cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2677-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 9211 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 49d56f99d9) cellbender:remove-background: 2024-06-06 14:52:32 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/2677-Schizophrenia-dACC.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: 32291 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5132 cellbender:remove-background: Prior on counts for empty droplets is 260 cellbender:remove-background: Excluding 5691 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 26600 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 130 cellbender:remove-background: Using 9211 probable cell barcodes, plus an additional 10789 barcodes, and 18424 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 256 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp16mexn6e 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: 8309.6707 cellbender:remove-background: [epoch 002] average training loss: 6556.4760 (6.0 seconds per epoch) cellbender:remove-background: Will checkpoint every 70 epochs cellbender:remove-background: [epoch 003] average training loss: 5515.2459 cellbender:remove-background: [epoch 004] average training loss: 4919.8542 cellbender:remove-background: [epoch 005] average training loss: 4705.1681 cellbender:remove-background: [epoch 005] average test loss: 4712.3686 cellbender:remove-background: [epoch 006] average training loss: 4625.6580 cellbender:remove-background: [epoch 007] average training loss: 4565.2503 cellbender:remove-background: [epoch 008] average training loss: 4532.8049 cellbender:remove-background: [epoch 009] average training loss: 4520.3385 cellbender:remove-background: [epoch 010] average training loss: 4478.6123 cellbender:remove-background: [epoch 010] average test loss: 4441.7996 cellbender:remove-background: [epoch 011] average training loss: 4469.4960 cellbender:remove-background: [epoch 012] average training loss: 4419.7411 cellbender:remove-background: [epoch 013] average training loss: 4375.3308 cellbender:remove-background: [epoch 014] average training loss: 4407.1187 cellbender:remove-background: [epoch 015] average training loss: 4378.1741 cellbender:remove-background: [epoch 015] average test loss: 4394.6159 cellbender:remove-background: [epoch 016] average training loss: 4358.0323 cellbender:remove-background: [epoch 017] average training loss: 4355.0216 cellbender:remove-background: [epoch 018] average training loss: 4320.5420 cellbender:remove-background: [epoch 019] average training loss: 4297.8018 cellbender:remove-background: [epoch 020] average training loss: 4277.4525 cellbender:remove-background: [epoch 020] average test loss: 4285.8550 cellbender:remove-background: [epoch 021] average training loss: 4269.9630 cellbender:remove-background: [epoch 022] average training loss: 4263.8107 cellbender:remove-background: [epoch 023] average training loss: 4260.6629 cellbender:remove-background: [epoch 024] average training loss: 4235.1796 cellbender:remove-background: [epoch 025] average training loss: 4224.0076 cellbender:remove-background: [epoch 025] average test loss: 4214.7312 cellbender:remove-background: [epoch 026] average training loss: 4212.0504 cellbender:remove-background: [epoch 027] average training loss: 4204.6617 cellbender:remove-background: [epoch 028] average training loss: 4201.1081 cellbender:remove-background: [epoch 029] average training loss: 4196.8850 cellbender:remove-background: [epoch 030] average training loss: 4195.7190 cellbender:remove-background: [epoch 030] average test loss: 4188.6517 cellbender:remove-background: [epoch 031] average training loss: 4194.1793 cellbender:remove-background: [epoch 032] average training loss: 4190.7904 cellbender:remove-background: [epoch 033] average training loss: 4186.8156 cellbender:remove-background: [epoch 034] average training loss: 4199.7449 cellbender:remove-background: [epoch 035] average training loss: 4197.5689 cellbender:remove-background: [epoch 035] average test loss: 4171.1429 cellbender:remove-background: [epoch 036] average training loss: 4206.6200 cellbender:remove-background: [epoch 037] average training loss: 4196.1621 cellbender:remove-background: [epoch 038] average training loss: 4191.0178 cellbender:remove-background: [epoch 039] average training loss: 4198.9484 cellbender:remove-background: [epoch 040] average training loss: 4194.5731 cellbender:remove-background: [epoch 040] average test loss: 4136.4054 cellbender:remove-background: [epoch 041] average training loss: 4188.0298 cellbender:remove-background: [epoch 042] average training loss: 4188.0091 cellbender:remove-background: [epoch 043] average training loss: 4187.1300 cellbender:remove-background: [epoch 044] average training loss: 4180.9300 cellbender:remove-background: [epoch 045] average training loss: 4182.0205 cellbender:remove-background: [epoch 045] average test loss: 4147.8177 cellbender:remove-background: [epoch 046] average training loss: 4184.8560 cellbender:remove-background: [epoch 047] average training loss: 4181.2890 cellbender:remove-background: [epoch 048] average training loss: 4177.5655 cellbender:remove-background: [epoch 049] average training loss: 4179.8401 cellbender:remove-background: [epoch 050] average training loss: 4178.5974 cellbender:remove-background: [epoch 050] average test loss: 4112.2101 cellbender:remove-background: [epoch 051] average training loss: 4181.0694 cellbender:remove-background: [epoch 052] average training loss: 4179.4077 cellbender:remove-background: [epoch 053] average training loss: 4179.6929 cellbender:remove-background: [epoch 054] average training loss: 4173.1218 cellbender:remove-background: [epoch 055] average training loss: 4176.1589 cellbender:remove-background: [epoch 055] average test loss: 4167.2726 cellbender:remove-background: [epoch 056] average training loss: 4174.6115 cellbender:remove-background: [epoch 057] average training loss: 4173.7091 cellbender:remove-background: [epoch 058] average training loss: 4172.1299 cellbender:remove-background: [epoch 059] average training loss: 4168.7192 cellbender:remove-background: [epoch 060] average training loss: 4172.5990 cellbender:remove-background: [epoch 060] average test loss: 4114.2465 cellbender:remove-background: [epoch 061] average training loss: 4171.5275 cellbender:remove-background: [epoch 062] average training loss: 4174.1520 cellbender:remove-background: [epoch 063] average training loss: 4173.0062 cellbender:remove-background: [epoch 064] average training loss: 4179.1122 cellbender:remove-background: [epoch 065] average training loss: 4187.1336 cellbender:remove-background: [epoch 065] average test loss: 4167.0144 cellbender:remove-background: [epoch 066] average training loss: 4178.5590 cellbender:remove-background: [epoch 067] average training loss: 4180.9099 cellbender:remove-background: [epoch 068] average training loss: 4184.0083 cellbender:remove-background: [epoch 069] average training loss: 4186.5388 cellbender:remove-background: [epoch 070] average training loss: 4196.5652 cellbender:remove-background: [epoch 070] average test loss: 4127.1476 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/2677-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 071] average training loss: 4218.0742 cellbender:remove-background: [epoch 072] average training loss: 4210.1406 cellbender:remove-background: [epoch 073] average training loss: 4219.6115 cellbender:remove-background: [epoch 074] average training loss: 4238.5738 cellbender:remove-background: [epoch 075] average training loss: 4234.2673 cellbender:remove-background: [epoch 075] average test loss: 4226.9023 cellbender:remove-background: [epoch 076] average training loss: 4239.6417 cellbender:remove-background: [epoch 077] average training loss: 4267.1545 cellbender:remove-background: [epoch 078] average training loss: 4251.3406 cellbender:remove-background: [epoch 079] average training loss: 4251.2929 cellbender:remove-background: [epoch 080] average training loss: 4270.2352 cellbender:remove-background: [epoch 080] average test loss: 4328.3385 cellbender:remove-background: [epoch 081] average training loss: 4258.7354 cellbender:remove-background: [epoch 082] average training loss: 4303.4013 cellbender:remove-background: [epoch 083] average training loss: 4328.3204 cellbender:remove-background: [epoch 084] average training loss: 4333.1970 cellbender:remove-background: [epoch 085] average training loss: 4387.6206 cellbender:remove-background: [epoch 085] average test loss: 4393.4274 cellbender:remove-background: [epoch 086] average training loss: 4340.8644 cellbender:remove-background: [epoch 087] average training loss: 4352.5394 cellbender:remove-background: [epoch 088] average training loss: 4367.4791 cellbender:remove-background: [epoch 089] average training loss: 4372.8585 cellbender:remove-background: [epoch 090] average training loss: 4397.7856 cellbender:remove-background: [epoch 090] average test loss: 4399.9212 cellbender:remove-background: [epoch 091] average training loss: 4396.0028 cellbender:remove-background: [epoch 092] average training loss: 4441.0480 cellbender:remove-background: [epoch 093] average training loss: 4411.2489 cellbender:remove-background: [epoch 094] average training loss: 4401.1157 cellbender:remove-background: [epoch 095] average training loss: 4433.0363 cellbender:remove-background: [epoch 095] average test loss: 4468.7883 cellbender:remove-background: [epoch 096] average training loss: 4439.0457 cellbender:remove-background: [epoch 097] average training loss: 4421.8004 cellbender:remove-background: [epoch 098] average training loss: 4453.2505 cellbender:remove-background: [epoch 099] average training loss: 4416.6733 cellbender:remove-background: [epoch 100] average training loss: 4444.1891 cellbender:remove-background: [epoch 100] average test loss: 4552.5109 cellbender:remove-background: [epoch 101] average training loss: 4464.3076 cellbender:remove-background: [epoch 102] average training loss: 4398.9435 cellbender:remove-background: [epoch 103] average training loss: 4440.8091 cellbender:remove-background: [epoch 104] average training loss: 4461.8211 cellbender:remove-background: [epoch 105] average training loss: 4464.8406 cellbender:remove-background: [epoch 105] average test loss: 4587.7729 cellbender:remove-background: [epoch 106] average training loss: 4423.3548 cellbender:remove-background: [epoch 107] average training loss: 4489.7049 cellbender:remove-background: [epoch 108] average training loss: 4504.8907 cellbender:remove-background: [epoch 109] average training loss: 4408.1099 cellbender:remove-background: [epoch 110] average training loss: 4462.4966 cellbender:remove-background: [epoch 110] average test loss: 4460.0151 cellbender:remove-background: [epoch 111] average training loss: 4450.6991 cellbender:remove-background: [epoch 112] average training loss: 4476.8772 cellbender:remove-background: [epoch 113] average training loss: 4493.0851 cellbender:remove-background: [epoch 114] average training loss: 4445.7256 cellbender:remove-background: [epoch 115] average training loss: 4456.3764 cellbender:remove-background: [epoch 115] average test loss: 4486.4085 cellbender:remove-background: [epoch 116] average training loss: 4438.5090 cellbender:remove-background: [epoch 117] average training loss: 4441.5969 cellbender:remove-background: [epoch 118] average training loss: 4503.9288 cellbender:remove-background: [epoch 119] average training loss: 4395.7642 cellbender:remove-background: [epoch 120] average training loss: 4527.9230 cellbender:remove-background: [epoch 120] average test loss: 4630.5951 cellbender:remove-background: [epoch 121] average training loss: 4481.7209 cellbender:remove-background: [epoch 122] average training loss: 4483.4720 cellbender:remove-background: [epoch 123] average training loss: 4443.4123 cellbender:remove-background: [epoch 124] average training loss: 4400.5943 cellbender:remove-background: [epoch 125] average training loss: 4478.5061 cellbender:remove-background: [epoch 125] average test loss: 4478.0351 cellbender:remove-background: [epoch 126] average training loss: 4405.8481 cellbender:remove-background: [epoch 127] average training loss: 4477.5873 cellbender:remove-background: [epoch 128] average training loss: 4520.7736 cellbender:remove-background: [epoch 129] average training loss: 4513.3446 cellbender:remove-background: [epoch 130] average training loss: 4480.4726 cellbender:remove-background: [epoch 130] average test loss: 4709.1137 cellbender:remove-background: [epoch 131] average training loss: 4474.5110 cellbender:remove-background: [epoch 132] average training loss: 4443.7227 cellbender:remove-background: [epoch 133] average training loss: 4454.7882 cellbender:remove-background: [epoch 134] average training loss: 4457.3482 cellbender:remove-background: [epoch 135] average training loss: 4392.5144 cellbender:remove-background: [epoch 135] average test loss: 4347.9639 cellbender:remove-background: [epoch 136] average training loss: 4501.8537 cellbender:remove-background: [epoch 137] average training loss: 4447.1593 cellbender:remove-background: [epoch 138] average training loss: 4442.5536 cellbender:remove-background: [epoch 139] average training loss: 4462.9575 cellbender:remove-background: [epoch 140] average training loss: 4437.7251 cellbender:remove-background: [epoch 140] average test loss: 4464.8448 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/2677-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 141] average training loss: 4485.9490 cellbender:remove-background: [epoch 142] average training loss: 4536.4754 cellbender:remove-background: [epoch 143] average training loss: 4487.0881 cellbender:remove-background: [epoch 144] average training loss: 4422.5490 cellbender:remove-background: [epoch 145] average training loss: 4452.4588 cellbender:remove-background: [epoch 145] average test loss: 4487.2335 cellbender:remove-background: [epoch 146] average training loss: 4479.4667 cellbender:remove-background: [epoch 147] average training loss: 4445.1716 cellbender:remove-background: [epoch 148] average training loss: 4486.7282 cellbender:remove-background: [epoch 149] average training loss: 4476.7984 cellbender:remove-background: [epoch 150] average training loss: 4500.0210 cellbender:remove-background: [epoch 150] average test loss: 4491.9511 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/2677-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:11:15 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp5rcdpykd cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp5rcdpykd /tmp/tmp5rcdpykd/49d56f99d9_random.pyro /tmp/tmp5rcdpykd/49d56f99d9_random.cuda /tmp/tmp5rcdpykd/49d56f99d9_model.torch /tmp/tmp5rcdpykd/49d56f99d9_optim.torch /tmp/tmp5rcdpykd/49d56f99d9_optim.pyro /tmp/tmp5rcdpykd/49d56f99d9_params.pyro /tmp/tmp5rcdpykd/49d56f99d9_train.loaderstate /tmp/tmp5rcdpykd/49d56f99d9_test.loaderstate /tmp/tmp5rcdpykd/49d56f99d9_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 (1/145) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/145) cellbender:remove-background: Working on chunk (3/145) cellbender:remove-background: Working on chunk (4/145) cellbender:remove-background: Working on chunk (5/145) cellbender:remove-background: Working on chunk (6/145) cellbender:remove-background: Working on chunk (7/145) cellbender:remove-background: Working on chunk (8/145) cellbender:remove-background: Working on chunk (9/145) cellbender:remove-background: Working on chunk (10/145) cellbender:remove-background: Working on chunk (11/145) cellbender:remove-background: Working on chunk (12/145) cellbender:remove-background: 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(48/145) cellbender:remove-background: Working on chunk (49/145) cellbender:remove-background: Working on chunk (50/145) cellbender:remove-background: Working on chunk (51/145) cellbender:remove-background: Working on chunk (52/145) cellbender:remove-background: Working on chunk (53/145) cellbender:remove-background: Working on chunk (54/145) cellbender:remove-background: Working on chunk (55/145) cellbender:remove-background: Working on chunk (56/145) cellbender:remove-background: Working on chunk (57/145) cellbender:remove-background: Working on chunk (58/145) cellbender:remove-background: Working on chunk (59/145) cellbender:remove-background: Working on chunk (60/145) cellbender:remove-background: Working on chunk (61/145) cellbender:remove-background: Working on chunk (62/145) cellbender:remove-background: Working on chunk (63/145) cellbender:remove-background: Working on chunk (64/145) cellbender:remove-background: Working on chunk (65/145) cellbender:remove-background: Working 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cellbender:remove-background: Working on chunk (102/145) cellbender:remove-background: Working on chunk (103/145) cellbender:remove-background: Working on chunk (104/145) cellbender:remove-background: Working on chunk (105/145) cellbender:remove-background: Working on chunk (106/145) cellbender:remove-background: Working on chunk (107/145) cellbender:remove-background: Working on chunk (108/145) cellbender:remove-background: Working on chunk (109/145) cellbender:remove-background: Working on chunk (110/145) cellbender:remove-background: Working on chunk (111/145) cellbender:remove-background: Working on chunk (112/145) cellbender:remove-background: Working on chunk (113/145) cellbender:remove-background: Working on chunk (114/145) cellbender:remove-background: Working on chunk (115/145) cellbender:remove-background: Working on chunk (116/145) cellbender:remove-background: Working on chunk (117/145) cellbender:remove-background: Working on chunk (118/145) cellbender:remove-background: Working on chunk (119/145) cellbender:remove-background: Working on chunk (120/145) cellbender:remove-background: Working on chunk (121/145) cellbender:remove-background: Working on chunk (122/145) cellbender:remove-background: Working on chunk (123/145) cellbender:remove-background: Working on chunk (124/145) cellbender:remove-background: Working on chunk (125/145) cellbender:remove-background: Working on chunk (126/145) cellbender:remove-background: Working on chunk (127/145) cellbender:remove-background: Working on chunk (128/145) cellbender:remove-background: Working on chunk (129/145) cellbender:remove-background: Working on chunk (130/145) cellbender:remove-background: Working on chunk (131/145) cellbender:remove-background: Working on chunk (132/145) cellbender:remove-background: Working on chunk (133/145) cellbender:remove-background: Working on chunk (134/145) cellbender:remove-background: Working on chunk (135/145) cellbender:remove-background: Working on chunk (136/145) cellbender:remove-background: Working on chunk (137/145) cellbender:remove-background: Working on chunk (138/145) cellbender:remove-background: Working on chunk (139/145) cellbender:remove-background: Working on chunk (140/145) cellbender:remove-background: Working on chunk (141/145) cellbender:remove-background: Working on chunk (142/145) cellbender:remove-background: Working on chunk (143/145) cellbender:remove-background: Working on chunk (144/145) cellbender:remove-background: Working on chunk (145/145) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.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/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:19:36 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.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: [2.14 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 15:35:18 Total MCKP estimation time = 902.06 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/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.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/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.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/2677-Schizophrenia-dACC/2677-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:35:39