cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2520-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 8673 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash ab874e6ca2) cellbender:remove-background: 2024-06-06 15:36:59 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/2520-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 32027 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5399 cellbender:remove-background: Prior on counts for empty droplets is 54 cellbender:remove-background: Excluding 10590 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21437 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 27 cellbender:remove-background: Using 8673 probable cell barcodes, plus an additional 11327 barcodes, and 8590 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 52 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpysjhykea 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: 7661.8209 cellbender:remove-background: [epoch 002] average training loss: 5869.1118 (5.8 seconds per epoch) cellbender:remove-background: Will checkpoint every 72 epochs cellbender:remove-background: [epoch 003] average training loss: 4968.5419 cellbender:remove-background: [epoch 004] average training loss: 4457.3944 cellbender:remove-background: [epoch 005] average training loss: 4357.2300 cellbender:remove-background: [epoch 005] average test loss: 4409.9734 cellbender:remove-background: [epoch 006] average training loss: 4327.1378 cellbender:remove-background: [epoch 007] average training loss: 4266.0035 cellbender:remove-background: [epoch 008] average training loss: 4221.0626 cellbender:remove-background: [epoch 009] average training loss: 4210.1976 cellbender:remove-background: [epoch 010] average training loss: 4128.2343 cellbender:remove-background: [epoch 010] average test loss: 4260.3180 cellbender:remove-background: [epoch 011] average training loss: 4003.5992 cellbender:remove-background: [epoch 012] average training loss: 3916.6822 cellbender:remove-background: [epoch 013] average training loss: 3875.1022 cellbender:remove-background: [epoch 014] average training loss: 3883.7584 cellbender:remove-background: [epoch 015] average training loss: 3840.6712 cellbender:remove-background: [epoch 015] average test loss: 3854.9778 cellbender:remove-background: [epoch 016] average training loss: 3817.3323 cellbender:remove-background: [epoch 017] average training loss: 3790.4056 cellbender:remove-background: [epoch 018] average training loss: 3701.0642 cellbender:remove-background: [epoch 019] average training loss: 3657.0275 cellbender:remove-background: [epoch 020] average training loss: 3616.8359 cellbender:remove-background: [epoch 020] average test loss: 3641.0243 cellbender:remove-background: [epoch 021] average training loss: 3608.3499 cellbender:remove-background: [epoch 022] average training loss: 3599.6403 cellbender:remove-background: [epoch 023] average training loss: 3586.6931 cellbender:remove-background: [epoch 024] average training loss: 3557.9555 cellbender:remove-background: [epoch 025] average training loss: 3546.7393 cellbender:remove-background: [epoch 025] average test loss: 3531.8308 cellbender:remove-background: [epoch 026] average training loss: 3518.4166 cellbender:remove-background: [epoch 027] average training loss: 3511.0876 cellbender:remove-background: [epoch 028] average training loss: 3507.0506 cellbender:remove-background: [epoch 029] average training loss: 3493.8142 cellbender:remove-background: [epoch 030] average training loss: 3486.2327 cellbender:remove-background: [epoch 030] average test loss: 3455.4237 cellbender:remove-background: [epoch 031] average training loss: 3482.3412 cellbender:remove-background: [epoch 032] average training loss: 3475.5568 cellbender:remove-background: [epoch 033] average training loss: 3474.5711 cellbender:remove-background: [epoch 034] average training loss: 3470.3659 cellbender:remove-background: [epoch 035] average training loss: 3464.6395 cellbender:remove-background: [epoch 035] average test loss: 3438.7739 cellbender:remove-background: [epoch 036] average training loss: 3462.3122 cellbender:remove-background: [epoch 037] average training loss: 3464.6209 cellbender:remove-background: [epoch 038] average training loss: 3464.9895 cellbender:remove-background: [epoch 039] average training loss: 3469.4398 cellbender:remove-background: [epoch 040] average training loss: 3471.0370 cellbender:remove-background: [epoch 040] average test loss: 3458.8474 cellbender:remove-background: [epoch 041] average training loss: 3468.9289 cellbender:remove-background: [epoch 042] average training loss: 3469.5526 cellbender:remove-background: [epoch 043] average training loss: 3476.6717 cellbender:remove-background: [epoch 044] average training loss: 3475.8916 cellbender:remove-background: [epoch 045] average training loss: 3475.4250 cellbender:remove-background: [epoch 045] average test loss: 3464.3407 cellbender:remove-background: [epoch 046] average training loss: 3474.2014 cellbender:remove-background: [epoch 047] average training loss: 3479.4170 cellbender:remove-background: [epoch 048] average training loss: 3469.9866 cellbender:remove-background: [epoch 049] average training loss: 3477.8507 cellbender:remove-background: [epoch 050] average training loss: 3470.9347 cellbender:remove-background: [epoch 050] average test loss: 3477.4868 cellbender:remove-background: [epoch 051] average training loss: 3476.1377 cellbender:remove-background: [epoch 052] average training loss: 3473.1563 cellbender:remove-background: [epoch 053] average training loss: 3483.4793 cellbender:remove-background: [epoch 054] average training loss: 3474.1533 cellbender:remove-background: [epoch 055] average training loss: 3481.7887 cellbender:remove-background: [epoch 055] average test loss: 3447.7277 cellbender:remove-background: [epoch 056] average training loss: 3480.9859 cellbender:remove-background: [epoch 057] average training loss: 3477.6158 cellbender:remove-background: [epoch 058] average training loss: 3478.8093 cellbender:remove-background: [epoch 059] average training loss: 3485.0129 cellbender:remove-background: [epoch 060] average training loss: 3476.4310 cellbender:remove-background: [epoch 060] average test loss: 3478.0578 cellbender:remove-background: [epoch 061] average training loss: 3479.8728 cellbender:remove-background: [epoch 062] average training loss: 3475.3320 cellbender:remove-background: [epoch 063] average training loss: 3480.8006 cellbender:remove-background: [epoch 064] average training loss: 3481.9402 cellbender:remove-background: [epoch 065] average training loss: 3491.0155 cellbender:remove-background: [epoch 065] average test loss: 3459.0658 cellbender:remove-background: [epoch 066] average training loss: 3491.1643 cellbender:remove-background: [epoch 067] average training loss: 3484.8668 cellbender:remove-background: [epoch 068] average training loss: 3490.2437 cellbender:remove-background: [epoch 069] average training loss: 3482.5260 cellbender:remove-background: [epoch 070] average training loss: 3490.0776 cellbender:remove-background: [epoch 070] average test loss: 3499.8632 cellbender:remove-background: [epoch 071] average training loss: 3485.6172 cellbender:remove-background: [epoch 072] average training loss: 3499.7999 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/2520-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 073] average training loss: 3492.7730 cellbender:remove-background: [epoch 074] average training loss: 3505.4829 cellbender:remove-background: [epoch 075] average training loss: 3494.5245 cellbender:remove-background: [epoch 075] average test loss: 3450.4675 cellbender:remove-background: [epoch 076] average training loss: 3493.2911 cellbender:remove-background: [epoch 077] average training loss: 3497.7870 cellbender:remove-background: [epoch 078] average training loss: 3488.5354 cellbender:remove-background: [epoch 079] average training loss: 3507.5899 cellbender:remove-background: [epoch 080] average training loss: 3489.0777 cellbender:remove-background: [epoch 080] average test loss: 3481.1408 cellbender:remove-background: [epoch 081] average training loss: 3505.6089 cellbender:remove-background: [epoch 082] average training loss: 3495.5804 cellbender:remove-background: [epoch 083] average training loss: 3488.0247 cellbender:remove-background: [epoch 084] average training loss: 3490.6451 cellbender:remove-background: [epoch 085] average training loss: 3489.9563 cellbender:remove-background: [epoch 085] average test loss: 3472.9426 cellbender:remove-background: [epoch 086] average training loss: 3491.8758 cellbender:remove-background: [epoch 087] average training loss: 3484.2389 cellbender:remove-background: [epoch 088] average training loss: 3480.1530 cellbender:remove-background: [epoch 089] average training loss: 3481.1196 cellbender:remove-background: [epoch 090] average training loss: 3483.3772 cellbender:remove-background: [epoch 090] average test loss: 3535.8109 cellbender:remove-background: [epoch 091] average training loss: 3478.3559 cellbender:remove-background: [epoch 092] average training loss: 3490.1195 cellbender:remove-background: [epoch 093] average training loss: 3491.5539 cellbender:remove-background: [epoch 094] average training loss: 3476.7663 cellbender:remove-background: [epoch 095] average training loss: 3487.4656 cellbender:remove-background: [epoch 095] average test loss: 3534.1844 cellbender:remove-background: [epoch 096] average training loss: 3483.0443 cellbender:remove-background: [epoch 097] average training loss: 3483.0827 cellbender:remove-background: [epoch 098] average training loss: 3484.7129 cellbender:remove-background: [epoch 099] average training loss: 3472.5070 cellbender:remove-background: [epoch 100] average training loss: 3482.0401 cellbender:remove-background: [epoch 100] average test loss: 3573.1114 cellbender:remove-background: [epoch 101] average training loss: 3474.7667 cellbender:remove-background: [epoch 102] average training loss: 3476.5905 cellbender:remove-background: [epoch 103] average training loss: 3473.8815 cellbender:remove-background: [epoch 104] average training loss: 3468.9514 cellbender:remove-background: [epoch 105] average training loss: 3481.3184 cellbender:remove-background: [epoch 105] average test loss: 3496.5580 cellbender:remove-background: [epoch 106] average training loss: 3471.1183 cellbender:remove-background: [epoch 107] average training loss: 3467.7799 cellbender:remove-background: [epoch 108] average training loss: 3467.2645 cellbender:remove-background: [epoch 109] average training loss: 3468.5593 cellbender:remove-background: [epoch 110] average training loss: 3468.0411 cellbender:remove-background: [epoch 110] average test loss: 3517.2185 cellbender:remove-background: [epoch 111] average training loss: 3464.8631 cellbender:remove-background: [epoch 112] average training loss: 3465.2653 cellbender:remove-background: [epoch 113] average training loss: 3467.5370 cellbender:remove-background: [epoch 114] average training loss: 3464.8495 cellbender:remove-background: [epoch 115] average training loss: 3462.1730 cellbender:remove-background: [epoch 115] average test loss: 3491.5375 cellbender:remove-background: [epoch 116] average training loss: 3471.2236 cellbender:remove-background: [epoch 117] average training loss: 3468.7655 cellbender:remove-background: [epoch 118] average training loss: 3468.8280 cellbender:remove-background: [epoch 119] average training loss: 3456.7671 cellbender:remove-background: [epoch 120] average training loss: 3459.3857 cellbender:remove-background: [epoch 120] average test loss: 3487.0029 cellbender:remove-background: [epoch 121] average training loss: 3461.9418 cellbender:remove-background: [epoch 122] average training loss: 3458.6199 cellbender:remove-background: [epoch 123] average training loss: 3459.1143 cellbender:remove-background: [epoch 124] average training loss: 3464.7254 cellbender:remove-background: [epoch 125] average training loss: 3470.1533 cellbender:remove-background: [epoch 125] average test loss: 3499.1722 cellbender:remove-background: [epoch 126] average training loss: 3468.0279 cellbender:remove-background: [epoch 127] average training loss: 3466.3553 cellbender:remove-background: [epoch 128] average training loss: 3461.0886 cellbender:remove-background: [epoch 129] average training loss: 3461.6582 cellbender:remove-background: [epoch 130] average training loss: 3452.5871 cellbender:remove-background: [epoch 130] average test loss: 3483.9126 cellbender:remove-background: [epoch 131] average training loss: 3452.4016 cellbender:remove-background: [epoch 132] average training loss: 3454.3550 cellbender:remove-background: [epoch 133] average training loss: 3458.1163 cellbender:remove-background: [epoch 134] average training loss: 3474.5259 cellbender:remove-background: [epoch 135] average training loss: 3455.4233 cellbender:remove-background: [epoch 135] average test loss: 3479.7878 cellbender:remove-background: [epoch 136] average training loss: 3453.4311 cellbender:remove-background: [epoch 137] average training loss: 3460.4319 cellbender:remove-background: [epoch 138] average training loss: 3453.9667 cellbender:remove-background: [epoch 139] average training loss: 3457.8897 cellbender:remove-background: [epoch 140] average training loss: 3455.8501 cellbender:remove-background: [epoch 140] average test loss: 3484.1721 cellbender:remove-background: [epoch 141] average training loss: 3465.4602 cellbender:remove-background: [epoch 142] average training loss: 3458.0940 cellbender:remove-background: [epoch 143] average training loss: 3451.5866 cellbender:remove-background: [epoch 144] average training loss: 3453.4004 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/2520-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 145] average training loss: 3460.4589 cellbender:remove-background: [epoch 145] average test loss: 3483.8683 cellbender:remove-background: [epoch 146] average training loss: 3460.8581 cellbender:remove-background: [epoch 147] average training loss: 3451.9405 cellbender:remove-background: [epoch 148] average training loss: 3459.2284 cellbender:remove-background: [epoch 149] average training loss: 3460.8470 cellbender:remove-background: [epoch 150] average training loss: 3452.7810 cellbender:remove-background: [epoch 150] average test loss: 3482.5931 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/2520-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:54:51 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpjkiusf62 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpjkiusf62 /tmp/tmpjkiusf62/ab874e6ca2_random.pyro /tmp/tmpjkiusf62/ab874e6ca2_random.cuda /tmp/tmpjkiusf62/ab874e6ca2_model.torch /tmp/tmpjkiusf62/ab874e6ca2_optim.torch /tmp/tmpjkiusf62/ab874e6ca2_optim.pyro /tmp/tmpjkiusf62/ab874e6ca2_params.pyro /tmp/tmpjkiusf62/ab874e6ca2_train.loaderstate /tmp/tmpjkiusf62/ab874e6ca2_test.loaderstate /tmp/tmpjkiusf62/ab874e6ca2_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 (1/120) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/120) cellbender:remove-background: Working on chunk (3/120) cellbender:remove-background: Working on chunk (4/120) cellbender:remove-background: Working on chunk (5/120) cellbender:remove-background: Working on chunk (6/120) cellbender:remove-background: Working on chunk (7/120) cellbender:remove-background: Working on chunk (8/120) cellbender:remove-background: Working on chunk (9/120) cellbender:remove-background: Working on chunk (10/120) cellbender:remove-background: Working on chunk (11/120) cellbender:remove-background: Working on chunk (12/120) cellbender:remove-background: 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cellbender:remove-background: Working on chunk (31/120) cellbender:remove-background: Working on chunk (32/120) cellbender:remove-background: Working on chunk (33/120) cellbender:remove-background: Working on chunk (34/120) cellbender:remove-background: Working on chunk (35/120) cellbender:remove-background: Working on chunk (36/120) cellbender:remove-background: Working on chunk (37/120) cellbender:remove-background: Working on chunk (38/120) cellbender:remove-background: Working on chunk (39/120) cellbender:remove-background: Working on chunk (40/120) cellbender:remove-background: Working on chunk (41/120) cellbender:remove-background: Working on chunk (42/120) cellbender:remove-background: Working on chunk (43/120) cellbender:remove-background: Working on chunk (44/120) cellbender:remove-background: Working on chunk (45/120) cellbender:remove-background: Working on chunk (46/120) cellbender:remove-background: Working on chunk (47/120) cellbender:remove-background: Working on chunk 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Working on chunk (84/120) cellbender:remove-background: Working on chunk (85/120) cellbender:remove-background: Working on chunk (86/120) cellbender:remove-background: Working on chunk (87/120) cellbender:remove-background: Working on chunk (88/120) cellbender:remove-background: Working on chunk (89/120) cellbender:remove-background: Working on chunk (90/120) cellbender:remove-background: Working on chunk (91/120) cellbender:remove-background: Working on chunk (92/120) cellbender:remove-background: Working on chunk (93/120) cellbender:remove-background: Working on chunk (94/120) cellbender:remove-background: Working on chunk (95/120) cellbender:remove-background: Working on chunk (96/120) cellbender:remove-background: Working on chunk (97/120) cellbender:remove-background: Working on chunk (98/120) cellbender:remove-background: Working on chunk (99/120) cellbender:remove-background: Working on chunk (100/120) cellbender:remove-background: Working on chunk (101/120) cellbender:remove-background: Working on chunk (102/120) cellbender:remove-background: Working on chunk (103/120) cellbender:remove-background: Working on chunk (104/120) cellbender:remove-background: Working on chunk (105/120) cellbender:remove-background: Working on chunk (106/120) cellbender:remove-background: Working on chunk (107/120) cellbender:remove-background: Working on chunk (108/120) cellbender:remove-background: Working on chunk (109/120) cellbender:remove-background: Working on chunk (110/120) cellbender:remove-background: Working on chunk (111/120) cellbender:remove-background: Working on chunk (112/120) cellbender:remove-background: Working on chunk (113/120) cellbender:remove-background: Working on chunk (114/120) cellbender:remove-background: Working on chunk (115/120) cellbender:remove-background: Working on chunk (116/120) cellbender:remove-background: Working on chunk (117/120) cellbender:remove-background: Working on chunk (118/120) cellbender:remove-background: Working on chunk (119/120) cellbender:remove-background: Working on chunk (120/120) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:00:41 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [2.19 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 16:16:59 Total MCKP estimation time = 943.61 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/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-Hippocampus/2520-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:17:23