cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1461-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-dACC/1461-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 8040 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 3e15abc37c) cellbender:remove-background: 2024-06-06 14:54:06 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/1461-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: 31241 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1515 cellbender:remove-background: Prior on counts for empty droplets is 69 cellbender:remove-background: Excluding 6462 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24779 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 34 cellbender:remove-background: Using 8040 probable cell barcodes, plus an additional 11960 barcodes, and 51849 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 69 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpg7dlj5k9 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: 3866.0756 cellbender:remove-background: [epoch 002] average training loss: 3140.5044 (7.9 seconds per epoch) cellbender:remove-background: Will checkpoint every 54 epochs cellbender:remove-background: [epoch 003] average training loss: 2754.6298 cellbender:remove-background: [epoch 004] average training loss: 2509.4534 cellbender:remove-background: [epoch 005] average training loss: 2427.8020 cellbender:remove-background: [epoch 005] average test loss: 2556.1242 cellbender:remove-background: [epoch 006] average training loss: 2386.5194 cellbender:remove-background: [epoch 007] average training loss: 2356.7028 cellbender:remove-background: [epoch 008] average training loss: 2335.0716 cellbender:remove-background: [epoch 009] average training loss: 2329.7485 cellbender:remove-background: [epoch 010] average training loss: 2306.9290 cellbender:remove-background: [epoch 010] average test loss: 2365.0874 cellbender:remove-background: [epoch 011] average training loss: 2305.6346 cellbender:remove-background: [epoch 012] average training loss: 2258.0628 cellbender:remove-background: [epoch 013] average training loss: 2186.2952 cellbender:remove-background: [epoch 014] average training loss: 2181.6250 cellbender:remove-background: [epoch 015] average training loss: 2160.4835 cellbender:remove-background: [epoch 015] average test loss: 2221.9877 cellbender:remove-background: [epoch 016] average training loss: 2147.0218 cellbender:remove-background: [epoch 017] average training loss: 2142.4597 cellbender:remove-background: [epoch 018] average training loss: 2135.9785 cellbender:remove-background: [epoch 019] average training loss: 2125.8218 cellbender:remove-background: [epoch 020] average training loss: 2113.7090 cellbender:remove-background: [epoch 020] average test loss: 2175.2019 cellbender:remove-background: [epoch 021] average training loss: 2111.3695 cellbender:remove-background: [epoch 022] average training loss: 2111.7891 cellbender:remove-background: [epoch 023] average training loss: 2105.8519 cellbender:remove-background: [epoch 024] average training loss: 2090.9114 cellbender:remove-background: [epoch 025] average training loss: 2080.9464 cellbender:remove-background: [epoch 025] average test loss: 2114.0252 cellbender:remove-background: [epoch 026] average training loss: 2066.0555 cellbender:remove-background: [epoch 027] average training loss: 2059.8489 cellbender:remove-background: [epoch 028] average training loss: 2052.7772 cellbender:remove-background: [epoch 029] average training loss: 2047.7367 cellbender:remove-background: [epoch 030] average training loss: 2042.8670 cellbender:remove-background: [epoch 030] average test loss: 2079.7290 cellbender:remove-background: [epoch 031] average training loss: 2039.9914 cellbender:remove-background: [epoch 032] average training loss: 2037.4113 cellbender:remove-background: [epoch 033] average training loss: 2035.6739 cellbender:remove-background: [epoch 034] average training loss: 2034.0280 cellbender:remove-background: [epoch 035] average training loss: 2031.6885 cellbender:remove-background: [epoch 035] average test loss: 2070.8634 cellbender:remove-background: [epoch 036] average training loss: 2029.1902 cellbender:remove-background: [epoch 037] average training loss: 2028.3145 cellbender:remove-background: [epoch 038] average training loss: 2026.7885 cellbender:remove-background: [epoch 039] average training loss: 2026.1767 cellbender:remove-background: [epoch 040] average training loss: 2024.9277 cellbender:remove-background: [epoch 040] average test loss: 2068.3953 cellbender:remove-background: [epoch 041] average training loss: 2023.1724 cellbender:remove-background: [epoch 042] average training loss: 2022.4677 cellbender:remove-background: [epoch 043] average training loss: 2022.4917 cellbender:remove-background: [epoch 044] average training loss: 2019.8584 cellbender:remove-background: [epoch 045] average training loss: 2019.2199 cellbender:remove-background: [epoch 045] average test loss: 2047.3277 cellbender:remove-background: [epoch 046] average training loss: 2021.8938 cellbender:remove-background: [epoch 047] average training loss: 2021.6004 cellbender:remove-background: [epoch 048] average training loss: 2023.9563 cellbender:remove-background: [epoch 049] average training loss: 2022.2359 cellbender:remove-background: [epoch 050] average training loss: 2026.3607 cellbender:remove-background: [epoch 050] average test loss: 2050.9737 cellbender:remove-background: [epoch 051] average training loss: 2016.1710 cellbender:remove-background: [epoch 052] average training loss: 2020.4781 cellbender:remove-background: [epoch 053] average training loss: 2013.8932 cellbender:remove-background: [epoch 054] average training loss: 2019.2330 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/1461-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 055] average training loss: 2016.1053 cellbender:remove-background: [epoch 055] average test loss: 2051.2382 cellbender:remove-background: [epoch 056] average training loss: 2017.3308 cellbender:remove-background: [epoch 057] average training loss: 2015.1875 cellbender:remove-background: [epoch 058] average training loss: 2013.9392 cellbender:remove-background: [epoch 059] average training loss: 2014.8433 cellbender:remove-background: [epoch 060] average training loss: 2018.1464 cellbender:remove-background: [epoch 060] average test loss: 2052.9152 cellbender:remove-background: [epoch 061] average training loss: 2012.3935 cellbender:remove-background: [epoch 062] average training loss: 2012.6407 cellbender:remove-background: [epoch 063] average training loss: 2014.1194 cellbender:remove-background: [epoch 064] average training loss: 2015.8439 cellbender:remove-background: [epoch 065] average training loss: 2012.4621 cellbender:remove-background: [epoch 065] average test loss: 2069.6600 cellbender:remove-background: [epoch 066] average training loss: 2014.8919 cellbender:remove-background: [epoch 067] average training loss: 2014.3933 cellbender:remove-background: [epoch 068] average training loss: 2015.6597 cellbender:remove-background: [epoch 069] average training loss: 2013.6053 cellbender:remove-background: [epoch 070] average training loss: 2015.4419 cellbender:remove-background: [epoch 070] average test loss: 2048.1603 cellbender:remove-background: [epoch 071] average training loss: 2016.3359 cellbender:remove-background: [epoch 072] average training loss: 2016.9105 cellbender:remove-background: [epoch 073] average training loss: 2014.8793 cellbender:remove-background: [epoch 074] average training loss: 2013.7690 cellbender:remove-background: [epoch 075] average training loss: 2016.3644 cellbender:remove-background: [epoch 075] average test loss: 2067.3267 cellbender:remove-background: [epoch 076] average training loss: 2017.8437 cellbender:remove-background: [epoch 077] average training loss: 2014.6576 cellbender:remove-background: [epoch 078] average training loss: 2018.8645 cellbender:remove-background: [epoch 079] average training loss: 2017.7969 cellbender:remove-background: [epoch 080] average training loss: 2016.0206 cellbender:remove-background: [epoch 080] average test loss: 2072.1088 cellbender:remove-background: [epoch 081] average training loss: 2017.1108 cellbender:remove-background: [epoch 082] average training loss: 2017.8944 cellbender:remove-background: [epoch 083] average training loss: 2020.8382 cellbender:remove-background: [epoch 084] average training loss: 2023.3386 cellbender:remove-background: [epoch 085] average training loss: 2017.0513 cellbender:remove-background: [epoch 085] average test loss: 2079.8791 cellbender:remove-background: [epoch 086] average training loss: 2020.0879 cellbender:remove-background: [epoch 087] average training loss: 2020.6810 cellbender:remove-background: [epoch 088] average training loss: 2020.9720 cellbender:remove-background: [epoch 089] average training loss: 2018.9427 cellbender:remove-background: [epoch 090] average training loss: 2019.9523 cellbender:remove-background: [epoch 090] average test loss: 2078.8963 cellbender:remove-background: [epoch 091] average training loss: 2019.9507 cellbender:remove-background: [epoch 092] average training loss: 2023.6626 cellbender:remove-background: [epoch 093] average training loss: 2022.2707 cellbender:remove-background: [epoch 094] average training loss: 2021.5685 cellbender:remove-background: [epoch 095] average training loss: 2022.6644 cellbender:remove-background: [epoch 095] average test loss: 2080.7506 cellbender:remove-background: [epoch 096] average training loss: 2021.6977 cellbender:remove-background: [epoch 097] average training loss: 2020.3778 cellbender:remove-background: [epoch 098] average training loss: 2023.9613 cellbender:remove-background: [epoch 099] average training loss: 2022.4692 cellbender:remove-background: [epoch 100] average training loss: 2023.2301 cellbender:remove-background: [epoch 100] average test loss: 2082.9303 cellbender:remove-background: [epoch 101] average training loss: 2020.9735 cellbender:remove-background: [epoch 102] average training loss: 2022.5383 cellbender:remove-background: [epoch 103] average training loss: 2020.9499 cellbender:remove-background: [epoch 104] average training loss: 2019.2747 cellbender:remove-background: [epoch 105] average training loss: 2021.9891 cellbender:remove-background: [epoch 105] average test loss: 2092.5286 cellbender:remove-background: [epoch 106] average training loss: 2021.8780 cellbender:remove-background: [epoch 107] average training loss: 2022.0551 cellbender:remove-background: [epoch 108] average training loss: 2019.8221 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/1461-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 109] average training loss: 2022.3764 cellbender:remove-background: [epoch 110] average training loss: 2021.1819 cellbender:remove-background: [epoch 110] average test loss: 2085.4602 cellbender:remove-background: [epoch 111] average training loss: 2023.3420 cellbender:remove-background: [epoch 112] average training loss: 2019.2207 cellbender:remove-background: [epoch 113] average training loss: 2022.4027 cellbender:remove-background: [epoch 114] average training loss: 2020.9492 cellbender:remove-background: [epoch 115] average training loss: 2018.5664 cellbender:remove-background: [epoch 115] average test loss: 2085.4531 cellbender:remove-background: [epoch 116] average training loss: 2021.7784 cellbender:remove-background: [epoch 117] average training loss: 2018.4721 cellbender:remove-background: [epoch 118] average training loss: 2020.8497 cellbender:remove-background: [epoch 119] average training loss: 2022.0278 cellbender:remove-background: [epoch 120] average training loss: 2021.2559 cellbender:remove-background: [epoch 120] average test loss: 2086.5732 cellbender:remove-background: [epoch 121] average training loss: 2019.5375 cellbender:remove-background: [epoch 122] average training loss: 2021.5380 cellbender:remove-background: [epoch 123] average training loss: 2019.5776 cellbender:remove-background: [epoch 124] average training loss: 2019.5314 cellbender:remove-background: [epoch 125] average training loss: 2020.3611 cellbender:remove-background: [epoch 125] average test loss: 2077.9287 cellbender:remove-background: [epoch 126] average training loss: 2020.3205 cellbender:remove-background: [epoch 127] average training loss: 2020.7881 cellbender:remove-background: [epoch 128] average training loss: 2019.6164 cellbender:remove-background: [epoch 129] average training loss: 2019.8130 cellbender:remove-background: [epoch 130] average training loss: 2019.7764 cellbender:remove-background: [epoch 130] average test loss: 2083.2113 cellbender:remove-background: [epoch 131] average training loss: 2018.2035 cellbender:remove-background: [epoch 132] average training loss: 2020.6105 cellbender:remove-background: [epoch 133] average training loss: 2018.5637 cellbender:remove-background: [epoch 134] average training loss: 2020.4095 cellbender:remove-background: [epoch 135] average training loss: 2019.5114 cellbender:remove-background: [epoch 135] average test loss: 2081.6719 cellbender:remove-background: [epoch 136] average training loss: 2021.2746 cellbender:remove-background: [epoch 137] average training loss: 2020.0375 cellbender:remove-background: [epoch 138] average training loss: 2020.2462 cellbender:remove-background: [epoch 139] average training loss: 2020.7452 cellbender:remove-background: [epoch 140] average training loss: 2021.2575 cellbender:remove-background: [epoch 140] average test loss: 2080.7663 cellbender:remove-background: [epoch 141] average training loss: 2018.0110 cellbender:remove-background: [epoch 142] average training loss: 2021.9629 cellbender:remove-background: [epoch 143] average training loss: 2019.3509 cellbender:remove-background: [epoch 144] average training loss: 2018.4179 cellbender:remove-background: [epoch 145] average training loss: 2020.6244 cellbender:remove-background: [epoch 145] average test loss: 2087.9447 cellbender:remove-background: [epoch 146] average training loss: 2021.9880 cellbender:remove-background: [epoch 147] average training loss: 2019.9440 cellbender:remove-background: [epoch 148] average training loss: 2019.1935 cellbender:remove-background: [epoch 149] average training loss: 2020.0107 cellbender:remove-background: [epoch 150] average training loss: 2019.7571 cellbender:remove-background: [epoch 150] average test loss: 2081.8012 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/1461-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:18:14 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpifiuw7my cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpifiuw7my /tmp/tmpifiuw7my/3e15abc37c_random.pyro /tmp/tmpifiuw7my/3e15abc37c_random.cuda /tmp/tmpifiuw7my/3e15abc37c_model.torch /tmp/tmpifiuw7my/3e15abc37c_optim.torch /tmp/tmpifiuw7my/3e15abc37c_optim.pyro /tmp/tmpifiuw7my/3e15abc37c_params.pyro /tmp/tmpifiuw7my/3e15abc37c_train.loaderstate /tmp/tmpifiuw7my/3e15abc37c_test.loaderstate /tmp/tmpifiuw7my/3e15abc37c_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 (1/75) cellbender:remove-background: [0.05 mins per chunk] cellbender:remove-background: Working on chunk (2/75) cellbender:remove-background: Working on chunk (3/75) cellbender:remove-background: Working on chunk (4/75) cellbender:remove-background: Working on chunk (5/75) cellbender:remove-background: Working on chunk (6/75) cellbender:remove-background: Working on chunk (7/75) cellbender:remove-background: Working on chunk (8/75) cellbender:remove-background: Working on chunk (9/75) cellbender:remove-background: Working on chunk (10/75) cellbender:remove-background: Working on chunk (11/75) cellbender:remove-background: Working on chunk (12/75) cellbender:remove-background: Working on chunk (13/75) cellbender:remove-background: Working on chunk (14/75) cellbender:remove-background: Working on chunk (15/75) cellbender:remove-background: Working on chunk (16/75) cellbender:remove-background: Working on chunk (17/75) cellbender:remove-background: Working on chunk (18/75) cellbender:remove-background: Working on chunk (19/75) cellbender:remove-background: Working on chunk (20/75) cellbender:remove-background: Working on chunk (21/75) cellbender:remove-background: Working on chunk (22/75) cellbender:remove-background: Working on chunk (23/75) cellbender:remove-background: Working on chunk (24/75) cellbender:remove-background: Working on chunk (25/75) cellbender:remove-background: Working on chunk (26/75) cellbender:remove-background: Working on chunk (27/75) cellbender:remove-background: Working on chunk (28/75) cellbender:remove-background: Working on chunk (29/75) cellbender:remove-background: Working on chunk (30/75) cellbender:remove-background: Working on chunk (31/75) cellbender:remove-background: Working on chunk (32/75) cellbender:remove-background: Working on chunk (33/75) cellbender:remove-background: Working on chunk (34/75) cellbender:remove-background: Working on chunk (35/75) cellbender:remove-background: Working on chunk (36/75) cellbender:remove-background: Working on chunk (37/75) cellbender:remove-background: Working on chunk (38/75) cellbender:remove-background: Working on chunk (39/75) cellbender:remove-background: Working on chunk (40/75) cellbender:remove-background: Working on chunk (41/75) cellbender:remove-background: Working on chunk (42/75) cellbender:remove-background: Working on chunk (43/75) cellbender:remove-background: Working on chunk (44/75) cellbender:remove-background: Working on chunk (45/75) cellbender:remove-background: Working on chunk (46/75) cellbender:remove-background: Working on chunk (47/75) cellbender:remove-background: Working on chunk (48/75) cellbender:remove-background: Working on chunk (49/75) cellbender:remove-background: Working on chunk (50/75) cellbender:remove-background: Working on chunk (51/75) cellbender:remove-background: Working on chunk (52/75) cellbender:remove-background: Working on chunk (53/75) cellbender:remove-background: Working on chunk (54/75) cellbender:remove-background: Working on chunk (55/75) cellbender:remove-background: Working on chunk (56/75) cellbender:remove-background: Working on chunk (57/75) cellbender:remove-background: Working on chunk (58/75) cellbender:remove-background: Working on chunk (59/75) cellbender:remove-background: Working on chunk (60/75) cellbender:remove-background: Working on chunk (61/75) cellbender:remove-background: Working on chunk (62/75) cellbender:remove-background: Working on chunk (63/75) cellbender:remove-background: Working on chunk (64/75) cellbender:remove-background: Working on chunk (65/75) cellbender:remove-background: Working on chunk (66/75) cellbender:remove-background: Working on chunk (67/75) cellbender:remove-background: Working on chunk (68/75) cellbender:remove-background: Working on chunk (69/75) cellbender:remove-background: Working on chunk (70/75) cellbender:remove-background: Working on chunk (71/75) cellbender:remove-background: Working on chunk (72/75) cellbender:remove-background: Working on chunk (73/75) cellbender:remove-background: Working on chunk (74/75) cellbender:remove-background: Working on chunk (75/75) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-dACC/1461-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/1461-Bipolar-dACC/1461-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:23:30 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-dACC/1461-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/1461-Bipolar-dACC/1461-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: [1.26 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 15:32:39 Total MCKP estimation time = 528.83 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/1461-Bipolar-dACC/1461-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/1461-Bipolar-dACC/1461-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/1461-Bipolar-dACC/1461-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/1461-Bipolar-dACC/1461-Bipolar-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:32:54