cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2653-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 11026 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 97fee23f6d) cellbender:remove-background: 2024-06-06 15:05:06 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/2653-Schizophrenia-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: 32161 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2838 cellbender:remove-background: Prior on counts for empty droplets is 150 cellbender:remove-background: Excluding 5959 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 26202 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 75 cellbender:remove-background: Using 11026 probable cell barcodes, plus an additional 8974 barcodes, and 41762 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 148 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpiixjxyqo 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: 7132.8820 cellbender:remove-background: [epoch 002] average training loss: 5587.7473 (8.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 49 epochs cellbender:remove-background: [epoch 003] average training loss: 4751.0087 cellbender:remove-background: [epoch 004] average training loss: 4217.0127 cellbender:remove-background: [epoch 005] average training loss: 4067.7709 cellbender:remove-background: [epoch 005] average test loss: 4065.9295 cellbender:remove-background: [epoch 006] average training loss: 4015.5045 cellbender:remove-background: [epoch 007] average training loss: 3957.7640 cellbender:remove-background: [epoch 008] average training loss: 3905.4924 cellbender:remove-background: [epoch 009] average training loss: 3885.9254 cellbender:remove-background: [epoch 010] average training loss: 3746.8979 cellbender:remove-background: [epoch 010] average test loss: 3898.4826 cellbender:remove-background: [epoch 011] average training loss: 3666.5557 cellbender:remove-background: [epoch 012] average training loss: 3634.7934 cellbender:remove-background: [epoch 013] average training loss: 3612.9650 cellbender:remove-background: [epoch 014] average training loss: 3626.6499 cellbender:remove-background: [epoch 015] average training loss: 3585.9704 cellbender:remove-background: [epoch 015] average test loss: 3635.9649 cellbender:remove-background: [epoch 016] average training loss: 3581.5939 cellbender:remove-background: [epoch 017] average training loss: 3583.4813 cellbender:remove-background: [epoch 018] average training loss: 3569.0914 cellbender:remove-background: [epoch 019] average training loss: 3541.1495 cellbender:remove-background: [epoch 020] average training loss: 3517.2350 cellbender:remove-background: [epoch 020] average test loss: 3516.6221 cellbender:remove-background: [epoch 021] average training loss: 3506.5903 cellbender:remove-background: [epoch 022] average training loss: 3494.7505 cellbender:remove-background: [epoch 023] average training loss: 3466.4164 cellbender:remove-background: [epoch 024] average training loss: 3434.8806 cellbender:remove-background: [epoch 025] average training loss: 3423.0984 cellbender:remove-background: [epoch 025] average test loss: 3390.9964 cellbender:remove-background: [epoch 026] average training loss: 3402.1875 cellbender:remove-background: [epoch 027] average training loss: 3390.8709 cellbender:remove-background: [epoch 028] average training loss: 3387.3776 cellbender:remove-background: [epoch 029] average training loss: 3380.4954 cellbender:remove-background: [epoch 030] average training loss: 3373.2628 cellbender:remove-background: [epoch 030] average test loss: 3359.2467 cellbender:remove-background: [epoch 031] average training loss: 3367.4215 cellbender:remove-background: [epoch 032] average training loss: 3365.0477 cellbender:remove-background: [epoch 033] average training loss: 3363.3124 cellbender:remove-background: [epoch 034] average training loss: 3360.6583 cellbender:remove-background: [epoch 035] average training loss: 3359.5518 cellbender:remove-background: [epoch 035] average test loss: 3341.4380 cellbender:remove-background: [epoch 036] average training loss: 3360.3151 cellbender:remove-background: [epoch 037] average training loss: 3357.6062 cellbender:remove-background: [epoch 038] average training loss: 3357.4497 cellbender:remove-background: [epoch 039] average training loss: 3355.6025 cellbender:remove-background: [epoch 040] average training loss: 3360.5568 cellbender:remove-background: [epoch 040] average test loss: 3325.5565 cellbender:remove-background: [epoch 041] average training loss: 3359.5655 cellbender:remove-background: [epoch 042] average training loss: 3359.1552 cellbender:remove-background: [epoch 043] average training loss: 3349.4874 cellbender:remove-background: [epoch 044] average training loss: 3355.6194 cellbender:remove-background: [epoch 045] average training loss: 3351.8956 cellbender:remove-background: [epoch 045] average test loss: 3300.4206 cellbender:remove-background: [epoch 046] average training loss: 3352.7873 cellbender:remove-background: [epoch 047] average training loss: 3350.6138 cellbender:remove-background: [epoch 048] average training loss: 3359.5902 cellbender:remove-background: [epoch 049] average training loss: 3359.9073 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/2653-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 050] average training loss: 3351.5607 cellbender:remove-background: [epoch 050] average test loss: 3320.2872 cellbender:remove-background: [epoch 051] average training loss: 3352.1711 cellbender:remove-background: [epoch 052] average training loss: 3355.5732 cellbender:remove-background: [epoch 053] average training loss: 3351.2565 cellbender:remove-background: [epoch 054] average training loss: 3357.8677 cellbender:remove-background: [epoch 055] average training loss: 3358.4798 cellbender:remove-background: [epoch 055] average test loss: 3335.7013 cellbender:remove-background: [epoch 056] average training loss: 3357.3336 cellbender:remove-background: [epoch 057] average training loss: 3370.6933 cellbender:remove-background: [epoch 058] average training loss: 3367.7095 cellbender:remove-background: [epoch 059] average training loss: 3365.9264 cellbender:remove-background: [epoch 060] average training loss: 3364.4314 cellbender:remove-background: [epoch 060] average test loss: 3372.9487 cellbender:remove-background: [epoch 061] average training loss: 3367.4556 cellbender:remove-background: [epoch 062] average training loss: 3374.9989 cellbender:remove-background: [epoch 063] average training loss: 3373.9262 cellbender:remove-background: [epoch 064] average training loss: 3373.1355 cellbender:remove-background: [epoch 065] average training loss: 3382.7591 cellbender:remove-background: [epoch 065] average test loss: 3351.1291 cellbender:remove-background: [epoch 066] average training loss: 3377.7809 cellbender:remove-background: [epoch 067] average training loss: 3381.1458 cellbender:remove-background: [epoch 068] average training loss: 3372.5525 cellbender:remove-background: [epoch 069] average training loss: 3385.9019 cellbender:remove-background: [epoch 070] average training loss: 3381.8250 cellbender:remove-background: [epoch 070] average test loss: 3401.6444 cellbender:remove-background: [epoch 071] average training loss: 3382.1151 cellbender:remove-background: [epoch 072] average training loss: 3384.2005 cellbender:remove-background: [epoch 073] average training loss: 3384.0362 cellbender:remove-background: [epoch 074] average training loss: 3384.9345 cellbender:remove-background: [epoch 075] average training loss: 3386.9776 cellbender:remove-background: [epoch 075] average test loss: 3381.4716 cellbender:remove-background: [epoch 076] average training loss: 3388.2486 cellbender:remove-background: [epoch 077] average training loss: 3392.6891 cellbender:remove-background: [epoch 078] average training loss: 3398.4141 cellbender:remove-background: [epoch 079] average training loss: 3396.6344 cellbender:remove-background: [epoch 080] average training loss: 3391.6581 cellbender:remove-background: [epoch 080] average test loss: 3345.9271 cellbender:remove-background: [epoch 081] average training loss: 3401.7799 cellbender:remove-background: [epoch 082] average training loss: 3402.6387 cellbender:remove-background: [epoch 083] average training loss: 3398.4970 cellbender:remove-background: [epoch 084] average training loss: 3391.1774 cellbender:remove-background: [epoch 085] average training loss: 3388.3647 cellbender:remove-background: [epoch 085] average test loss: 3370.6920 cellbender:remove-background: [epoch 086] average training loss: 3398.6940 cellbender:remove-background: [epoch 087] average training loss: 3389.0229 cellbender:remove-background: [epoch 088] average training loss: 3396.1230 cellbender:remove-background: [epoch 089] average training loss: 3392.5025 cellbender:remove-background: [epoch 090] average training loss: 3399.4313 cellbender:remove-background: [epoch 090] average test loss: 3395.1601 cellbender:remove-background: [epoch 091] average training loss: 3398.3686 cellbender:remove-background: [epoch 092] average training loss: 3397.0075 cellbender:remove-background: [epoch 093] average training loss: 3402.4140 cellbender:remove-background: [epoch 094] average training loss: 3406.2582 cellbender:remove-background: [epoch 095] average training loss: 3400.7147 cellbender:remove-background: [epoch 095] average test loss: 3414.2644 cellbender:remove-background: [epoch 096] average training loss: 3406.3721 cellbender:remove-background: [epoch 097] average training loss: 3406.4071 cellbender:remove-background: [epoch 098] average training loss: 3399.1359 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/2653-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 099] average training loss: 3390.8955 cellbender:remove-background: [epoch 100] average training loss: 3400.9522 cellbender:remove-background: [epoch 100] average test loss: 3392.2781 cellbender:remove-background: [epoch 101] average training loss: 3393.6250 cellbender:remove-background: [epoch 102] average training loss: 3400.0985 cellbender:remove-background: [epoch 103] average training loss: 3388.7106 cellbender:remove-background: [epoch 104] average training loss: 3387.6235 cellbender:remove-background: [epoch 105] average training loss: 3386.8051 cellbender:remove-background: [epoch 105] average test loss: 3427.5792 cellbender:remove-background: [epoch 106] average training loss: 3396.3009 cellbender:remove-background: [epoch 107] average training loss: 3386.5360 cellbender:remove-background: [epoch 108] average training loss: 3394.3250 cellbender:remove-background: [epoch 109] average training loss: 3388.5829 cellbender:remove-background: [epoch 110] average training loss: 3387.2212 cellbender:remove-background: [epoch 110] average test loss: 3403.6217 cellbender:remove-background: [epoch 111] average training loss: 3383.1419 cellbender:remove-background: [epoch 112] average training loss: 3384.7733 cellbender:remove-background: [epoch 113] average training loss: 3384.4745 cellbender:remove-background: [epoch 114] average training loss: 3377.3381 cellbender:remove-background: [epoch 115] average training loss: 3379.3658 cellbender:remove-background: [epoch 115] average test loss: 3401.5106 cellbender:remove-background: [epoch 116] average training loss: 3383.5772 cellbender:remove-background: [epoch 117] average training loss: 3384.5485 cellbender:remove-background: [epoch 118] average training loss: 3374.5104 cellbender:remove-background: [epoch 119] average training loss: 3376.6974 cellbender:remove-background: [epoch 120] average training loss: 3384.3081 cellbender:remove-background: [epoch 120] average test loss: 3390.1750 cellbender:remove-background: [epoch 121] average training loss: 3377.9305 cellbender:remove-background: [epoch 122] average training loss: 3373.4286 cellbender:remove-background: [epoch 123] average training loss: 3375.2967 cellbender:remove-background: [epoch 124] average training loss: 3372.3765 cellbender:remove-background: [epoch 125] average training loss: 3378.7881 cellbender:remove-background: [epoch 125] average test loss: 3383.6400 cellbender:remove-background: [epoch 126] average training loss: 3370.7857 cellbender:remove-background: [epoch 127] average training loss: 3374.6100 cellbender:remove-background: [epoch 128] average training loss: 3380.3470 cellbender:remove-background: [epoch 129] average training loss: 3370.0777 cellbender:remove-background: [epoch 130] average training loss: 3371.9557 cellbender:remove-background: [epoch 130] average test loss: 3379.0630 cellbender:remove-background: [epoch 131] average training loss: 3369.7505 cellbender:remove-background: [epoch 132] average training loss: 3374.2146 cellbender:remove-background: [epoch 133] average training loss: 3371.8937 cellbender:remove-background: [epoch 134] average training loss: 3370.4325 cellbender:remove-background: [epoch 135] average training loss: 3371.7079 cellbender:remove-background: [epoch 135] average test loss: 3402.2668 cellbender:remove-background: [epoch 136] average training loss: 3377.5067 cellbender:remove-background: [epoch 137] average training loss: 3367.4026 cellbender:remove-background: [epoch 138] average training loss: 3368.2182 cellbender:remove-background: [epoch 139] average training loss: 3366.7844 cellbender:remove-background: [epoch 140] average training loss: 3364.3665 cellbender:remove-background: [epoch 140] average test loss: 3389.9082 cellbender:remove-background: [epoch 141] average training loss: 3369.3907 cellbender:remove-background: [epoch 142] average training loss: 3364.3209 cellbender:remove-background: [epoch 143] average training loss: 3368.9894 cellbender:remove-background: [epoch 144] average training loss: 3365.3533 cellbender:remove-background: [epoch 145] average training loss: 3368.6761 cellbender:remove-background: [epoch 145] average test loss: 3382.2483 cellbender:remove-background: [epoch 146] average training loss: 3369.5340 cellbender:remove-background: [epoch 147] average training loss: 3366.2924 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/2653-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 148] average training loss: 3369.9985 cellbender:remove-background: [epoch 149] average training loss: 3365.3403 cellbender:remove-background: [epoch 150] average training loss: 3369.1786 cellbender:remove-background: [epoch 150] average test loss: 3377.5482 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/2653-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:31:45 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpyzgg_zkj cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpyzgg_zkj /tmp/tmpyzgg_zkj/97fee23f6d_random.pyro /tmp/tmpyzgg_zkj/97fee23f6d_random.cuda /tmp/tmpyzgg_zkj/97fee23f6d_model.torch /tmp/tmpyzgg_zkj/97fee23f6d_optim.torch /tmp/tmpyzgg_zkj/97fee23f6d_optim.pyro /tmp/tmpyzgg_zkj/97fee23f6d_params.pyro /tmp/tmpyzgg_zkj/97fee23f6d_train.loaderstate /tmp/tmpyzgg_zkj/97fee23f6d_test.loaderstate /tmp/tmpyzgg_zkj/97fee23f6d_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 (1/107) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/107) cellbender:remove-background: Working on chunk (3/107) cellbender:remove-background: Working on chunk (4/107) cellbender:remove-background: Working on chunk (5/107) cellbender:remove-background: Working on chunk (6/107) cellbender:remove-background: Working on chunk (7/107) cellbender:remove-background: Working on chunk (8/107) cellbender:remove-background: Working on chunk (9/107) cellbender:remove-background: Working on chunk (10/107) cellbender:remove-background: Working on chunk (11/107) cellbender:remove-background: Working on chunk (12/107) cellbender:remove-background: Working on chunk (13/107) cellbender:remove-background: Working on chunk (14/107) cellbender:remove-background: Working on chunk (15/107) cellbender:remove-background: Working on chunk (16/107) cellbender:remove-background: Working on chunk (17/107) cellbender:remove-background: Working on chunk (18/107) cellbender:remove-background: Working on chunk (19/107) cellbender:remove-background: Working on chunk (20/107) cellbender:remove-background: Working on chunk (21/107) cellbender:remove-background: Working on chunk (22/107) cellbender:remove-background: Working on chunk (23/107) cellbender:remove-background: Working on chunk (24/107) cellbender:remove-background: Working on chunk 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Working on chunk (61/107) cellbender:remove-background: Working on chunk (62/107) cellbender:remove-background: Working on chunk (63/107) cellbender:remove-background: Working on chunk (64/107) cellbender:remove-background: Working on chunk (65/107) cellbender:remove-background: Working on chunk (66/107) cellbender:remove-background: Working on chunk (67/107) cellbender:remove-background: Working on chunk (68/107) cellbender:remove-background: Working on chunk (69/107) cellbender:remove-background: Working on chunk (70/107) cellbender:remove-background: Working on chunk (71/107) cellbender:remove-background: Working on chunk (72/107) cellbender:remove-background: Working on chunk (73/107) cellbender:remove-background: Working on chunk (74/107) cellbender:remove-background: Working on chunk (75/107) cellbender:remove-background: Working on chunk (76/107) cellbender:remove-background: Working on chunk (77/107) cellbender:remove-background: Working on chunk (78/107) cellbender:remove-background: Working on chunk (79/107) cellbender:remove-background: Working on chunk (80/107) cellbender:remove-background: Working on chunk (81/107) cellbender:remove-background: Working on chunk (82/107) cellbender:remove-background: Working on chunk (83/107) cellbender:remove-background: Working on chunk (84/107) cellbender:remove-background: Working on chunk (85/107) cellbender:remove-background: Working on chunk (86/107) cellbender:remove-background: Working on chunk (87/107) cellbender:remove-background: Working on chunk (88/107) cellbender:remove-background: Working on chunk (89/107) cellbender:remove-background: Working on chunk (90/107) cellbender:remove-background: Working on chunk (91/107) cellbender:remove-background: Working on chunk (92/107) cellbender:remove-background: Working on chunk (93/107) cellbender:remove-background: Working on chunk (94/107) cellbender:remove-background: Working on chunk (95/107) cellbender:remove-background: Working on chunk (96/107) cellbender:remove-background: Working on chunk (97/107) cellbender:remove-background: Working on chunk (98/107) cellbender:remove-background: Working on chunk (99/107) cellbender:remove-background: Working on chunk (100/107) cellbender:remove-background: Working on chunk (101/107) cellbender:remove-background: Working on chunk (102/107) cellbender:remove-background: Working on chunk (103/107) cellbender:remove-background: Working on chunk (104/107) cellbender:remove-background: Working on chunk (105/107) cellbender:remove-background: Working on chunk (106/107) cellbender:remove-background: Working on chunk (107/107) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-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/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:38:59 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-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: [2.43 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 15:56:45 Total MCKP estimation time = 1029.94 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/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-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/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-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/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-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/2653-Schizophrenia-Hippocampus/2653-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:57:08