cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2042-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2042-Bipolar-DLPFC/2042-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 6051 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 0001c75099) cellbender:remove-background: 2024-06-06 15:26:05 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/2042-Bipolar-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: 33194 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 6439 cellbender:remove-background: Prior on counts for empty droplets is 67 cellbender:remove-background: Excluding 11233 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21961 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 33 cellbender:remove-background: Using 6051 probable cell barcodes, plus an additional 13949 barcodes, and 53167 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 66 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpyk6p1oij 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: 7041.0567 cellbender:remove-background: [epoch 002] average training loss: 5180.5061 (14.6 seconds per epoch) cellbender:remove-background: Will checkpoint every 29 epochs cellbender:remove-background: [epoch 003] average training loss: 4079.6150 cellbender:remove-background: [epoch 004] average training loss: 3582.7871 cellbender:remove-background: [epoch 005] average training loss: 3443.9152 cellbender:remove-background: [epoch 005] average test loss: 3480.3510 cellbender:remove-background: [epoch 006] average training loss: 3400.7460 cellbender:remove-background: [epoch 007] average training loss: 3344.3740 cellbender:remove-background: [epoch 008] average training loss: 3317.6391 cellbender:remove-background: [epoch 009] average training loss: 3307.1925 cellbender:remove-background: [epoch 010] average training loss: 3266.5414 cellbender:remove-background: [epoch 010] average test loss: 3223.4363 cellbender:remove-background: [epoch 011] average training loss: 3235.5246 cellbender:remove-background: [epoch 012] average training loss: 3138.4379 cellbender:remove-background: [epoch 013] average training loss: 3103.7503 cellbender:remove-background: [epoch 014] average training loss: 3111.8555 cellbender:remove-background: [epoch 015] average training loss: 3079.3517 cellbender:remove-background: [epoch 015] average test loss: 3082.2005 cellbender:remove-background: [epoch 016] average training loss: 3069.5463 cellbender:remove-background: [epoch 017] average training loss: 3077.4608 cellbender:remove-background: [epoch 018] average training loss: 3068.3182 cellbender:remove-background: [epoch 019] average training loss: 3050.1194 cellbender:remove-background: [epoch 020] average training loss: 3024.4520 cellbender:remove-background: [epoch 020] average test loss: 3021.6381 cellbender:remove-background: [epoch 021] average training loss: 3021.1632 cellbender:remove-background: [epoch 022] average training loss: 3016.2938 cellbender:remove-background: [epoch 023] average training loss: 2992.2133 cellbender:remove-background: [epoch 024] average training loss: 2962.4674 cellbender:remove-background: [epoch 025] average training loss: 2944.8205 cellbender:remove-background: [epoch 025] average test loss: 2913.1916 cellbender:remove-background: [epoch 026] average training loss: 2922.0767 cellbender:remove-background: [epoch 027] average training loss: 2913.6003 cellbender:remove-background: [epoch 028] average training loss: 2909.3938 cellbender:remove-background: [epoch 029] average training loss: 2898.2827 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 030] average training loss: 2889.2760 cellbender:remove-background: [epoch 030] average test loss: 2864.1872 cellbender:remove-background: [epoch 031] average training loss: 2884.9704 cellbender:remove-background: [epoch 032] average training loss: 2877.7199 cellbender:remove-background: [epoch 033] average training loss: 2874.9727 cellbender:remove-background: [epoch 034] average training loss: 2869.9446 cellbender:remove-background: [epoch 035] average training loss: 2864.9733 cellbender:remove-background: [epoch 035] average test loss: 2836.3075 cellbender:remove-background: [epoch 036] average training loss: 2860.0421 cellbender:remove-background: [epoch 037] average training loss: 2859.0308 cellbender:remove-background: [epoch 038] average training loss: 2857.6815 cellbender:remove-background: [epoch 039] average training loss: 2854.0789 cellbender:remove-background: [epoch 040] average training loss: 2856.1277 cellbender:remove-background: [epoch 040] average test loss: 2841.9174 cellbender:remove-background: [epoch 041] average training loss: 2854.3180 cellbender:remove-background: [epoch 042] average training loss: 2852.7897 cellbender:remove-background: [epoch 043] average training loss: 2851.7652 cellbender:remove-background: [epoch 044] average training loss: 2850.4290 cellbender:remove-background: [epoch 045] average training loss: 2847.6647 cellbender:remove-background: [epoch 045] average test loss: 2810.4904 cellbender:remove-background: [epoch 046] average training loss: 2847.6992 cellbender:remove-background: [epoch 047] average training loss: 2848.4016 cellbender:remove-background: [epoch 048] average training loss: 2844.7441 cellbender:remove-background: [epoch 049] average training loss: 2844.1115 cellbender:remove-background: [epoch 050] average training loss: 2842.4370 cellbender:remove-background: [epoch 050] average test loss: 2807.1636 cellbender:remove-background: [epoch 051] average training loss: 2841.5720 cellbender:remove-background: [epoch 052] average training loss: 2848.4909 cellbender:remove-background: [epoch 053] average training loss: 2850.8829 cellbender:remove-background: [epoch 054] average training loss: 2843.7010 cellbender:remove-background: [epoch 055] average training loss: 2847.5860 cellbender:remove-background: [epoch 055] average test loss: 2814.7586 cellbender:remove-background: [epoch 056] average training loss: 2848.7652 cellbender:remove-background: [epoch 057] average training loss: 2849.7142 cellbender:remove-background: [epoch 058] average training loss: 2849.4572 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 059] average training loss: 2843.3530 cellbender:remove-background: [epoch 060] average training loss: 2840.0046 cellbender:remove-background: [epoch 060] average test loss: 2822.5763 cellbender:remove-background: [epoch 061] average training loss: 2841.8880 cellbender:remove-background: [epoch 062] average training loss: 2845.0138 cellbender:remove-background: [epoch 063] average training loss: 2843.3046 cellbender:remove-background: [epoch 064] average training loss: 2838.9067 cellbender:remove-background: [epoch 065] average training loss: 2843.1890 cellbender:remove-background: [epoch 065] average test loss: 2818.7490 cellbender:remove-background: [epoch 066] average training loss: 2840.2130 cellbender:remove-background: [epoch 067] average training loss: 2844.5042 cellbender:remove-background: [epoch 068] average training loss: 2842.6119 cellbender:remove-background: [epoch 069] average training loss: 2844.5130 cellbender:remove-background: [epoch 070] average training loss: 2842.5973 cellbender:remove-background: [epoch 070] average test loss: 2800.7577 cellbender:remove-background: [epoch 071] average training loss: 2842.8119 cellbender:remove-background: [epoch 072] average training loss: 2836.1276 cellbender:remove-background: [epoch 073] average training loss: 2839.1839 cellbender:remove-background: [epoch 074] average training loss: 2839.5539 cellbender:remove-background: [epoch 075] average training loss: 2841.8522 cellbender:remove-background: [epoch 075] average test loss: 2843.9189 cellbender:remove-background: [epoch 076] average training loss: 2849.5422 cellbender:remove-background: [epoch 077] average training loss: 2847.4771 cellbender:remove-background: [epoch 078] average training loss: 2837.5606 cellbender:remove-background: [epoch 079] average training loss: 2832.1824 cellbender:remove-background: [epoch 080] average training loss: 2835.9963 cellbender:remove-background: [epoch 080] average test loss: 2826.6188 cellbender:remove-background: [epoch 081] average training loss: 2835.2967 cellbender:remove-background: [epoch 082] average training loss: 2839.8738 cellbender:remove-background: [epoch 083] average training loss: 2831.9863 cellbender:remove-background: [epoch 084] average training loss: 2836.3051 cellbender:remove-background: [epoch 085] average training loss: 2834.1826 cellbender:remove-background: [epoch 085] average test loss: 2846.3298 cellbender:remove-background: [epoch 086] average training loss: 2835.8465 cellbender:remove-background: [epoch 087] average training loss: 2829.6722 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 088] average training loss: 2833.1763 cellbender:remove-background: [epoch 089] average training loss: 2833.9754 cellbender:remove-background: [epoch 090] average training loss: 2830.9957 cellbender:remove-background: [epoch 090] average test loss: 2827.4160 cellbender:remove-background: [epoch 091] average training loss: 2831.1740 cellbender:remove-background: [epoch 092] average training loss: 2832.8671 cellbender:remove-background: [epoch 093] average training loss: 2828.7386 cellbender:remove-background: [epoch 094] average training loss: 2829.6957 cellbender:remove-background: [epoch 095] average training loss: 2833.2623 cellbender:remove-background: [epoch 095] average test loss: 2824.4876 cellbender:remove-background: [epoch 096] average training loss: 2825.8964 cellbender:remove-background: [epoch 097] average training loss: 2829.5655 cellbender:remove-background: [epoch 098] average training loss: 2828.1176 cellbender:remove-background: [epoch 099] average training loss: 2829.2908 cellbender:remove-background: [epoch 100] average training loss: 2831.9657 cellbender:remove-background: [epoch 100] average test loss: 2840.6566 cellbender:remove-background: [epoch 101] average training loss: 2827.4955 cellbender:remove-background: [epoch 102] average training loss: 2826.0014 cellbender:remove-background: [epoch 103] average training loss: 2828.9029 cellbender:remove-background: [epoch 104] average training loss: 2825.7160 cellbender:remove-background: [epoch 105] average training loss: 2827.1547 cellbender:remove-background: [epoch 105] average test loss: 2826.3302 cellbender:remove-background: [epoch 106] average training loss: 2830.7063 cellbender:remove-background: [epoch 107] average training loss: 2829.1524 cellbender:remove-background: [epoch 108] average training loss: 2825.5353 cellbender:remove-background: [epoch 109] average training loss: 2828.7217 cellbender:remove-background: [epoch 110] average training loss: 2826.6369 cellbender:remove-background: [epoch 110] average test loss: 2823.9347 cellbender:remove-background: [epoch 111] average training loss: 2824.6072 cellbender:remove-background: [epoch 112] average training loss: 2828.6164 cellbender:remove-background: [epoch 113] average training loss: 2825.6926 cellbender:remove-background: [epoch 114] average training loss: 2826.8524 cellbender:remove-background: [epoch 115] average training loss: 2828.1619 cellbender:remove-background: [epoch 115] average test loss: 2826.6952 cellbender:remove-background: [epoch 116] average training loss: 2821.6950 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 117] average training loss: 2826.8986 cellbender:remove-background: [epoch 118] average training loss: 2823.0375 cellbender:remove-background: [epoch 119] average training loss: 2826.5962 cellbender:remove-background: [epoch 120] average training loss: 2826.6541 cellbender:remove-background: [epoch 120] average test loss: 2843.2829 cellbender:remove-background: [epoch 121] average training loss: 2824.3597 cellbender:remove-background: [epoch 122] average training loss: 2825.5724 cellbender:remove-background: [epoch 123] average training loss: 2827.0397 cellbender:remove-background: [epoch 124] average training loss: 2823.3570 cellbender:remove-background: [epoch 125] average training loss: 2819.3738 cellbender:remove-background: [epoch 125] average test loss: 2831.7460 cellbender:remove-background: [epoch 126] average training loss: 2827.5739 cellbender:remove-background: [epoch 127] average training loss: 2826.7338 cellbender:remove-background: [epoch 128] average training loss: 2825.4721 cellbender:remove-background: [epoch 129] average training loss: 2822.6756 cellbender:remove-background: [epoch 130] average training loss: 2824.6234 cellbender:remove-background: [epoch 130] average test loss: 2826.4158 cellbender:remove-background: [epoch 131] average training loss: 2819.6978 cellbender:remove-background: [epoch 132] average training loss: 2826.1905 cellbender:remove-background: [epoch 133] average training loss: 2823.1430 cellbender:remove-background: [epoch 134] average training loss: 2822.4717 cellbender:remove-background: [epoch 135] average training loss: 2822.0453 cellbender:remove-background: [epoch 135] average test loss: 2835.0799 cellbender:remove-background: [epoch 136] average training loss: 2827.3773 cellbender:remove-background: [epoch 137] average training loss: 2822.8589 cellbender:remove-background: [epoch 138] average training loss: 2825.9794 cellbender:remove-background: [epoch 139] average training loss: 2823.6151 cellbender:remove-background: [epoch 140] average training loss: 2829.3743 cellbender:remove-background: [epoch 140] average test loss: 2834.7364 cellbender:remove-background: [epoch 141] average training loss: 2823.2919 cellbender:remove-background: [epoch 142] average training loss: 2825.0418 cellbender:remove-background: [epoch 143] average training loss: 2822.6310 cellbender:remove-background: [epoch 144] average training loss: 2823.0879 cellbender:remove-background: [epoch 145] average training loss: 2821.7907 cellbender:remove-background: [epoch 145] average test loss: 2837.6711 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 146] average training loss: 2821.9375 cellbender:remove-background: [epoch 147] average training loss: 2821.4364 cellbender:remove-background: [epoch 148] average training loss: 2824.1832 cellbender:remove-background: [epoch 149] average training loss: 2821.9956 cellbender:remove-background: [epoch 150] average training loss: 2823.8274 cellbender:remove-background: [epoch 150] average test loss: 2850.8235 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/2042-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:10:23 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp59xmm9tm cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp59xmm9tm /tmp/tmp59xmm9tm/0001c75099_random.pyro /tmp/tmp59xmm9tm/0001c75099_random.cuda /tmp/tmp59xmm9tm/0001c75099_model.torch /tmp/tmp59xmm9tm/0001c75099_optim.torch /tmp/tmp59xmm9tm/0001c75099_optim.pyro /tmp/tmp59xmm9tm/0001c75099_params.pyro /tmp/tmp59xmm9tm/0001c75099_train.loaderstate /tmp/tmp59xmm9tm/0001c75099_test.loaderstate /tmp/tmp59xmm9tm/0001c75099_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 (1/59) cellbender:remove-background: [0.07 mins per chunk] cellbender:remove-background: Working on chunk (2/59) cellbender:remove-background: Working on chunk (3/59) cellbender:remove-background: Working on chunk (4/59) cellbender:remove-background: Working on chunk (5/59) cellbender:remove-background: Working on chunk (6/59) cellbender:remove-background: Working on chunk (7/59) cellbender:remove-background: Working on chunk (8/59) cellbender:remove-background: Working on chunk (9/59) cellbender:remove-background: Working on chunk (10/59) cellbender:remove-background: Working on chunk (11/59) cellbender:remove-background: Working on chunk (12/59) cellbender:remove-background: Working on chunk (13/59) cellbender:remove-background: Working on chunk (14/59) cellbender:remove-background: Working on chunk (15/59) cellbender:remove-background: Working on chunk (16/59) cellbender:remove-background: Working on chunk (17/59) cellbender:remove-background: Working on chunk (18/59) cellbender:remove-background: Working on chunk (19/59) cellbender:remove-background: Working on chunk (20/59) cellbender:remove-background: Working on chunk (21/59) cellbender:remove-background: Working on chunk (22/59) cellbender:remove-background: Working on chunk (23/59) cellbender:remove-background: Working on chunk (24/59) cellbender:remove-background: Working on chunk (25/59) cellbender:remove-background: Working on chunk (26/59) cellbender:remove-background: Working on chunk (27/59) cellbender:remove-background: Working on chunk (28/59) cellbender:remove-background: Working on chunk (29/59) cellbender:remove-background: Working on chunk (30/59) cellbender:remove-background: Working on chunk (31/59) cellbender:remove-background: Working on chunk (32/59) cellbender:remove-background: Working on chunk (33/59) cellbender:remove-background: Working on chunk (34/59) cellbender:remove-background: Working on chunk (35/59) cellbender:remove-background: Working on chunk (36/59) cellbender:remove-background: Working on chunk (37/59) cellbender:remove-background: Working on chunk (38/59) cellbender:remove-background: Working on chunk (39/59) cellbender:remove-background: Working on chunk (40/59) cellbender:remove-background: Working on chunk (41/59) cellbender:remove-background: Working on chunk (42/59) cellbender:remove-background: Working on chunk (43/59) cellbender:remove-background: Working on chunk (44/59) cellbender:remove-background: Working on chunk (45/59) cellbender:remove-background: Working on chunk (46/59) cellbender:remove-background: Working on chunk (47/59) cellbender:remove-background: Working on chunk (48/59) cellbender:remove-background: Working on chunk (49/59) cellbender:remove-background: Working on chunk (50/59) cellbender:remove-background: Working on chunk (51/59) cellbender:remove-background: Working on chunk (52/59) cellbender:remove-background: Working on chunk (53/59) cellbender:remove-background: Working on chunk (54/59) cellbender:remove-background: Working on chunk (55/59) cellbender:remove-background: Working on chunk (56/59) cellbender:remove-background: Working on chunk (57/59) cellbender:remove-background: Working on chunk (58/59) cellbender:remove-background: Working on chunk (59/59) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2042-Bipolar-DLPFC/2042-Bipolar-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/2042-Bipolar-DLPFC/2042-Bipolar-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:16:52 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2042-Bipolar-DLPFC/2042-Bipolar-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2042-Bipolar-DLPFC/2042-Bipolar-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: [2.12 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 16:32:39 Total MCKP estimation time = 900.76 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/2042-Bipolar-DLPFC/2042-Bipolar-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/2042-Bipolar-DLPFC/2042-Bipolar-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/2042-Bipolar-DLPFC/2042-Bipolar-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/2042-Bipolar-DLPFC/2042-Bipolar-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:33:10