cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2275-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-DLPFC/2275-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 7807 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash fab33b8666) cellbender:remove-background: 2024-06-06 15:39:47 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/2275-Bipolar-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: 30791 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2101 cellbender:remove-background: Prior on counts for empty droplets is 97 cellbender:remove-background: Excluding 6580 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24211 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 48 cellbender:remove-background: Using 7807 probable cell barcodes, plus an additional 12193 barcodes, and 19618 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 96 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp58no2szb 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: 4077.6883 cellbender:remove-background: [epoch 002] average training loss: 3368.3339 (14.8 seconds per epoch) cellbender:remove-background: Will checkpoint every 29 epochs cellbender:remove-background: [epoch 003] average training loss: 2954.2037 cellbender:remove-background: [epoch 004] average training loss: 2706.5125 cellbender:remove-background: [epoch 005] average training loss: 2615.9961 cellbender:remove-background: [epoch 005] average test loss: 2644.8570 cellbender:remove-background: [epoch 006] average training loss: 2583.0036 cellbender:remove-background: [epoch 007] average training loss: 2543.4444 cellbender:remove-background: [epoch 008] average training loss: 2526.9569 cellbender:remove-background: [epoch 009] average training loss: 2522.6389 cellbender:remove-background: [epoch 010] average training loss: 2504.1795 cellbender:remove-background: [epoch 010] average test loss: 2488.1131 cellbender:remove-background: [epoch 011] average training loss: 2487.0392 cellbender:remove-background: [epoch 012] average training loss: 2415.6058 cellbender:remove-background: [epoch 013] average training loss: 2385.2402 cellbender:remove-background: [epoch 014] average training loss: 2387.7706 cellbender:remove-background: [epoch 015] average training loss: 2370.3594 cellbender:remove-background: [epoch 015] average test loss: 2383.1385 cellbender:remove-background: [epoch 016] average training loss: 2364.0290 cellbender:remove-background: [epoch 017] average training loss: 2364.6896 cellbender:remove-background: [epoch 018] average training loss: 2359.6795 cellbender:remove-background: [epoch 019] average training loss: 2350.2886 cellbender:remove-background: [epoch 020] average training loss: 2339.9281 cellbender:remove-background: [epoch 020] average test loss: 2354.7118 cellbender:remove-background: [epoch 021] average training loss: 2338.0280 cellbender:remove-background: [epoch 022] average training loss: 2334.6182 cellbender:remove-background: [epoch 023] average training loss: 2329.7485 cellbender:remove-background: [epoch 024] average training loss: 2314.0713 cellbender:remove-background: [epoch 025] average training loss: 2301.0237 cellbender:remove-background: [epoch 025] average test loss: 2287.9745 cellbender:remove-background: [epoch 026] average training loss: 2285.7187 cellbender:remove-background: [epoch 027] average training loss: 2278.4231 cellbender:remove-background: [epoch 028] average training loss: 2274.1788 cellbender:remove-background: [epoch 029] average training loss: 2268.4244 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 030] average training loss: 2267.5824 cellbender:remove-background: [epoch 030] average test loss: 2265.8276 cellbender:remove-background: [epoch 031] average training loss: 2264.2813 cellbender:remove-background: [epoch 032] average training loss: 2264.8124 cellbender:remove-background: [epoch 033] average training loss: 2262.7435 cellbender:remove-background: [epoch 034] average training loss: 2259.9650 cellbender:remove-background: [epoch 035] average training loss: 2259.8949 cellbender:remove-background: [epoch 035] average test loss: 2253.5070 cellbender:remove-background: [epoch 036] average training loss: 2266.4447 cellbender:remove-background: [epoch 037] average training loss: 2264.1666 cellbender:remove-background: [epoch 038] average training loss: 2265.0922 cellbender:remove-background: [epoch 039] average training loss: 2263.9769 cellbender:remove-background: [epoch 040] average training loss: 2266.6260 cellbender:remove-background: [epoch 040] average test loss: 2258.5082 cellbender:remove-background: [epoch 041] average training loss: 2263.8179 cellbender:remove-background: [epoch 042] average training loss: 2268.2725 cellbender:remove-background: [epoch 043] average training loss: 2265.0883 cellbender:remove-background: [epoch 044] average training loss: 2268.0920 cellbender:remove-background: [epoch 045] average training loss: 2268.7505 cellbender:remove-background: [epoch 045] average test loss: 2270.7163 cellbender:remove-background: [epoch 046] average training loss: 2268.0186 cellbender:remove-background: [epoch 047] average training loss: 2269.1626 cellbender:remove-background: [epoch 048] average training loss: 2270.0605 cellbender:remove-background: [epoch 049] average training loss: 2265.7311 cellbender:remove-background: [epoch 050] average training loss: 2269.4553 cellbender:remove-background: [epoch 050] average test loss: 2262.2541 cellbender:remove-background: [epoch 051] average training loss: 2268.5025 cellbender:remove-background: [epoch 052] average training loss: 2270.2564 cellbender:remove-background: [epoch 053] average training loss: 2269.7318 cellbender:remove-background: [epoch 054] average training loss: 2271.8854 cellbender:remove-background: [epoch 055] average training loss: 2265.0798 cellbender:remove-background: [epoch 055] average test loss: 2267.2444 cellbender:remove-background: [epoch 056] average training loss: 2269.3646 cellbender:remove-background: [epoch 057] average training loss: 2268.9007 cellbender:remove-background: [epoch 058] average training loss: 2275.1928 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 059] average training loss: 2276.3282 cellbender:remove-background: [epoch 060] average training loss: 2283.0371 cellbender:remove-background: [epoch 060] average test loss: 2312.1935 cellbender:remove-background: [epoch 061] average training loss: 2272.9896 cellbender:remove-background: [epoch 062] average training loss: 2276.8251 cellbender:remove-background: [epoch 063] average training loss: 2285.3206 cellbender:remove-background: [epoch 064] average training loss: 2295.6939 cellbender:remove-background: [epoch 065] average training loss: 2278.2918 cellbender:remove-background: [epoch 065] average test loss: 2329.2791 cellbender:remove-background: [epoch 066] average training loss: 2279.1429 cellbender:remove-background: [epoch 067] average training loss: 2278.9593 cellbender:remove-background: [epoch 068] average training loss: 2278.2710 cellbender:remove-background: [epoch 069] average training loss: 2281.9045 cellbender:remove-background: [epoch 070] average training loss: 2285.9649 cellbender:remove-background: [epoch 070] average test loss: 2329.7877 cellbender:remove-background: [epoch 071] average training loss: 2284.4145 cellbender:remove-background: [epoch 072] average training loss: 2284.5871 cellbender:remove-background: [epoch 073] average training loss: 2288.6187 cellbender:remove-background: [epoch 074] average training loss: 2291.2620 cellbender:remove-background: [epoch 075] average training loss: 2285.0856 cellbender:remove-background: [epoch 075] average test loss: 2307.5355 cellbender:remove-background: [epoch 076] average training loss: 2277.8163 cellbender:remove-background: [epoch 077] average training loss: 2276.9010 cellbender:remove-background: [epoch 078] average training loss: 2277.8111 cellbender:remove-background: [epoch 079] average training loss: 2281.6331 cellbender:remove-background: [epoch 080] average training loss: 2282.1869 cellbender:remove-background: [epoch 080] average test loss: 2314.8485 cellbender:remove-background: [epoch 081] average training loss: 2284.8234 cellbender:remove-background: [epoch 082] average training loss: 2273.7630 cellbender:remove-background: [epoch 083] average training loss: 2276.2603 cellbender:remove-background: [epoch 084] average training loss: 2278.3831 cellbender:remove-background: [epoch 085] average training loss: 2276.0642 cellbender:remove-background: [epoch 085] average test loss: 2325.9800 cellbender:remove-background: [epoch 086] average training loss: 2272.6491 cellbender:remove-background: [epoch 087] average training loss: 2275.4269 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 088] average training loss: 2270.7221 cellbender:remove-background: [epoch 089] average training loss: 2277.1085 cellbender:remove-background: [epoch 090] average training loss: 2272.1108 cellbender:remove-background: [epoch 090] average test loss: 2307.8253 cellbender:remove-background: [epoch 091] average training loss: 2271.3891 cellbender:remove-background: [epoch 092] average training loss: 2270.8114 cellbender:remove-background: [epoch 093] average training loss: 2272.3694 cellbender:remove-background: [epoch 094] average training loss: 2271.0753 cellbender:remove-background: [epoch 095] average training loss: 2270.2372 cellbender:remove-background: [epoch 095] average test loss: 2330.8353 cellbender:remove-background: [epoch 096] average training loss: 2272.4033 cellbender:remove-background: [epoch 097] average training loss: 2261.8141 cellbender:remove-background: [epoch 098] average training loss: 2260.1088 cellbender:remove-background: [epoch 099] average training loss: 2261.8805 cellbender:remove-background: [epoch 100] average training loss: 2262.8201 cellbender:remove-background: [epoch 100] average test loss: 2290.7933 cellbender:remove-background: [epoch 101] average training loss: 2266.7011 cellbender:remove-background: [epoch 102] average training loss: 2260.4531 cellbender:remove-background: [epoch 103] average training loss: 2261.0207 cellbender:remove-background: [epoch 104] average training loss: 2256.3799 cellbender:remove-background: [epoch 105] average training loss: 2259.9119 cellbender:remove-background: [epoch 105] average test loss: 2299.9935 cellbender:remove-background: [epoch 106] average training loss: 2260.2941 cellbender:remove-background: [epoch 107] average training loss: 2260.1251 cellbender:remove-background: [epoch 108] average training loss: 2257.3999 cellbender:remove-background: [epoch 109] average training loss: 2257.9531 cellbender:remove-background: [epoch 110] average training loss: 2261.2285 cellbender:remove-background: [epoch 110] average test loss: 2299.0516 cellbender:remove-background: [epoch 111] average training loss: 2262.0413 cellbender:remove-background: [epoch 112] average training loss: 2257.6649 cellbender:remove-background: [epoch 113] average training loss: 2256.1487 cellbender:remove-background: [epoch 114] average training loss: 2256.9556 cellbender:remove-background: [epoch 115] average training loss: 2257.3567 cellbender:remove-background: [epoch 115] average test loss: 2297.2903 cellbender:remove-background: [epoch 116] average training loss: 2260.0626 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 117] average training loss: 2252.8355 cellbender:remove-background: [epoch 118] average training loss: 2253.1231 cellbender:remove-background: [epoch 119] average training loss: 2255.6537 cellbender:remove-background: [epoch 120] average training loss: 2255.2671 cellbender:remove-background: [epoch 120] average test loss: 2294.1245 cellbender:remove-background: [epoch 121] average training loss: 2254.2700 cellbender:remove-background: [epoch 122] average training loss: 2255.7791 cellbender:remove-background: [epoch 123] average training loss: 2258.0846 cellbender:remove-background: [epoch 124] average training loss: 2255.0250 cellbender:remove-background: [epoch 125] average training loss: 2252.1867 cellbender:remove-background: [epoch 125] average test loss: 2291.7392 cellbender:remove-background: [epoch 126] average training loss: 2257.4017 cellbender:remove-background: [epoch 127] average training loss: 2253.3979 cellbender:remove-background: [epoch 128] average training loss: 2251.3747 cellbender:remove-background: [epoch 129] average training loss: 2250.2617 cellbender:remove-background: [epoch 130] average training loss: 2248.8164 cellbender:remove-background: [epoch 130] average test loss: 2290.3851 cellbender:remove-background: [epoch 131] average training loss: 2251.5396 cellbender:remove-background: [epoch 132] average training loss: 2253.2037 cellbender:remove-background: [epoch 133] average training loss: 2250.4013 cellbender:remove-background: [epoch 134] average training loss: 2251.3952 cellbender:remove-background: [epoch 135] average training loss: 2251.6083 cellbender:remove-background: [epoch 135] average test loss: 2288.4454 cellbender:remove-background: [epoch 136] average training loss: 2250.5960 cellbender:remove-background: [epoch 137] average training loss: 2250.8862 cellbender:remove-background: [epoch 138] average training loss: 2249.3032 cellbender:remove-background: [epoch 139] average training loss: 2250.8514 cellbender:remove-background: [epoch 140] average training loss: 2250.6865 cellbender:remove-background: [epoch 140] average test loss: 2289.0685 cellbender:remove-background: [epoch 141] average training loss: 2251.8661 cellbender:remove-background: [epoch 142] average training loss: 2249.7095 cellbender:remove-background: [epoch 143] average training loss: 2248.6564 cellbender:remove-background: [epoch 144] average training loss: 2249.4579 cellbender:remove-background: [epoch 145] average training loss: 2247.8243 cellbender:remove-background: [epoch 145] average test loss: 2294.4363 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 146] average training loss: 2252.9116 cellbender:remove-background: [epoch 147] average training loss: 2251.7181 cellbender:remove-background: [epoch 148] average training loss: 2251.1509 cellbender:remove-background: [epoch 149] average training loss: 2249.3330 cellbender:remove-background: [epoch 150] average training loss: 2250.0845 cellbender:remove-background: [epoch 150] average test loss: 2294.8348 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/2275-Bipolar-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:25:05 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpdw80qgwx cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpdw80qgwx /tmp/tmpdw80qgwx/fab33b8666_random.pyro /tmp/tmpdw80qgwx/fab33b8666_random.cuda /tmp/tmpdw80qgwx/fab33b8666_model.torch /tmp/tmpdw80qgwx/fab33b8666_optim.torch /tmp/tmpdw80qgwx/fab33b8666_optim.pyro /tmp/tmpdw80qgwx/fab33b8666_params.pyro /tmp/tmpdw80qgwx/fab33b8666_train.loaderstate /tmp/tmpdw80qgwx/fab33b8666_test.loaderstate /tmp/tmpdw80qgwx/fab33b8666_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 (1/82) cellbender:remove-background: [0.07 mins per chunk] cellbender:remove-background: Working on chunk (2/82) cellbender:remove-background: Working on chunk (3/82) cellbender:remove-background: Working on chunk (4/82) cellbender:remove-background: Working on chunk (5/82) cellbender:remove-background: Working on chunk (6/82) cellbender:remove-background: Working on chunk (7/82) cellbender:remove-background: Working on chunk (8/82) cellbender:remove-background: Working on chunk (9/82) cellbender:remove-background: Working on chunk (10/82) cellbender:remove-background: Working on chunk (11/82) cellbender:remove-background: Working on chunk (12/82) cellbender:remove-background: Working on chunk (13/82) cellbender:remove-background: Working on chunk (14/82) cellbender:remove-background: Working on chunk (15/82) cellbender:remove-background: Working on chunk (16/82) cellbender:remove-background: Working on chunk (17/82) cellbender:remove-background: Working on chunk (18/82) cellbender:remove-background: Working on chunk (19/82) cellbender:remove-background: Working on chunk (20/82) cellbender:remove-background: Working on chunk (21/82) cellbender:remove-background: Working on chunk (22/82) cellbender:remove-background: Working on chunk (23/82) cellbender:remove-background: Working on chunk (24/82) cellbender:remove-background: Working on chunk (25/82) cellbender:remove-background: Working on chunk (26/82) cellbender:remove-background: Working on chunk (27/82) cellbender:remove-background: Working on chunk (28/82) cellbender:remove-background: Working on chunk (29/82) cellbender:remove-background: Working on chunk (30/82) cellbender:remove-background: Working on chunk (31/82) cellbender:remove-background: Working on chunk (32/82) cellbender:remove-background: Working on chunk (33/82) cellbender:remove-background: Working on chunk (34/82) cellbender:remove-background: Working on chunk (35/82) cellbender:remove-background: Working on chunk (36/82) cellbender:remove-background: Working on chunk (37/82) cellbender:remove-background: Working on chunk (38/82) cellbender:remove-background: Working on chunk (39/82) cellbender:remove-background: Working on chunk (40/82) cellbender:remove-background: Working on chunk (41/82) cellbender:remove-background: Working on chunk (42/82) cellbender:remove-background: Working on chunk (43/82) cellbender:remove-background: Working on chunk (44/82) cellbender:remove-background: Working on chunk (45/82) cellbender:remove-background: Working on chunk (46/82) cellbender:remove-background: Working on chunk (47/82) cellbender:remove-background: Working on chunk (48/82) cellbender:remove-background: Working on chunk (49/82) cellbender:remove-background: Working on chunk (50/82) cellbender:remove-background: Working on chunk (51/82) cellbender:remove-background: Working on chunk (52/82) cellbender:remove-background: Working on chunk (53/82) cellbender:remove-background: Working on chunk (54/82) cellbender:remove-background: Working on chunk (55/82) cellbender:remove-background: Working on chunk (56/82) cellbender:remove-background: Working on chunk (57/82) cellbender:remove-background: Working on chunk (58/82) cellbender:remove-background: Working on chunk (59/82) cellbender:remove-background: Working on chunk (60/82) cellbender:remove-background: Working on chunk (61/82) cellbender:remove-background: Working on chunk (62/82) cellbender:remove-background: Working on chunk (63/82) cellbender:remove-background: Working on chunk (64/82) cellbender:remove-background: Working on chunk (65/82) cellbender:remove-background: Working on chunk (66/82) cellbender:remove-background: Working on chunk (67/82) cellbender:remove-background: Working on chunk (68/82) cellbender:remove-background: Working on chunk (69/82) cellbender:remove-background: Working on chunk (70/82) cellbender:remove-background: Working on chunk (71/82) cellbender:remove-background: Working on chunk (72/82) cellbender:remove-background: Working on chunk (73/82) cellbender:remove-background: Working on chunk (74/82) cellbender:remove-background: Working on chunk (75/82) cellbender:remove-background: Working on chunk (76/82) cellbender:remove-background: Working on chunk (77/82) cellbender:remove-background: Working on chunk (78/82) cellbender:remove-background: Working on chunk (79/82) cellbender:remove-background: Working on chunk (80/82) cellbender:remove-background: Working on chunk (81/82) cellbender:remove-background: Working on chunk (82/82) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-DLPFC/2275-Bipolar-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/2275-Bipolar-DLPFC/2275-Bipolar-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:32:42 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-DLPFC/2275-Bipolar-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2275-Bipolar-DLPFC/2275-Bipolar-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: [1.44 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 16:43:21 Total MCKP estimation time = 603.61 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/2275-Bipolar-DLPFC/2275-Bipolar-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/2275-Bipolar-DLPFC/2275-Bipolar-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/2275-Bipolar-DLPFC/2275-Bipolar-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/2275-Bipolar-DLPFC/2275-Bipolar-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:43:46