cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1390-Control-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-Hippocampus/1390-Control-Hippocampus.cellbender.output.h5 --cuda --expected-cells 9642 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash b476218c8a) cellbender:remove-background: 2024-06-06 14:52:07 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/1390-Control-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: 31422 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2722 cellbender:remove-background: Prior on counts for empty droplets is 105 cellbender:remove-background: Excluding 7723 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23699 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 52 cellbender:remove-background: Using 9642 probable cell barcodes, plus an additional 10358 barcodes, and 12499 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 103 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpbmsrl3u7 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: 5449.9980 cellbender:remove-background: [epoch 002] average training loss: 4389.9489 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 68 epochs cellbender:remove-background: [epoch 003] average training loss: 3777.1474 cellbender:remove-background: [epoch 004] average training loss: 3418.2239 cellbender:remove-background: [epoch 005] average training loss: 3312.3211 cellbender:remove-background: [epoch 005] average test loss: 3359.2585 cellbender:remove-background: [epoch 006] average training loss: 3274.7277 cellbender:remove-background: [epoch 007] average training loss: 3230.9723 cellbender:remove-background: [epoch 008] average training loss: 3210.8703 cellbender:remove-background: [epoch 009] average training loss: 3196.2646 cellbender:remove-background: [epoch 010] average training loss: 3121.9349 cellbender:remove-background: [epoch 010] average test loss: 3237.7920 cellbender:remove-background: [epoch 011] average training loss: 3018.0944 cellbender:remove-background: [epoch 012] average training loss: 2980.5759 cellbender:remove-background: [epoch 013] average training loss: 2955.4681 cellbender:remove-background: [epoch 014] average training loss: 2946.2537 cellbender:remove-background: [epoch 015] average training loss: 2919.7210 cellbender:remove-background: [epoch 015] average test loss: 2960.3455 cellbender:remove-background: [epoch 016] average training loss: 2908.0185 cellbender:remove-background: [epoch 017] average training loss: 2906.0197 cellbender:remove-background: [epoch 018] average training loss: 2900.5648 cellbender:remove-background: [epoch 019] average training loss: 2892.4672 cellbender:remove-background: [epoch 020] average training loss: 2883.0625 cellbender:remove-background: [epoch 020] average test loss: 2917.4755 cellbender:remove-background: [epoch 021] average training loss: 2881.5076 cellbender:remove-background: [epoch 022] average training loss: 2877.4436 cellbender:remove-background: [epoch 023] average training loss: 2863.7244 cellbender:remove-background: [epoch 024] average training loss: 2837.0140 cellbender:remove-background: [epoch 025] average training loss: 2822.9601 cellbender:remove-background: [epoch 025] average test loss: 2835.5937 cellbender:remove-background: [epoch 026] average training loss: 2804.2568 cellbender:remove-background: [epoch 027] average training loss: 2793.5586 cellbender:remove-background: [epoch 028] average training loss: 2784.8386 cellbender:remove-background: [epoch 029] average training loss: 2774.0480 cellbender:remove-background: [epoch 030] average training loss: 2768.8602 cellbender:remove-background: [epoch 030] average test loss: 2777.5705 cellbender:remove-background: [epoch 031] average training loss: 2762.1900 cellbender:remove-background: [epoch 032] average training loss: 2759.3171 cellbender:remove-background: [epoch 033] average training loss: 2758.5169 cellbender:remove-background: [epoch 034] average training loss: 2755.9049 cellbender:remove-background: [epoch 035] average training loss: 2755.7055 cellbender:remove-background: [epoch 035] average test loss: 2770.6897 cellbender:remove-background: [epoch 036] average training loss: 2757.9767 cellbender:remove-background: [epoch 037] average training loss: 2761.0431 cellbender:remove-background: [epoch 038] average training loss: 2758.4308 cellbender:remove-background: [epoch 039] average training loss: 2757.8809 cellbender:remove-background: [epoch 040] average training loss: 2756.5068 cellbender:remove-background: [epoch 040] average test loss: 2765.6187 cellbender:remove-background: [epoch 041] average training loss: 2756.7101 cellbender:remove-background: [epoch 042] average training loss: 2755.3266 cellbender:remove-background: [epoch 043] average training loss: 2757.8579 cellbender:remove-background: [epoch 044] average training loss: 2760.0520 cellbender:remove-background: [epoch 045] average training loss: 2758.9150 cellbender:remove-background: [epoch 045] average test loss: 2761.2583 cellbender:remove-background: [epoch 046] average training loss: 2755.4484 cellbender:remove-background: [epoch 047] average training loss: 2753.8036 cellbender:remove-background: [epoch 048] average training loss: 2757.4054 cellbender:remove-background: [epoch 049] average training loss: 2755.3460 cellbender:remove-background: [epoch 050] average training loss: 2750.0113 cellbender:remove-background: [epoch 050] average test loss: 2775.1585 cellbender:remove-background: [epoch 051] average training loss: 2755.1980 cellbender:remove-background: [epoch 052] average training loss: 2755.8941 cellbender:remove-background: [epoch 053] average training loss: 2752.1233 cellbender:remove-background: [epoch 054] average training loss: 2755.1760 cellbender:remove-background: [epoch 055] average training loss: 2753.5513 cellbender:remove-background: [epoch 055] average test loss: 2761.5908 cellbender:remove-background: [epoch 056] average training loss: 2752.2219 cellbender:remove-background: [epoch 057] average training loss: 2752.8101 cellbender:remove-background: [epoch 058] average training loss: 2751.9413 cellbender:remove-background: [epoch 059] average training loss: 2754.4794 cellbender:remove-background: [epoch 060] average training loss: 2755.6842 cellbender:remove-background: [epoch 060] average test loss: 2758.2863 cellbender:remove-background: [epoch 061] average training loss: 2749.7853 cellbender:remove-background: [epoch 062] average training loss: 2748.5775 cellbender:remove-background: [epoch 063] average training loss: 2754.4521 cellbender:remove-background: [epoch 064] average training loss: 2749.6193 cellbender:remove-background: [epoch 065] average training loss: 2750.9533 cellbender:remove-background: [epoch 065] average test loss: 2776.7103 cellbender:remove-background: [epoch 066] average training loss: 2749.9609 cellbender:remove-background: [epoch 067] average training loss: 2753.2539 cellbender:remove-background: [epoch 068] average training loss: 2747.8436 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/1390-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 069] average training loss: 2751.7699 cellbender:remove-background: [epoch 070] average training loss: 2751.6667 cellbender:remove-background: [epoch 070] average test loss: 2767.1479 cellbender:remove-background: [epoch 071] average training loss: 2750.2860 cellbender:remove-background: [epoch 072] average training loss: 2751.4475 cellbender:remove-background: [epoch 073] average training loss: 2749.8468 cellbender:remove-background: [epoch 074] average training loss: 2750.7484 cellbender:remove-background: [epoch 075] average training loss: 2753.8493 cellbender:remove-background: [epoch 075] average test loss: 2771.9414 cellbender:remove-background: [epoch 076] average training loss: 2751.1405 cellbender:remove-background: [epoch 077] average training loss: 2749.5842 cellbender:remove-background: [epoch 078] average training loss: 2753.0112 cellbender:remove-background: [epoch 079] average training loss: 2749.4162 cellbender:remove-background: [epoch 080] average training loss: 2748.3128 cellbender:remove-background: [epoch 080] average test loss: 2799.4029 cellbender:remove-background: [epoch 081] average training loss: 2754.3175 cellbender:remove-background: [epoch 082] average training loss: 2749.9759 cellbender:remove-background: [epoch 083] average training loss: 2751.4863 cellbender:remove-background: [epoch 084] average training loss: 2750.8593 cellbender:remove-background: [epoch 085] average training loss: 2755.2081 cellbender:remove-background: [epoch 085] average test loss: 2773.3828 cellbender:remove-background: [epoch 086] average training loss: 2752.1569 cellbender:remove-background: [epoch 087] average training loss: 2756.9754 cellbender:remove-background: [epoch 088] average training loss: 2753.9339 cellbender:remove-background: [epoch 089] average training loss: 2749.2964 cellbender:remove-background: [epoch 090] average training loss: 2754.0945 cellbender:remove-background: [epoch 090] average test loss: 2777.8705 cellbender:remove-background: [epoch 091] average training loss: 2756.8002 cellbender:remove-background: [epoch 092] average training loss: 2751.5113 cellbender:remove-background: [epoch 093] average training loss: 2754.7658 cellbender:remove-background: [epoch 094] average training loss: 2757.6707 cellbender:remove-background: [epoch 095] average training loss: 2753.5056 cellbender:remove-background: [epoch 095] average test loss: 2788.6738 cellbender:remove-background: [epoch 096] average training loss: 2752.7648 cellbender:remove-background: [epoch 097] average training loss: 2759.6708 cellbender:remove-background: [epoch 098] average training loss: 2758.1063 cellbender:remove-background: [epoch 099] average training loss: 2760.0367 cellbender:remove-background: [epoch 100] average training loss: 2758.1319 cellbender:remove-background: [epoch 100] average test loss: 2787.1456 cellbender:remove-background: [epoch 101] average training loss: 2756.6965 cellbender:remove-background: [epoch 102] average training loss: 2756.6115 cellbender:remove-background: [epoch 103] average training loss: 2759.8553 cellbender:remove-background: [epoch 104] average training loss: 2756.3773 cellbender:remove-background: [epoch 105] average training loss: 2755.0108 cellbender:remove-background: [epoch 105] average test loss: 2779.7370 cellbender:remove-background: [epoch 106] average training loss: 2756.2814 cellbender:remove-background: [epoch 107] average training loss: 2758.9363 cellbender:remove-background: [epoch 108] average training loss: 2754.7968 cellbender:remove-background: [epoch 109] average training loss: 2755.0426 cellbender:remove-background: [epoch 110] average training loss: 2757.3079 cellbender:remove-background: [epoch 110] average test loss: 2792.8634 cellbender:remove-background: [epoch 111] average training loss: 2755.7643 cellbender:remove-background: [epoch 112] average training loss: 2754.1229 cellbender:remove-background: [epoch 113] average training loss: 2755.7719 cellbender:remove-background: [epoch 114] average training loss: 2755.7579 cellbender:remove-background: [epoch 115] average training loss: 2757.6176 cellbender:remove-background: [epoch 115] average test loss: 2794.0759 cellbender:remove-background: [epoch 116] average training loss: 2757.3598 cellbender:remove-background: [epoch 117] average training loss: 2753.6410 cellbender:remove-background: [epoch 118] average training loss: 2754.3943 cellbender:remove-background: [epoch 119] average training loss: 2755.3236 cellbender:remove-background: [epoch 120] average training loss: 2753.2338 cellbender:remove-background: [epoch 120] average test loss: 2771.1380 cellbender:remove-background: [epoch 121] average training loss: 2755.4936 cellbender:remove-background: [epoch 122] average training loss: 2752.1472 cellbender:remove-background: [epoch 123] average training loss: 2757.9207 cellbender:remove-background: [epoch 124] average training loss: 2755.0438 cellbender:remove-background: [epoch 125] average training loss: 2758.8516 cellbender:remove-background: [epoch 125] average test loss: 2787.3475 cellbender:remove-background: [epoch 126] average training loss: 2754.3793 cellbender:remove-background: [epoch 127] average training loss: 2755.0086 cellbender:remove-background: [epoch 128] average training loss: 2754.2277 cellbender:remove-background: [epoch 129] average training loss: 2752.5042 cellbender:remove-background: [epoch 130] average training loss: 2752.6853 cellbender:remove-background: [epoch 130] average test loss: 2791.5876 cellbender:remove-background: [epoch 131] average training loss: 2754.7924 cellbender:remove-background: [epoch 132] average training loss: 2754.6097 cellbender:remove-background: [epoch 133] average training loss: 2753.2930 cellbender:remove-background: [epoch 134] average training loss: 2753.0000 cellbender:remove-background: [epoch 135] average training loss: 2756.7685 cellbender:remove-background: [epoch 135] average test loss: 2795.3443 cellbender:remove-background: [epoch 136] average training loss: 2755.4773 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/1390-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 137] average training loss: 2753.6670 cellbender:remove-background: [epoch 138] average training loss: 2755.5394 cellbender:remove-background: [epoch 139] average training loss: 2752.0282 cellbender:remove-background: [epoch 140] average training loss: 2756.2951 cellbender:remove-background: [epoch 140] average test loss: 2798.3818 cellbender:remove-background: [epoch 141] average training loss: 2754.2336 cellbender:remove-background: [epoch 142] average training loss: 2751.3231 cellbender:remove-background: [epoch 143] average training loss: 2753.8381 cellbender:remove-background: [epoch 144] average training loss: 2751.8536 cellbender:remove-background: [epoch 145] average training loss: 2752.2735 cellbender:remove-background: [epoch 145] average test loss: 2791.9902 cellbender:remove-background: [epoch 146] average training loss: 2752.9402 cellbender:remove-background: [epoch 147] average training loss: 2753.3516 cellbender:remove-background: [epoch 148] average training loss: 2751.7867 cellbender:remove-background: [epoch 149] average training loss: 2749.4670 cellbender:remove-background: [epoch 150] average training loss: 2751.8251 cellbender:remove-background: [epoch 150] average test loss: 2785.2021 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/1390-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:11:33 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzzf45ukv cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpzzf45ukv /tmp/tmpzzf45ukv/b476218c8a_random.pyro /tmp/tmpzzf45ukv/b476218c8a_random.cuda /tmp/tmpzzf45ukv/b476218c8a_model.torch /tmp/tmpzzf45ukv/b476218c8a_optim.torch /tmp/tmpzzf45ukv/b476218c8a_optim.pyro /tmp/tmpzzf45ukv/b476218c8a_params.pyro /tmp/tmpzzf45ukv/b476218c8a_train.loaderstate /tmp/tmpzzf45ukv/b476218c8a_test.loaderstate /tmp/tmpzzf45ukv/b476218c8a_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 (1/103) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/103) cellbender:remove-background: Working on chunk (3/103) cellbender:remove-background: Working on chunk (4/103) cellbender:remove-background: Working on chunk (5/103) cellbender:remove-background: Working on chunk (6/103) cellbender:remove-background: Working on chunk (7/103) cellbender:remove-background: Working on chunk (8/103) cellbender:remove-background: Working on chunk (9/103) cellbender:remove-background: Working on chunk (10/103) cellbender:remove-background: Working on chunk (11/103) cellbender:remove-background: Working on chunk (12/103) cellbender:remove-background: Working on chunk (13/103) cellbender:remove-background: Working on chunk (14/103) cellbender:remove-background: Working on chunk (15/103) cellbender:remove-background: Working on chunk (16/103) cellbender:remove-background: Working on chunk (17/103) cellbender:remove-background: Working on chunk (18/103) cellbender:remove-background: Working on chunk (19/103) cellbender:remove-background: Working on chunk (20/103) cellbender:remove-background: Working on chunk (21/103) cellbender:remove-background: Working on chunk (22/103) cellbender:remove-background: Working on chunk (23/103) cellbender:remove-background: Working on chunk (24/103) cellbender:remove-background: Working on chunk (25/103) cellbender:remove-background: Working on chunk (26/103) cellbender:remove-background: Working on chunk (27/103) cellbender:remove-background: Working on chunk (28/103) cellbender:remove-background: Working on chunk (29/103) cellbender:remove-background: Working on chunk (30/103) cellbender:remove-background: Working on chunk (31/103) cellbender:remove-background: Working on chunk (32/103) cellbender:remove-background: Working on chunk (33/103) cellbender:remove-background: Working on chunk (34/103) cellbender:remove-background: Working on chunk (35/103) cellbender:remove-background: Working on chunk (36/103) cellbender:remove-background: Working on chunk (37/103) cellbender:remove-background: Working on chunk (38/103) cellbender:remove-background: Working on chunk (39/103) cellbender:remove-background: Working on chunk (40/103) cellbender:remove-background: Working on chunk (41/103) cellbender:remove-background: Working on chunk (42/103) cellbender:remove-background: Working on chunk (43/103) cellbender:remove-background: Working on chunk (44/103) cellbender:remove-background: Working on chunk (45/103) cellbender:remove-background: Working on chunk (46/103) cellbender:remove-background: Working on chunk (47/103) cellbender:remove-background: Working on chunk (48/103) cellbender:remove-background: Working on chunk (49/103) cellbender:remove-background: Working on chunk (50/103) cellbender:remove-background: Working on chunk (51/103) cellbender:remove-background: Working on chunk (52/103) cellbender:remove-background: Working on chunk (53/103) cellbender:remove-background: Working on chunk (54/103) cellbender:remove-background: Working on chunk (55/103) cellbender:remove-background: Working on chunk (56/103) cellbender:remove-background: Working on chunk (57/103) cellbender:remove-background: Working on chunk (58/103) cellbender:remove-background: Working on chunk (59/103) cellbender:remove-background: Working on chunk (60/103) cellbender:remove-background: Working on chunk (61/103) cellbender:remove-background: Working on chunk (62/103) cellbender:remove-background: Working on chunk (63/103) cellbender:remove-background: Working on chunk (64/103) cellbender:remove-background: Working on chunk (65/103) cellbender:remove-background: Working on chunk (66/103) cellbender:remove-background: Working on chunk (67/103) cellbender:remove-background: Working on chunk (68/103) cellbender:remove-background: Working on chunk (69/103) cellbender:remove-background: Working on chunk (70/103) cellbender:remove-background: Working on chunk (71/103) cellbender:remove-background: Working on chunk (72/103) cellbender:remove-background: Working on chunk (73/103) cellbender:remove-background: Working on chunk (74/103) cellbender:remove-background: Working on chunk (75/103) cellbender:remove-background: Working on chunk (76/103) cellbender:remove-background: Working on chunk (77/103) cellbender:remove-background: Working on chunk (78/103) cellbender:remove-background: Working on chunk (79/103) cellbender:remove-background: Working on chunk (80/103) cellbender:remove-background: Working on chunk (81/103) cellbender:remove-background: Working on chunk (82/103) cellbender:remove-background: Working on chunk (83/103) cellbender:remove-background: Working on chunk (84/103) cellbender:remove-background: Working on chunk (85/103) cellbender:remove-background: Working on chunk (86/103) cellbender:remove-background: Working on chunk (87/103) cellbender:remove-background: Working on chunk (88/103) cellbender:remove-background: Working on chunk (89/103) cellbender:remove-background: Working on chunk (90/103) cellbender:remove-background: Working on chunk (91/103) cellbender:remove-background: Working on chunk (92/103) cellbender:remove-background: Working on chunk (93/103) cellbender:remove-background: Working on chunk (94/103) cellbender:remove-background: Working on chunk (95/103) cellbender:remove-background: Working on chunk (96/103) cellbender:remove-background: Working on chunk (97/103) cellbender:remove-background: Working on chunk (98/103) cellbender:remove-background: Working on chunk (99/103) cellbender:remove-background: Working on chunk (100/103) cellbender:remove-background: Working on chunk (101/103) cellbender:remove-background: Working on chunk (102/103) cellbender:remove-background: Working on chunk (103/103) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-Hippocampus/1390-Control-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/1390-Control-Hippocampus/1390-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:17:04 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-Hippocampus/1390-Control-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-Hippocampus/1390-Control-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 15:30:38 Total MCKP estimation time = 785.96 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/1390-Control-Hippocampus/1390-Control-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/1390-Control-Hippocampus/1390-Control-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/1390-Control-Hippocampus/1390-Control-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/1390-Control-Hippocampus/1390-Control-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:30:57