cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2653-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 8067 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 4de42cc3b1) cellbender:remove-background: 2024-06-06 15:05:08 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-DLPFC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 32516 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 4212 cellbender:remove-background: Prior on counts for empty droplets is 186 cellbender:remove-background: Excluding 4952 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 27564 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 93 cellbender:remove-background: Using 8067 probable cell barcodes, plus an additional 11933 barcodes, and 50454 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 184 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpfwfjizsj 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: 6713.6655 cellbender:remove-background: [epoch 002] average training loss: 5374.3064 (7.0 seconds per epoch) cellbender:remove-background: Will checkpoint every 60 epochs cellbender:remove-background: [epoch 003] average training loss: 4615.6907 cellbender:remove-background: [epoch 004] average training loss: 4144.8211 cellbender:remove-background: [epoch 005] average training loss: 3999.4625 cellbender:remove-background: [epoch 005] average test loss: 4063.0403 cellbender:remove-background: [epoch 006] average training loss: 3945.5743 cellbender:remove-background: [epoch 007] average training loss: 3893.4695 cellbender:remove-background: [epoch 008] average training loss: 3850.8007 cellbender:remove-background: [epoch 009] average training loss: 3841.6479 cellbender:remove-background: [epoch 010] average training loss: 3776.1725 cellbender:remove-background: [epoch 010] average test loss: 3821.4944 cellbender:remove-background: [epoch 011] average training loss: 3669.9886 cellbender:remove-background: [epoch 012] average training loss: 3619.7235 cellbender:remove-background: [epoch 013] average training loss: 3593.1739 cellbender:remove-background: [epoch 014] average training loss: 3606.6449 cellbender:remove-background: [epoch 015] average training loss: 3570.5175 cellbender:remove-background: [epoch 015] average test loss: 3575.0755 cellbender:remove-background: [epoch 016] average training loss: 3555.7575 cellbender:remove-background: [epoch 017] average training loss: 3565.8563 cellbender:remove-background: [epoch 018] average training loss: 3549.9853 cellbender:remove-background: [epoch 019] average training loss: 3531.2433 cellbender:remove-background: [epoch 020] average training loss: 3506.5801 cellbender:remove-background: [epoch 020] average test loss: 3522.2342 cellbender:remove-background: [epoch 021] average training loss: 3506.1033 cellbender:remove-background: [epoch 022] average training loss: 3498.6247 cellbender:remove-background: [epoch 023] average training loss: 3481.1828 cellbender:remove-background: [epoch 024] average training loss: 3446.0715 cellbender:remove-background: [epoch 025] average training loss: 3422.2538 cellbender:remove-background: [epoch 025] average test loss: 3402.9666 cellbender:remove-background: [epoch 026] average training loss: 3393.6771 cellbender:remove-background: [epoch 027] average training loss: 3384.7950 cellbender:remove-background: [epoch 028] average training loss: 3380.3053 cellbender:remove-background: [epoch 029] average training loss: 3370.9532 cellbender:remove-background: [epoch 030] average training loss: 3363.0629 cellbender:remove-background: [epoch 030] average test loss: 3341.1552 cellbender:remove-background: [epoch 031] average training loss: 3359.8298 cellbender:remove-background: [epoch 032] average training loss: 3356.6292 cellbender:remove-background: [epoch 033] average training loss: 3359.3685 cellbender:remove-background: [epoch 034] average training loss: 3357.4506 cellbender:remove-background: [epoch 035] average training loss: 3357.3834 cellbender:remove-background: [epoch 035] average test loss: 3344.1658 cellbender:remove-background: [epoch 036] average training loss: 3359.8329 cellbender:remove-background: [epoch 037] average training loss: 3358.8871 cellbender:remove-background: [epoch 038] average training loss: 3356.1481 cellbender:remove-background: [epoch 039] average training loss: 3356.9416 cellbender:remove-background: [epoch 040] average training loss: 3358.7990 cellbender:remove-background: [epoch 040] average test loss: 3318.0854 cellbender:remove-background: [epoch 041] average training loss: 3362.2783 cellbender:remove-background: [epoch 042] average training loss: 3364.7792 cellbender:remove-background: [epoch 043] average training loss: 3366.8300 cellbender:remove-background: [epoch 044] average training loss: 3367.3120 cellbender:remove-background: [epoch 045] average training loss: 3366.7355 cellbender:remove-background: [epoch 045] average test loss: 3366.8140 cellbender:remove-background: [epoch 046] average training loss: 3372.3440 cellbender:remove-background: [epoch 047] average training loss: 3374.5772 cellbender:remove-background: [epoch 048] average training loss: 3371.8807 cellbender:remove-background: [epoch 049] average training loss: 3373.7222 cellbender:remove-background: [epoch 050] average training loss: 3381.0504 cellbender:remove-background: [epoch 050] average test loss: 3378.4261 cellbender:remove-background: [epoch 051] average training loss: 3374.8457 cellbender:remove-background: [epoch 052] average training loss: 3378.9023 cellbender:remove-background: [epoch 053] average training loss: 3381.3100 cellbender:remove-background: [epoch 054] average training loss: 3387.9392 cellbender:remove-background: [epoch 055] average training loss: 3386.2232 cellbender:remove-background: [epoch 055] average test loss: 3371.4708 cellbender:remove-background: [epoch 056] average training loss: 3381.6793 cellbender:remove-background: [epoch 057] average training loss: 3393.7974 cellbender:remove-background: [epoch 058] average training loss: 3391.3197 cellbender:remove-background: [epoch 059] average training loss: 3415.1683 cellbender:remove-background: [epoch 060] average training loss: 3410.3572 cellbender:remove-background: [epoch 060] average test loss: 3450.4663 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 061] average training loss: 3429.8626 cellbender:remove-background: [epoch 062] average training loss: 3411.5763 cellbender:remove-background: [epoch 063] average training loss: 3424.3391 cellbender:remove-background: [epoch 064] average training loss: 3421.5632 cellbender:remove-background: [epoch 065] average training loss: 3412.6793 cellbender:remove-background: [epoch 065] average test loss: 3426.1016 cellbender:remove-background: [epoch 066] average training loss: 3407.0721 cellbender:remove-background: [epoch 067] average training loss: 3409.4204 cellbender:remove-background: [epoch 068] average training loss: 3412.7046 cellbender:remove-background: [epoch 069] average training loss: 3415.2241 cellbender:remove-background: [epoch 070] average training loss: 3441.9517 cellbender:remove-background: [epoch 070] average test loss: 3437.4476 cellbender:remove-background: [epoch 071] average training loss: 3450.0886 cellbender:remove-background: [epoch 072] average training loss: 3447.0781 cellbender:remove-background: [epoch 073] average training loss: 3420.1823 cellbender:remove-background: [epoch 074] average training loss: 3416.9232 cellbender:remove-background: [epoch 075] average training loss: 3426.6658 cellbender:remove-background: [epoch 075] average test loss: 3448.1631 cellbender:remove-background: [epoch 076] average training loss: 3413.6150 cellbender:remove-background: [epoch 077] average training loss: 3406.9939 cellbender:remove-background: [epoch 078] average training loss: 3406.6045 cellbender:remove-background: [epoch 079] average training loss: 3401.6479 cellbender:remove-background: [epoch 080] average training loss: 3396.9251 cellbender:remove-background: [epoch 080] average test loss: 3385.4141 cellbender:remove-background: [epoch 081] average training loss: 3402.0302 cellbender:remove-background: [epoch 082] average training loss: 3398.5499 cellbender:remove-background: [epoch 083] average training loss: 3416.4629 cellbender:remove-background: [epoch 084] average training loss: 3411.5921 cellbender:remove-background: [epoch 085] average training loss: 3407.6305 cellbender:remove-background: [epoch 085] average test loss: 3428.7847 cellbender:remove-background: [epoch 086] average training loss: 3404.5414 cellbender:remove-background: [epoch 087] average training loss: 3396.8363 cellbender:remove-background: [epoch 088] average training loss: 3405.5158 cellbender:remove-background: [epoch 089] average training loss: 3385.4060 cellbender:remove-background: [epoch 090] average training loss: 3403.4835 cellbender:remove-background: [epoch 090] average test loss: 3420.3977 cellbender:remove-background: [epoch 091] average training loss: 3384.3416 cellbender:remove-background: [epoch 092] average training loss: 3389.5262 cellbender:remove-background: [epoch 093] average training loss: 3387.1099 cellbender:remove-background: [epoch 094] average training loss: 3379.4756 cellbender:remove-background: [epoch 095] average training loss: 3395.0860 cellbender:remove-background: [epoch 095] average test loss: 3416.4951 cellbender:remove-background: [epoch 096] average training loss: 3382.1128 cellbender:remove-background: [epoch 097] average training loss: 3385.4967 cellbender:remove-background: [epoch 098] average training loss: 3372.3248 cellbender:remove-background: [epoch 099] average training loss: 3376.8316 cellbender:remove-background: [epoch 100] average training loss: 3380.4360 cellbender:remove-background: [epoch 100] average test loss: 3416.0164 cellbender:remove-background: [epoch 101] average training loss: 3378.7975 cellbender:remove-background: [epoch 102] average training loss: 3372.2486 cellbender:remove-background: [epoch 103] average training loss: 3373.7971 cellbender:remove-background: [epoch 104] average training loss: 3367.0856 cellbender:remove-background: [epoch 105] average training loss: 3371.7778 cellbender:remove-background: [epoch 105] average test loss: 3406.2663 cellbender:remove-background: [epoch 106] average training loss: 3368.8327 cellbender:remove-background: [epoch 107] average training loss: 3371.2737 cellbender:remove-background: [epoch 108] average training loss: 3367.7869 cellbender:remove-background: [epoch 109] average training loss: 3363.5876 cellbender:remove-background: [epoch 110] average training loss: 3362.5136 cellbender:remove-background: [epoch 110] average test loss: 3373.8697 cellbender:remove-background: [epoch 111] average training loss: 3357.3791 cellbender:remove-background: [epoch 112] average training loss: 3356.9323 cellbender:remove-background: [epoch 113] average training loss: 3362.7038 cellbender:remove-background: [epoch 114] average training loss: 3360.1541 cellbender:remove-background: [epoch 115] average training loss: 3354.1632 cellbender:remove-background: [epoch 115] average test loss: 3413.0176 cellbender:remove-background: [epoch 116] average training loss: 3356.0100 cellbender:remove-background: [epoch 117] average training loss: 3360.8050 cellbender:remove-background: [epoch 118] average training loss: 3353.7970 cellbender:remove-background: [epoch 119] average training loss: 3355.4210 cellbender:remove-background: [epoch 120] average training loss: 3357.4066 cellbender:remove-background: [epoch 120] average test loss: 3401.7312 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-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 121] average training loss: 3353.3965 cellbender:remove-background: [epoch 122] average training loss: 3351.8052 cellbender:remove-background: [epoch 123] average training loss: 3351.0143 cellbender:remove-background: [epoch 124] average training loss: 3357.6467 cellbender:remove-background: [epoch 125] average training loss: 3354.0000 cellbender:remove-background: [epoch 125] average test loss: 3401.6495 cellbender:remove-background: [epoch 126] average training loss: 3355.0764 cellbender:remove-background: [epoch 127] average training loss: 3355.4713 cellbender:remove-background: [epoch 128] average training loss: 3351.4523 cellbender:remove-background: [epoch 129] average training loss: 3347.2648 cellbender:remove-background: [epoch 130] average training loss: 3356.7051 cellbender:remove-background: [epoch 130] average test loss: 3388.4305 cellbender:remove-background: [epoch 131] average training loss: 3351.7050 cellbender:remove-background: [epoch 132] average training loss: 3351.9148 cellbender:remove-background: [epoch 133] average training loss: 3353.3277 cellbender:remove-background: [epoch 134] average training loss: 3353.4851 cellbender:remove-background: [epoch 135] average training loss: 3348.0975 cellbender:remove-background: [epoch 135] average test loss: 3399.6690 cellbender:remove-background: [epoch 136] average training loss: 3354.9848 cellbender:remove-background: [epoch 137] average training loss: 3351.1456 cellbender:remove-background: [epoch 138] average training loss: 3350.7218 cellbender:remove-background: [epoch 139] average training loss: 3347.6290 cellbender:remove-background: [epoch 140] average training loss: 3350.1089 cellbender:remove-background: [epoch 140] average test loss: 3398.3372 cellbender:remove-background: [epoch 141] average training loss: 3351.1748 cellbender:remove-background: [epoch 142] average training loss: 3350.0158 cellbender:remove-background: [epoch 143] average training loss: 3346.3529 cellbender:remove-background: [epoch 144] average training loss: 3351.1410 cellbender:remove-background: [epoch 145] average training loss: 3350.3280 cellbender:remove-background: [epoch 145] average test loss: 3392.8866 cellbender:remove-background: [epoch 146] average training loss: 3354.2949 cellbender:remove-background: [epoch 147] average training loss: 3352.0553 cellbender:remove-background: [epoch 148] average training loss: 3348.9077 cellbender:remove-background: [epoch 149] average training loss: 3347.8701 cellbender:remove-background: [epoch 150] average training loss: 3349.6373 cellbender:remove-background: [epoch 150] average test loss: 3396.7577 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-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:27:31 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpw6t5m4na cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpw6t5m4na /tmp/tmpw6t5m4na/4de42cc3b1_random.pyro /tmp/tmpw6t5m4na/4de42cc3b1_random.cuda /tmp/tmpw6t5m4na/4de42cc3b1_model.torch /tmp/tmpw6t5m4na/4de42cc3b1_optim.torch /tmp/tmpw6t5m4na/4de42cc3b1_optim.pyro /tmp/tmpw6t5m4na/4de42cc3b1_params.pyro /tmp/tmpw6t5m4na/4de42cc3b1_train.loaderstate /tmp/tmpw6t5m4na/4de42cc3b1_test.loaderstate /tmp/tmpw6t5m4na/4de42cc3b1_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 (1/79) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/79) cellbender:remove-background: Working on chunk (3/79) cellbender:remove-background: Working on chunk (4/79) cellbender:remove-background: Working on chunk (5/79) cellbender:remove-background: Working on chunk (6/79) cellbender:remove-background: Working on chunk (7/79) cellbender:remove-background: Working on chunk (8/79) cellbender:remove-background: Working on chunk (9/79) cellbender:remove-background: Working on chunk (10/79) cellbender:remove-background: Working on chunk (11/79) cellbender:remove-background: Working on chunk (12/79) cellbender:remove-background: Working on chunk (13/79) cellbender:remove-background: Working on chunk (14/79) cellbender:remove-background: Working on chunk (15/79) cellbender:remove-background: Working on chunk (16/79) cellbender:remove-background: Working on chunk (17/79) cellbender:remove-background: Working on chunk (18/79) cellbender:remove-background: Working on chunk (19/79) cellbender:remove-background: Working on chunk (20/79) cellbender:remove-background: Working on chunk (21/79) cellbender:remove-background: Working on chunk (22/79) cellbender:remove-background: Working on chunk (23/79) cellbender:remove-background: Working on chunk (24/79) cellbender:remove-background: Working on chunk (25/79) cellbender:remove-background: Working on chunk (26/79) cellbender:remove-background: Working on chunk (27/79) cellbender:remove-background: Working on chunk (28/79) cellbender:remove-background: Working on chunk (29/79) cellbender:remove-background: Working on chunk (30/79) cellbender:remove-background: Working on chunk (31/79) cellbender:remove-background: Working on chunk (32/79) cellbender:remove-background: Working on chunk (33/79) cellbender:remove-background: Working on chunk (34/79) cellbender:remove-background: Working on chunk (35/79) cellbender:remove-background: Working on chunk (36/79) cellbender:remove-background: Working on chunk (37/79) cellbender:remove-background: Working on chunk (38/79) cellbender:remove-background: Working on chunk (39/79) cellbender:remove-background: Working on chunk (40/79) cellbender:remove-background: Working on chunk (41/79) cellbender:remove-background: Working on chunk (42/79) cellbender:remove-background: Working on chunk (43/79) cellbender:remove-background: Working on chunk (44/79) cellbender:remove-background: Working on chunk (45/79) cellbender:remove-background: Working on chunk (46/79) cellbender:remove-background: Working on chunk (47/79) cellbender:remove-background: Working on chunk (48/79) cellbender:remove-background: Working on chunk (49/79) cellbender:remove-background: Working on chunk (50/79) cellbender:remove-background: Working on chunk (51/79) cellbender:remove-background: Working on chunk (52/79) cellbender:remove-background: Working on chunk (53/79) cellbender:remove-background: Working on chunk (54/79) cellbender:remove-background: Working on chunk (55/79) cellbender:remove-background: Working on chunk (56/79) cellbender:remove-background: Working on chunk (57/79) cellbender:remove-background: Working on chunk (58/79) cellbender:remove-background: Working on chunk (59/79) cellbender:remove-background: Working on chunk (60/79) cellbender:remove-background: Working on chunk (61/79) cellbender:remove-background: Working on chunk (62/79) cellbender:remove-background: Working on chunk (63/79) cellbender:remove-background: Working on chunk (64/79) cellbender:remove-background: Working on chunk (65/79) cellbender:remove-background: Working on chunk (66/79) cellbender:remove-background: Working on chunk (67/79) cellbender:remove-background: Working on chunk (68/79) cellbender:remove-background: Working on chunk (69/79) cellbender:remove-background: Working on chunk (70/79) cellbender:remove-background: Working on chunk (71/79) cellbender:remove-background: Working on chunk (72/79) cellbender:remove-background: Working on chunk (73/79) cellbender:remove-background: Working on chunk (74/79) cellbender:remove-background: Working on chunk (75/79) cellbender:remove-background: Working on chunk (76/79) cellbender:remove-background: Working on chunk (77/79) cellbender:remove-background: Working on chunk (78/79) cellbender:remove-background: Working on chunk (79/79) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:33:15 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [2.37 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 15:50:35 Total MCKP estimation time = 988.62 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-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2653-Schizophrenia-DLPFC/2653-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:50:56