cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1713-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-Hippocampus/1713-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 7242 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash ae35385020) 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/1713-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: 31504 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2412 cellbender:remove-background: Prior on counts for empty droplets is 73 cellbender:remove-background: Excluding 7944 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23560 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 36 cellbender:remove-background: Using 7242 probable cell barcodes, plus an additional 12758 barcodes, and 14108 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 71 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpziydzmjt 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: 4607.1232 cellbender:remove-background: [epoch 002] average training loss: 3730.7527 (6.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 69 epochs cellbender:remove-background: [epoch 003] average training loss: 3257.2497 cellbender:remove-background: [epoch 004] average training loss: 2917.5417 cellbender:remove-background: [epoch 005] average training loss: 2788.4717 cellbender:remove-background: [epoch 005] average test loss: 2839.2784 cellbender:remove-background: [epoch 006] average training loss: 2742.9742 cellbender:remove-background: [epoch 007] average training loss: 2696.6570 cellbender:remove-background: [epoch 008] average training loss: 2667.9912 cellbender:remove-background: [epoch 009] average training loss: 2651.4525 cellbender:remove-background: [epoch 010] average training loss: 2587.9685 cellbender:remove-background: [epoch 010] average test loss: 2610.0246 cellbender:remove-background: [epoch 011] average training loss: 2531.7217 cellbender:remove-background: [epoch 012] average training loss: 2511.7014 cellbender:remove-background: [epoch 013] average training loss: 2491.8131 cellbender:remove-background: [epoch 014] average training loss: 2495.5319 cellbender:remove-background: [epoch 015] average training loss: 2476.5170 cellbender:remove-background: [epoch 015] average test loss: 2508.0589 cellbender:remove-background: [epoch 016] average training loss: 2468.4026 cellbender:remove-background: [epoch 017] average training loss: 2471.6436 cellbender:remove-background: [epoch 018] average training loss: 2460.2305 cellbender:remove-background: [epoch 019] average training loss: 2451.7383 cellbender:remove-background: [epoch 020] average training loss: 2436.9660 cellbender:remove-background: [epoch 020] average test loss: 2470.9095 cellbender:remove-background: [epoch 021] average training loss: 2431.9229 cellbender:remove-background: [epoch 022] average training loss: 2430.5621 cellbender:remove-background: [epoch 023] average training loss: 2420.2068 cellbender:remove-background: [epoch 024] average training loss: 2394.9635 cellbender:remove-background: [epoch 025] average training loss: 2383.3655 cellbender:remove-background: [epoch 025] average test loss: 2396.6468 cellbender:remove-background: [epoch 026] average training loss: 2369.4378 cellbender:remove-background: [epoch 027] average training loss: 2358.0176 cellbender:remove-background: [epoch 028] average training loss: 2345.7476 cellbender:remove-background: [epoch 029] average training loss: 2335.4591 cellbender:remove-background: [epoch 030] average training loss: 2328.0690 cellbender:remove-background: [epoch 030] average test loss: 2336.3901 cellbender:remove-background: [epoch 031] average training loss: 2320.3920 cellbender:remove-background: [epoch 032] average training loss: 2316.6848 cellbender:remove-background: [epoch 033] average training loss: 2315.3300 cellbender:remove-background: [epoch 034] average training loss: 2311.5197 cellbender:remove-background: [epoch 035] average training loss: 2309.5124 cellbender:remove-background: [epoch 035] average test loss: 2318.9731 cellbender:remove-background: [epoch 036] average training loss: 2308.1230 cellbender:remove-background: [epoch 037] average training loss: 2307.3509 cellbender:remove-background: [epoch 038] average training loss: 2305.2965 cellbender:remove-background: [epoch 039] average training loss: 2304.5793 cellbender:remove-background: [epoch 040] average training loss: 2303.3306 cellbender:remove-background: [epoch 040] average test loss: 2308.6902 cellbender:remove-background: [epoch 041] average training loss: 2301.6171 cellbender:remove-background: [epoch 042] average training loss: 2306.1858 cellbender:remove-background: [epoch 043] average training loss: 2302.8447 cellbender:remove-background: [epoch 044] average training loss: 2302.4330 cellbender:remove-background: [epoch 045] average training loss: 2305.5369 cellbender:remove-background: [epoch 045] average test loss: 2308.4846 cellbender:remove-background: [epoch 046] average training loss: 2317.4965 cellbender:remove-background: [epoch 047] average training loss: 2308.8080 cellbender:remove-background: [epoch 048] average training loss: 2311.0282 cellbender:remove-background: [epoch 049] average training loss: 2310.0892 cellbender:remove-background: [epoch 050] average training loss: 2313.1753 cellbender:remove-background: [epoch 050] average test loss: 2309.5368 cellbender:remove-background: [epoch 051] average training loss: 2321.7098 cellbender:remove-background: [epoch 052] average training loss: 2313.5817 cellbender:remove-background: [epoch 053] average training loss: 2318.8133 cellbender:remove-background: [epoch 054] average training loss: 2328.2933 cellbender:remove-background: [epoch 055] average training loss: 2334.0416 cellbender:remove-background: [epoch 055] average test loss: 2307.2911 cellbender:remove-background: [epoch 056] average training loss: 2321.5757 cellbender:remove-background: [epoch 057] average training loss: 2337.1106 cellbender:remove-background: [epoch 058] average training loss: 2343.1141 cellbender:remove-background: [epoch 059] average training loss: 2343.0204 cellbender:remove-background: [epoch 060] average training loss: 2360.3121 cellbender:remove-background: [epoch 060] average test loss: 2348.4112 cellbender:remove-background: [epoch 061] average training loss: 2345.0076 cellbender:remove-background: [epoch 062] average training loss: 2341.7633 cellbender:remove-background: [epoch 063] average training loss: 2357.1604 cellbender:remove-background: [epoch 064] average training loss: 2361.7423 cellbender:remove-background: [epoch 065] average training loss: 2359.3566 cellbender:remove-background: [epoch 065] average test loss: 2358.8021 cellbender:remove-background: [epoch 066] average training loss: 2346.0554 cellbender:remove-background: [epoch 067] average training loss: 2360.6188 cellbender:remove-background: [epoch 068] average training loss: 2360.3757 cellbender:remove-background: [epoch 069] average training loss: 2363.0788 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/1713-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 070] average training loss: 2351.1739 cellbender:remove-background: [epoch 070] average test loss: 2367.1278 cellbender:remove-background: [epoch 071] average training loss: 2353.3319 cellbender:remove-background: [epoch 072] average training loss: 2372.9840 cellbender:remove-background: [epoch 073] average training loss: 2371.8982 cellbender:remove-background: [epoch 074] average training loss: 2371.6272 cellbender:remove-background: [epoch 075] average training loss: 2374.5672 cellbender:remove-background: [epoch 075] average test loss: 2406.3117 cellbender:remove-background: [epoch 076] average training loss: 2382.9779 cellbender:remove-background: [epoch 077] average training loss: 2391.9090 cellbender:remove-background: [epoch 078] average training loss: 2378.4510 cellbender:remove-background: [epoch 079] average training loss: 2395.7928 cellbender:remove-background: [epoch 080] average training loss: 2391.5554 cellbender:remove-background: [epoch 080] average test loss: 2468.3491 cellbender:remove-background: [epoch 081] average training loss: 2396.1960 cellbender:remove-background: [epoch 082] average training loss: 2390.6779 cellbender:remove-background: [epoch 083] average training loss: 2392.1161 cellbender:remove-background: [epoch 084] average training loss: 2388.6342 cellbender:remove-background: [epoch 085] average training loss: 2384.9734 cellbender:remove-background: [epoch 085] average test loss: 2450.2343 cellbender:remove-background: [epoch 086] average training loss: 2383.6865 cellbender:remove-background: [epoch 087] average training loss: 2396.2615 cellbender:remove-background: [epoch 088] average training loss: 2405.4302 cellbender:remove-background: [epoch 089] average training loss: 2410.7347 cellbender:remove-background: [epoch 090] average training loss: 2401.3160 cellbender:remove-background: [epoch 090] average test loss: 2413.2321 cellbender:remove-background: [epoch 091] average training loss: 2399.9372 cellbender:remove-background: [epoch 092] average training loss: 2407.7317 cellbender:remove-background: [epoch 093] average training loss: 2385.3066 cellbender:remove-background: [epoch 094] average training loss: 2407.0528 cellbender:remove-background: [epoch 095] average training loss: 2388.6168 cellbender:remove-background: [epoch 095] average test loss: 2467.9229 cellbender:remove-background: [epoch 096] average training loss: 2406.8719 cellbender:remove-background: [epoch 097] average training loss: 2396.4194 cellbender:remove-background: [epoch 098] average training loss: 2399.6391 cellbender:remove-background: [epoch 099] average training loss: 2404.0630 cellbender:remove-background: [epoch 100] average training loss: 2407.8399 cellbender:remove-background: [epoch 100] average test loss: 2456.6211 cellbender:remove-background: [epoch 101] average training loss: 2413.0284 cellbender:remove-background: [epoch 102] average training loss: 2408.2955 cellbender:remove-background: [epoch 103] average training loss: 2407.0286 cellbender:remove-background: [epoch 104] average training loss: 2417.0402 cellbender:remove-background: [epoch 105] average training loss: 2404.0682 cellbender:remove-background: [epoch 105] average test loss: 2449.4474 cellbender:remove-background: [epoch 106] average training loss: 2405.5025 cellbender:remove-background: [epoch 107] average training loss: 2404.6357 cellbender:remove-background: [epoch 108] average training loss: 2406.4112 cellbender:remove-background: [epoch 109] average training loss: 2416.4088 cellbender:remove-background: [epoch 110] average training loss: 2398.1266 cellbender:remove-background: [epoch 110] average test loss: 2514.0970 cellbender:remove-background: [epoch 111] average training loss: 2410.7015 cellbender:remove-background: [epoch 112] average training loss: 2427.8510 cellbender:remove-background: [epoch 113] average training loss: 2400.3943 cellbender:remove-background: [epoch 114] average training loss: 2407.6182 cellbender:remove-background: [epoch 115] average training loss: 2404.8233 cellbender:remove-background: [epoch 115] average test loss: 2483.7055 cellbender:remove-background: [epoch 116] average training loss: 2402.6328 cellbender:remove-background: [epoch 117] average training loss: 2409.2216 cellbender:remove-background: [epoch 118] average training loss: 2426.4606 cellbender:remove-background: [epoch 119] average training loss: 2410.6072 cellbender:remove-background: [epoch 120] average training loss: 2405.9173 cellbender:remove-background: [epoch 120] average test loss: 2487.0281 cellbender:remove-background: [epoch 121] average training loss: 2413.5955 cellbender:remove-background: [epoch 122] average training loss: 2403.0925 cellbender:remove-background: [epoch 123] average training loss: 2414.8933 cellbender:remove-background: [epoch 124] average training loss: 2417.0290 cellbender:remove-background: [epoch 125] average training loss: 2415.1441 cellbender:remove-background: [epoch 125] average test loss: 2455.2081 cellbender:remove-background: [epoch 126] average training loss: 2402.1998 cellbender:remove-background: [epoch 127] average training loss: 2422.6338 cellbender:remove-background: [epoch 128] average training loss: 2414.3764 cellbender:remove-background: [epoch 129] average training loss: 2406.1514 cellbender:remove-background: [epoch 130] average training loss: 2402.9946 cellbender:remove-background: [epoch 130] average test loss: 2480.3461 cellbender:remove-background: [epoch 131] average training loss: 2404.0530 cellbender:remove-background: [epoch 132] average training loss: 2406.8990 cellbender:remove-background: [epoch 133] average training loss: 2408.9502 cellbender:remove-background: [epoch 134] average training loss: 2406.4078 cellbender:remove-background: [epoch 135] average training loss: 2411.7647 cellbender:remove-background: [epoch 135] average test loss: 2522.3434 cellbender:remove-background: [epoch 136] average training loss: 2419.1867 cellbender:remove-background: [epoch 137] average training loss: 2394.8559 cellbender:remove-background: [epoch 138] average training loss: 2405.0236 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/1713-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 139] average training loss: 2403.8709 cellbender:remove-background: [epoch 140] average training loss: 2407.1925 cellbender:remove-background: [epoch 140] average test loss: 2497.1786 cellbender:remove-background: [epoch 141] average training loss: 2399.1960 cellbender:remove-background: [epoch 142] average training loss: 2396.4835 cellbender:remove-background: [epoch 143] average training loss: 2418.8269 cellbender:remove-background: [epoch 144] average training loss: 2416.9513 cellbender:remove-background: [epoch 145] average training loss: 2415.3055 cellbender:remove-background: [epoch 145] average test loss: 2510.2628 cellbender:remove-background: [epoch 146] average training loss: 2408.2705 cellbender:remove-background: [epoch 147] average training loss: 2403.2163 cellbender:remove-background: [epoch 148] average training loss: 2407.7467 cellbender:remove-background: [epoch 149] average training loss: 2408.6476 cellbender:remove-background: [epoch 150] average training loss: 2411.7440 cellbender:remove-background: [epoch 150] average test loss: 2501.1044 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/1713-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:11:18 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpwq1flxec cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpwq1flxec /tmp/tmpwq1flxec/ae35385020_random.pyro /tmp/tmpwq1flxec/ae35385020_random.cuda /tmp/tmpwq1flxec/ae35385020_model.torch /tmp/tmpwq1flxec/ae35385020_optim.torch /tmp/tmpwq1flxec/ae35385020_optim.pyro /tmp/tmpwq1flxec/ae35385020_params.pyro /tmp/tmpwq1flxec/ae35385020_train.loaderstate /tmp/tmpwq1flxec/ae35385020_test.loaderstate /tmp/tmpwq1flxec/ae35385020_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 (1/93) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/93) cellbender:remove-background: Working on chunk (3/93) cellbender:remove-background: Working on chunk (4/93) cellbender:remove-background: Working on chunk (5/93) cellbender:remove-background: Working on chunk (6/93) cellbender:remove-background: Working on chunk (7/93) cellbender:remove-background: Working on chunk (8/93) cellbender:remove-background: Working on chunk (9/93) cellbender:remove-background: Working on chunk (10/93) cellbender:remove-background: Working on chunk (11/93) cellbender:remove-background: Working on chunk (12/93) cellbender:remove-background: Working on chunk (13/93) cellbender:remove-background: Working on chunk (14/93) cellbender:remove-background: Working on chunk (15/93) cellbender:remove-background: Working on chunk (16/93) cellbender:remove-background: Working on chunk (17/93) cellbender:remove-background: Working on chunk (18/93) cellbender:remove-background: Working on chunk (19/93) cellbender:remove-background: Working on chunk (20/93) cellbender:remove-background: Working on chunk (21/93) cellbender:remove-background: Working on chunk (22/93) cellbender:remove-background: Working on chunk (23/93) cellbender:remove-background: Working on chunk (24/93) cellbender:remove-background: Working on chunk (25/93) cellbender:remove-background: Working on chunk (26/93) cellbender:remove-background: Working on chunk (27/93) cellbender:remove-background: Working on chunk (28/93) cellbender:remove-background: Working on chunk (29/93) cellbender:remove-background: Working on chunk (30/93) cellbender:remove-background: Working on chunk (31/93) cellbender:remove-background: Working on chunk (32/93) cellbender:remove-background: Working on chunk (33/93) cellbender:remove-background: Working on chunk (34/93) cellbender:remove-background: Working on chunk (35/93) cellbender:remove-background: Working on chunk (36/93) cellbender:remove-background: Working on chunk (37/93) cellbender:remove-background: Working on chunk (38/93) cellbender:remove-background: Working on chunk (39/93) cellbender:remove-background: Working on chunk (40/93) cellbender:remove-background: Working on chunk (41/93) cellbender:remove-background: Working on chunk (42/93) cellbender:remove-background: Working on chunk (43/93) cellbender:remove-background: Working on chunk (44/93) cellbender:remove-background: Working on chunk (45/93) cellbender:remove-background: Working on chunk (46/93) cellbender:remove-background: Working on chunk (47/93) cellbender:remove-background: Working on chunk (48/93) cellbender:remove-background: Working on chunk (49/93) cellbender:remove-background: Working on chunk (50/93) cellbender:remove-background: Working on chunk (51/93) cellbender:remove-background: Working on chunk (52/93) cellbender:remove-background: Working on chunk (53/93) cellbender:remove-background: Working on chunk (54/93) cellbender:remove-background: Working on chunk (55/93) cellbender:remove-background: Working on chunk (56/93) cellbender:remove-background: Working on chunk (57/93) cellbender:remove-background: Working on chunk (58/93) cellbender:remove-background: Working on chunk (59/93) cellbender:remove-background: Working on chunk (60/93) cellbender:remove-background: Working on chunk (61/93) cellbender:remove-background: Working on chunk (62/93) cellbender:remove-background: Working on chunk (63/93) cellbender:remove-background: Working on chunk (64/93) cellbender:remove-background: Working on chunk (65/93) cellbender:remove-background: Working on chunk (66/93) cellbender:remove-background: Working on chunk (67/93) cellbender:remove-background: Working on chunk (68/93) cellbender:remove-background: Working on chunk (69/93) cellbender:remove-background: Working on chunk (70/93) cellbender:remove-background: Working on chunk (71/93) cellbender:remove-background: Working on chunk (72/93) cellbender:remove-background: Working on chunk (73/93) cellbender:remove-background: Working on chunk (74/93) cellbender:remove-background: Working on chunk (75/93) cellbender:remove-background: Working on chunk (76/93) cellbender:remove-background: Working on chunk (77/93) cellbender:remove-background: Working on chunk (78/93) cellbender:remove-background: Working on chunk (79/93) cellbender:remove-background: Working on chunk (80/93) cellbender:remove-background: Working on chunk (81/93) cellbender:remove-background: Working on chunk (82/93) cellbender:remove-background: Working on chunk (83/93) cellbender:remove-background: Working on chunk (84/93) cellbender:remove-background: Working on chunk (85/93) cellbender:remove-background: Working on chunk (86/93) cellbender:remove-background: Working on chunk (87/93) cellbender:remove-background: Working on chunk (88/93) cellbender:remove-background: Working on chunk (89/93) cellbender:remove-background: Working on chunk (90/93) cellbender:remove-background: Working on chunk (91/93) cellbender:remove-background: Working on chunk (92/93) cellbender:remove-background: Working on chunk (93/93) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-Hippocampus/1713-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/1713-Bipolar-Hippocampus/1713-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:16:20 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-Hippocampus/1713-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/1713-Bipolar-Hippocampus/1713-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: [1.43 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 15:26:55 Total MCKP estimation time = 612.59 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/1713-Bipolar-Hippocampus/1713-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/1713-Bipolar-Hippocampus/1713-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/1713-Bipolar-Hippocampus/1713-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/1713-Bipolar-Hippocampus/1713-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:27:11