cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1041-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1041-Schizophrenia-DLPFC/1041-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 8212 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 7ba4405a85) cellbender:remove-background: 2024-06-06 15:04:05 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/1041-Schizophrenia-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: 32956 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 7397 cellbender:remove-background: Prior on counts for empty droplets is 253 cellbender:remove-background: Excluding 8431 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24525 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 126 cellbender:remove-background: Using 8212 probable cell barcodes, plus an additional 11788 barcodes, and 28547 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 250 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp2o5md4xu 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: 9865.5247 cellbender:remove-background: [epoch 002] average training loss: 7581.0322 (5.7 seconds per epoch) cellbender:remove-background: Will checkpoint every 74 epochs cellbender:remove-background: [epoch 003] average training loss: 6409.9862 cellbender:remove-background: [epoch 004] average training loss: 5716.8647 cellbender:remove-background: [epoch 005] average training loss: 5530.6459 cellbender:remove-background: [epoch 005] average test loss: 5637.2848 cellbender:remove-background: [epoch 006] average training loss: 5494.0252 cellbender:remove-background: [epoch 007] average training loss: 5416.9141 cellbender:remove-background: [epoch 008] average training loss: 5340.0217 cellbender:remove-background: [epoch 009] average training loss: 5309.4227 cellbender:remove-background: [epoch 010] average training loss: 5081.1905 cellbender:remove-background: [epoch 010] average test loss: 5271.4268 cellbender:remove-background: [epoch 011] average training loss: 4942.7544 cellbender:remove-background: [epoch 012] average training loss: 4899.8680 cellbender:remove-background: [epoch 013] average training loss: 4851.6751 cellbender:remove-background: [epoch 014] average training loss: 4847.4846 cellbender:remove-background: [epoch 015] average training loss: 4793.2292 cellbender:remove-background: [epoch 015] average test loss: 4872.5894 cellbender:remove-background: [epoch 016] average training loss: 4767.6799 cellbender:remove-background: [epoch 017] average training loss: 4776.6760 cellbender:remove-background: [epoch 018] average training loss: 4768.4993 cellbender:remove-background: [epoch 019] average training loss: 4742.2137 cellbender:remove-background: [epoch 020] average training loss: 4714.4706 cellbender:remove-background: [epoch 020] average test loss: 4772.9626 cellbender:remove-background: [epoch 021] average training loss: 4713.9074 cellbender:remove-background: [epoch 022] average training loss: 4711.8730 cellbender:remove-background: [epoch 023] average training loss: 4704.3430 cellbender:remove-background: [epoch 024] average training loss: 4682.4937 cellbender:remove-background: [epoch 025] average training loss: 4665.4533 cellbender:remove-background: [epoch 025] average test loss: 4677.9625 cellbender:remove-background: [epoch 026] average training loss: 4622.3967 cellbender:remove-background: [epoch 027] average training loss: 4606.0039 cellbender:remove-background: [epoch 028] average training loss: 4595.2604 cellbender:remove-background: [epoch 029] average training loss: 4582.9981 cellbender:remove-background: [epoch 030] average training loss: 4578.3151 cellbender:remove-background: [epoch 030] average test loss: 4567.9495 cellbender:remove-background: [epoch 031] average training loss: 4565.8097 cellbender:remove-background: [epoch 032] average training loss: 4570.3757 cellbender:remove-background: [epoch 033] average training loss: 4558.5780 cellbender:remove-background: [epoch 034] average training loss: 4563.9742 cellbender:remove-background: [epoch 035] average training loss: 4557.5478 cellbender:remove-background: [epoch 035] average test loss: 4573.2369 cellbender:remove-background: [epoch 036] average training loss: 4554.3053 cellbender:remove-background: [epoch 037] average training loss: 4557.2999 cellbender:remove-background: [epoch 038] average training loss: 4562.5104 cellbender:remove-background: [epoch 039] average training loss: 4555.7057 cellbender:remove-background: [epoch 040] average training loss: 4556.1882 cellbender:remove-background: [epoch 040] average test loss: 4551.6784 cellbender:remove-background: [epoch 041] average training loss: 4550.4007 cellbender:remove-background: [epoch 042] average training loss: 4548.1006 cellbender:remove-background: [epoch 043] average training loss: 4543.9428 cellbender:remove-background: [epoch 044] average training loss: 4541.7700 cellbender:remove-background: [epoch 045] average training loss: 4539.0494 cellbender:remove-background: [epoch 045] average test loss: 4525.3220 cellbender:remove-background: [epoch 046] average training loss: 4540.9443 cellbender:remove-background: [epoch 047] average training loss: 4545.3711 cellbender:remove-background: [epoch 048] average training loss: 4543.4231 cellbender:remove-background: [epoch 049] average training loss: 4540.7781 cellbender:remove-background: [epoch 050] average training loss: 4534.2647 cellbender:remove-background: [epoch 050] average test loss: 4561.5393 cellbender:remove-background: [epoch 051] average training loss: 4534.6184 cellbender:remove-background: [epoch 052] average training loss: 4532.3334 cellbender:remove-background: [epoch 053] average training loss: 4531.3163 cellbender:remove-background: [epoch 054] average training loss: 4530.2473 cellbender:remove-background: [epoch 055] average training loss: 4528.7609 cellbender:remove-background: [epoch 055] average test loss: 4520.6991 cellbender:remove-background: [epoch 056] average training loss: 4529.0006 cellbender:remove-background: [epoch 057] average training loss: 4542.7129 cellbender:remove-background: [epoch 058] average training loss: 4530.2247 cellbender:remove-background: [epoch 059] average training loss: 4535.8112 cellbender:remove-background: [epoch 060] average training loss: 4525.4030 cellbender:remove-background: [epoch 060] average test loss: 4520.4816 cellbender:remove-background: [epoch 061] average training loss: 4536.0762 cellbender:remove-background: [epoch 062] average training loss: 4526.2222 cellbender:remove-background: [epoch 063] average training loss: 4529.7641 cellbender:remove-background: [epoch 064] average training loss: 4523.1679 cellbender:remove-background: [epoch 065] average training loss: 4524.4958 cellbender:remove-background: [epoch 065] average test loss: 4515.6741 cellbender:remove-background: [epoch 066] average training loss: 4537.0138 cellbender:remove-background: [epoch 067] average training loss: 4518.2470 cellbender:remove-background: [epoch 068] average training loss: 4520.3024 cellbender:remove-background: [epoch 069] average training loss: 4525.3360 cellbender:remove-background: [epoch 070] average training loss: 4519.9978 cellbender:remove-background: [epoch 070] average test loss: 4542.0798 cellbender:remove-background: [epoch 071] average training loss: 4517.4249 cellbender:remove-background: [epoch 072] average training loss: 4506.7188 cellbender:remove-background: [epoch 073] average training loss: 4499.2361 cellbender:remove-background: [epoch 074] average training loss: 4496.0748 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/1041-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 075] average training loss: 4496.4427 cellbender:remove-background: [epoch 075] average test loss: 4490.2070 cellbender:remove-background: [epoch 076] average training loss: 4500.5138 cellbender:remove-background: [epoch 077] average training loss: 4499.2978 cellbender:remove-background: [epoch 078] average training loss: 4504.7821 cellbender:remove-background: [epoch 079] average training loss: 4493.9766 cellbender:remove-background: [epoch 080] average training loss: 4497.3899 cellbender:remove-background: [epoch 080] average test loss: 4512.8503 cellbender:remove-background: [epoch 081] average training loss: 4496.6040 cellbender:remove-background: [epoch 082] average training loss: 4498.5287 cellbender:remove-background: [epoch 083] average training loss: 4498.4425 cellbender:remove-background: [epoch 084] average training loss: 4509.9421 cellbender:remove-background: [epoch 085] average training loss: 4498.4920 cellbender:remove-background: [epoch 085] average test loss: 4554.8208 cellbender:remove-background: [epoch 086] average training loss: 4495.9407 cellbender:remove-background: [epoch 087] average training loss: 4494.9069 cellbender:remove-background: [epoch 088] average training loss: 4501.4513 cellbender:remove-background: [epoch 089] average training loss: 4501.0773 cellbender:remove-background: [epoch 090] average training loss: 4505.4893 cellbender:remove-background: [epoch 090] average test loss: 4547.9915 cellbender:remove-background: [epoch 091] average training loss: 4502.6882 cellbender:remove-background: [epoch 092] average training loss: 4497.6586 cellbender:remove-background: [epoch 093] average training loss: 4498.5608 cellbender:remove-background: [epoch 094] average training loss: 4495.1056 cellbender:remove-background: [epoch 095] average training loss: 4497.7221 cellbender:remove-background: [epoch 095] average test loss: 4505.0962 cellbender:remove-background: [epoch 096] average training loss: 4502.7020 cellbender:remove-background: [epoch 097] average training loss: 4494.2314 cellbender:remove-background: [epoch 098] average training loss: 4496.1548 cellbender:remove-background: [epoch 099] average training loss: 4499.4307 cellbender:remove-background: [epoch 100] average training loss: 4497.0952 cellbender:remove-background: [epoch 100] average test loss: 4534.7768 cellbender:remove-background: [epoch 101] average training loss: 4486.2525 cellbender:remove-background: [epoch 102] average training loss: 4486.8052 cellbender:remove-background: [epoch 103] average training loss: 4488.8341 cellbender:remove-background: [epoch 104] average training loss: 4484.1011 cellbender:remove-background: [epoch 105] average training loss: 4486.0781 cellbender:remove-background: [epoch 105] average test loss: 4512.3255 cellbender:remove-background: [epoch 106] average training loss: 4485.3660 cellbender:remove-background: [epoch 107] average training loss: 4490.6554 cellbender:remove-background: [epoch 108] average training loss: 4487.4505 cellbender:remove-background: [epoch 109] average training loss: 4486.3582 cellbender:remove-background: [epoch 110] average training loss: 4485.6904 cellbender:remove-background: [epoch 110] average test loss: 4520.9809 cellbender:remove-background: [epoch 111] average training loss: 4480.0897 cellbender:remove-background: [epoch 112] average training loss: 4478.4133 cellbender:remove-background: [epoch 113] average training loss: 4482.0013 cellbender:remove-background: [epoch 114] average training loss: 4482.2576 cellbender:remove-background: [epoch 115] average training loss: 4471.0829 cellbender:remove-background: [epoch 115] average test loss: 4504.4938 cellbender:remove-background: [epoch 116] average training loss: 4473.6991 cellbender:remove-background: [epoch 117] average training loss: 4473.0806 cellbender:remove-background: [epoch 118] average training loss: 4470.6519 cellbender:remove-background: [epoch 119] average training loss: 4472.4927 cellbender:remove-background: [epoch 120] average training loss: 4473.6000 cellbender:remove-background: [epoch 120] average test loss: 4501.0582 cellbender:remove-background: [epoch 121] average training loss: 4472.2753 cellbender:remove-background: [epoch 122] average training loss: 4474.3083 cellbender:remove-background: [epoch 123] average training loss: 4467.5448 cellbender:remove-background: [epoch 124] average training loss: 4471.4853 cellbender:remove-background: [epoch 125] average training loss: 4467.9793 cellbender:remove-background: [epoch 125] average test loss: 4493.2315 cellbender:remove-background: [epoch 126] average training loss: 4470.4944 cellbender:remove-background: [epoch 127] average training loss: 4472.1131 cellbender:remove-background: [epoch 128] average training loss: 4465.3224 cellbender:remove-background: [epoch 129] average training loss: 4471.4528 cellbender:remove-background: [epoch 130] average training loss: 4467.3870 cellbender:remove-background: [epoch 130] average test loss: 4509.2086 cellbender:remove-background: [epoch 131] average training loss: 4463.7204 cellbender:remove-background: [epoch 132] average training loss: 4466.5277 cellbender:remove-background: [epoch 133] average training loss: 4466.5868 cellbender:remove-background: [epoch 134] average training loss: 4464.1868 cellbender:remove-background: [epoch 135] average training loss: 4465.6078 cellbender:remove-background: [epoch 135] average test loss: 4500.1244 cellbender:remove-background: [epoch 136] average training loss: 4461.2618 cellbender:remove-background: [epoch 137] average training loss: 4464.1328 cellbender:remove-background: [epoch 138] average training loss: 4464.2174 cellbender:remove-background: [epoch 139] average training loss: 4466.3407 cellbender:remove-background: [epoch 140] average training loss: 4466.3174 cellbender:remove-background: [epoch 140] average test loss: 4504.7038 cellbender:remove-background: [epoch 141] average training loss: 4465.3748 cellbender:remove-background: [epoch 142] average training loss: 4466.4169 cellbender:remove-background: [epoch 143] average training loss: 4462.8283 cellbender:remove-background: [epoch 144] average training loss: 4465.0658 cellbender:remove-background: [epoch 145] average training loss: 4466.7160 cellbender:remove-background: [epoch 145] average test loss: 4505.2522 cellbender:remove-background: [epoch 146] average training loss: 4463.7941 cellbender:remove-background: [epoch 147] average training loss: 4466.5393 cellbender:remove-background: [epoch 148] average training loss: 4463.3518 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/1041-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 149] average training loss: 4463.2109 cellbender:remove-background: [epoch 150] average training loss: 4465.4448 cellbender:remove-background: [epoch 150] average test loss: 4508.0565 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/1041-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:21:53 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpkcfd2u1e cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpkcfd2u1e /tmp/tmpkcfd2u1e/7ba4405a85_random.pyro /tmp/tmpkcfd2u1e/7ba4405a85_random.cuda /tmp/tmpkcfd2u1e/7ba4405a85_model.torch /tmp/tmpkcfd2u1e/7ba4405a85_optim.torch /tmp/tmpkcfd2u1e/7ba4405a85_optim.pyro /tmp/tmpkcfd2u1e/7ba4405a85_params.pyro /tmp/tmpkcfd2u1e/7ba4405a85_train.loaderstate /tmp/tmpkcfd2u1e/7ba4405a85_test.loaderstate /tmp/tmpkcfd2u1e/7ba4405a85_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 (1/91) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/91) cellbender:remove-background: Working on chunk (3/91) cellbender:remove-background: Working on chunk (4/91) cellbender:remove-background: Working on chunk (5/91) cellbender:remove-background: Working on chunk (6/91) cellbender:remove-background: Working on chunk (7/91) cellbender:remove-background: Working on chunk (8/91) cellbender:remove-background: Working on chunk (9/91) cellbender:remove-background: Working on chunk (10/91) cellbender:remove-background: Working on chunk (11/91) cellbender:remove-background: Working on chunk (12/91) cellbender:remove-background: Working on chunk (13/91) cellbender:remove-background: Working on chunk (14/91) cellbender:remove-background: Working on chunk (15/91) cellbender:remove-background: Working on chunk (16/91) cellbender:remove-background: Working on chunk (17/91) cellbender:remove-background: Working on chunk (18/91) cellbender:remove-background: Working on chunk (19/91) cellbender:remove-background: Working on chunk (20/91) cellbender:remove-background: Working on chunk (21/91) cellbender:remove-background: Working on chunk (22/91) cellbender:remove-background: Working on chunk (23/91) cellbender:remove-background: Working on chunk (24/91) cellbender:remove-background: Working on chunk (25/91) cellbender:remove-background: Working on chunk (26/91) cellbender:remove-background: Working on chunk (27/91) cellbender:remove-background: Working on chunk (28/91) cellbender:remove-background: Working on chunk (29/91) cellbender:remove-background: Working on chunk (30/91) cellbender:remove-background: Working on chunk (31/91) cellbender:remove-background: Working on chunk (32/91) cellbender:remove-background: Working on chunk (33/91) cellbender:remove-background: Working on chunk (34/91) cellbender:remove-background: Working on chunk (35/91) cellbender:remove-background: Working on chunk (36/91) cellbender:remove-background: Working on chunk (37/91) cellbender:remove-background: Working on chunk (38/91) cellbender:remove-background: Working on chunk (39/91) cellbender:remove-background: Working on chunk (40/91) cellbender:remove-background: Working on chunk (41/91) cellbender:remove-background: Working on chunk (42/91) cellbender:remove-background: Working on chunk (43/91) cellbender:remove-background: Working on chunk (44/91) cellbender:remove-background: Working on chunk (45/91) cellbender:remove-background: Working on chunk (46/91) cellbender:remove-background: Working on chunk (47/91) cellbender:remove-background: Working on chunk (48/91) cellbender:remove-background: Working on chunk (49/91) cellbender:remove-background: Working on chunk (50/91) cellbender:remove-background: Working on chunk (51/91) cellbender:remove-background: Working on chunk (52/91) cellbender:remove-background: Working on chunk (53/91) cellbender:remove-background: Working on chunk (54/91) cellbender:remove-background: Working on chunk (55/91) cellbender:remove-background: Working on chunk (56/91) cellbender:remove-background: Working on chunk (57/91) cellbender:remove-background: Working on chunk (58/91) cellbender:remove-background: Working on chunk (59/91) cellbender:remove-background: Working on chunk (60/91) cellbender:remove-background: Working on chunk (61/91) cellbender:remove-background: Working on chunk (62/91) cellbender:remove-background: Working on chunk (63/91) cellbender:remove-background: Working on chunk (64/91) cellbender:remove-background: Working on chunk (65/91) cellbender:remove-background: Working on chunk (66/91) cellbender:remove-background: Working on chunk (67/91) cellbender:remove-background: Working on chunk (68/91) cellbender:remove-background: Working on chunk (69/91) cellbender:remove-background: Working on chunk (70/91) cellbender:remove-background: Working on chunk (71/91) cellbender:remove-background: Working on chunk (72/91) cellbender:remove-background: Working on chunk (73/91) cellbender:remove-background: Working on chunk (74/91) cellbender:remove-background: Working on chunk (75/91) cellbender:remove-background: Working on chunk (76/91) cellbender:remove-background: Working on chunk (77/91) cellbender:remove-background: Working on chunk (78/91) cellbender:remove-background: Working on chunk (79/91) cellbender:remove-background: Working on chunk (80/91) cellbender:remove-background: Working on chunk (81/91) cellbender:remove-background: Working on chunk (82/91) cellbender:remove-background: Working on chunk (83/91) cellbender:remove-background: Working on chunk (84/91) cellbender:remove-background: Working on chunk (85/91) cellbender:remove-background: Working on chunk (86/91) cellbender:remove-background: Working on chunk (87/91) cellbender:remove-background: Working on chunk (88/91) cellbender:remove-background: Working on chunk (89/91) cellbender:remove-background: Working on chunk (90/91) cellbender:remove-background: Working on chunk (91/91) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1041-Schizophrenia-DLPFC/1041-Schizophrenia-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/1041-Schizophrenia-DLPFC/1041-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:27:13 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1041-Schizophrenia-DLPFC/1041-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1041-Schizophrenia-DLPFC/1041-Schizophrenia-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: [2.29 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 15:43:36 Total MCKP estimation time = 941.72 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/1041-Schizophrenia-DLPFC/1041-Schizophrenia-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/1041-Schizophrenia-DLPFC/1041-Schizophrenia-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/1041-Schizophrenia-DLPFC/1041-Schizophrenia-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/1041-Schizophrenia-DLPFC/1041-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:43:59