cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2781-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 10188 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 9a0fa141b8) cellbender:remove-background: 2024-06-06 14:48:29 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/2781-Control-DLPFC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 30804 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2039 cellbender:remove-background: Prior on counts for empty droplets is 92 cellbender:remove-background: Excluding 7873 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22931 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 46 cellbender:remove-background: Using 10188 probable cell barcodes, plus an additional 9812 barcodes, and 13724 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 91 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpcep0uu7v cellbender:remove-background: No saved checkpoint. cellbender:remove-background: No checkpoint loaded. cellbender:remove-background: Running inference... /home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/torch/distributions/gamma.py:77: UserWarning: Specified kernel cache directory could not be created! This disables kernel caching. Specified directory is /home/users/guozy/.cache/torch/kernels. This warning will appear only once per process. (Triggered internally at ../aten/src/ATen/native/cuda/jit_utils.cpp:1443.) self.rate * value - torch.lgamma(self.concentration)) cellbender:remove-background: [epoch 001] average training loss: 4342.6469 cellbender:remove-background: [epoch 002] average training loss: 3602.3078 (6.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 65 epochs cellbender:remove-background: [epoch 003] average training loss: 3155.4411 cellbender:remove-background: [epoch 004] average training loss: 2882.6035 cellbender:remove-background: [epoch 005] average training loss: 2783.5505 cellbender:remove-background: [epoch 005] average test loss: 2762.0109 cellbender:remove-background: [epoch 006] average training loss: 2746.8065 cellbender:remove-background: [epoch 007] average training loss: 2723.9101 cellbender:remove-background: [epoch 008] average training loss: 2707.4004 cellbender:remove-background: [epoch 009] average training loss: 2704.7889 cellbender:remove-background: [epoch 010] average training loss: 2690.6959 cellbender:remove-background: [epoch 010] average test loss: 2679.0469 cellbender:remove-background: [epoch 011] average training loss: 2688.8508 cellbender:remove-background: [epoch 012] average training loss: 2677.1386 cellbender:remove-background: [epoch 013] average training loss: 2632.9141 cellbender:remove-background: [epoch 014] average training loss: 2615.4125 cellbender:remove-background: [epoch 015] average training loss: 2601.0026 cellbender:remove-background: [epoch 015] average test loss: 2598.7781 cellbender:remove-background: [epoch 016] average training loss: 2596.9611 cellbender:remove-background: [epoch 017] average training loss: 2596.0438 cellbender:remove-background: [epoch 018] average training loss: 2588.5241 cellbender:remove-background: [epoch 019] average training loss: 2581.6165 cellbender:remove-background: [epoch 020] average training loss: 2573.1795 cellbender:remove-background: [epoch 020] average test loss: 2560.5733 cellbender:remove-background: [epoch 021] average training loss: 2570.8725 cellbender:remove-background: [epoch 022] average training loss: 2568.6758 cellbender:remove-background: [epoch 023] average training loss: 2567.9300 cellbender:remove-background: [epoch 024] average training loss: 2566.7349 cellbender:remove-background: [epoch 025] average training loss: 2563.1998 cellbender:remove-background: [epoch 025] average test loss: 2542.5999 cellbender:remove-background: [epoch 026] average training loss: 2559.5531 cellbender:remove-background: [epoch 027] average training loss: 2551.5047 cellbender:remove-background: [epoch 028] average training loss: 2542.2030 cellbender:remove-background: [epoch 029] average training loss: 2534.6214 cellbender:remove-background: [epoch 030] average training loss: 2534.3774 cellbender:remove-background: [epoch 030] average test loss: 2505.8297 cellbender:remove-background: [epoch 031] average training loss: 2531.2131 cellbender:remove-background: [epoch 032] average training loss: 2529.5301 cellbender:remove-background: [epoch 033] average training loss: 2527.4783 cellbender:remove-background: [epoch 034] average training loss: 2526.6617 cellbender:remove-background: [epoch 035] average training loss: 2525.3807 cellbender:remove-background: [epoch 035] average test loss: 2488.0570 cellbender:remove-background: [epoch 036] average training loss: 2521.9349 cellbender:remove-background: [epoch 037] average training loss: 2522.8067 cellbender:remove-background: [epoch 038] average training loss: 2519.3753 cellbender:remove-background: [epoch 039] average training loss: 2520.6015 cellbender:remove-background: [epoch 040] average training loss: 2520.5336 cellbender:remove-background: [epoch 040] average test loss: 2488.5054 cellbender:remove-background: [epoch 041] average training loss: 2519.3960 cellbender:remove-background: [epoch 042] average training loss: 2516.1163 cellbender:remove-background: [epoch 043] average training loss: 2520.4255 cellbender:remove-background: [epoch 044] average training loss: 2520.3106 cellbender:remove-background: [epoch 045] average training loss: 2518.1699 cellbender:remove-background: [epoch 045] average test loss: 2491.8610 cellbender:remove-background: [epoch 046] average training loss: 2518.9137 cellbender:remove-background: [epoch 047] average training loss: 2515.6560 cellbender:remove-background: [epoch 048] average training loss: 2516.5428 cellbender:remove-background: [epoch 049] average training loss: 2516.1148 cellbender:remove-background: [epoch 050] average training loss: 2514.0009 cellbender:remove-background: [epoch 050] average test loss: 2481.7260 cellbender:remove-background: [epoch 051] average training loss: 2510.2059 cellbender:remove-background: [epoch 052] average training loss: 2512.6599 cellbender:remove-background: [epoch 053] average training loss: 2508.5917 cellbender:remove-background: [epoch 054] average training loss: 2509.1506 cellbender:remove-background: [epoch 055] average training loss: 2510.8933 cellbender:remove-background: [epoch 055] average test loss: 2470.2480 cellbender:remove-background: [epoch 056] average training loss: 2510.3272 cellbender:remove-background: [epoch 057] average training loss: 2511.0293 cellbender:remove-background: [epoch 058] average training loss: 2510.9130 cellbender:remove-background: [epoch 059] average training loss: 2511.9852 cellbender:remove-background: [epoch 060] average training loss: 2506.7131 cellbender:remove-background: [epoch 060] average test loss: 2473.5125 cellbender:remove-background: [epoch 061] average training loss: 2507.0817 cellbender:remove-background: [epoch 062] average training loss: 2506.9823 cellbender:remove-background: [epoch 063] average training loss: 2509.7844 cellbender:remove-background: [epoch 064] average training loss: 2509.3977 cellbender:remove-background: [epoch 065] average training loss: 2507.5502 cellbender:remove-background: [epoch 065] average test loss: 2471.2636 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/2781-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 066] average training loss: 2508.9603 cellbender:remove-background: [epoch 067] average training loss: 2505.5996 cellbender:remove-background: [epoch 068] average training loss: 2507.2122 cellbender:remove-background: [epoch 069] average training loss: 2502.0293 cellbender:remove-background: [epoch 070] average training loss: 2502.6376 cellbender:remove-background: [epoch 070] average test loss: 2480.9667 cellbender:remove-background: [epoch 071] average training loss: 2501.0402 cellbender:remove-background: [epoch 072] average training loss: 2503.6099 cellbender:remove-background: [epoch 073] average training loss: 2504.3484 cellbender:remove-background: [epoch 074] average training loss: 2503.4201 cellbender:remove-background: [epoch 075] average training loss: 2502.8610 cellbender:remove-background: [epoch 075] average test loss: 2480.2111 cellbender:remove-background: [epoch 076] average training loss: 2499.6568 cellbender:remove-background: [epoch 077] average training loss: 2502.8933 cellbender:remove-background: [epoch 078] average training loss: 2503.0678 cellbender:remove-background: [epoch 079] average training loss: 2499.8620 cellbender:remove-background: [epoch 080] average training loss: 2502.1934 cellbender:remove-background: [epoch 080] average test loss: 2473.3093 cellbender:remove-background: [epoch 081] average training loss: 2501.7853 cellbender:remove-background: [epoch 082] average training loss: 2498.7204 cellbender:remove-background: [epoch 083] average training loss: 2501.3520 cellbender:remove-background: [epoch 084] average training loss: 2501.8715 cellbender:remove-background: [epoch 085] average training loss: 2499.6580 cellbender:remove-background: [epoch 085] average test loss: 2469.3050 cellbender:remove-background: [epoch 086] average training loss: 2497.6835 cellbender:remove-background: [epoch 087] average training loss: 2501.3463 cellbender:remove-background: [epoch 088] average training loss: 2499.6371 cellbender:remove-background: [epoch 089] average training loss: 2496.5194 cellbender:remove-background: [epoch 090] average training loss: 2499.3402 cellbender:remove-background: [epoch 090] average test loss: 2471.7382 cellbender:remove-background: [epoch 091] average training loss: 2497.5159 cellbender:remove-background: [epoch 092] average training loss: 2499.9005 cellbender:remove-background: [epoch 093] average training loss: 2497.2571 cellbender:remove-background: [epoch 094] average training loss: 2494.4819 cellbender:remove-background: [epoch 095] average training loss: 2496.7944 cellbender:remove-background: [epoch 095] average test loss: 2490.9743 cellbender:remove-background: [epoch 096] average training loss: 2497.6977 cellbender:remove-background: [epoch 097] average training loss: 2498.4946 cellbender:remove-background: [epoch 098] average training loss: 2495.9091 cellbender:remove-background: [epoch 099] average training loss: 2494.8060 cellbender:remove-background: [epoch 100] average training loss: 2497.9219 cellbender:remove-background: [epoch 100] average test loss: 2483.5098 cellbender:remove-background: [epoch 101] average training loss: 2494.7089 cellbender:remove-background: [epoch 102] average training loss: 2494.0556 cellbender:remove-background: [epoch 103] average training loss: 2494.5265 cellbender:remove-background: [epoch 104] average training loss: 2495.7884 cellbender:remove-background: [epoch 105] average training loss: 2497.0326 cellbender:remove-background: [epoch 105] average test loss: 2466.2703 cellbender:remove-background: [epoch 106] average training loss: 2493.6728 cellbender:remove-background: [epoch 107] average training loss: 2493.8081 cellbender:remove-background: [epoch 108] average training loss: 2494.5514 cellbender:remove-background: [epoch 109] average training loss: 2492.9134 cellbender:remove-background: [epoch 110] average training loss: 2492.3013 cellbender:remove-background: [epoch 110] average test loss: 2475.6120 cellbender:remove-background: [epoch 111] average training loss: 2492.7100 cellbender:remove-background: [epoch 112] average training loss: 2492.1841 cellbender:remove-background: [epoch 113] average training loss: 2494.0730 cellbender:remove-background: [epoch 114] average training loss: 2493.8931 cellbender:remove-background: [epoch 115] average training loss: 2493.2798 cellbender:remove-background: [epoch 115] average test loss: 2476.0923 cellbender:remove-background: [epoch 116] average training loss: 2492.1826 cellbender:remove-background: [epoch 117] average training loss: 2490.2160 cellbender:remove-background: [epoch 118] average training loss: 2491.8767 cellbender:remove-background: [epoch 119] average training loss: 2488.3262 cellbender:remove-background: [epoch 120] average training loss: 2491.3090 cellbender:remove-background: [epoch 120] average test loss: 2463.6713 cellbender:remove-background: [epoch 121] average training loss: 2489.9577 cellbender:remove-background: [epoch 122] average training loss: 2488.8358 cellbender:remove-background: [epoch 123] average training loss: 2489.6727 cellbender:remove-background: [epoch 124] average training loss: 2489.4618 cellbender:remove-background: [epoch 125] average training loss: 2490.5872 cellbender:remove-background: [epoch 125] average test loss: 2476.2797 cellbender:remove-background: [epoch 126] average training loss: 2491.0076 cellbender:remove-background: [epoch 127] average training loss: 2490.4805 cellbender:remove-background: [epoch 128] average training loss: 2491.4597 cellbender:remove-background: [epoch 129] average training loss: 2488.9046 cellbender:remove-background: [epoch 130] average training loss: 2492.1548 cellbender:remove-background: [epoch 130] average test loss: 2462.7808 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/2781-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 131] average training loss: 2492.1285 cellbender:remove-background: [epoch 132] average training loss: 2491.0510 cellbender:remove-background: [epoch 133] average training loss: 2487.4273 cellbender:remove-background: [epoch 134] average training loss: 2489.8561 cellbender:remove-background: [epoch 135] average training loss: 2490.8887 cellbender:remove-background: [epoch 135] average test loss: 2473.5206 cellbender:remove-background: [epoch 136] average training loss: 2490.7043 cellbender:remove-background: [epoch 137] average training loss: 2490.1155 cellbender:remove-background: [epoch 138] average training loss: 2489.4748 cellbender:remove-background: [epoch 139] average training loss: 2489.3371 cellbender:remove-background: [epoch 140] average training loss: 2488.3346 cellbender:remove-background: [epoch 140] average test loss: 2480.3264 cellbender:remove-background: [epoch 141] average training loss: 2489.8126 cellbender:remove-background: [epoch 142] average training loss: 2488.9017 cellbender:remove-background: [epoch 143] average training loss: 2489.8714 cellbender:remove-background: [epoch 144] average training loss: 2489.3232 cellbender:remove-background: [epoch 145] average training loss: 2489.8798 cellbender:remove-background: [epoch 145] average test loss: 2472.6544 cellbender:remove-background: [epoch 146] average training loss: 2492.4333 cellbender:remove-background: [epoch 147] average training loss: 2489.3668 cellbender:remove-background: [epoch 148] average training loss: 2489.3819 cellbender:remove-background: [epoch 149] average training loss: 2488.6153 cellbender:remove-background: [epoch 150] average training loss: 2490.0562 cellbender:remove-background: [epoch 150] average test loss: 2474.7234 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/2781-Control-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:07:12 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpy94lyukc cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpy94lyukc /tmp/tmpy94lyukc/9a0fa141b8_random.pyro /tmp/tmpy94lyukc/9a0fa141b8_random.cuda /tmp/tmpy94lyukc/9a0fa141b8_model.torch /tmp/tmpy94lyukc/9a0fa141b8_optim.torch /tmp/tmpy94lyukc/9a0fa141b8_optim.pyro /tmp/tmpy94lyukc/9a0fa141b8_params.pyro /tmp/tmpy94lyukc/9a0fa141b8_train.loaderstate /tmp/tmpy94lyukc/9a0fa141b8_test.loaderstate /tmp/tmpy94lyukc/9a0fa141b8_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 (1/96) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/96) cellbender:remove-background: Working on chunk (3/96) cellbender:remove-background: Working on chunk (4/96) cellbender:remove-background: Working on chunk (5/96) cellbender:remove-background: Working on chunk (6/96) cellbender:remove-background: Working on chunk (7/96) cellbender:remove-background: Working on chunk (8/96) cellbender:remove-background: Working on chunk (9/96) cellbender:remove-background: Working on chunk (10/96) cellbender:remove-background: Working on chunk (11/96) cellbender:remove-background: Working on chunk (12/96) cellbender:remove-background: Working on chunk (13/96) cellbender:remove-background: Working on chunk (14/96) cellbender:remove-background: Working on chunk (15/96) cellbender:remove-background: Working on chunk (16/96) cellbender:remove-background: Working on chunk (17/96) cellbender:remove-background: Working on chunk (18/96) cellbender:remove-background: Working on chunk (19/96) cellbender:remove-background: Working on chunk (20/96) cellbender:remove-background: Working on chunk (21/96) cellbender:remove-background: Working on chunk (22/96) cellbender:remove-background: Working on chunk (23/96) cellbender:remove-background: Working on chunk (24/96) cellbender:remove-background: Working on chunk (25/96) cellbender:remove-background: Working on chunk (26/96) cellbender:remove-background: Working on chunk (27/96) cellbender:remove-background: Working on chunk (28/96) cellbender:remove-background: Working on chunk (29/96) cellbender:remove-background: Working on chunk (30/96) cellbender:remove-background: Working on chunk (31/96) cellbender:remove-background: Working on chunk (32/96) cellbender:remove-background: Working on chunk (33/96) cellbender:remove-background: Working on chunk (34/96) cellbender:remove-background: Working on chunk (35/96) cellbender:remove-background: Working on chunk (36/96) cellbender:remove-background: Working on chunk (37/96) cellbender:remove-background: Working on chunk (38/96) cellbender:remove-background: Working on chunk (39/96) cellbender:remove-background: Working on chunk (40/96) cellbender:remove-background: Working on chunk (41/96) cellbender:remove-background: Working on chunk (42/96) cellbender:remove-background: Working on chunk (43/96) cellbender:remove-background: Working on chunk (44/96) cellbender:remove-background: Working on chunk (45/96) cellbender:remove-background: Working on chunk (46/96) cellbender:remove-background: Working on chunk (47/96) cellbender:remove-background: Working on chunk (48/96) cellbender:remove-background: Working on chunk (49/96) cellbender:remove-background: Working on chunk (50/96) cellbender:remove-background: Working on chunk (51/96) cellbender:remove-background: Working on chunk (52/96) cellbender:remove-background: Working on chunk (53/96) cellbender:remove-background: Working on chunk (54/96) cellbender:remove-background: Working on chunk (55/96) cellbender:remove-background: Working on chunk (56/96) cellbender:remove-background: Working on chunk (57/96) cellbender:remove-background: Working on chunk (58/96) cellbender:remove-background: Working on chunk (59/96) cellbender:remove-background: Working on chunk (60/96) cellbender:remove-background: Working on chunk (61/96) cellbender:remove-background: Working on chunk (62/96) cellbender:remove-background: Working on chunk (63/96) cellbender:remove-background: Working on chunk (64/96) cellbender:remove-background: Working on chunk (65/96) cellbender:remove-background: Working on chunk (66/96) cellbender:remove-background: Working on chunk (67/96) cellbender:remove-background: Working on chunk (68/96) cellbender:remove-background: Working on chunk (69/96) cellbender:remove-background: Working on chunk (70/96) cellbender:remove-background: Working on chunk (71/96) cellbender:remove-background: Working on chunk (72/96) cellbender:remove-background: Working on chunk (73/96) cellbender:remove-background: Working on chunk (74/96) cellbender:remove-background: Working on chunk (75/96) cellbender:remove-background: Working on chunk (76/96) cellbender:remove-background: Working on chunk (77/96) cellbender:remove-background: Working on chunk (78/96) cellbender:remove-background: Working on chunk (79/96) cellbender:remove-background: Working on chunk (80/96) cellbender:remove-background: Working on chunk (81/96) cellbender:remove-background: Working on chunk (82/96) cellbender:remove-background: Working on chunk (83/96) cellbender:remove-background: Working on chunk (84/96) cellbender:remove-background: Working on chunk (85/96) cellbender:remove-background: Working on chunk (86/96) cellbender:remove-background: Working on chunk (87/96) cellbender:remove-background: Working on chunk (88/96) cellbender:remove-background: Working on chunk (89/96) cellbender:remove-background: Working on chunk (90/96) cellbender:remove-background: Working on chunk (91/96) cellbender:remove-background: Working on chunk (92/96) cellbender:remove-background: Working on chunk (93/96) cellbender:remove-background: Working on chunk (94/96) cellbender:remove-background: Working on chunk (95/96) cellbender:remove-background: Working on chunk (96/96) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:12:25 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.42 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 15:22:42 Total MCKP estimation time = 592.76 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/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-DLPFC/2781-Control-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:22:59