cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1676-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-Hippocampus/1676-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 4421 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash d14a953df4) cellbender:remove-background: 2024-06-06 14:49:44 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/1676-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: 31499 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 6892 cellbender:remove-background: Prior on counts for empty droplets is 113 cellbender:remove-background: Excluding 9962 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21537 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 56 cellbender:remove-background: Using 4421 probable cell barcodes, plus an additional 15579 barcodes, and 6445 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 112 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp8pkht54j 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: 4940.5331 cellbender:remove-background: [epoch 002] average training loss: 4067.1095 (6.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 69 epochs cellbender:remove-background: [epoch 003] average training loss: 3640.3790 cellbender:remove-background: [epoch 004] average training loss: 3333.8404 cellbender:remove-background: [epoch 005] average training loss: 3297.6904 cellbender:remove-background: [epoch 005] average test loss: 3397.8080 cellbender:remove-background: [epoch 006] average training loss: 3280.6134 cellbender:remove-background: [epoch 007] average training loss: 3234.5427 cellbender:remove-background: [epoch 008] average training loss: 3199.4537 cellbender:remove-background: [epoch 009] average training loss: 3167.2926 cellbender:remove-background: [epoch 010] average training loss: 3062.7598 cellbender:remove-background: [epoch 010] average test loss: 3131.7066 cellbender:remove-background: [epoch 011] average training loss: 3043.6569 cellbender:remove-background: [epoch 012] average training loss: 3027.6430 cellbender:remove-background: [epoch 013] average training loss: 2991.8598 cellbender:remove-background: [epoch 014] average training loss: 2999.7411 cellbender:remove-background: [epoch 015] average training loss: 2882.6575 cellbender:remove-background: [epoch 015] average test loss: 2905.0928 cellbender:remove-background: [epoch 016] average training loss: 2843.0607 cellbender:remove-background: [epoch 017] average training loss: 2843.1940 cellbender:remove-background: [epoch 018] average training loss: 2824.3563 cellbender:remove-background: [epoch 019] average training loss: 2803.3434 cellbender:remove-background: [epoch 020] average training loss: 2774.7135 cellbender:remove-background: [epoch 020] average test loss: 2847.6496 cellbender:remove-background: [epoch 021] average training loss: 2760.1849 cellbender:remove-background: [epoch 022] average training loss: 2750.6602 cellbender:remove-background: [epoch 023] average training loss: 2740.0397 cellbender:remove-background: [epoch 024] average training loss: 2726.3434 cellbender:remove-background: [epoch 025] average training loss: 2724.9397 cellbender:remove-background: [epoch 025] average test loss: 2760.2617 cellbender:remove-background: [epoch 026] average training loss: 2706.8672 cellbender:remove-background: [epoch 027] average training loss: 2701.2345 cellbender:remove-background: [epoch 028] average training loss: 2698.1972 cellbender:remove-background: [epoch 029] average training loss: 2691.0484 cellbender:remove-background: [epoch 030] average training loss: 2682.9862 cellbender:remove-background: [epoch 030] average test loss: 2707.5219 cellbender:remove-background: [epoch 031] average training loss: 2682.8174 cellbender:remove-background: [epoch 032] average training loss: 2675.8191 cellbender:remove-background: [epoch 033] average training loss: 2679.6435 cellbender:remove-background: [epoch 034] average training loss: 2668.9541 cellbender:remove-background: [epoch 035] average training loss: 2673.3173 cellbender:remove-background: [epoch 035] average test loss: 2671.4444 cellbender:remove-background: [epoch 036] average training loss: 2671.8467 cellbender:remove-background: [epoch 037] average training loss: 2676.0845 cellbender:remove-background: [epoch 038] average training loss: 2667.7290 cellbender:remove-background: [epoch 039] average training loss: 2672.2340 cellbender:remove-background: [epoch 040] average training loss: 2672.8988 cellbender:remove-background: [epoch 040] average test loss: 2655.8689 cellbender:remove-background: [epoch 041] average training loss: 2673.4951 cellbender:remove-background: [epoch 042] average training loss: 2680.4400 cellbender:remove-background: [epoch 043] average training loss: 2683.1059 cellbender:remove-background: [epoch 044] average training loss: 2680.6454 cellbender:remove-background: [epoch 045] average training loss: 2683.3757 cellbender:remove-background: [epoch 045] average test loss: 2669.0261 cellbender:remove-background: [epoch 046] average training loss: 2688.0729 cellbender:remove-background: [epoch 047] average training loss: 2692.2288 cellbender:remove-background: [epoch 048] average training loss: 2703.4022 cellbender:remove-background: [epoch 049] average training loss: 2703.8407 cellbender:remove-background: [epoch 050] average training loss: 2720.3296 cellbender:remove-background: [epoch 050] average test loss: 2766.6292 cellbender:remove-background: [epoch 051] average training loss: 2728.0336 cellbender:remove-background: [epoch 052] average training loss: 2751.1900 cellbender:remove-background: [epoch 053] average training loss: 2754.6441 cellbender:remove-background: [epoch 054] average training loss: 2733.4814 cellbender:remove-background: [epoch 055] average training loss: 2748.2027 cellbender:remove-background: [epoch 055] average test loss: 2869.7601 cellbender:remove-background: [epoch 056] average training loss: 2765.4572 cellbender:remove-background: [epoch 057] average training loss: 2776.4511 cellbender:remove-background: [epoch 058] average training loss: 2789.7723 cellbender:remove-background: [epoch 059] average training loss: 2786.0196 cellbender:remove-background: [epoch 060] average training loss: 2812.1617 cellbender:remove-background: [epoch 060] average test loss: 2885.7179 cellbender:remove-background: [epoch 061] average training loss: 2829.0231 cellbender:remove-background: [epoch 062] average training loss: 2833.6537 cellbender:remove-background: [epoch 063] average training loss: 2811.0012 cellbender:remove-background: [epoch 064] average training loss: 2830.3534 cellbender:remove-background: [epoch 065] average training loss: 2795.4690 cellbender:remove-background: [epoch 065] average test loss: 2834.4584 cellbender:remove-background: [epoch 066] average training loss: 2822.0045 cellbender:remove-background: [epoch 067] average training loss: 2831.8318 cellbender:remove-background: [epoch 068] average training loss: 2854.3145 cellbender:remove-background: [epoch 069] average training loss: 2847.5515 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/1676-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 070] average training loss: 2860.2415 cellbender:remove-background: [epoch 070] average test loss: 2846.4544 cellbender:remove-background: [epoch 071] average training loss: 2852.2621 cellbender:remove-background: [epoch 072] average training loss: 2836.4392 cellbender:remove-background: [epoch 073] average training loss: 2823.7587 cellbender:remove-background: [epoch 074] average training loss: 2826.4784 cellbender:remove-background: [epoch 075] average training loss: 2819.7085 cellbender:remove-background: [epoch 075] average test loss: 2906.4349 cellbender:remove-background: [epoch 076] average training loss: 2895.5137 cellbender:remove-background: [epoch 077] average training loss: 2857.6731 cellbender:remove-background: [epoch 078] average training loss: 2827.9319 cellbender:remove-background: [epoch 079] average training loss: 2842.6466 cellbender:remove-background: [epoch 080] average training loss: 2873.4863 cellbender:remove-background: [epoch 080] average test loss: 3187.1133 cellbender:remove-background: [epoch 081] average training loss: 2884.2151 cellbender:remove-background: [epoch 082] average training loss: 2818.8094 cellbender:remove-background: [epoch 083] average training loss: 2809.2855 cellbender:remove-background: [epoch 084] average training loss: 2853.7990 cellbender:remove-background: [epoch 085] average training loss: 2872.6709 cellbender:remove-background: [epoch 085] average test loss: 2950.1379 cellbender:remove-background: [epoch 086] average training loss: 2831.4012 cellbender:remove-background: [epoch 087] average training loss: 2853.9882 cellbender:remove-background: [epoch 088] average training loss: 2845.6434 cellbender:remove-background: [epoch 089] average training loss: 2817.7423 cellbender:remove-background: [epoch 090] average training loss: 2809.6868 cellbender:remove-background: [epoch 090] average test loss: 2887.4323 cellbender:remove-background: [epoch 091] average training loss: 2852.7821 cellbender:remove-background: [epoch 092] average training loss: 2821.3392 cellbender:remove-background: [epoch 093] average training loss: 2843.3821 cellbender:remove-background: [epoch 094] average training loss: 2896.1914 cellbender:remove-background: [epoch 095] average training loss: 2835.1537 cellbender:remove-background: [epoch 095] average test loss: 2826.2936 cellbender:remove-background: [epoch 096] average training loss: 2893.3562 cellbender:remove-background: [epoch 097] average training loss: 2863.7805 cellbender:remove-background: [epoch 098] average training loss: 2843.9075 cellbender:remove-background: [epoch 099] average training loss: 2884.7503 cellbender:remove-background: [epoch 100] average training loss: 2846.0425 cellbender:remove-background: [epoch 100] average test loss: 2911.2864 cellbender:remove-background: [epoch 101] average training loss: 2863.8187 cellbender:remove-background: [epoch 102] average training loss: 2825.3417 cellbender:remove-background: [epoch 103] average training loss: 2848.0052 cellbender:remove-background: [epoch 104] average training loss: 2866.4011 cellbender:remove-background: [epoch 105] average training loss: 2817.9123 cellbender:remove-background: [epoch 105] average test loss: 3000.8831 cellbender:remove-background: [epoch 106] average training loss: 2839.3284 cellbender:remove-background: [epoch 107] average training loss: 2863.1179 cellbender:remove-background: [epoch 108] average training loss: 2876.9825 cellbender:remove-background: [epoch 109] average training loss: 2853.4125 cellbender:remove-background: [epoch 110] average training loss: 2854.6096 cellbender:remove-background: [epoch 110] average test loss: 2991.0847 cellbender:remove-background: [epoch 111] average training loss: 2840.7435 cellbender:remove-background: [epoch 112] average training loss: 2865.7231 cellbender:remove-background: [epoch 113] average training loss: 2845.4881 cellbender:remove-background: [epoch 114] average training loss: 2830.7192 cellbender:remove-background: [epoch 115] average training loss: 2835.2127 cellbender:remove-background: [epoch 115] average test loss: 2872.8842 cellbender:remove-background: [epoch 116] average training loss: 2827.4730 cellbender:remove-background: [epoch 117] average training loss: 2845.4599 cellbender:remove-background: [epoch 118] average training loss: 2855.4838 cellbender:remove-background: [epoch 119] average training loss: 2822.4496 cellbender:remove-background: [epoch 120] average training loss: 2891.0596 cellbender:remove-background: [epoch 120] average test loss: 2954.3573 cellbender:remove-background: [epoch 121] average training loss: 2837.4053 cellbender:remove-background: [epoch 122] average training loss: 2806.5202 cellbender:remove-background: [epoch 123] average training loss: 2858.3818 cellbender:remove-background: [epoch 124] average training loss: 2845.9541 cellbender:remove-background: [epoch 125] average training loss: 2869.2965 cellbender:remove-background: [epoch 125] average test loss: 2839.8744 cellbender:remove-background: [epoch 126] average training loss: 2872.3269 cellbender:remove-background: [epoch 127] average training loss: 2856.2548 cellbender:remove-background: [epoch 128] average training loss: 2854.5772 cellbender:remove-background: [epoch 129] average training loss: 2826.3894 cellbender:remove-background: [epoch 130] average training loss: 2823.8348 cellbender:remove-background: [epoch 130] average test loss: 2931.8117 cellbender:remove-background: [epoch 131] average training loss: 2863.5423 cellbender:remove-background: [epoch 132] average training loss: 2823.4939 cellbender:remove-background: [epoch 133] average training loss: 2833.4717 cellbender:remove-background: [epoch 134] average training loss: 2818.0276 cellbender:remove-background: [epoch 135] average training loss: 2841.7050 cellbender:remove-background: [epoch 135] average test loss: 3011.3108 cellbender:remove-background: [epoch 136] average training loss: 2824.5073 cellbender:remove-background: [epoch 137] average training loss: 2804.2227 cellbender:remove-background: [epoch 138] average training loss: 2873.6532 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/1676-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 139] average training loss: 2815.7457 cellbender:remove-background: [epoch 140] average training loss: 2825.2731 cellbender:remove-background: [epoch 140] average test loss: 2839.0926 cellbender:remove-background: [epoch 141] average training loss: 2843.8481 cellbender:remove-background: [epoch 142] average training loss: 2843.0665 cellbender:remove-background: [epoch 143] average training loss: 2812.5143 cellbender:remove-background: [epoch 144] average training loss: 2834.1194 cellbender:remove-background: [epoch 145] average training loss: 2861.9595 cellbender:remove-background: [epoch 145] average test loss: 2981.0221 cellbender:remove-background: [epoch 146] average training loss: 2851.1550 cellbender:remove-background: [epoch 147] average training loss: 2797.4873 cellbender:remove-background: [epoch 148] average training loss: 2838.5895 cellbender:remove-background: [epoch 149] average training loss: 2847.4391 cellbender:remove-background: [epoch 150] average training loss: 2854.8718 cellbender:remove-background: [epoch 150] average test loss: 2850.7759 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/1676-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:10:26 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp4iopys74 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp4iopys74 /tmp/tmp4iopys74/d14a953df4_random.pyro /tmp/tmp4iopys74/d14a953df4_random.cuda /tmp/tmp4iopys74/d14a953df4_model.torch /tmp/tmp4iopys74/d14a953df4_optim.torch /tmp/tmp4iopys74/d14a953df4_optim.pyro /tmp/tmp4iopys74/d14a953df4_params.pyro /tmp/tmp4iopys74/d14a953df4_train.loaderstate /tmp/tmp4iopys74/d14a953df4_test.loaderstate /tmp/tmp4iopys74/d14a953df4_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: [0.03 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/1676-Schizophrenia-Hippocampus/1676-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/1676-Schizophrenia-Hippocampus/1676-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:15:00 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-Hippocampus/1676-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/1676-Schizophrenia-Hippocampus/1676-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: [1.85 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 15:28:27 Total MCKP estimation time = 777.90 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/1676-Schizophrenia-Hippocampus/1676-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/1676-Schizophrenia-Hippocampus/1676-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/1676-Schizophrenia-Hippocampus/1676-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/1676-Schizophrenia-Hippocampus/1676-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:28:46