cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2780-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-DLPFC/2780-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 7177 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash aef205abf6) cellbender:remove-background: 2024-06-06 14:52:18 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/2780-Control-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: 32311 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3556 cellbender:remove-background: Prior on counts for empty droplets is 130 cellbender:remove-background: Excluding 9430 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22881 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 65 cellbender:remove-background: Using 7177 probable cell barcodes, plus an additional 12823 barcodes, and 24169 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 128 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpoj6fxip4 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: 5956.9402 cellbender:remove-background: [epoch 002] average training loss: 4663.7544 (5.9 seconds per epoch) cellbender:remove-background: Will checkpoint every 71 epochs cellbender:remove-background: [epoch 003] average training loss: 4011.1473 cellbender:remove-background: [epoch 004] average training loss: 3619.9272 cellbender:remove-background: [epoch 005] average training loss: 3518.0462 cellbender:remove-background: [epoch 005] average test loss: 3639.2789 cellbender:remove-background: [epoch 006] average training loss: 3478.8954 cellbender:remove-background: [epoch 007] average training loss: 3414.7479 cellbender:remove-background: [epoch 008] average training loss: 3386.9424 cellbender:remove-background: [epoch 009] average training loss: 3374.7723 cellbender:remove-background: [epoch 010] average training loss: 3305.5218 cellbender:remove-background: [epoch 010] average test loss: 3297.1095 cellbender:remove-background: [epoch 011] average training loss: 3234.8479 cellbender:remove-background: [epoch 012] average training loss: 3194.5729 cellbender:remove-background: [epoch 013] average training loss: 3173.0108 cellbender:remove-background: [epoch 014] average training loss: 3180.5666 cellbender:remove-background: [epoch 015] average training loss: 3155.5007 cellbender:remove-background: [epoch 015] average test loss: 3186.7776 cellbender:remove-background: [epoch 016] average training loss: 3143.6166 cellbender:remove-background: [epoch 017] average training loss: 3149.7722 cellbender:remove-background: [epoch 018] average training loss: 3137.4355 cellbender:remove-background: [epoch 019] average training loss: 3123.8940 cellbender:remove-background: [epoch 020] average training loss: 3105.8994 cellbender:remove-background: [epoch 020] average test loss: 3162.9788 cellbender:remove-background: [epoch 021] average training loss: 3101.5371 cellbender:remove-background: [epoch 022] average training loss: 3092.6868 cellbender:remove-background: [epoch 023] average training loss: 3077.0248 cellbender:remove-background: [epoch 024] average training loss: 3053.3128 cellbender:remove-background: [epoch 025] average training loss: 3044.0679 cellbender:remove-background: [epoch 025] average test loss: 3061.9161 cellbender:remove-background: [epoch 026] average training loss: 3021.1504 cellbender:remove-background: [epoch 027] average training loss: 3010.1136 cellbender:remove-background: [epoch 028] average training loss: 3004.0213 cellbender:remove-background: [epoch 029] average training loss: 2992.0416 cellbender:remove-background: [epoch 030] average training loss: 2987.6067 cellbender:remove-background: [epoch 030] average test loss: 3012.4698 cellbender:remove-background: [epoch 031] average training loss: 2984.8114 cellbender:remove-background: [epoch 032] average training loss: 2980.0443 cellbender:remove-background: [epoch 033] average training loss: 2979.4002 cellbender:remove-background: [epoch 034] average training loss: 2974.6220 cellbender:remove-background: [epoch 035] average training loss: 2971.6281 cellbender:remove-background: [epoch 035] average test loss: 2981.2357 cellbender:remove-background: [epoch 036] average training loss: 2968.1255 cellbender:remove-background: [epoch 037] average training loss: 2966.6965 cellbender:remove-background: [epoch 038] average training loss: 2965.2799 cellbender:remove-background: [epoch 039] average training loss: 2963.3669 cellbender:remove-background: [epoch 040] average training loss: 2961.7457 cellbender:remove-background: [epoch 040] average test loss: 2962.8158 cellbender:remove-background: [epoch 041] average training loss: 2961.2918 cellbender:remove-background: [epoch 042] average training loss: 2959.8316 cellbender:remove-background: [epoch 043] average training loss: 2959.1988 cellbender:remove-background: [epoch 044] average training loss: 2962.4883 cellbender:remove-background: [epoch 045] average training loss: 2962.2547 cellbender:remove-background: [epoch 045] average test loss: 2978.3349 cellbender:remove-background: [epoch 046] average training loss: 2958.7907 cellbender:remove-background: [epoch 047] average training loss: 2962.9156 cellbender:remove-background: [epoch 048] average training loss: 2961.9848 cellbender:remove-background: [epoch 049] average training loss: 2963.4770 cellbender:remove-background: [epoch 050] average training loss: 2962.0889 cellbender:remove-background: [epoch 050] average test loss: 2977.3300 cellbender:remove-background: [epoch 051] average training loss: 2956.1650 cellbender:remove-background: [epoch 052] average training loss: 2968.2196 cellbender:remove-background: [epoch 053] average training loss: 2963.4035 cellbender:remove-background: [epoch 054] average training loss: 2967.7355 cellbender:remove-background: [epoch 055] average training loss: 2966.5916 cellbender:remove-background: [epoch 055] average test loss: 2976.1914 cellbender:remove-background: [epoch 056] average training loss: 2964.7510 cellbender:remove-background: [epoch 057] average training loss: 2971.6992 cellbender:remove-background: [epoch 058] average training loss: 2963.8547 cellbender:remove-background: [epoch 059] average training loss: 2968.6404 cellbender:remove-background: [epoch 060] average training loss: 2967.9035 cellbender:remove-background: [epoch 060] average test loss: 2971.8201 cellbender:remove-background: [epoch 061] average training loss: 2970.0461 cellbender:remove-background: [epoch 062] average training loss: 2970.4702 cellbender:remove-background: [epoch 063] average training loss: 2974.5454 cellbender:remove-background: [epoch 064] average training loss: 2973.7426 cellbender:remove-background: [epoch 065] average training loss: 2970.9904 cellbender:remove-background: [epoch 065] average test loss: 2998.7798 cellbender:remove-background: [epoch 066] average training loss: 2968.8191 cellbender:remove-background: [epoch 067] average training loss: 2965.1717 cellbender:remove-background: [epoch 068] average training loss: 2970.5069 cellbender:remove-background: [epoch 069] average training loss: 2966.6305 cellbender:remove-background: [epoch 070] average training loss: 2967.5617 cellbender:remove-background: [epoch 070] average test loss: 3030.8530 cellbender:remove-background: [epoch 071] average training loss: 2975.2225 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/2780-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 072] average training loss: 2973.7903 cellbender:remove-background: [epoch 073] average training loss: 2972.5092 cellbender:remove-background: [epoch 074] average training loss: 2974.4598 cellbender:remove-background: [epoch 075] average training loss: 2973.1534 cellbender:remove-background: [epoch 075] average test loss: 3014.5064 cellbender:remove-background: [epoch 076] average training loss: 2969.7692 cellbender:remove-background: [epoch 077] average training loss: 2976.2211 cellbender:remove-background: [epoch 078] average training loss: 2967.7727 cellbender:remove-background: [epoch 079] average training loss: 2969.0962 cellbender:remove-background: [epoch 080] average training loss: 2970.0727 cellbender:remove-background: [epoch 080] average test loss: 3034.2196 cellbender:remove-background: [epoch 081] average training loss: 2977.5460 cellbender:remove-background: [epoch 082] average training loss: 2975.2857 cellbender:remove-background: [epoch 083] average training loss: 2967.6302 cellbender:remove-background: [epoch 084] average training loss: 2972.4227 cellbender:remove-background: [epoch 085] average training loss: 2973.7867 cellbender:remove-background: [epoch 085] average test loss: 3013.1205 cellbender:remove-background: [epoch 086] average training loss: 2964.2808 cellbender:remove-background: [epoch 087] average training loss: 2975.0809 cellbender:remove-background: [epoch 088] average training loss: 2969.9342 cellbender:remove-background: [epoch 089] average training loss: 2968.7306 cellbender:remove-background: [epoch 090] average training loss: 2965.3167 cellbender:remove-background: [epoch 090] average test loss: 3049.3253 cellbender:remove-background: [epoch 091] average training loss: 2968.7209 cellbender:remove-background: [epoch 092] average training loss: 2971.1255 cellbender:remove-background: [epoch 093] average training loss: 2966.9529 cellbender:remove-background: [epoch 094] average training loss: 2967.2783 cellbender:remove-background: [epoch 095] average training loss: 2973.1050 cellbender:remove-background: [epoch 095] average test loss: 3014.6163 cellbender:remove-background: [epoch 096] average training loss: 2970.8388 cellbender:remove-background: [epoch 097] average training loss: 2969.2658 cellbender:remove-background: [epoch 098] average training loss: 2978.2902 cellbender:remove-background: [epoch 099] average training loss: 2970.2158 cellbender:remove-background: [epoch 100] average training loss: 2971.9253 cellbender:remove-background: [epoch 100] average test loss: 3027.0004 cellbender:remove-background: [epoch 101] average training loss: 2970.6459 cellbender:remove-background: [epoch 102] average training loss: 2972.0959 cellbender:remove-background: [epoch 103] average training loss: 2977.7095 cellbender:remove-background: [epoch 104] average training loss: 2972.8138 cellbender:remove-background: [epoch 105] average training loss: 2973.6275 cellbender:remove-background: [epoch 105] average test loss: 3055.0459 cellbender:remove-background: [epoch 106] average training loss: 2972.2257 cellbender:remove-background: [epoch 107] average training loss: 2973.9277 cellbender:remove-background: [epoch 108] average training loss: 2971.9613 cellbender:remove-background: [epoch 109] average training loss: 2967.0885 cellbender:remove-background: [epoch 110] average training loss: 2968.5961 cellbender:remove-background: [epoch 110] average test loss: 3022.6344 cellbender:remove-background: [epoch 111] average training loss: 2968.9946 cellbender:remove-background: [epoch 112] average training loss: 2966.9288 cellbender:remove-background: [epoch 113] average training loss: 2968.2474 cellbender:remove-background: [epoch 114] average training loss: 2973.7445 cellbender:remove-background: [epoch 115] average training loss: 2963.3900 cellbender:remove-background: [epoch 115] average test loss: 3045.1503 cellbender:remove-background: [epoch 116] average training loss: 2968.0442 cellbender:remove-background: [epoch 117] average training loss: 2965.0437 cellbender:remove-background: [epoch 118] average training loss: 2968.1790 cellbender:remove-background: [epoch 119] average training loss: 2968.9458 cellbender:remove-background: [epoch 120] average training loss: 2968.8531 cellbender:remove-background: [epoch 120] average test loss: 3027.2435 cellbender:remove-background: [epoch 121] average training loss: 2969.4532 cellbender:remove-background: [epoch 122] average training loss: 2966.1679 cellbender:remove-background: [epoch 123] average training loss: 2965.5512 cellbender:remove-background: [epoch 124] average training loss: 2967.8607 cellbender:remove-background: [epoch 125] average training loss: 2965.9275 cellbender:remove-background: [epoch 125] average test loss: 3041.4628 cellbender:remove-background: [epoch 126] average training loss: 2962.2329 cellbender:remove-background: [epoch 127] average training loss: 2967.3041 cellbender:remove-background: [epoch 128] average training loss: 2966.5836 cellbender:remove-background: [epoch 129] average training loss: 2966.0026 cellbender:remove-background: [epoch 130] average training loss: 2964.9023 cellbender:remove-background: [epoch 130] average test loss: 3040.2494 cellbender:remove-background: [epoch 131] average training loss: 2964.8216 cellbender:remove-background: [epoch 132] average training loss: 2967.2645 cellbender:remove-background: [epoch 133] average training loss: 2968.0905 cellbender:remove-background: [epoch 134] average training loss: 2965.9348 cellbender:remove-background: [epoch 135] average training loss: 2961.9572 cellbender:remove-background: [epoch 135] average test loss: 3038.0590 cellbender:remove-background: [epoch 136] average training loss: 2965.0210 cellbender:remove-background: [epoch 137] average training loss: 2964.0109 cellbender:remove-background: [epoch 138] average training loss: 2964.8575 cellbender:remove-background: [epoch 139] average training loss: 2964.5817 cellbender:remove-background: [epoch 140] average training loss: 2963.7833 cellbender:remove-background: [epoch 140] average test loss: 3036.5400 cellbender:remove-background: [epoch 141] average training loss: 2963.2628 cellbender:remove-background: [epoch 142] average training loss: 2964.9543 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/2780-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 143] average training loss: 2963.1071 cellbender:remove-background: [epoch 144] average training loss: 2964.8368 cellbender:remove-background: [epoch 145] average training loss: 2962.3987 cellbender:remove-background: [epoch 145] average test loss: 3040.9416 cellbender:remove-background: [epoch 146] average training loss: 2964.2264 cellbender:remove-background: [epoch 147] average training loss: 2962.9267 cellbender:remove-background: [epoch 148] average training loss: 2963.1835 cellbender:remove-background: [epoch 149] average training loss: 2963.3737 cellbender:remove-background: [epoch 150] average training loss: 2961.3972 cellbender:remove-background: [epoch 150] average test loss: 3038.9128 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/2780-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:11:41 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp2xcqd20x cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp2xcqd20x /tmp/tmp2xcqd20x/aef205abf6_random.pyro /tmp/tmp2xcqd20x/aef205abf6_random.cuda /tmp/tmp2xcqd20x/aef205abf6_model.torch /tmp/tmp2xcqd20x/aef205abf6_optim.torch /tmp/tmp2xcqd20x/aef205abf6_optim.pyro /tmp/tmp2xcqd20x/aef205abf6_params.pyro /tmp/tmp2xcqd20x/aef205abf6_train.loaderstate /tmp/tmp2xcqd20x/aef205abf6_test.loaderstate /tmp/tmp2xcqd20x/aef205abf6_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 (1/80) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/80) cellbender:remove-background: Working on chunk (3/80) cellbender:remove-background: Working on chunk (4/80) cellbender:remove-background: Working on chunk (5/80) cellbender:remove-background: Working on chunk (6/80) cellbender:remove-background: Working on chunk (7/80) cellbender:remove-background: Working on chunk (8/80) cellbender:remove-background: Working on chunk (9/80) cellbender:remove-background: Working on chunk (10/80) cellbender:remove-background: Working on chunk (11/80) cellbender:remove-background: Working on chunk (12/80) cellbender:remove-background: Working on chunk (13/80) cellbender:remove-background: Working on chunk (14/80) cellbender:remove-background: Working on chunk (15/80) cellbender:remove-background: Working on chunk (16/80) cellbender:remove-background: Working on chunk (17/80) cellbender:remove-background: Working on chunk (18/80) cellbender:remove-background: Working on chunk (19/80) cellbender:remove-background: Working on chunk (20/80) cellbender:remove-background: Working on chunk (21/80) cellbender:remove-background: Working on chunk (22/80) cellbender:remove-background: Working on chunk (23/80) cellbender:remove-background: Working on chunk (24/80) cellbender:remove-background: Working on chunk (25/80) cellbender:remove-background: Working on chunk (26/80) cellbender:remove-background: Working on chunk (27/80) cellbender:remove-background: Working on chunk (28/80) cellbender:remove-background: Working on chunk (29/80) cellbender:remove-background: Working on chunk (30/80) cellbender:remove-background: Working on chunk (31/80) cellbender:remove-background: Working on chunk (32/80) cellbender:remove-background: Working on chunk (33/80) cellbender:remove-background: Working on chunk (34/80) cellbender:remove-background: Working on chunk (35/80) cellbender:remove-background: Working on chunk (36/80) cellbender:remove-background: Working on chunk (37/80) cellbender:remove-background: Working on chunk (38/80) cellbender:remove-background: Working on chunk (39/80) cellbender:remove-background: Working on chunk (40/80) cellbender:remove-background: Working on chunk (41/80) cellbender:remove-background: Working on chunk (42/80) cellbender:remove-background: Working on chunk (43/80) cellbender:remove-background: Working on chunk (44/80) cellbender:remove-background: Working on chunk (45/80) cellbender:remove-background: Working on chunk (46/80) cellbender:remove-background: Working on chunk (47/80) cellbender:remove-background: Working on chunk (48/80) cellbender:remove-background: Working on chunk (49/80) cellbender:remove-background: Working on chunk (50/80) cellbender:remove-background: Working on chunk (51/80) cellbender:remove-background: Working on chunk (52/80) cellbender:remove-background: Working on chunk (53/80) cellbender:remove-background: Working on chunk (54/80) cellbender:remove-background: Working on chunk (55/80) cellbender:remove-background: Working on chunk (56/80) cellbender:remove-background: Working on chunk (57/80) cellbender:remove-background: Working on chunk (58/80) cellbender:remove-background: Working on chunk (59/80) cellbender:remove-background: Working on chunk (60/80) cellbender:remove-background: Working on chunk (61/80) cellbender:remove-background: Working on chunk (62/80) cellbender:remove-background: Working on chunk (63/80) cellbender:remove-background: Working on chunk (64/80) cellbender:remove-background: Working on chunk (65/80) cellbender:remove-background: Working on chunk (66/80) cellbender:remove-background: Working on chunk (67/80) cellbender:remove-background: Working on chunk (68/80) cellbender:remove-background: Working on chunk (69/80) cellbender:remove-background: Working on chunk (70/80) cellbender:remove-background: Working on chunk (71/80) cellbender:remove-background: Working on chunk (72/80) cellbender:remove-background: Working on chunk (73/80) cellbender:remove-background: Working on chunk (74/80) cellbender:remove-background: Working on chunk (75/80) cellbender:remove-background: Working on chunk (76/80) cellbender:remove-background: Working on chunk (77/80) cellbender:remove-background: Working on chunk (78/80) cellbender:remove-background: Working on chunk (79/80) cellbender:remove-background: Working on chunk (80/80) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-DLPFC/2780-Control-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/2780-Control-DLPFC/2780-Control-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:16:29 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-DLPFC/2780-Control-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-DLPFC/2780-Control-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: [1.97 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 15:30:53 Total MCKP estimation time = 834.46 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/2780-Control-DLPFC/2780-Control-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/2780-Control-DLPFC/2780-Control-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/2780-Control-DLPFC/2780-Control-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/2780-Control-DLPFC/2780-Control-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:31:16