cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1436-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-dACC/1436-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 4928 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash c98198b03a) cellbender:remove-background: 2024-06-06 15:32:56 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/1436-Schizophrenia-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: 32599 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 9218 cellbender:remove-background: Prior on counts for empty droplets is 36 cellbender:remove-background: Excluding 13376 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19223 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 18 cellbender:remove-background: Using 4928 probable cell barcodes, plus an additional 15072 barcodes, and 45087 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 36 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpano9tncj 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: 5615.3178 cellbender:remove-background: [epoch 002] average training loss: 4322.7652 (12.7 seconds per epoch) cellbender:remove-background: Will checkpoint every 33 epochs cellbender:remove-background: [epoch 003] average training loss: 3692.7992 cellbender:remove-background: [epoch 004] average training loss: 3358.1097 cellbender:remove-background: [epoch 005] average training loss: 3292.1841 cellbender:remove-background: [epoch 005] average test loss: 3276.3180 cellbender:remove-background: [epoch 006] average training loss: 3269.9054 cellbender:remove-background: [epoch 007] average training loss: 3236.0209 cellbender:remove-background: [epoch 008] average training loss: 3195.6967 cellbender:remove-background: [epoch 009] average training loss: 3184.2180 cellbender:remove-background: [epoch 010] average training loss: 3081.3104 cellbender:remove-background: [epoch 010] average test loss: 3159.7387 cellbender:remove-background: [epoch 011] average training loss: 2983.0344 cellbender:remove-background: [epoch 012] average training loss: 2952.6827 cellbender:remove-background: [epoch 013] average training loss: 2928.5030 cellbender:remove-background: [epoch 014] average training loss: 2933.0422 cellbender:remove-background: [epoch 015] average training loss: 2902.7414 cellbender:remove-background: [epoch 015] average test loss: 2866.5358 cellbender:remove-background: [epoch 016] average training loss: 2883.1178 cellbender:remove-background: [epoch 017] average training loss: 2891.4789 cellbender:remove-background: [epoch 018] average training loss: 2862.2868 cellbender:remove-background: [epoch 019] average training loss: 2828.9127 cellbender:remove-background: [epoch 020] average training loss: 2806.1596 cellbender:remove-background: [epoch 020] average test loss: 2773.4625 cellbender:remove-background: [epoch 021] average training loss: 2792.7722 cellbender:remove-background: [epoch 022] average training loss: 2778.0496 cellbender:remove-background: [epoch 023] average training loss: 2762.2778 cellbender:remove-background: [epoch 024] average training loss: 2742.7109 cellbender:remove-background: [epoch 025] average training loss: 2736.3017 cellbender:remove-background: [epoch 025] average test loss: 2701.5529 cellbender:remove-background: [epoch 026] average training loss: 2721.4490 cellbender:remove-background: [epoch 027] average training loss: 2718.8959 cellbender:remove-background: [epoch 028] average training loss: 2715.9205 cellbender:remove-background: [epoch 029] average training loss: 2706.6095 cellbender:remove-background: [epoch 030] average training loss: 2701.7360 cellbender:remove-background: [epoch 030] average test loss: 2660.2347 cellbender:remove-background: [epoch 031] average training loss: 2695.4833 cellbender:remove-background: [epoch 032] average training loss: 2691.8877 cellbender:remove-background: [epoch 033] average training loss: 2691.0491 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/1436-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 034] average training loss: 2691.5405 cellbender:remove-background: [epoch 035] average training loss: 2689.5572 cellbender:remove-background: [epoch 035] average test loss: 2650.0935 cellbender:remove-background: [epoch 036] average training loss: 2693.8434 cellbender:remove-background: [epoch 037] average training loss: 2717.3813 cellbender:remove-background: [epoch 038] average training loss: 2706.2015 cellbender:remove-background: [epoch 039] average training loss: 2705.1053 cellbender:remove-background: [epoch 040] average training loss: 2801.0214 cellbender:remove-background: [epoch 040] average test loss: 2656.0373 cellbender:remove-background: [epoch 041] average training loss: 2702.6877 cellbender:remove-background: [epoch 042] average training loss: 2710.9842 cellbender:remove-background: [epoch 043] average training loss: 2757.6603 cellbender:remove-background: [epoch 044] average training loss: 2737.8851 cellbender:remove-background: [epoch 045] average training loss: 2746.4108 cellbender:remove-background: [epoch 045] average test loss: 2670.4128 cellbender:remove-background: [epoch 046] average training loss: 2786.1604 cellbender:remove-background: [epoch 047] average training loss: 2728.5434 cellbender:remove-background: [epoch 048] average training loss: 2824.2038 cellbender:remove-background: [epoch 049] average training loss: 2707.7252 cellbender:remove-background: [epoch 050] average training loss: 2680.3168 cellbender:remove-background: [epoch 050] average test loss: 2787.7335 cellbender:remove-background: [epoch 051] average training loss: 2698.6765 cellbender:remove-background: [epoch 052] average training loss: 2697.9720 cellbender:remove-background: [epoch 053] average training loss: 2689.7326 cellbender:remove-background: [epoch 054] average training loss: 2727.4642 cellbender:remove-background: [epoch 055] average training loss: 2681.5340 cellbender:remove-background: [epoch 055] average test loss: 2677.7827 cellbender:remove-background: [epoch 056] average training loss: 2690.8526 cellbender:remove-background: [epoch 057] average training loss: 2684.5433 cellbender:remove-background: [epoch 058] average training loss: 2714.1041 cellbender:remove-background: [epoch 059] average training loss: 2756.9000 cellbender:remove-background: [epoch 060] average training loss: 2715.6099 cellbender:remove-background: [epoch 060] average test loss: 2669.0438 cellbender:remove-background: [epoch 061] average training loss: 2695.6076 cellbender:remove-background: [epoch 062] average training loss: 2697.7475 cellbender:remove-background: [epoch 063] average training loss: 2687.1043 cellbender:remove-background: [epoch 064] average training loss: 2754.9656 cellbender:remove-background: [epoch 065] average training loss: 2706.0594 cellbender:remove-background: [epoch 065] average test loss: 2678.2120 cellbender:remove-background: [epoch 066] average training loss: 2695.5891 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/1436-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 067] average training loss: 2677.8890 cellbender:remove-background: [epoch 068] average training loss: 2757.1212 cellbender:remove-background: [epoch 069] average training loss: 2695.2886 cellbender:remove-background: [epoch 070] average training loss: 2670.8365 cellbender:remove-background: [epoch 070] average test loss: 2668.5698 cellbender:remove-background: [epoch 071] average training loss: 2672.3206 cellbender:remove-background: [epoch 072] average training loss: 2674.7051 cellbender:remove-background: [epoch 073] average training loss: 2680.5779 cellbender:remove-background: [epoch 074] average training loss: 2680.0512 cellbender:remove-background: [epoch 075] average training loss: 2675.3228 cellbender:remove-background: [epoch 075] average test loss: 2671.3080 cellbender:remove-background: [epoch 076] average training loss: 2666.8743 cellbender:remove-background: [epoch 077] average training loss: 2670.8866 cellbender:remove-background: [epoch 078] average training loss: 2676.4324 cellbender:remove-background: [epoch 079] average training loss: 2681.6067 cellbender:remove-background: [epoch 080] average training loss: 2678.5982 cellbender:remove-background: [epoch 080] average test loss: 2692.1122 cellbender:remove-background: [epoch 081] average training loss: 2679.8380 cellbender:remove-background: [epoch 082] average training loss: 2671.0931 cellbender:remove-background: [epoch 083] average training loss: 2669.7358 cellbender:remove-background: [epoch 084] average training loss: 2669.3141 cellbender:remove-background: [epoch 085] average training loss: 2667.9610 cellbender:remove-background: [epoch 085] average test loss: 2669.1975 cellbender:remove-background: [epoch 086] average training loss: 2664.0456 cellbender:remove-background: [epoch 087] average training loss: 2680.7587 cellbender:remove-background: [epoch 088] average training loss: 2676.7554 cellbender:remove-background: [epoch 089] average training loss: 2673.3093 cellbender:remove-background: [epoch 090] average training loss: 2689.0264 cellbender:remove-background: [epoch 090] average test loss: 2673.2689 cellbender:remove-background: [epoch 091] average training loss: 2676.6470 cellbender:remove-background: [epoch 092] average training loss: 2675.5368 cellbender:remove-background: [epoch 093] average training loss: 2673.6541 cellbender:remove-background: [epoch 094] average training loss: 2667.9318 cellbender:remove-background: [epoch 095] average training loss: 2665.6451 cellbender:remove-background: [epoch 095] average test loss: 2690.7298 cellbender:remove-background: [epoch 096] average training loss: 2667.6386 cellbender:remove-background: [epoch 097] average training loss: 2666.7795 cellbender:remove-background: [epoch 098] average training loss: 2665.6811 cellbender:remove-background: [epoch 099] average training loss: 2665.0727 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/1436-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 100] average training loss: 2671.4167 cellbender:remove-background: [epoch 100] average test loss: 2695.7419 cellbender:remove-background: [epoch 101] average training loss: 2673.5233 cellbender:remove-background: [epoch 102] average training loss: 2666.0572 cellbender:remove-background: [epoch 103] average training loss: 2671.2665 cellbender:remove-background: [epoch 104] average training loss: 2667.9378 cellbender:remove-background: [epoch 105] average training loss: 2664.6534 cellbender:remove-background: [epoch 105] average test loss: 2650.7354 cellbender:remove-background: [epoch 106] average training loss: 2667.2333 cellbender:remove-background: [epoch 107] average training loss: 2667.4233 cellbender:remove-background: [epoch 108] average training loss: 2668.1887 cellbender:remove-background: [epoch 109] average training loss: 2680.3752 cellbender:remove-background: [epoch 110] average training loss: 2664.9664 cellbender:remove-background: [epoch 110] average test loss: 2669.7802 cellbender:remove-background: [epoch 111] average training loss: 2667.1463 cellbender:remove-background: [epoch 112] average training loss: 2665.8356 cellbender:remove-background: [epoch 113] average training loss: 2663.5100 cellbender:remove-background: [epoch 114] average training loss: 2665.9109 cellbender:remove-background: [epoch 115] average training loss: 2660.2028 cellbender:remove-background: [epoch 115] average test loss: 2670.4135 cellbender:remove-background: [epoch 116] average training loss: 2667.1465 cellbender:remove-background: [epoch 117] average training loss: 2662.5790 cellbender:remove-background: [epoch 118] average training loss: 2666.9398 cellbender:remove-background: [epoch 119] average training loss: 2662.3044 cellbender:remove-background: [epoch 120] average training loss: 2662.5023 cellbender:remove-background: [epoch 120] average test loss: 2663.4452 cellbender:remove-background: [epoch 121] average training loss: 2659.6832 cellbender:remove-background: [epoch 122] average training loss: 2666.3595 cellbender:remove-background: [epoch 123] average training loss: 2668.2517 cellbender:remove-background: [epoch 124] average training loss: 2662.7122 cellbender:remove-background: [epoch 125] average training loss: 2662.6636 cellbender:remove-background: [epoch 125] average test loss: 2666.0762 cellbender:remove-background: [epoch 126] average training loss: 2657.6928 cellbender:remove-background: [epoch 127] average training loss: 2663.7603 cellbender:remove-background: [epoch 128] average training loss: 2663.4915 cellbender:remove-background: [epoch 129] average training loss: 2659.0761 cellbender:remove-background: [epoch 130] average training loss: 2667.1639 cellbender:remove-background: [epoch 130] average test loss: 2676.7705 cellbender:remove-background: [epoch 131] average training loss: 2665.2936 cellbender:remove-background: [epoch 132] average training loss: 2661.5572 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/1436-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 133] average training loss: 2662.0493 cellbender:remove-background: [epoch 134] average training loss: 2658.3239 cellbender:remove-background: [epoch 135] average training loss: 2664.3877 cellbender:remove-background: [epoch 135] average test loss: 2661.4924 cellbender:remove-background: [epoch 136] average training loss: 2658.5872 cellbender:remove-background: [epoch 137] average training loss: 2664.6155 cellbender:remove-background: [epoch 138] average training loss: 2659.2497 cellbender:remove-background: [epoch 139] average training loss: 2660.1496 cellbender:remove-background: [epoch 140] average training loss: 2660.0534 cellbender:remove-background: [epoch 140] average test loss: 2747.5146 cellbender:remove-background: [epoch 141] average training loss: 2659.2156 cellbender:remove-background: [epoch 142] average training loss: 2657.2119 cellbender:remove-background: [epoch 143] average training loss: 2660.8396 cellbender:remove-background: [epoch 144] average training loss: 2658.2101 cellbender:remove-background: [epoch 145] average training loss: 2661.7914 cellbender:remove-background: [epoch 145] average test loss: 2695.2209 cellbender:remove-background: [epoch 146] average training loss: 2663.2333 cellbender:remove-background: [epoch 147] average training loss: 2657.0134 cellbender:remove-background: [epoch 148] average training loss: 2666.1732 cellbender:remove-background: [epoch 149] average training loss: 2660.5515 cellbender:remove-background: [epoch 150] average training loss: 2663.0612 cellbender:remove-background: [epoch 150] average test loss: 2665.6098 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/1436-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:09:21 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpz0d0akwd cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpz0d0akwd /tmp/tmpz0d0akwd/c98198b03a_random.pyro /tmp/tmpz0d0akwd/c98198b03a_random.cuda /tmp/tmpz0d0akwd/c98198b03a_model.torch /tmp/tmpz0d0akwd/c98198b03a_optim.torch /tmp/tmpz0d0akwd/c98198b03a_optim.pyro /tmp/tmpz0d0akwd/c98198b03a_params.pyro /tmp/tmpz0d0akwd/c98198b03a_train.loaderstate /tmp/tmpz0d0akwd/c98198b03a_test.loaderstate /tmp/tmpz0d0akwd/c98198b03a_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 (1/50) cellbender:remove-background: [0.05 mins per chunk] cellbender:remove-background: Working on chunk (2/50) cellbender:remove-background: Working on chunk (3/50) cellbender:remove-background: Working on chunk (4/50) cellbender:remove-background: Working on chunk (5/50) cellbender:remove-background: Working on chunk (6/50) cellbender:remove-background: Working on chunk (7/50) cellbender:remove-background: Working on chunk (8/50) cellbender:remove-background: Working on chunk (9/50) cellbender:remove-background: Working on chunk (10/50) cellbender:remove-background: Working on chunk (11/50) cellbender:remove-background: Working on chunk (12/50) cellbender:remove-background: Working on chunk (13/50) cellbender:remove-background: Working on chunk (14/50) cellbender:remove-background: Working on chunk (15/50) cellbender:remove-background: Working on chunk (16/50) cellbender:remove-background: Working on chunk (17/50) cellbender:remove-background: Working on chunk (18/50) cellbender:remove-background: Working on chunk (19/50) cellbender:remove-background: Working on chunk (20/50) cellbender:remove-background: Working on chunk (21/50) cellbender:remove-background: Working on chunk (22/50) cellbender:remove-background: Working on chunk (23/50) cellbender:remove-background: Working on chunk (24/50) cellbender:remove-background: Working on chunk (25/50) cellbender:remove-background: Working on chunk (26/50) cellbender:remove-background: Working on chunk (27/50) cellbender:remove-background: Working on chunk (28/50) cellbender:remove-background: Working on chunk (29/50) cellbender:remove-background: Working on chunk (30/50) cellbender:remove-background: Working on chunk (31/50) cellbender:remove-background: Working on chunk (32/50) cellbender:remove-background: Working on chunk (33/50) cellbender:remove-background: Working on chunk (34/50) cellbender:remove-background: Working on chunk (35/50) cellbender:remove-background: Working on chunk (36/50) cellbender:remove-background: Working on chunk (37/50) cellbender:remove-background: Working on chunk (38/50) cellbender:remove-background: Working on chunk (39/50) cellbender:remove-background: Working on chunk (40/50) cellbender:remove-background: Working on chunk (41/50) cellbender:remove-background: Working on chunk (42/50) cellbender:remove-background: Working on chunk (43/50) cellbender:remove-background: Working on chunk (44/50) cellbender:remove-background: Working on chunk (45/50) cellbender:remove-background: Working on chunk (46/50) cellbender:remove-background: Working on chunk (47/50) cellbender:remove-background: Working on chunk (48/50) cellbender:remove-background: Working on chunk (49/50) cellbender:remove-background: Working on chunk (50/50) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-dACC/1436-Schizophrenia-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/1436-Schizophrenia-dACC/1436-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:14:11 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-dACC/1436-Schizophrenia-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1436-Schizophrenia-dACC/1436-Schizophrenia-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: [1.82 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 16:27:58 Total MCKP estimation time = 784.16 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/1436-Schizophrenia-dACC/1436-Schizophrenia-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/1436-Schizophrenia-dACC/1436-Schizophrenia-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/1436-Schizophrenia-dACC/1436-Schizophrenia-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/1436-Schizophrenia-dACC/1436-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:28:28