 2044.8444 cellbender:remove-background: [epoch 045] average training loss: 2045.1816 cellbender:remove-background: [epoch 045] average test loss: 2040.1346 cellbender:remove-background: [epoch 046] average training loss: 2042.2949 cellbender:remove-background: [epoch 047] average training loss: 2043.3030 cellbender:remove-background: [epoch 048] average training loss: 2041.4050 cellbender:remove-background: [epoch 049] average training loss: 2041.8203 cellbender:remove-background: [epoch 050] average training loss: 2041.1968 cellbender:remove-background: [epoch 050] average test loss: 2028.3645 cellbender:remove-background: [epoch 051] average training loss: 2039.9442 cellbender:remove-background: [epoch 052] average training loss: 2038.5160 cellbender:remove-background: [epoch 053] average training loss: 2036.6440 cellbender:remove-background: [epoch 054] average training loss: 2035.4262 cellbender:remove-background: [epoch 055] average training loss: 2034.9967 cellbender:remove-background: [epoch 055] average test loss: 2009.0988 cellbender:remove-background: [epoch 056] average training loss: 2033.9968 cellbender:remove-background: [epoch 057] average training loss: 2032.5851 cellbender:remove-background: [epoch 058] average training loss: 2031.2699 cellbender:remove-background: [epoch 059] average training loss: 2031.1273 cellbender:remove-background: [epoch 060] average training loss: 2029.7973 cellbender:remove-background: [epoch 060] average test loss: 2016.2447 cellbender:remove-background: [epoch 061] average training loss: 2030.0560 cellbender:remove-background: [epoch 062] average training loss: 2027.5080 cellbender:remove-background: [epoch 063] average training loss: 2027.5233 cellbender:remove-background: [epoch 064] average training loss: 2027.4748 cellbender:remove-background: [epoch 065] average training loss: 2027.5219 cellbender:remove-background: [epoch 065] average test loss: 2017.0991 cellbender:remove-background: [epoch 066] average training loss: 2026.6199 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/2275-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 067] average training loss: 2027.1591 cellbender:remove-background: [epoch 068] average training loss: 2026.6842 cellbender:remove-background: [epoch 069] average training loss: 2026.1000 cellbender:remove-background: [epoch 070] average training loss: 2023.6188 cellbender:remove-background: [epoch 070] average test loss: 2012.2697 cellbender:remove-background: [epoch 071] average training loss: 2025.0090 cellbender:remove-background: [epoch 072] average training loss: 2025.1608 cellbender:remove-background: [epoch 073] average training loss: 2025.9930 cellbender:remove-background: [epoch 074] average training loss: 2023.7039 cellbender:remove-background: [epoch 075] average training loss: 2021.6474 cellbender:remove-background: [epoch 075] average test loss: 2005.2627 cellbender:remove-background: [epoch 076] average training loss: 2022.6699 cellbender:remove-background: [epoch 077] average training loss: 2022.5600 cellbender:remove-background: [epoch 078] average training loss: 2021.6626 cellbender:remove-background: [epoch 079] average training loss: 2022.2070 cellbender:remove-background: [epoch 080] average training loss: 2021.0123 cellbender:remove-background: [epoch 080] average test loss: 2004.9162 cellbender:remove-background: [epoch 081] average training loss: 2020.7151 cellbender:remove-background: [epoch 082] average training loss: 2020.0341 cellbender:remove-background: [epoch 083] average training loss: 2020.3097 cellbender:remove-background: [epoch 084] average training loss: 2020.8649 cellbender:remove-background: [epoch 085] average training loss: 2020.3359 cellbender:remove-background: [epoch 085] average test loss: 2009.1627 cellbender:remove-background: [epoch 086] average training loss: 2018.9895 cellbender:remove-background: [epoch 087] average training loss: 2018.9893 cellbender:remove-background: [epoch 088] average training loss: 2019.5090 cellbender:remove-background: [epoch 089] average training loss: 2018.4353 cellbender:remove-background: [epoch 090] average training loss: 2019.1121 cellbender:remove-background: [epoch 090] average test loss: 2009.0959 cellbender:remove-background: [epoch 091] average training loss: 2017.9153 cellbender:remove-background: [epoch 092] average training loss: 2019.7115 cellbender:remove-background: [epoch 093] average training loss: 2018.0839 cellbender:remove-background: [epoch 094] average training loss: 2015.1732 cellbender:remove-background: [epoch 095] average training loss: 2017.8013 cellbender:remove-background: [epoch 095] average test loss: 2019.2103 cellbender:remove-background: [epoch 096] average training loss: 2017.1504 cellbender:remove-background: [epoch 097] average training loss: 2016.3704 cellbender:remove-background: [epoch 098] average training loss: 2015.5888 cellbender:remove-background: [epoch 099] average training loss: 2017.5761 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/2275-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 100] average training loss: 2017.8128 cellbender:remove-background: [epoch 100] average test loss: 2020.0011 cellbender:remove-background: [epoch 101] average training loss: 2017.4720 cellbender:remove-background: [epoch 102] average training loss: 2016.3883 cellbender:remove-background: [epoch 103] average training loss: 2017.2495 cellbender:remove-background: [epoch 104] average training loss: 2016.2325 cellbender:remove-background: [epoch 105] average training loss: 2015.4317 cellbender:remove-background: [epoch 105] average test loss: 2002.2706 cellbender:remove-background: [epoch 106] average training loss: 2011.4165 cellbender:remove-background: [epoch 107] average training loss: 2014.8486 cellbender:remove-background: [epoch 108] average training loss: 2014.9674 cellbender:remove-background: [epoch 109] average training loss: 2015.6260 cellbender:remove-background: [epoch 110] average training loss: 2014.7790 cellbender:remove-background: [epoch 110] average test loss: 2011.3995 cellbender:remove-background: [epoch 111] average training loss: 2013.5913 cellbender:remove-background: [epoch 112] average training loss: 2013.4856 cellbender:remove-background: [epoch 113] average training loss: 2012.9573 cellbender:remove-background: [epoch 114] average training loss: 2015.2899 cellbender:remove-background: [epoch 115] average training loss: 2012.7346 cellbender:remove-background: [epoch 115] average test loss: 2015.9367 cellbender:remove-background: [epoch 116] average training loss: 2013.1956 cellbender:remove-background: [epoch 117] average training loss: 2013.3443 cellbender:remove-background: [epoch 118] average training loss: 2012.4014 cellbender:remove-background: [epoch 119] average training loss: 2012.6856 cellbender:remove-background: [epoch 120] average training loss: 2010.9519 cellbender:remove-background: [epoch 120] average test loss: 2012.8447 cellbender:remove-background: [epoch 121] average training loss: 2012.9226 cellbender:remove-background: [epoch 122] average training loss: 2011.8095 cellbender:remove-background: [epoch 123] average training loss: 2012.9734 cellbender:remove-background: [epoch 124] average training loss: 2011.5755 cellbender:remove-background: [epoch 125] average training loss: 2012.7854 cellbender:remove-background: [epoch 125] average test loss: 2009.3597 cellbender:remove-background: [epoch 126] average training loss: 2012.2826 cellbender:remove-background: [epoch 127] average training loss: 2011.6845 cellbender:remove-background: [epoch 128] average training loss: 2011.0444 cellbender:remove-background: [epoch 129] average training loss: 2011.4610 cellbender:remove-background: [epoch 130] average training loss: 2012.1712 cellbender:remove-background: [epoch 130] average test loss: 2009.9753 cellbender:remove-background: [epoch 131] average training loss: 2011.2614 cellbender:remove-background: [epoch 132] average training loss: 2010.6121 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/2275-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 133] average training loss: 2011.8893 cellbender:remove-background: [epoch 134] average training loss: 2010.5823 cellbender:remove-background: [epoch 135] average training loss: 2009.3625 cellbender:remove-background: [epoch 135] average test loss: 2006.7782 cellbender:remove-background: [epoch 136] average training loss: 2009.5450 cellbender:remove-background: [epoch 137] average training loss: 2009.6938 cellbender:remove-background: [epoch 138] average training loss: 2010.4048 cellbender:remove-background: [epoch 139] average training loss: 2009.1910 cellbender:remove-background: [epoch 140] average training loss: 2009.6145 cellbender:remove-background: [epoch 140] average test loss: 2007.4729 cellbender:remove-background: [epoch 141] average training loss: 2009.5986 cellbender:remove-background: [epoch 142] average training loss: 2010.2536 cellbender:remove-background: [epoch 143] average training loss: 2011.4145 cellbender:remove-background: [epoch 144] average training loss: 2008.7756 cellbender:remove-background: [epoch 145] average training loss: 2010.4905 cellbender:remove-background: [epoch 145] average test loss: 2011.6869 cellbender:remove-background: [epoch 146] average training loss: 2010.1229 cellbender:remove-background: [epoch 147] average training loss: 2009.8522 cellbender:remove-background: [epoch 148] average training loss: 2010.7022 cellbender:remove-background: [epoch 149] average training loss: 2009.4641 cellbender:remove-background: [epoch 150] average training loss: 2010.0037 cellbender:remove-background: [epoch 150] average test loss: 2009.6476 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/2275-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:29:14 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpm07euouw cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpm07euouw /tmp/tmpm07euouw/dc53e14360_random.pyro /tmp/tmpm07euouw/dc53e14360_random.cuda /tmp/tmpm07euouw/dc53e14360_model.torch /tmp/tmpm07euouw/dc53e14360_optim.torch /tmp/tmpm07euouw/dc53e14360_optim.pyro /tmp/tmpm07euouw/dc53e14360_params.pyro /tmp/tmpm07euouw/dc53e14360_train.loaderstate /tmp/tmpm07euouw/dc53e14360_test.loaderstate /tmp/tmpm07euouw/dc53e14360_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 (1/89) cellbender:remove-background: [0.07 mins per chunk] cellbender:remove-background: Working on chunk (2/89) cellbender:remove-background: Working on chunk (3/89) cellbender:remove-background: Working on chunk (4/89) cellbender:remove-background: Working on chunk (5/89) cellbender:remove-background: Working on chunk (6/89) cellbender:remove-background: Working on chunk (7/89) cellbender:remove-background: Working on chunk (8/89) cellbender:remove-background: Working on chunk (9/89) cellbender:remove-background: Working on chunk (10/89) cellbender:remove-background: Working on chunk (11/89) cellbender:remove-background: Working on chunk (12/89) cellbender:remove-background: Working on chunk (13/89) cellbender:remove-background: Working on chunk (14/89) cellbender:remove-background: Working on chunk (15/89) cellbender:remove-background: Working on chunk (16/89) cellbender:remove-background: Working on chunk (17/89) cellbender:remove-background: Working on chunk (18/89) cellbender:remove-background: Working on chunk (19/89) cellbender:remove-background: Working on chunk (20/89) cellbender:remove-background: Working on chunk (21/89) cellbender:remove-background: Working on chunk (22/89) cellbender:remove-background: Working on chunk (23/89) cellbender:remove-background: Working on chunk (24/89) cellbender:remove-background: Working on chunk (25/89) cellbender:remove-background: Working on chunk (26/89) cellbender:remove-background: Working on chunk (27/89) cellbender:remove-background: Working on chunk (28/89) cellbender:remove-background: Working on chunk (29/89) cellbender:remove-background: Working on chunk (30/89) cellbender:remove-background: Working on chunk (31/89) cellbender:remove-background: Working on chunk (32/89) cellbender:remove-background: Working on chunk (33/89) cellbender:remove-background: Working on chunk (34/89) cellbender:remove-background: Working on chunk (35/89) cellbender:remove-background: Working on chunk (36/89) cellbender:remove-background: Working on chunk (37/89) cellbender:remove-background: Working on chunk (38/89) cellbender:remove-background: Working on chunk (39/89) cellbender:remove-background: Working on chunk (40/89) cellbender:remove-background: Working on chunk (41/89) cellbender:remove-background: Working on chunk (42/89) cellbender:remove-background: Working on chunk (43/89) cellbender:remove-background: Working on chunk (44/89) cellbender:remove-background: Working on chunk (45/89) cellbender:remove-background: Working on chunk (46/89) cellbender:remove-background: Working on chunk (47/89) cellbender:remove-background: Working on chunk (48/89) cellbender:remove-background: Working on chunk (49/89) cellbender:remove-background: Working on chunk (50/89) cellbender:remove-background: Working on chunk (51/89) cellbender:remove-background: Working on chunk (52/89) cellbender:remove-background: Working on chunk (53/89) cellbender:remove-background: Working on chunk (54/89) cellbender:remove-background: Working on chunk (55/89) cellbender:remove-background: Working on chunk (56/89) cellbender:remove-background: Working on chunk (57/89) cellbender:remove-background: Working on chunk (58/89) cellbender:remove-background: Working on chunk (59/89) cellbender:remove-background: Working on chunk (60/89) cellbender:remove-background: Working on chunk (61/89) cellbender:remove-background: Working on chunk (62/89) cellbender:remove-background: Working on chunk (63/89) cellbender:remove-background: Working on chunk (64/89) cellbender:remove-background: Working on chunk (65/89) cellbender:remove-background: Working on chunk (66/89) cellbender:remove-background: Working on chunk (67/89) cellbender:remove-background: Working on chunk (68/89) cellbender:remove-background: Working on chunk (69/89) cellbender:remove-background: Working on chunk (70/89) cellbender:remove-background: Working on chunk (71/89) cellbender:remove-background: Working on chunk (72/89) cellbender:remove-background: Working on chunk (73/89) cellbender:remove-background: Working on chunk (74/89) cellbender:remove-background: Working on chunk (75/89) cellbender:remove-background: Working on chunk (76/89) cellbender:remove-background: Working on chunk (77/89) cellbender:remove-background: Working on chunk (78/89) cellbender:remove-background: Working on chunk (79/89) cellbender:remove-background: Working on chunk (80/89) cellbender:remove-background: Working on chunk (81/89) cellbender:remove-background: Working on chunk (82/89) cellbender:remove-background: Working on chunk (83/89) cellbender:remove-background: Working on chunk (84/89) cellbender:remove-background: Working on chunk (85/89) cellbender:remove-background: Working on chunk (86/89) cellbender:remove-background: Working on chunk (87/89) cellbender:remove-background: Working on chunk (88/89) cellbender:remove-background: Working on chunk (89/89) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:37:26 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.53 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 15:48:37 Total MCKP estimation time = 628.91 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/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-dACC/2275-Bipolar-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:49:01