cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2477-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-dACC/2477-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 3696 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 78b547e7aa)
cellbender:remove-background: 2024-06-06 15:14:58
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/2477-Bipolar-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: 31483 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 2537
cellbender:remove-background: Prior on counts for empty droplets is 57
cellbender:remove-background: Excluding 10681 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 20802 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 28
cellbender:remove-background: Using 3696 probable cell barcodes, plus an additional 16304 barcodes, and 51027 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 57 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpdixo159q
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: 2897.5903
cellbender:remove-background: [epoch 002]  average training loss: 2356.9584  (5.8 seconds per epoch)
cellbender:remove-background: Will checkpoint every 73 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2051.9695
cellbender:remove-background: [epoch 004]  average training loss: 1876.3901
cellbender:remove-background: [epoch 005]  average training loss: 1826.3669
cellbender:remove-background: [epoch 005] average test loss: 2031.7930
cellbender:remove-background: [epoch 006]  average training loss: 1817.6665
cellbender:remove-background: [epoch 007]  average training loss: 1790.3196
cellbender:remove-background: [epoch 008]  average training loss: 1768.2071
cellbender:remove-background: [epoch 009]  average training loss: 1761.8918
cellbender:remove-background: [epoch 010]  average training loss: 1725.4053
cellbender:remove-background: [epoch 010] average test loss: 1758.9715
cellbender:remove-background: [epoch 011]  average training loss: 1700.3837
cellbender:remove-background: [epoch 012]  average training loss: 1677.9412
cellbender:remove-background: [epoch 013]  average training loss: 1659.3404
cellbender:remove-background: [epoch 014]  average training loss: 1672.1855
cellbender:remove-background: [epoch 015]  average training loss: 1650.3149
cellbender:remove-background: [epoch 015] average test loss: 1692.2658
cellbender:remove-background: [epoch 016]  average training loss: 1638.9939
cellbender:remove-background: [epoch 017]  average training loss: 1648.7074
cellbender:remove-background: [epoch 018]  average training loss: 1642.5185
cellbender:remove-background: [epoch 019]  average training loss: 1631.5940
cellbender:remove-background: [epoch 020]  average training loss: 1620.8907
cellbender:remove-background: [epoch 020] average test loss: 1699.3993
cellbender:remove-background: [epoch 021]  average training loss: 1618.1195
cellbender:remove-background: [epoch 022]  average training loss: 1621.2825
cellbender:remove-background: [epoch 023]  average training loss: 1616.6888
cellbender:remove-background: [epoch 024]  average training loss: 1605.1082
cellbender:remove-background: [epoch 025]  average training loss: 1594.7793
cellbender:remove-background: [epoch 025] average test loss: 1628.2973
cellbender:remove-background: [epoch 026]  average training loss: 1572.5263
cellbender:remove-background: [epoch 027]  average training loss: 1567.5724
cellbender:remove-background: [epoch 028]  average training loss: 1563.0758
cellbender:remove-background: [epoch 029]  average training loss: 1557.9314
cellbender:remove-background: [epoch 030]  average training loss: 1551.5962
cellbender:remove-background: [epoch 030] average test loss: 1599.2547
cellbender:remove-background: [epoch 031]  average training loss: 1548.0441
cellbender:remove-background: [epoch 032]  average training loss: 1547.7138
cellbender:remove-background: [epoch 033]  average training loss: 1545.6288
cellbender:remove-background: [epoch 034]  average training loss: 1542.1000
cellbender:remove-background: [epoch 035]  average training loss: 1540.3036
cellbender:remove-background: [epoch 035] average test loss: 1575.4831
cellbender:remove-background: [epoch 036]  average training loss: 1542.0963
cellbender:remove-background: [epoch 037]  average training loss: 1537.6874
cellbender:remove-background: [epoch 038]  average training loss: 1536.9207
cellbender:remove-background: [epoch 039]  average training loss: 1536.7752
cellbender:remove-background: [epoch 040]  average training loss: 1534.4372
cellbender:remove-background: [epoch 040] average test loss: 1566.0380
cellbender:remove-background: [epoch 041]  average training loss: 1537.8848
cellbender:remove-background: [epoch 042]  average training loss: 1535.3567
cellbender:remove-background: [epoch 043]  average training loss: 1537.5658
cellbender:remove-background: [epoch 044]  average training loss: 1537.0994
cellbender:remove-background: [epoch 045]  average training loss: 1538.6782
cellbender:remove-background: [epoch 045] average test loss: 1569.4000
cellbender:remove-background: [epoch 046]  average training loss: 1541.2059
cellbender:remove-background: [epoch 047]  average training loss: 1543.1400
cellbender:remove-background: [epoch 048]  average training loss: 1548.7462
cellbender:remove-background: [epoch 049]  average training loss: 1552.6199
cellbender:remove-background: [epoch 050]  average training loss: 1557.3098
cellbender:remove-background: [epoch 050] average test loss: 1611.6096
cellbender:remove-background: [epoch 051]  average training loss: 1569.8467
cellbender:remove-background: [epoch 052]  average training loss: 1562.8545
cellbender:remove-background: [epoch 053]  average training loss: 1568.3223
cellbender:remove-background: [epoch 054]  average training loss: 1578.3618
cellbender:remove-background: [epoch 055]  average training loss: 1569.5735
cellbender:remove-background: [epoch 055] average test loss: 1605.4887
cellbender:remove-background: [epoch 056]  average training loss: 1572.7337
cellbender:remove-background: [epoch 057]  average training loss: 1573.6276
cellbender:remove-background: [epoch 058]  average training loss: 1564.4163
cellbender:remove-background: [epoch 059]  average training loss: 1580.2759
cellbender:remove-background: [epoch 060]  average training loss: 1561.4560
cellbender:remove-background: [epoch 060] average test loss: 1592.5808
cellbender:remove-background: [epoch 061]  average training loss: 1563.1744
cellbender:remove-background: [epoch 062]  average training loss: 1564.0786
cellbender:remove-background: [epoch 063]  average training loss: 1570.4956
cellbender:remove-background: [epoch 064]  average training loss: 1561.5849
cellbender:remove-background: [epoch 065]  average training loss: 1566.8854
cellbender:remove-background: [epoch 065] average test loss: 1603.2983
cellbender:remove-background: [epoch 066]  average training loss: 1566.9401
cellbender:remove-background: [epoch 067]  average training loss: 1566.4317
cellbender:remove-background: [epoch 068]  average training loss: 1569.9222
cellbender:remove-background: [epoch 069]  average training loss: 1570.3928
cellbender:remove-background: [epoch 070]  average training loss: 1559.5976
cellbender:remove-background: [epoch 070] average test loss: 1669.5134
cellbender:remove-background: [epoch 071]  average training loss: 1565.6793
cellbender:remove-background: [epoch 072]  average training loss: 1560.4789
cellbender:remove-background: [epoch 073]  average training loss: 1566.5282
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/2477-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 074]  average training loss: 1561.4218
cellbender:remove-background: [epoch 075]  average training loss: 1573.5348
cellbender:remove-background: [epoch 075] average test loss: 1616.0376
cellbender:remove-background: [epoch 076]  average training loss: 1589.2554
cellbender:remove-background: [epoch 077]  average training loss: 1579.6841
cellbender:remove-background: [epoch 078]  average training loss: 1577.8515
cellbender:remove-background: [epoch 079]  average training loss: 1569.6384
cellbender:remove-background: [epoch 080]  average training loss: 1573.3739
cellbender:remove-background: [epoch 080] average test loss: 1637.5723
cellbender:remove-background: [epoch 081]  average training loss: 1573.0542
cellbender:remove-background: [epoch 082]  average training loss: 1573.4895
cellbender:remove-background: [epoch 083]  average training loss: 1566.7366
cellbender:remove-background: [epoch 084]  average training loss: 1572.5838
cellbender:remove-background: [epoch 085]  average training loss: 1577.4540
cellbender:remove-background: [epoch 085] average test loss: 1629.8034
cellbender:remove-background: [epoch 086]  average training loss: 1578.0716
cellbender:remove-background: [epoch 087]  average training loss: 1575.7333
cellbender:remove-background: [epoch 088]  average training loss: 1569.7502
cellbender:remove-background: [epoch 089]  average training loss: 1581.6806
cellbender:remove-background: [epoch 090]  average training loss: 1577.2131
cellbender:remove-background: [epoch 090] average test loss: 1634.6683
cellbender:remove-background: [epoch 091]  average training loss: 1582.5887
cellbender:remove-background: [epoch 092]  average training loss: 1587.5116
cellbender:remove-background: [epoch 093]  average training loss: 1577.4532
cellbender:remove-background: [epoch 094]  average training loss: 1586.0325
cellbender:remove-background: [epoch 095]  average training loss: 1578.1966
cellbender:remove-background: [epoch 095] average test loss: 1610.2211
cellbender:remove-background: [epoch 096]  average training loss: 1578.5387
cellbender:remove-background: [epoch 097]  average training loss: 1583.0628
cellbender:remove-background: [epoch 098]  average training loss: 1583.4563
cellbender:remove-background: [epoch 099]  average training loss: 1578.3340
cellbender:remove-background: [epoch 100]  average training loss: 1570.5963
cellbender:remove-background: [epoch 100] average test loss: 1653.3954
cellbender:remove-background: [epoch 101]  average training loss: 1590.4308
cellbender:remove-background: [epoch 102]  average training loss: 1577.7269
cellbender:remove-background: [epoch 103]  average training loss: 1579.8716
cellbender:remove-background: [epoch 104]  average training loss: 1582.7281
cellbender:remove-background: [epoch 105]  average training loss: 1583.5435
cellbender:remove-background: [epoch 105] average test loss: 1648.8681
cellbender:remove-background: [epoch 106]  average training loss: 1587.8354
cellbender:remove-background: [epoch 107]  average training loss: 1580.8582
cellbender:remove-background: [epoch 108]  average training loss: 1573.1104
cellbender:remove-background: [epoch 109]  average training loss: 1579.2151
cellbender:remove-background: [epoch 110]  average training loss: 1580.3074
cellbender:remove-background: [epoch 110] average test loss: 1645.2170
cellbender:remove-background: [epoch 111]  average training loss: 1576.7869
cellbender:remove-background: [epoch 112]  average training loss: 1575.0930
cellbender:remove-background: [epoch 113]  average training loss: 1580.7921
cellbender:remove-background: [epoch 114]  average training loss: 1576.6557
cellbender:remove-background: [epoch 115]  average training loss: 1583.1541
cellbender:remove-background: [epoch 115] average test loss: 1677.4423
cellbender:remove-background: [epoch 116]  average training loss: 1576.6752
cellbender:remove-background: [epoch 117]  average training loss: 1579.7537
cellbender:remove-background: [epoch 118]  average training loss: 1580.1909
cellbender:remove-background: [epoch 119]  average training loss: 1573.1226
cellbender:remove-background: [epoch 120]  average training loss: 1577.3943
cellbender:remove-background: [epoch 120] average test loss: 1647.8610
cellbender:remove-background: [epoch 121]  average training loss: 1584.1290
cellbender:remove-background: [epoch 122]  average training loss: 1585.4300
cellbender:remove-background: [epoch 123]  average training loss: 1588.4459
cellbender:remove-background: [epoch 124]  average training loss: 1570.4236
cellbender:remove-background: [epoch 125]  average training loss: 1590.6976
cellbender:remove-background: [epoch 125] average test loss: 1685.1353
cellbender:remove-background: [epoch 126]  average training loss: 1573.8174
cellbender:remove-background: [epoch 127]  average training loss: 1576.2276
cellbender:remove-background: [epoch 128]  average training loss: 1582.5709
cellbender:remove-background: [epoch 129]  average training loss: 1578.0324
cellbender:remove-background: [epoch 130]  average training loss: 1573.2366
cellbender:remove-background: [epoch 130] average test loss: 1652.1380
cellbender:remove-background: [epoch 131]  average training loss: 1574.9456
cellbender:remove-background: [epoch 132]  average training loss: 1572.7869
cellbender:remove-background: [epoch 133]  average training loss: 1575.9170
cellbender:remove-background: [epoch 134]  average training loss: 1572.6368
cellbender:remove-background: [epoch 135]  average training loss: 1575.6591
cellbender:remove-background: [epoch 135] average test loss: 1665.1744
cellbender:remove-background: [epoch 136]  average training loss: 1582.6334
cellbender:remove-background: [epoch 137]  average training loss: 1571.5858
cellbender:remove-background: [epoch 138]  average training loss: 1579.6387
cellbender:remove-background: [epoch 139]  average training loss: 1572.8152
cellbender:remove-background: [epoch 140]  average training loss: 1571.3836
cellbender:remove-background: [epoch 140] average test loss: 1674.7153
cellbender:remove-background: [epoch 141]  average training loss: 1571.4934
cellbender:remove-background: [epoch 142]  average training loss: 1582.9948
cellbender:remove-background: [epoch 143]  average training loss: 1573.3690
cellbender:remove-background: [epoch 144]  average training loss: 1572.7128
cellbender:remove-background: [epoch 145]  average training loss: 1585.4811
cellbender:remove-background: [epoch 145] average test loss: 1656.1278
cellbender:remove-background: [epoch 146]  average training loss: 1572.3628
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/2477-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 147]  average training loss: 1577.9529
cellbender:remove-background: [epoch 148]  average training loss: 1580.0706
cellbender:remove-background: [epoch 149]  average training loss: 1576.0473
cellbender:remove-background: [epoch 150]  average training loss: 1583.3606
cellbender:remove-background: [epoch 150] average test loss: 1649.6162
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/2477-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:32:54
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpjqsqx4ni
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpjqsqx4ni
/tmp/tmpjqsqx4ni/78b547e7aa_random.pyro
/tmp/tmpjqsqx4ni/78b547e7aa_random.cuda
/tmp/tmpjqsqx4ni/78b547e7aa_model.torch
/tmp/tmpjqsqx4ni/78b547e7aa_optim.torch
/tmp/tmpjqsqx4ni/78b547e7aa_optim.pyro
/tmp/tmpjqsqx4ni/78b547e7aa_params.pyro
/tmp/tmpjqsqx4ni/78b547e7aa_train.loaderstate
/tmp/tmpjqsqx4ni/78b547e7aa_test.loaderstate
/tmp/tmpjqsqx4ni/78b547e7aa_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 (1/45)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/45)
cellbender:remove-background: Working on chunk (3/45)
cellbender:remove-background: Working on chunk (4/45)
cellbender:remove-background: Working on chunk (5/45)
cellbender:remove-background: Working on chunk (6/45)
cellbender:remove-background: Working on chunk (7/45)
cellbender:remove-background: Working on chunk (8/45)
cellbender:remove-background: Working on chunk (9/45)
cellbender:remove-background: Working on chunk (10/45)
cellbender:remove-background: Working on chunk (11/45)
cellbender:remove-background: Working on chunk (12/45)
cellbender:remove-background: Working on chunk (13/45)
cellbender:remove-background: Working on chunk (14/45)
cellbender:remove-background: Working on chunk (15/45)
cellbender:remove-background: Working on chunk (16/45)
cellbender:remove-background: Working on chunk (17/45)
cellbender:remove-background: Working on chunk (18/45)
cellbender:remove-background: Working on chunk (19/45)
cellbender:remove-background: Working on chunk (20/45)
cellbender:remove-background: Working on chunk (21/45)
cellbender:remove-background: Working on chunk (22/45)
cellbender:remove-background: Working on chunk (23/45)
cellbender:remove-background: Working on chunk (24/45)
cellbender:remove-background: Working on chunk (25/45)
cellbender:remove-background: Working on chunk (26/45)
cellbender:remove-background: Working on chunk (27/45)
cellbender:remove-background: Working on chunk (28/45)
cellbender:remove-background: Working on chunk (29/45)
cellbender:remove-background: Working on chunk (30/45)
cellbender:remove-background: Working on chunk (31/45)
cellbender:remove-background: Working on chunk (32/45)
cellbender:remove-background: Working on chunk (33/45)
cellbender:remove-background: Working on chunk (34/45)
cellbender:remove-background: Working on chunk (35/45)
cellbender:remove-background: Working on chunk (36/45)
cellbender:remove-background: Working on chunk (37/45)
cellbender:remove-background: Working on chunk (38/45)
cellbender:remove-background: Working on chunk (39/45)
cellbender:remove-background: Working on chunk (40/45)
cellbender:remove-background: Working on chunk (41/45)
cellbender:remove-background: Working on chunk (42/45)
cellbender:remove-background: Working on chunk (43/45)
cellbender:remove-background: Working on chunk (44/45)
cellbender:remove-background: Working on chunk (45/45)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-dACC/2477-Bipolar-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/2477-Bipolar-dACC/2477-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:35:47

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-dACC/2477-Bipolar-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-dACC/2477-Bipolar-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:     [0.81 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 15:41:39 Total MCKP estimation time = 339.29 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/2477-Bipolar-dACC/2477-Bipolar-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/2477-Bipolar-dACC/2477-Bipolar-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/2477-Bipolar-dACC/2477-Bipolar-dACC.cellbender.output_metrics.csv
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    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 <module>
    ) 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 <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    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 <module>
    ) 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/2477-Bipolar-dACC/2477-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:41:49