cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1734-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-Hippocampus/1734-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 8307 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash de4727ab1f) cellbender:remove-background: 2024-06-06 14:52:08 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/1734-Bipolar-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: 32261 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3853 cellbender:remove-background: Prior on counts for empty droplets is 57 cellbender:remove-background: Excluding 8437 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23824 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 28 cellbender:remove-background: Using 8307 probable cell barcodes, plus an additional 11693 barcodes, and 43604 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 57 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpyl86wfeq 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: 6518.6507 cellbender:remove-background: [epoch 002] average training loss: 5008.7680 (5.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 77 epochs cellbender:remove-background: [epoch 003] average training loss: 4235.1465 cellbender:remove-background: [epoch 004] average training loss: 3784.9684 cellbender:remove-background: [epoch 005] average training loss: 3656.3241 cellbender:remove-background: [epoch 005] average test loss: 3741.6372 cellbender:remove-background: [epoch 006] average training loss: 3608.3793 cellbender:remove-background: [epoch 007] average training loss: 3543.8648 cellbender:remove-background: [epoch 008] average training loss: 3472.6898 cellbender:remove-background: [epoch 009] average training loss: 3357.3747 cellbender:remove-background: [epoch 010] average training loss: 3267.9345 cellbender:remove-background: [epoch 010] average test loss: 3260.8304 cellbender:remove-background: [epoch 011] average training loss: 3261.7965 cellbender:remove-background: [epoch 012] average training loss: 3248.3893 cellbender:remove-background: [epoch 013] average training loss: 3218.3201 cellbender:remove-background: [epoch 014] average training loss: 3223.0988 cellbender:remove-background: [epoch 015] average training loss: 3184.8040 cellbender:remove-background: [epoch 015] average test loss: 3187.2120 cellbender:remove-background: [epoch 016] average training loss: 3165.7881 cellbender:remove-background: [epoch 017] average training loss: 3169.2971 cellbender:remove-background: [epoch 018] average training loss: 3157.8032 cellbender:remove-background: [epoch 019] average training loss: 3137.4611 cellbender:remove-background: [epoch 020] average training loss: 3117.2638 cellbender:remove-background: [epoch 020] average test loss: 3125.0770 cellbender:remove-background: [epoch 021] average training loss: 3110.4175 cellbender:remove-background: [epoch 022] average training loss: 3085.6266 cellbender:remove-background: [epoch 023] average training loss: 3063.6187 cellbender:remove-background: [epoch 024] average training loss: 3041.1613 cellbender:remove-background: [epoch 025] average training loss: 3027.8553 cellbender:remove-background: [epoch 025] average test loss: 3008.0537 cellbender:remove-background: [epoch 026] average training loss: 3002.2111 cellbender:remove-background: [epoch 027] average training loss: 2985.0613 cellbender:remove-background: [epoch 028] average training loss: 2973.3611 cellbender:remove-background: [epoch 029] average training loss: 2960.8479 cellbender:remove-background: [epoch 030] average training loss: 2954.2853 cellbender:remove-background: [epoch 030] average test loss: 2927.0455 cellbender:remove-background: [epoch 031] average training loss: 2947.0222 cellbender:remove-background: [epoch 032] average training loss: 2939.0833 cellbender:remove-background: [epoch 033] average training loss: 2937.6169 cellbender:remove-background: [epoch 034] average training loss: 2935.1554 cellbender:remove-background: [epoch 035] average training loss: 2930.1366 cellbender:remove-background: [epoch 035] average test loss: 2897.6209 cellbender:remove-background: [epoch 036] average training loss: 2928.2597 cellbender:remove-background: [epoch 037] average training loss: 2926.2381 cellbender:remove-background: [epoch 038] average training loss: 2925.4612 cellbender:remove-background: [epoch 039] average training loss: 2919.0349 cellbender:remove-background: [epoch 040] average training loss: 2919.7341 cellbender:remove-background: [epoch 040] average test loss: 2891.5205 cellbender:remove-background: [epoch 041] average training loss: 2920.1987 cellbender:remove-background: [epoch 042] average training loss: 2919.2340 cellbender:remove-background: [epoch 043] average training loss: 2916.5661 cellbender:remove-background: [epoch 044] average training loss: 2919.5026 cellbender:remove-background: [epoch 045] average training loss: 2914.0308 cellbender:remove-background: [epoch 045] average test loss: 2892.6916 cellbender:remove-background: [epoch 046] average training loss: 2918.7620 cellbender:remove-background: [epoch 047] average training loss: 2927.8858 cellbender:remove-background: [epoch 048] average training loss: 2910.0229 cellbender:remove-background: [epoch 049] average training loss: 2911.3099 cellbender:remove-background: [epoch 050] average training loss: 2906.5869 cellbender:remove-background: [epoch 050] average test loss: 2876.7301 cellbender:remove-background: [epoch 051] average training loss: 2905.8368 cellbender:remove-background: [epoch 052] average training loss: 2906.9738 cellbender:remove-background: [epoch 053] average training loss: 2902.9256 cellbender:remove-background: [epoch 054] average training loss: 2901.4613 cellbender:remove-background: [epoch 055] average training loss: 2904.3159 cellbender:remove-background: [epoch 055] average test loss: 2878.5104 cellbender:remove-background: [epoch 056] average training loss: 2902.8758 cellbender:remove-background: [epoch 057] average training loss: 2898.7109 cellbender:remove-background: [epoch 058] average training loss: 2899.2962 cellbender:remove-background: [epoch 059] average training loss: 2897.5411 cellbender:remove-background: [epoch 060] average training loss: 2902.3032 cellbender:remove-background: [epoch 060] average test loss: 2871.7131 cellbender:remove-background: [epoch 061] average training loss: 2894.5452 cellbender:remove-background: [epoch 062] average training loss: 2897.6804 cellbender:remove-background: [epoch 063] average training loss: 2897.1173 cellbender:remove-background: [epoch 064] average training loss: 2892.8172 cellbender:remove-background: [epoch 065] average training loss: 2894.7480 cellbender:remove-background: [epoch 065] average test loss: 2871.4368 cellbender:remove-background: [epoch 066] average training loss: 2893.2547 cellbender:remove-background: [epoch 067] average training loss: 2890.8335 cellbender:remove-background: [epoch 068] average training loss: 2898.2333 cellbender:remove-background: [epoch 069] average training loss: 2899.8517 cellbender:remove-background: [epoch 070] average training loss: 2894.1053 cellbender:remove-background: [epoch 070] average test loss: 2875.2464 cellbender:remove-background: [epoch 071] average training loss: 2894.2600 cellbender:remove-background: [epoch 072] average training loss: 2891.8513 cellbender:remove-background: [epoch 073] average training loss: 2886.7673 cellbender:remove-background: [epoch 074] average training loss: 2891.3477 cellbender:remove-background: [epoch 075] average training loss: 2894.4597 cellbender:remove-background: [epoch 075] average test loss: 2875.0366 cellbender:remove-background: [epoch 076] average training loss: 2891.3526 cellbender:remove-background: [epoch 077] average training loss: 2884.2307 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/1734-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 078] average training loss: 2889.3900 cellbender:remove-background: [epoch 079] average training loss: 2887.8329 cellbender:remove-background: [epoch 080] average training loss: 2891.1416 cellbender:remove-background: [epoch 080] average test loss: 2875.6132 cellbender:remove-background: [epoch 081] average training loss: 2888.8519 cellbender:remove-background: [epoch 082] average training loss: 2886.4434 cellbender:remove-background: [epoch 083] average training loss: 2886.9072 cellbender:remove-background: [epoch 084] average training loss: 2889.0219 cellbender:remove-background: [epoch 085] average training loss: 2888.1227 cellbender:remove-background: [epoch 085] average test loss: 2878.1686 cellbender:remove-background: [epoch 086] average training loss: 2887.4301 cellbender:remove-background: [epoch 087] average training loss: 2890.5836 cellbender:remove-background: [epoch 088] average training loss: 2886.6591 cellbender:remove-background: [epoch 089] average training loss: 2887.9195 cellbender:remove-background: [epoch 090] average training loss: 2889.1223 cellbender:remove-background: [epoch 090] average test loss: 2888.4952 cellbender:remove-background: [epoch 091] average training loss: 2888.3459 cellbender:remove-background: [epoch 092] average training loss: 2888.6558 cellbender:remove-background: [epoch 093] average training loss: 2888.4003 cellbender:remove-background: [epoch 094] average training loss: 2886.0158 cellbender:remove-background: [epoch 095] average training loss: 2887.0134 cellbender:remove-background: [epoch 095] average test loss: 2879.2164 cellbender:remove-background: [epoch 096] average training loss: 2888.6405 cellbender:remove-background: [epoch 097] average training loss: 2886.8855 cellbender:remove-background: [epoch 098] average training loss: 2890.3027 cellbender:remove-background: [epoch 099] average training loss: 2888.3791 cellbender:remove-background: [epoch 100] average training loss: 2886.4672 cellbender:remove-background: [epoch 100] average test loss: 2888.5555 cellbender:remove-background: [epoch 101] average training loss: 2886.5496 cellbender:remove-background: [epoch 102] average training loss: 2890.0966 cellbender:remove-background: [epoch 103] average training loss: 2890.0124 cellbender:remove-background: [epoch 104] average training loss: 2885.9314 cellbender:remove-background: [epoch 105] average training loss: 2884.8984 cellbender:remove-background: [epoch 105] average test loss: 2885.5984 cellbender:remove-background: [epoch 106] average training loss: 2883.2465 cellbender:remove-background: [epoch 107] average training loss: 2887.3080 cellbender:remove-background: [epoch 108] average training loss: 2887.4965 cellbender:remove-background: [epoch 109] average training loss: 2885.7202 cellbender:remove-background: [epoch 110] average training loss: 2888.1381 cellbender:remove-background: [epoch 110] average test loss: 2894.0225 cellbender:remove-background: [epoch 111] average training loss: 2886.4841 cellbender:remove-background: [epoch 112] average training loss: 2888.7777 cellbender:remove-background: [epoch 113] average training loss: 2884.4987 cellbender:remove-background: [epoch 114] average training loss: 2885.7140 cellbender:remove-background: [epoch 115] average training loss: 2884.6076 cellbender:remove-background: [epoch 115] average test loss: 2884.3765 cellbender:remove-background: [epoch 116] average training loss: 2886.4541 cellbender:remove-background: [epoch 117] average training loss: 2884.1507 cellbender:remove-background: [epoch 118] average training loss: 2884.0113 cellbender:remove-background: [epoch 119] average training loss: 2882.8772 cellbender:remove-background: [epoch 120] average training loss: 2886.8676 cellbender:remove-background: [epoch 120] average test loss: 2878.2217 cellbender:remove-background: [epoch 121] average training loss: 2884.4603 cellbender:remove-background: [epoch 122] average training loss: 2882.4612 cellbender:remove-background: [epoch 123] average training loss: 2882.3209 cellbender:remove-background: [epoch 124] average training loss: 2884.0515 cellbender:remove-background: [epoch 125] average training loss: 2882.8738 cellbender:remove-background: [epoch 125] average test loss: 2889.3191 cellbender:remove-background: [epoch 126] average training loss: 2885.4784 cellbender:remove-background: [epoch 127] average training loss: 2884.6079 cellbender:remove-background: [epoch 128] average training loss: 2882.2158 cellbender:remove-background: [epoch 129] average training loss: 2883.2323 cellbender:remove-background: [epoch 130] average training loss: 2882.9945 cellbender:remove-background: [epoch 130] average test loss: 2879.2586 cellbender:remove-background: [epoch 131] average training loss: 2881.7838 cellbender:remove-background: [epoch 132] average training loss: 2884.8415 cellbender:remove-background: [epoch 133] average training loss: 2884.8722 cellbender:remove-background: [epoch 134] average training loss: 2882.2670 cellbender:remove-background: [epoch 135] average training loss: 2880.3921 cellbender:remove-background: [epoch 135] average test loss: 2886.1291 cellbender:remove-background: [epoch 136] average training loss: 2883.1749 cellbender:remove-background: [epoch 137] average training loss: 2884.8241 cellbender:remove-background: [epoch 138] average training loss: 2881.3835 cellbender:remove-background: [epoch 139] average training loss: 2882.5398 cellbender:remove-background: [epoch 140] average training loss: 2881.5924 cellbender:remove-background: [epoch 140] average test loss: 2884.3594 cellbender:remove-background: [epoch 141] average training loss: 2881.6954 cellbender:remove-background: [epoch 142] average training loss: 2882.5382 cellbender:remove-background: [epoch 143] average training loss: 2880.5840 cellbender:remove-background: [epoch 144] average training loss: 2881.9449 cellbender:remove-background: [epoch 145] average training loss: 2883.1036 cellbender:remove-background: [epoch 145] average test loss: 2885.2575 cellbender:remove-background: [epoch 146] average training loss: 2881.1934 cellbender:remove-background: [epoch 147] average training loss: 2879.9446 cellbender:remove-background: [epoch 148] average training loss: 2881.9062 cellbender:remove-background: [epoch 149] average training loss: 2880.8810 cellbender:remove-background: [epoch 150] average training loss: 2881.6246 cellbender:remove-background: [epoch 150] average test loss: 2888.5078 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/1734-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:08:14 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpsglz8w01 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpsglz8w01 /tmp/tmpsglz8w01/de4727ab1f_random.pyro /tmp/tmpsglz8w01/de4727ab1f_random.cuda /tmp/tmpsglz8w01/de4727ab1f_model.torch /tmp/tmpsglz8w01/de4727ab1f_optim.torch /tmp/tmpsglz8w01/de4727ab1f_optim.pyro /tmp/tmpsglz8w01/de4727ab1f_params.pyro /tmp/tmpsglz8w01/de4727ab1f_train.loaderstate /tmp/tmpsglz8w01/de4727ab1f_test.loaderstate /tmp/tmpsglz8w01/de4727ab1f_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 (1/73) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/73) cellbender:remove-background: Working on chunk (3/73) cellbender:remove-background: Working on chunk (4/73) cellbender:remove-background: Working on chunk (5/73) cellbender:remove-background: Working on chunk (6/73) cellbender:remove-background: Working on chunk (7/73) cellbender:remove-background: Working on chunk (8/73) cellbender:remove-background: Working on chunk (9/73) cellbender:remove-background: Working on chunk (10/73) cellbender:remove-background: Working on chunk (11/73) cellbender:remove-background: Working on chunk (12/73) cellbender:remove-background: Working on chunk (13/73) cellbender:remove-background: Working on chunk (14/73) cellbender:remove-background: Working on chunk (15/73) cellbender:remove-background: Working on chunk (16/73) cellbender:remove-background: Working on chunk (17/73) cellbender:remove-background: Working on chunk (18/73) cellbender:remove-background: Working on chunk (19/73) cellbender:remove-background: Working on chunk (20/73) cellbender:remove-background: Working on chunk (21/73) cellbender:remove-background: Working on chunk (22/73) cellbender:remove-background: Working on chunk (23/73) cellbender:remove-background: Working on chunk (24/73) cellbender:remove-background: Working on chunk (25/73) cellbender:remove-background: Working on chunk (26/73) cellbender:remove-background: Working on chunk (27/73) cellbender:remove-background: Working on chunk (28/73) cellbender:remove-background: Working on chunk (29/73) cellbender:remove-background: Working on chunk (30/73) cellbender:remove-background: Working on chunk (31/73) cellbender:remove-background: Working on chunk (32/73) cellbender:remove-background: Working on chunk (33/73) cellbender:remove-background: Working on chunk (34/73) cellbender:remove-background: Working on chunk (35/73) cellbender:remove-background: Working on chunk (36/73) cellbender:remove-background: Working on chunk (37/73) cellbender:remove-background: Working on chunk (38/73) cellbender:remove-background: Working on chunk (39/73) cellbender:remove-background: Working on chunk (40/73) cellbender:remove-background: Working on chunk (41/73) cellbender:remove-background: Working on chunk (42/73) cellbender:remove-background: Working on chunk (43/73) cellbender:remove-background: Working on chunk (44/73) cellbender:remove-background: Working on chunk (45/73) cellbender:remove-background: Working on chunk (46/73) cellbender:remove-background: Working on chunk (47/73) cellbender:remove-background: Working on chunk (48/73) cellbender:remove-background: Working on chunk (49/73) cellbender:remove-background: Working on chunk (50/73) cellbender:remove-background: Working on chunk (51/73) cellbender:remove-background: Working on chunk (52/73) cellbender:remove-background: Working on chunk (53/73) cellbender:remove-background: Working on chunk (54/73) cellbender:remove-background: Working on chunk (55/73) cellbender:remove-background: Working on chunk (56/73) cellbender:remove-background: Working on chunk (57/73) cellbender:remove-background: Working on chunk (58/73) cellbender:remove-background: Working on chunk (59/73) cellbender:remove-background: Working on chunk (60/73) cellbender:remove-background: Working on chunk (61/73) cellbender:remove-background: Working on chunk (62/73) cellbender:remove-background: Working on chunk (63/73) cellbender:remove-background: Working on chunk (64/73) cellbender:remove-background: Working on chunk (65/73) cellbender:remove-background: Working on chunk (66/73) cellbender:remove-background: Working on chunk (67/73) cellbender:remove-background: Working on chunk (68/73) cellbender:remove-background: Working on chunk (69/73) cellbender:remove-background: Working on chunk (70/73) cellbender:remove-background: Working on chunk (71/73) cellbender:remove-background: Working on chunk (72/73) cellbender:remove-background: Working on chunk (73/73) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-Hippocampus/1734-Bipolar-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/1734-Bipolar-Hippocampus/1734-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:12:39 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-Hippocampus/1734-Bipolar-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-Hippocampus/1734-Bipolar-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: [1.35 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 15:22:37 Total MCKP estimation time = 572.81 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/1734-Bipolar-Hippocampus/1734-Bipolar-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/1734-Bipolar-Hippocampus/1734-Bipolar-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/1734-Bipolar-Hippocampus/1734-Bipolar-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/1734-Bipolar-Hippocampus/1734-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:22:56