cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1227-Control-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output.h5 --cuda --expected-cells 8275 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 8dfd6820d7) cellbender:remove-background: 2024-06-06 15:12:35 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/1227-Control-Hippocampus.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 32006 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3871 cellbender:remove-background: Prior on counts for empty droplets is 106 cellbender:remove-background: Excluding 8422 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23584 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 53 cellbender:remove-background: Using 8275 probable cell barcodes, plus an additional 11725 barcodes, and 14583 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 104 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpjoht0kvd 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: 5855.6379 cellbender:remove-background: [epoch 002] average training loss: 4660.6461 (6.4 seconds per epoch) cellbender:remove-background: Will checkpoint every 66 epochs cellbender:remove-background: [epoch 003] average training loss: 4052.4931 cellbender:remove-background: [epoch 004] average training loss: 3682.3311 cellbender:remove-background: [epoch 005] average training loss: 3598.4918 cellbender:remove-background: [epoch 005] average test loss: 3654.4113 cellbender:remove-background: [epoch 006] average training loss: 3565.8705 cellbender:remove-background: [epoch 007] average training loss: 3512.0015 cellbender:remove-background: [epoch 008] average training loss: 3488.0408 cellbender:remove-background: [epoch 009] average training loss: 3476.0899 cellbender:remove-background: [epoch 010] average training loss: 3426.1921 cellbender:remove-background: [epoch 010] average test loss: 3434.2370 cellbender:remove-background: [epoch 011] average training loss: 3331.2508 cellbender:remove-background: [epoch 012] average training loss: 3203.2757 cellbender:remove-background: [epoch 013] average training loss: 3168.7454 cellbender:remove-background: [epoch 014] average training loss: 3166.1734 cellbender:remove-background: [epoch 015] average training loss: 3119.6982 cellbender:remove-background: [epoch 015] average test loss: 3160.0262 cellbender:remove-background: [epoch 016] average training loss: 3097.0679 cellbender:remove-background: [epoch 017] average training loss: 3100.4491 cellbender:remove-background: [epoch 018] average training loss: 3088.4323 cellbender:remove-background: [epoch 019] average training loss: 3068.0661 cellbender:remove-background: [epoch 020] average training loss: 3046.9118 cellbender:remove-background: [epoch 020] average test loss: 3071.4943 cellbender:remove-background: [epoch 021] average training loss: 3034.0280 cellbender:remove-background: [epoch 022] average training loss: 3012.5468 cellbender:remove-background: [epoch 023] average training loss: 2981.1819 cellbender:remove-background: [epoch 024] average training loss: 2954.7385 cellbender:remove-background: [epoch 025] average training loss: 2944.8307 cellbender:remove-background: [epoch 025] average test loss: 2941.3254 cellbender:remove-background: [epoch 026] average training loss: 2925.8080 cellbender:remove-background: [epoch 027] average training loss: 2919.0709 cellbender:remove-background: [epoch 028] average training loss: 2913.7771 cellbender:remove-background: [epoch 029] average training loss: 2905.6216 cellbender:remove-background: [epoch 030] average training loss: 2900.0053 cellbender:remove-background: [epoch 030] average test loss: 2897.3140 cellbender:remove-background: [epoch 031] average training loss: 2896.0498 cellbender:remove-background: [epoch 032] average training loss: 2893.5984 cellbender:remove-background: [epoch 033] average training loss: 2889.9260 cellbender:remove-background: [epoch 034] average training loss: 2890.9386 cellbender:remove-background: [epoch 035] average training loss: 2887.2574 cellbender:remove-background: [epoch 035] average test loss: 2879.8378 cellbender:remove-background: [epoch 036] average training loss: 2887.1174 cellbender:remove-background: [epoch 037] average training loss: 2886.6003 cellbender:remove-background: [epoch 038] average training loss: 2883.6901 cellbender:remove-background: [epoch 039] average training loss: 2888.4655 cellbender:remove-background: [epoch 040] average training loss: 2885.6601 cellbender:remove-background: [epoch 040] average test loss: 2879.7661 cellbender:remove-background: [epoch 041] average training loss: 2887.2916 cellbender:remove-background: [epoch 042] average training loss: 2886.3838 cellbender:remove-background: [epoch 043] average training loss: 2885.2840 cellbender:remove-background: [epoch 044] average training loss: 2888.7317 cellbender:remove-background: [epoch 045] average training loss: 2891.2827 cellbender:remove-background: [epoch 045] average test loss: 2873.8532 cellbender:remove-background: [epoch 046] average training loss: 2895.0117 cellbender:remove-background: [epoch 047] average training loss: 2893.5927 cellbender:remove-background: [epoch 048] average training loss: 2894.6762 cellbender:remove-background: [epoch 049] average training loss: 2900.7691 cellbender:remove-background: [epoch 050] average training loss: 2903.3874 cellbender:remove-background: [epoch 050] average test loss: 2894.6330 cellbender:remove-background: [epoch 051] average training loss: 2903.9648 cellbender:remove-background: [epoch 052] average training loss: 2899.3250 cellbender:remove-background: [epoch 053] average training loss: 2904.5833 cellbender:remove-background: [epoch 054] average training loss: 2901.0562 cellbender:remove-background: [epoch 055] average training loss: 2901.7750 cellbender:remove-background: [epoch 055] average test loss: 2892.7225 cellbender:remove-background: [epoch 056] average training loss: 2899.0390 cellbender:remove-background: [epoch 057] average training loss: 2899.7374 cellbender:remove-background: [epoch 058] average training loss: 2899.9705 cellbender:remove-background: [epoch 059] average training loss: 2898.4338 cellbender:remove-background: [epoch 060] average training loss: 2896.5979 cellbender:remove-background: [epoch 060] average test loss: 2895.3687 cellbender:remove-background: [epoch 061] average training loss: 2897.6592 cellbender:remove-background: [epoch 062] average training loss: 2894.6336 cellbender:remove-background: [epoch 063] average training loss: 2891.8232 cellbender:remove-background: [epoch 064] average training loss: 2887.0794 cellbender:remove-background: [epoch 065] average training loss: 2896.6804 cellbender:remove-background: [epoch 065] average test loss: 2908.1464 cellbender:remove-background: [epoch 066] average training loss: 2900.6658 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/1227-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 067] average training loss: 2902.1744 cellbender:remove-background: [epoch 068] average training loss: 2898.0730 cellbender:remove-background: [epoch 069] average training loss: 2892.3851 cellbender:remove-background: [epoch 070] average training loss: 2891.6455 cellbender:remove-background: [epoch 070] average test loss: 2902.9414 cellbender:remove-background: [epoch 071] average training loss: 2898.4669 cellbender:remove-background: [epoch 072] average training loss: 2895.1299 cellbender:remove-background: [epoch 073] average training loss: 2902.5464 cellbender:remove-background: [epoch 074] average training loss: 2902.6980 cellbender:remove-background: [epoch 075] average training loss: 2907.1298 cellbender:remove-background: [epoch 075] average test loss: 2903.5805 cellbender:remove-background: [epoch 076] average training loss: 2899.3436 cellbender:remove-background: [epoch 077] average training loss: 2897.6420 cellbender:remove-background: [epoch 078] average training loss: 2897.5564 cellbender:remove-background: [epoch 079] average training loss: 2903.6132 cellbender:remove-background: [epoch 080] average training loss: 2896.1912 cellbender:remove-background: [epoch 080] average test loss: 2929.2695 cellbender:remove-background: [epoch 081] average training loss: 2900.5096 cellbender:remove-background: [epoch 082] average training loss: 2895.0223 cellbender:remove-background: [epoch 083] average training loss: 2894.0064 cellbender:remove-background: [epoch 084] average training loss: 2899.4227 cellbender:remove-background: [epoch 085] average training loss: 2895.7746 cellbender:remove-background: [epoch 085] average test loss: 2898.4172 cellbender:remove-background: [epoch 086] average training loss: 2902.1800 cellbender:remove-background: [epoch 087] average training loss: 2904.5602 cellbender:remove-background: [epoch 088] average training loss: 2905.6296 cellbender:remove-background: [epoch 089] average training loss: 2897.7646 cellbender:remove-background: [epoch 090] average training loss: 2890.8981 cellbender:remove-background: [epoch 090] average test loss: 2910.8490 cellbender:remove-background: [epoch 091] average training loss: 2891.7626 cellbender:remove-background: [epoch 092] average training loss: 2900.9711 cellbender:remove-background: [epoch 093] average training loss: 2899.9327 cellbender:remove-background: [epoch 094] average training loss: 2890.5156 cellbender:remove-background: [epoch 095] average training loss: 2893.9859 cellbender:remove-background: [epoch 095] average test loss: 2918.4529 cellbender:remove-background: [epoch 096] average training loss: 2891.1363 cellbender:remove-background: [epoch 097] average training loss: 2888.9029 cellbender:remove-background: [epoch 098] average training loss: 2892.4954 cellbender:remove-background: [epoch 099] average training loss: 2888.5075 cellbender:remove-background: [epoch 100] average training loss: 2890.2704 cellbender:remove-background: [epoch 100] average test loss: 2902.1273 cellbender:remove-background: [epoch 101] average training loss: 2882.8344 cellbender:remove-background: [epoch 102] average training loss: 2881.3141 cellbender:remove-background: [epoch 103] average training loss: 2876.7910 cellbender:remove-background: [epoch 104] average training loss: 2880.0524 cellbender:remove-background: [epoch 105] average training loss: 2881.7552 cellbender:remove-background: [epoch 105] average test loss: 2903.6727 cellbender:remove-background: [epoch 106] average training loss: 2874.2127 cellbender:remove-background: [epoch 107] average training loss: 2876.9625 cellbender:remove-background: [epoch 108] average training loss: 2876.1143 cellbender:remove-background: [epoch 109] average training loss: 2879.2034 cellbender:remove-background: [epoch 110] average training loss: 2876.0421 cellbender:remove-background: [epoch 110] average test loss: 2900.2457 cellbender:remove-background: [epoch 111] average training loss: 2875.2559 cellbender:remove-background: [epoch 112] average training loss: 2875.3320 cellbender:remove-background: [epoch 113] average training loss: 2872.8915 cellbender:remove-background: [epoch 114] average training loss: 2872.9795 cellbender:remove-background: [epoch 115] average training loss: 2870.5220 cellbender:remove-background: [epoch 115] average test loss: 2908.5132 cellbender:remove-background: [epoch 116] average training loss: 2869.7571 cellbender:remove-background: [epoch 117] average training loss: 2872.9560 cellbender:remove-background: [epoch 118] average training loss: 2868.1008 cellbender:remove-background: [epoch 119] average training loss: 2872.5821 cellbender:remove-background: [epoch 120] average training loss: 2869.6944 cellbender:remove-background: [epoch 120] average test loss: 2902.6968 cellbender:remove-background: [epoch 121] average training loss: 2869.5545 cellbender:remove-background: [epoch 122] average training loss: 2872.4556 cellbender:remove-background: [epoch 123] average training loss: 2868.9290 cellbender:remove-background: [epoch 124] average training loss: 2869.9258 cellbender:remove-background: [epoch 125] average training loss: 2866.0562 cellbender:remove-background: [epoch 125] average test loss: 2892.6157 cellbender:remove-background: [epoch 126] average training loss: 2866.0848 cellbender:remove-background: [epoch 127] average training loss: 2868.0392 cellbender:remove-background: [epoch 128] average training loss: 2870.9443 cellbender:remove-background: [epoch 129] average training loss: 2865.6413 cellbender:remove-background: [epoch 130] average training loss: 2871.2975 cellbender:remove-background: [epoch 130] average test loss: 2889.3526 cellbender:remove-background: [epoch 131] average training loss: 2864.6503 cellbender:remove-background: [epoch 132] average training loss: 2871.5911 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/1227-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 133] average training loss: 2867.8955 cellbender:remove-background: [epoch 134] average training loss: 2867.7342 cellbender:remove-background: [epoch 135] average training loss: 2866.0019 cellbender:remove-background: [epoch 135] average test loss: 2899.3431 cellbender:remove-background: [epoch 136] average training loss: 2869.2309 cellbender:remove-background: [epoch 137] average training loss: 2868.1288 cellbender:remove-background: [epoch 138] average training loss: 2868.6074 cellbender:remove-background: [epoch 139] average training loss: 2869.5235 cellbender:remove-background: [epoch 140] average training loss: 2863.1454 cellbender:remove-background: [epoch 140] average test loss: 2909.9973 cellbender:remove-background: [epoch 141] average training loss: 2869.8755 cellbender:remove-background: [epoch 142] average training loss: 2868.1397 cellbender:remove-background: [epoch 143] average training loss: 2866.0144 cellbender:remove-background: [epoch 144] average training loss: 2864.4432 cellbender:remove-background: [epoch 145] average training loss: 2864.2598 cellbender:remove-background: [epoch 145] average test loss: 2900.1583 cellbender:remove-background: [epoch 146] average training loss: 2867.2664 cellbender:remove-background: [epoch 147] average training loss: 2868.3666 cellbender:remove-background: [epoch 148] average training loss: 2865.0323 cellbender:remove-background: [epoch 149] average training loss: 2866.6085 cellbender:remove-background: [epoch 150] average training loss: 2865.7219 cellbender:remove-background: [epoch 150] average test loss: 2897.7287 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/1227-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:32:37 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpoysfeptx cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpoysfeptx /tmp/tmpoysfeptx/8dfd6820d7_random.pyro /tmp/tmpoysfeptx/8dfd6820d7_random.cuda /tmp/tmpoysfeptx/8dfd6820d7_model.torch /tmp/tmpoysfeptx/8dfd6820d7_optim.torch /tmp/tmpoysfeptx/8dfd6820d7_optim.pyro /tmp/tmpoysfeptx/8dfd6820d7_params.pyro /tmp/tmpoysfeptx/8dfd6820d7_train.loaderstate /tmp/tmpoysfeptx/8dfd6820d7_test.loaderstate /tmp/tmpoysfeptx/8dfd6820d7_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 (1/87) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/87) cellbender:remove-background: Working on chunk (3/87) cellbender:remove-background: Working on chunk (4/87) cellbender:remove-background: Working on chunk (5/87) cellbender:remove-background: Working on chunk (6/87) cellbender:remove-background: Working on chunk (7/87) cellbender:remove-background: Working on chunk (8/87) cellbender:remove-background: Working on chunk (9/87) cellbender:remove-background: Working on chunk (10/87) cellbender:remove-background: Working on chunk (11/87) cellbender:remove-background: Working on chunk (12/87) cellbender:remove-background: Working on chunk (13/87) cellbender:remove-background: Working on chunk (14/87) cellbender:remove-background: Working on chunk (15/87) cellbender:remove-background: Working on chunk (16/87) cellbender:remove-background: Working on chunk (17/87) cellbender:remove-background: Working on chunk (18/87) cellbender:remove-background: Working on chunk (19/87) cellbender:remove-background: Working on chunk (20/87) cellbender:remove-background: Working on chunk (21/87) cellbender:remove-background: Working on chunk (22/87) cellbender:remove-background: Working on chunk (23/87) cellbender:remove-background: Working on chunk (24/87) cellbender:remove-background: Working on chunk (25/87) cellbender:remove-background: Working on chunk (26/87) cellbender:remove-background: Working on chunk (27/87) cellbender:remove-background: Working on chunk (28/87) cellbender:remove-background: Working on chunk (29/87) cellbender:remove-background: Working on chunk (30/87) cellbender:remove-background: Working on chunk (31/87) cellbender:remove-background: Working on chunk (32/87) cellbender:remove-background: Working on chunk (33/87) cellbender:remove-background: Working on chunk (34/87) cellbender:remove-background: Working on chunk (35/87) cellbender:remove-background: Working on chunk (36/87) cellbender:remove-background: Working on chunk (37/87) cellbender:remove-background: Working on chunk (38/87) cellbender:remove-background: Working on chunk (39/87) cellbender:remove-background: Working on chunk (40/87) cellbender:remove-background: Working on chunk (41/87) cellbender:remove-background: Working on chunk (42/87) cellbender:remove-background: Working on chunk (43/87) cellbender:remove-background: Working on chunk (44/87) cellbender:remove-background: Working on chunk (45/87) cellbender:remove-background: Working on chunk (46/87) cellbender:remove-background: Working on chunk (47/87) cellbender:remove-background: Working on chunk (48/87) cellbender:remove-background: Working on chunk (49/87) cellbender:remove-background: Working on chunk (50/87) cellbender:remove-background: Working on chunk (51/87) cellbender:remove-background: Working on chunk (52/87) cellbender:remove-background: Working on chunk (53/87) cellbender:remove-background: Working on chunk (54/87) cellbender:remove-background: Working on chunk (55/87) cellbender:remove-background: Working on chunk (56/87) cellbender:remove-background: Working on chunk (57/87) cellbender:remove-background: Working on chunk (58/87) cellbender:remove-background: Working on chunk (59/87) cellbender:remove-background: Working on chunk (60/87) cellbender:remove-background: Working on chunk (61/87) cellbender:remove-background: Working on chunk (62/87) cellbender:remove-background: Working on chunk (63/87) cellbender:remove-background: Working on chunk (64/87) cellbender:remove-background: Working on chunk (65/87) cellbender:remove-background: Working on chunk (66/87) cellbender:remove-background: Working on chunk (67/87) cellbender:remove-background: Working on chunk (68/87) cellbender:remove-background: Working on chunk (69/87) cellbender:remove-background: Working on chunk (70/87) cellbender:remove-background: Working on chunk (71/87) cellbender:remove-background: Working on chunk (72/87) cellbender:remove-background: Working on chunk (73/87) cellbender:remove-background: Working on chunk (74/87) cellbender:remove-background: Working on chunk (75/87) cellbender:remove-background: Working on chunk (76/87) cellbender:remove-background: Working on chunk (77/87) cellbender:remove-background: Working on chunk (78/87) cellbender:remove-background: Working on chunk (79/87) cellbender:remove-background: Working on chunk (80/87) cellbender:remove-background: Working on chunk (81/87) cellbender:remove-background: Working on chunk (82/87) cellbender:remove-background: Working on chunk (83/87) cellbender:remove-background: Working on chunk (84/87) cellbender:remove-background: Working on chunk (85/87) cellbender:remove-background: Working on chunk (86/87) cellbender:remove-background: Working on chunk (87/87) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:37:43 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.94 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 15:52:21 Total MCKP estimation time = 821.97 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/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-Hippocampus/1227-Control-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:52:42