cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2343-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 6669 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash d6cbc59ea0) cellbender:remove-background: 2024-06-06 15:04:08 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/2343-Schizophrenia-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: 32878 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3435 cellbender:remove-background: Prior on counts for empty droplets is 135 cellbender:remove-background: Excluding 6450 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 26428 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 67 cellbender:remove-background: Using 6669 probable cell barcodes, plus an additional 13331 barcodes, and 30833 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 134 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmppkw8_11p 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: 4407.9109 cellbender:remove-background: [epoch 002] average training loss: 3635.5494 (13.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 32 epochs cellbender:remove-background: [epoch 003] average training loss: 3211.7810 cellbender:remove-background: [epoch 004] average training loss: 2951.0272 cellbender:remove-background: [epoch 005] average training loss: 2881.8857 cellbender:remove-background: [epoch 005] average test loss: 2867.3825 cellbender:remove-background: [epoch 006] average training loss: 2853.6826 cellbender:remove-background: [epoch 007] average training loss: 2814.9972 cellbender:remove-background: [epoch 008] average training loss: 2796.6507 cellbender:remove-background: [epoch 009] average training loss: 2790.4105 cellbender:remove-background: [epoch 010] average training loss: 2754.0027 cellbender:remove-background: [epoch 010] average test loss: 2739.5712 cellbender:remove-background: [epoch 011] average training loss: 2720.1629 cellbender:remove-background: [epoch 012] average training loss: 2641.8224 cellbender:remove-background: [epoch 013] average training loss: 2597.8849 cellbender:remove-background: [epoch 014] average training loss: 2599.6932 cellbender:remove-background: [epoch 015] average training loss: 2567.7745 cellbender:remove-background: [epoch 015] average test loss: 2532.8539 cellbender:remove-background: [epoch 016] average training loss: 2537.4320 cellbender:remove-background: [epoch 017] average training loss: 2507.2334 cellbender:remove-background: [epoch 018] average training loss: 2467.4211 cellbender:remove-background: [epoch 019] average training loss: 2449.4575 cellbender:remove-background: [epoch 020] average training loss: 2433.1410 cellbender:remove-background: [epoch 020] average test loss: 2411.9218 cellbender:remove-background: [epoch 021] average training loss: 2427.8703 cellbender:remove-background: [epoch 022] average training loss: 2423.5168 cellbender:remove-background: [epoch 023] average training loss: 2424.7556 cellbender:remove-background: [epoch 024] average training loss: 2419.2255 cellbender:remove-background: [epoch 025] average training loss: 2419.7713 cellbender:remove-background: [epoch 025] average test loss: 2395.9046 cellbender:remove-background: [epoch 026] average training loss: 2416.9427 cellbender:remove-background: [epoch 027] average training loss: 2415.2374 cellbender:remove-background: [epoch 028] average training loss: 2414.7025 cellbender:remove-background: [epoch 029] average training loss: 2413.0284 cellbender:remove-background: [epoch 030] average training loss: 2411.6867 cellbender:remove-background: [epoch 030] average test loss: 2384.5415 cellbender:remove-background: [epoch 031] average training loss: 2415.9411 cellbender:remove-background: [epoch 032] average training loss: 2414.9221 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/2343-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 033] average training loss: 2414.6048 cellbender:remove-background: [epoch 034] average training loss: 2417.6005 cellbender:remove-background: [epoch 035] average training loss: 2418.3365 cellbender:remove-background: [epoch 035] average test loss: 2392.0735 cellbender:remove-background: [epoch 036] average training loss: 2421.9947 cellbender:remove-background: [epoch 037] average training loss: 2421.5857 cellbender:remove-background: [epoch 038] average training loss: 2422.0794 cellbender:remove-background: [epoch 039] average training loss: 2423.7278 cellbender:remove-background: [epoch 040] average training loss: 2430.2862 cellbender:remove-background: [epoch 040] average test loss: 2397.1477 cellbender:remove-background: [epoch 041] average training loss: 2432.3334 cellbender:remove-background: [epoch 042] average training loss: 2436.7729 cellbender:remove-background: [epoch 043] average training loss: 2449.6534 cellbender:remove-background: [epoch 044] average training loss: 2447.4971 cellbender:remove-background: [epoch 045] average training loss: 2452.9007 cellbender:remove-background: [epoch 045] average test loss: 2411.7997 cellbender:remove-background: [epoch 046] average training loss: 2460.8941 cellbender:remove-background: [epoch 047] average training loss: 2468.7499 cellbender:remove-background: [epoch 048] average training loss: 2452.8653 cellbender:remove-background: [epoch 049] average training loss: 2460.8127 cellbender:remove-background: [epoch 050] average training loss: 2456.5382 cellbender:remove-background: [epoch 050] average test loss: 2482.4680 cellbender:remove-background: [epoch 051] average training loss: 2469.9435 cellbender:remove-background: [epoch 052] average training loss: 2461.0707 cellbender:remove-background: [epoch 053] average training loss: 2449.3280 cellbender:remove-background: [epoch 054] average training loss: 2453.8626 cellbender:remove-background: [epoch 055] average training loss: 2450.1996 cellbender:remove-background: [epoch 055] average test loss: 2426.5099 cellbender:remove-background: [epoch 056] average training loss: 2459.5120 cellbender:remove-background: [epoch 057] average training loss: 2463.8406 cellbender:remove-background: [epoch 058] average training loss: 2463.7905 cellbender:remove-background: [epoch 059] average training loss: 2464.1971 cellbender:remove-background: [epoch 060] average training loss: 2460.6673 cellbender:remove-background: [epoch 060] average test loss: 2442.4609 cellbender:remove-background: [epoch 061] average training loss: 2463.4473 cellbender:remove-background: [epoch 062] average training loss: 2460.8664 cellbender:remove-background: [epoch 063] average training loss: 2453.0565 cellbender:remove-background: [epoch 064] average training loss: 2457.0234 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/2343-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 065] average training loss: 2459.2056 cellbender:remove-background: [epoch 065] average test loss: 2423.7527 cellbender:remove-background: [epoch 066] average training loss: 2452.4095 cellbender:remove-background: [epoch 067] average training loss: 2462.0796 cellbender:remove-background: [epoch 068] average training loss: 2464.6442 cellbender:remove-background: [epoch 069] average training loss: 2462.9131 cellbender:remove-background: [epoch 070] average training loss: 2464.0670 cellbender:remove-background: [epoch 070] average test loss: 2469.0563 cellbender:remove-background: [epoch 071] average training loss: 2460.6854 cellbender:remove-background: [epoch 072] average training loss: 2451.4942 cellbender:remove-background: [epoch 073] average training loss: 2457.8506 cellbender:remove-background: [epoch 074] average training loss: 2464.0665 cellbender:remove-background: [epoch 075] average training loss: 2453.5064 cellbender:remove-background: [epoch 075] average test loss: 2467.8533 cellbender:remove-background: [epoch 076] average training loss: 2450.1327 cellbender:remove-background: [epoch 077] average training loss: 2461.0902 cellbender:remove-background: [epoch 078] average training loss: 2452.3437 cellbender:remove-background: [epoch 079] average training loss: 2451.0316 cellbender:remove-background: [epoch 080] average training loss: 2461.5651 cellbender:remove-background: [epoch 080] average test loss: 2474.9362 cellbender:remove-background: [epoch 081] average training loss: 2452.0270 cellbender:remove-background: [epoch 082] average training loss: 2453.2382 cellbender:remove-background: [epoch 083] average training loss: 2459.3782 cellbender:remove-background: [epoch 084] average training loss: 2451.3371 cellbender:remove-background: [epoch 085] average training loss: 2450.7183 cellbender:remove-background: [epoch 085] average test loss: 2456.3895 cellbender:remove-background: [epoch 086] average training loss: 2449.2125 cellbender:remove-background: [epoch 087] average training loss: 2449.1189 cellbender:remove-background: [epoch 088] average training loss: 2454.7556 cellbender:remove-background: [epoch 089] average training loss: 2453.2337 cellbender:remove-background: [epoch 090] average training loss: 2452.8011 cellbender:remove-background: [epoch 090] average test loss: 2458.6960 cellbender:remove-background: [epoch 091] average training loss: 2445.9088 cellbender:remove-background: [epoch 092] average training loss: 2441.1670 cellbender:remove-background: [epoch 093] average training loss: 2445.4250 cellbender:remove-background: [epoch 094] average training loss: 2441.9269 cellbender:remove-background: [epoch 095] average training loss: 2442.3320 cellbender:remove-background: [epoch 095] average test loss: 2456.3246 cellbender:remove-background: [epoch 096] average training loss: 2443.6565 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/2343-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 097] average training loss: 2442.2960 cellbender:remove-background: [epoch 098] average training loss: 2441.3786 cellbender:remove-background: [epoch 099] average training loss: 2438.3107 cellbender:remove-background: [epoch 100] average training loss: 2436.2283 cellbender:remove-background: [epoch 100] average test loss: 2432.4295 cellbender:remove-background: [epoch 101] average training loss: 2437.9441 cellbender:remove-background: [epoch 102] average training loss: 2437.2211 cellbender:remove-background: [epoch 103] average training loss: 2436.0258 cellbender:remove-background: [epoch 104] average training loss: 2437.8530 cellbender:remove-background: [epoch 105] average training loss: 2439.1475 cellbender:remove-background: [epoch 105] average test loss: 2439.0395 cellbender:remove-background: [epoch 106] average training loss: 2441.5181 cellbender:remove-background: [epoch 107] average training loss: 2436.3626 cellbender:remove-background: [epoch 108] average training loss: 2438.5858 cellbender:remove-background: [epoch 109] average training loss: 2436.7372 cellbender:remove-background: [epoch 110] average training loss: 2440.4235 cellbender:remove-background: [epoch 110] average test loss: 2441.0519 cellbender:remove-background: [epoch 111] average training loss: 2437.9005 cellbender:remove-background: [epoch 112] average training loss: 2439.6136 cellbender:remove-background: [epoch 113] average training loss: 2442.4381 cellbender:remove-background: [epoch 114] average training loss: 2433.1298 cellbender:remove-background: [epoch 115] average training loss: 2434.9056 cellbender:remove-background: [epoch 115] average test loss: 2449.7076 cellbender:remove-background: [epoch 116] average training loss: 2438.7337 cellbender:remove-background: [epoch 117] average training loss: 2433.5399 cellbender:remove-background: [epoch 118] average training loss: 2432.7909 cellbender:remove-background: [epoch 119] average training loss: 2439.0709 cellbender:remove-background: [epoch 120] average training loss: 2434.6131 cellbender:remove-background: [epoch 120] average test loss: 2449.2528 cellbender:remove-background: [epoch 121] average training loss: 2436.3104 cellbender:remove-background: [epoch 122] average training loss: 2435.2632 cellbender:remove-background: [epoch 123] average training loss: 2436.4521 cellbender:remove-background: [epoch 124] average training loss: 2433.3195 cellbender:remove-background: [epoch 125] average training loss: 2431.9031 cellbender:remove-background: [epoch 125] average test loss: 2443.7480 cellbender:remove-background: [epoch 126] average training loss: 2433.4493 cellbender:remove-background: [epoch 127] average training loss: 2432.6313 cellbender:remove-background: [epoch 128] average training loss: 2437.3863 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/2343-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 129] average training loss: 2431.3853 cellbender:remove-background: [epoch 130] average training loss: 2433.3205 cellbender:remove-background: [epoch 130] average test loss: 2445.2158 cellbender:remove-background: [epoch 131] average training loss: 2428.7868 cellbender:remove-background: [epoch 132] average training loss: 2433.3798 cellbender:remove-background: [epoch 133] average training loss: 2432.0349 cellbender:remove-background: [epoch 134] average training loss: 2434.5166 cellbender:remove-background: [epoch 135] average training loss: 2430.8446 cellbender:remove-background: [epoch 135] average test loss: 2440.3465 cellbender:remove-background: [epoch 136] average training loss: 2427.8530 cellbender:remove-background: [epoch 137] average training loss: 2430.6289 cellbender:remove-background: [epoch 138] average training loss: 2429.3819 cellbender:remove-background: [epoch 139] average training loss: 2429.1486 cellbender:remove-background: [epoch 140] average training loss: 2431.0133 cellbender:remove-background: [epoch 140] average test loss: 2462.6171 cellbender:remove-background: [epoch 141] average training loss: 2429.7038 cellbender:remove-background: [epoch 142] average training loss: 2430.5710 cellbender:remove-background: [epoch 143] average training loss: 2429.9145 cellbender:remove-background: [epoch 144] average training loss: 2428.6821 cellbender:remove-background: [epoch 145] average training loss: 2428.7065 cellbender:remove-background: [epoch 145] average test loss: 2451.5464 cellbender:remove-background: [epoch 146] average training loss: 2430.2601 cellbender:remove-background: [epoch 147] average training loss: 2431.3961 cellbender:remove-background: [epoch 148] average training loss: 2429.9317 cellbender:remove-background: [epoch 149] average training loss: 2430.6117 cellbender:remove-background: [epoch 150] average training loss: 2428.7292 cellbender:remove-background: [epoch 150] average test loss: 2452.3384 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/2343-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:45:22 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpaa98w4by cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpaa98w4by /tmp/tmpaa98w4by/d6cbc59ea0_random.pyro /tmp/tmpaa98w4by/d6cbc59ea0_random.cuda /tmp/tmpaa98w4by/d6cbc59ea0_model.torch /tmp/tmpaa98w4by/d6cbc59ea0_optim.torch /tmp/tmpaa98w4by/d6cbc59ea0_optim.pyro /tmp/tmpaa98w4by/d6cbc59ea0_params.pyro /tmp/tmpaa98w4by/d6cbc59ea0_train.loaderstate /tmp/tmpaa98w4by/d6cbc59ea0_test.loaderstate /tmp/tmpaa98w4by/d6cbc59ea0_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: [0.06 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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:52:21 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-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: [1.33 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 16:02:11 Total MCKP estimation time = 557.78 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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-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/2343-Schizophrenia-Hippocampus/2343-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:02:32