cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2780-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-dACC/2780-Control-dACC.cellbender.output.h5 --cuda --expected-cells 6206 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash a9ce7f9a9a)
cellbender:remove-background: 2024-06-06 14:54:30
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/2780-Control-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: 30901 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 1331
cellbender:remove-background: Prior on counts for empty droplets is 84
cellbender:remove-background: Excluding 7967 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 22934 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 42
cellbender:remove-background: Using 6206 probable cell barcodes, plus an additional 13794 barcodes, and 56787 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 83 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpuum07ys8
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: 2749.5097
cellbender:remove-background: [epoch 002]  average training loss: 2336.3115  (6.9 seconds per epoch)
cellbender:remove-background: Will checkpoint every 61 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2112.3619
cellbender:remove-background: [epoch 004]  average training loss: 1967.7503
cellbender:remove-background: [epoch 005]  average training loss: 1932.8916
cellbender:remove-background: [epoch 005] average test loss: 2012.7125
cellbender:remove-background: [epoch 006]  average training loss: 1912.3853
cellbender:remove-background: [epoch 007]  average training loss: 1889.1299
cellbender:remove-background: [epoch 008]  average training loss: 1878.4324
cellbender:remove-background: [epoch 009]  average training loss: 1880.1424
cellbender:remove-background: [epoch 010]  average training loss: 1864.3925
cellbender:remove-background: [epoch 010] average test loss: 1887.6246
cellbender:remove-background: [epoch 011]  average training loss: 1864.9356
cellbender:remove-background: [epoch 012]  average training loss: 1844.3450
cellbender:remove-background: [epoch 013]  average training loss: 1803.8448
cellbender:remove-background: [epoch 014]  average training loss: 1791.3401
cellbender:remove-background: [epoch 015]  average training loss: 1777.9314
cellbender:remove-background: [epoch 015] average test loss: 1819.1814
cellbender:remove-background: [epoch 016]  average training loss: 1771.9527
cellbender:remove-background: [epoch 017]  average training loss: 1775.6920
cellbender:remove-background: [epoch 018]  average training loss: 1766.7254
cellbender:remove-background: [epoch 019]  average training loss: 1756.2840
cellbender:remove-background: [epoch 020]  average training loss: 1739.1289
cellbender:remove-background: [epoch 020] average test loss: 1773.6078
cellbender:remove-background: [epoch 021]  average training loss: 1728.5192
cellbender:remove-background: [epoch 022]  average training loss: 1718.0149
cellbender:remove-background: [epoch 023]  average training loss: 1712.8541
cellbender:remove-background: [epoch 024]  average training loss: 1703.4743
cellbender:remove-background: [epoch 025]  average training loss: 1699.8076
cellbender:remove-background: [epoch 025] average test loss: 1725.7965
cellbender:remove-background: [epoch 026]  average training loss: 1692.5003
cellbender:remove-background: [epoch 027]  average training loss: 1687.3499
cellbender:remove-background: [epoch 028]  average training loss: 1685.5694
cellbender:remove-background: [epoch 029]  average training loss: 1683.4134
cellbender:remove-background: [epoch 030]  average training loss: 1681.4849
cellbender:remove-background: [epoch 030] average test loss: 1701.8620
cellbender:remove-background: [epoch 031]  average training loss: 1680.6571
cellbender:remove-background: [epoch 032]  average training loss: 1678.7556
cellbender:remove-background: [epoch 033]  average training loss: 1677.9026
cellbender:remove-background: [epoch 034]  average training loss: 1679.2430
cellbender:remove-background: [epoch 035]  average training loss: 1678.3040
cellbender:remove-background: [epoch 035] average test loss: 1708.0719
cellbender:remove-background: [epoch 036]  average training loss: 1679.0202
cellbender:remove-background: [epoch 037]  average training loss: 1680.8609
cellbender:remove-background: [epoch 038]  average training loss: 1678.8390
cellbender:remove-background: [epoch 039]  average training loss: 1676.9794
cellbender:remove-background: [epoch 040]  average training loss: 1675.0754
cellbender:remove-background: [epoch 040] average test loss: 1694.9450
cellbender:remove-background: [epoch 041]  average training loss: 1675.3994
cellbender:remove-background: [epoch 042]  average training loss: 1677.3228
cellbender:remove-background: [epoch 043]  average training loss: 1673.3107
cellbender:remove-background: [epoch 044]  average training loss: 1673.0939
cellbender:remove-background: [epoch 045]  average training loss: 1674.2526
cellbender:remove-background: [epoch 045] average test loss: 1706.3498
cellbender:remove-background: [epoch 046]  average training loss: 1671.6665
cellbender:remove-background: [epoch 047]  average training loss: 1673.2749
cellbender:remove-background: [epoch 048]  average training loss: 1673.5603
cellbender:remove-background: [epoch 049]  average training loss: 1674.5989
cellbender:remove-background: [epoch 050]  average training loss: 1673.6656
cellbender:remove-background: [epoch 050] average test loss: 1699.1315
cellbender:remove-background: [epoch 051]  average training loss: 1673.4568
cellbender:remove-background: [epoch 052]  average training loss: 1672.6045
cellbender:remove-background: [epoch 053]  average training loss: 1675.2362
cellbender:remove-background: [epoch 054]  average training loss: 1673.6712
cellbender:remove-background: [epoch 055]  average training loss: 1673.6900
cellbender:remove-background: [epoch 055] average test loss: 1709.0111
cellbender:remove-background: [epoch 056]  average training loss: 1675.3558
cellbender:remove-background: [epoch 057]  average training loss: 1673.9278
cellbender:remove-background: [epoch 058]  average training loss: 1676.6218
cellbender:remove-background: [epoch 059]  average training loss: 1675.4969
cellbender:remove-background: [epoch 060]  average training loss: 1678.4869
cellbender:remove-background: [epoch 060] average test loss: 1714.9250
cellbender:remove-background: [epoch 061]  average training loss: 1681.7521
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/2780-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 062]  average training loss: 1679.6463
cellbender:remove-background: [epoch 063]  average training loss: 1681.6401
cellbender:remove-background: [epoch 064]  average training loss: 1684.1526
cellbender:remove-background: [epoch 065]  average training loss: 1690.6964
cellbender:remove-background: [epoch 065] average test loss: 1689.6185
cellbender:remove-background: [epoch 066]  average training loss: 1686.6918
cellbender:remove-background: [epoch 067]  average training loss: 1686.7353
cellbender:remove-background: [epoch 068]  average training loss: 1692.0484
cellbender:remove-background: [epoch 069]  average training loss: 1684.9745
cellbender:remove-background: [epoch 070]  average training loss: 1693.4285
cellbender:remove-background: [epoch 070] average test loss: 1724.1264
cellbender:remove-background: [epoch 071]  average training loss: 1697.4078
cellbender:remove-background: [epoch 072]  average training loss: 1698.3203
cellbender:remove-background: [epoch 073]  average training loss: 1695.5510
cellbender:remove-background: [epoch 074]  average training loss: 1694.9138
cellbender:remove-background: [epoch 075]  average training loss: 1707.7331
cellbender:remove-background: [epoch 075] average test loss: 1731.4538
cellbender:remove-background: [epoch 076]  average training loss: 1701.0357
cellbender:remove-background: [epoch 077]  average training loss: 1705.6541
cellbender:remove-background: [epoch 078]  average training loss: 1697.0197
cellbender:remove-background: [epoch 079]  average training loss: 1696.4076
cellbender:remove-background: [epoch 080]  average training loss: 1700.4911
cellbender:remove-background: [epoch 080] average test loss: 1761.7267
cellbender:remove-background: [epoch 081]  average training loss: 1699.1486
cellbender:remove-background: [epoch 082]  average training loss: 1701.8564
cellbender:remove-background: [epoch 083]  average training loss: 1698.3980
cellbender:remove-background: [epoch 084]  average training loss: 1703.9538
cellbender:remove-background: [epoch 085]  average training loss: 1712.2476
cellbender:remove-background: [epoch 085] average test loss: 1758.6029
cellbender:remove-background: [epoch 086]  average training loss: 1710.2126
cellbender:remove-background: [epoch 087]  average training loss: 1700.8460
cellbender:remove-background: [epoch 088]  average training loss: 1708.3482
cellbender:remove-background: [epoch 089]  average training loss: 1702.1685
cellbender:remove-background: [epoch 090]  average training loss: 1705.4367
cellbender:remove-background: [epoch 090] average test loss: 1737.6961
cellbender:remove-background: [epoch 091]  average training loss: 1694.6481
cellbender:remove-background: [epoch 092]  average training loss: 1698.4284
cellbender:remove-background: [epoch 093]  average training loss: 1703.2480
cellbender:remove-background: [epoch 094]  average training loss: 1701.7680
cellbender:remove-background: [epoch 095]  average training loss: 1696.3862
cellbender:remove-background: [epoch 095] average test loss: 1767.1183
cellbender:remove-background: [epoch 096]  average training loss: 1695.2317
cellbender:remove-background: [epoch 097]  average training loss: 1701.0787
cellbender:remove-background: [epoch 098]  average training loss: 1700.9361
cellbender:remove-background: [epoch 099]  average training loss: 1693.8080
cellbender:remove-background: [epoch 100]  average training loss: 1699.9879
cellbender:remove-background: [epoch 100] average test loss: 1742.6680
cellbender:remove-background: [epoch 101]  average training loss: 1693.0710
cellbender:remove-background: [epoch 102]  average training loss: 1693.9614
cellbender:remove-background: [epoch 103]  average training loss: 1696.7252
cellbender:remove-background: [epoch 104]  average training loss: 1695.0863
cellbender:remove-background: [epoch 105]  average training loss: 1695.5624
cellbender:remove-background: [epoch 105] average test loss: 1772.8102
cellbender:remove-background: [epoch 106]  average training loss: 1701.4754
cellbender:remove-background: [epoch 107]  average training loss: 1696.0250
cellbender:remove-background: [epoch 108]  average training loss: 1703.7795
cellbender:remove-background: [epoch 109]  average training loss: 1697.3340
cellbender:remove-background: [epoch 110]  average training loss: 1695.2909
cellbender:remove-background: [epoch 110] average test loss: 1764.6283
cellbender:remove-background: [epoch 111]  average training loss: 1689.2476
cellbender:remove-background: [epoch 112]  average training loss: 1692.2744
cellbender:remove-background: [epoch 113]  average training loss: 1696.5055
cellbender:remove-background: [epoch 114]  average training loss: 1692.9987
cellbender:remove-background: [epoch 115]  average training loss: 1696.2893
cellbender:remove-background: [epoch 115] average test loss: 1769.1852
cellbender:remove-background: [epoch 116]  average training loss: 1695.5350
cellbender:remove-background: [epoch 117]  average training loss: 1690.6281
cellbender:remove-background: [epoch 118]  average training loss: 1693.0770
cellbender:remove-background: [epoch 119]  average training loss: 1695.2345
cellbender:remove-background: [epoch 120]  average training loss: 1694.0633
cellbender:remove-background: [epoch 120] average test loss: 1755.1660
cellbender:remove-background: [epoch 121]  average training loss: 1694.7639
cellbender:remove-background: [epoch 122]  average training loss: 1695.1651
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/2780-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 123]  average training loss: 1688.3138
cellbender:remove-background: [epoch 124]  average training loss: 1690.8860
cellbender:remove-background: [epoch 125]  average training loss: 1684.3728
cellbender:remove-background: [epoch 125] average test loss: 1761.5064
cellbender:remove-background: [epoch 126]  average training loss: 1694.9365
cellbender:remove-background: [epoch 127]  average training loss: 1689.2092
cellbender:remove-background: [epoch 128]  average training loss: 1691.1508
cellbender:remove-background: [epoch 129]  average training loss: 1691.2371
cellbender:remove-background: [epoch 130]  average training loss: 1691.8182
cellbender:remove-background: [epoch 130] average test loss: 1761.5379
cellbender:remove-background: [epoch 131]  average training loss: 1692.4665
cellbender:remove-background: [epoch 132]  average training loss: 1688.1809
cellbender:remove-background: [epoch 133]  average training loss: 1690.1021
cellbender:remove-background: [epoch 134]  average training loss: 1688.1383
cellbender:remove-background: [epoch 135]  average training loss: 1688.9129
cellbender:remove-background: [epoch 135] average test loss: 1760.0209
cellbender:remove-background: [epoch 136]  average training loss: 1687.6100
cellbender:remove-background: [epoch 137]  average training loss: 1686.6237
cellbender:remove-background: [epoch 138]  average training loss: 1686.8527
cellbender:remove-background: [epoch 139]  average training loss: 1690.8038
cellbender:remove-background: [epoch 140]  average training loss: 1688.4884
cellbender:remove-background: [epoch 140] average test loss: 1769.2357
cellbender:remove-background: [epoch 141]  average training loss: 1691.7950
cellbender:remove-background: [epoch 142]  average training loss: 1687.8201
cellbender:remove-background: [epoch 143]  average training loss: 1691.0793
cellbender:remove-background: [epoch 144]  average training loss: 1687.9174
cellbender:remove-background: [epoch 145]  average training loss: 1686.2286
cellbender:remove-background: [epoch 145] average test loss: 1766.1024
cellbender:remove-background: [epoch 146]  average training loss: 1688.8805
cellbender:remove-background: [epoch 147]  average training loss: 1692.8737
cellbender:remove-background: [epoch 148]  average training loss: 1689.7621
cellbender:remove-background: [epoch 149]  average training loss: 1689.8186
cellbender:remove-background: [epoch 150]  average training loss: 1687.9280
cellbender:remove-background: [epoch 150] average test loss: 1758.5818
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/2780-Control-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:15:26
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzyrgup4w
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpzyrgup4w
/tmp/tmpzyrgup4w/a9ce7f9a9a_random.pyro
/tmp/tmpzyrgup4w/a9ce7f9a9a_random.cuda
/tmp/tmpzyrgup4w/a9ce7f9a9a_model.torch
/tmp/tmpzyrgup4w/a9ce7f9a9a_optim.torch
/tmp/tmpzyrgup4w/a9ce7f9a9a_optim.pyro
/tmp/tmpzyrgup4w/a9ce7f9a9a_params.pyro
/tmp/tmpzyrgup4w/a9ce7f9a9a_train.loaderstate
/tmp/tmpzyrgup4w/a9ce7f9a9a_test.loaderstate
/tmp/tmpzyrgup4w/a9ce7f9a9a_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 (1/52)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/52)
cellbender:remove-background: Working on chunk (3/52)
cellbender:remove-background: Working on chunk (4/52)
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cellbender:remove-background: Working on chunk (7/52)
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cellbender:remove-background: Working on chunk (9/52)
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cellbender:remove-background: Working on chunk (15/52)
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cellbender:remove-background: Working on chunk (17/52)
cellbender:remove-background: Working on chunk (18/52)
cellbender:remove-background: Working on chunk (19/52)
cellbender:remove-background: Working on chunk (20/52)
cellbender:remove-background: Working on chunk (21/52)
cellbender:remove-background: Working on chunk (22/52)
cellbender:remove-background: Working on chunk (23/52)
cellbender:remove-background: Working on chunk (24/52)
cellbender:remove-background: Working on chunk (25/52)
cellbender:remove-background: Working on chunk (26/52)
cellbender:remove-background: Working on chunk (27/52)
cellbender:remove-background: Working on chunk (28/52)
cellbender:remove-background: Working on chunk (29/52)
cellbender:remove-background: Working on chunk (30/52)
cellbender:remove-background: Working on chunk (31/52)
cellbender:remove-background: Working on chunk (32/52)
cellbender:remove-background: Working on chunk (33/52)
cellbender:remove-background: Working on chunk (34/52)
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cellbender:remove-background: Working on chunk (36/52)
cellbender:remove-background: Working on chunk (37/52)
cellbender:remove-background: Working on chunk (38/52)
cellbender:remove-background: Working on chunk (39/52)
cellbender:remove-background: Working on chunk (40/52)
cellbender:remove-background: Working on chunk (41/52)
cellbender:remove-background: Working on chunk (42/52)
cellbender:remove-background: Working on chunk (43/52)
cellbender:remove-background: Working on chunk (44/52)
cellbender:remove-background: Working on chunk (45/52)
cellbender:remove-background: Working on chunk (46/52)
cellbender:remove-background: Working on chunk (47/52)
cellbender:remove-background: Working on chunk (48/52)
cellbender:remove-background: Working on chunk (49/52)
cellbender:remove-background: Working on chunk (50/52)
cellbender:remove-background: Working on chunk (51/52)
cellbender:remove-background: Working on chunk (52/52)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-dACC/2780-Control-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/2780-Control-dACC/2780-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:18:55

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-dACC/2780-Control-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-dACC/2780-Control-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:     [0.89 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 15:25:33 Total MCKP estimation time = 382.67 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/2780-Control-dACC/2780-Control-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/2780-Control-dACC/2780-Control-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/2780-Control-dACC/2780-Control-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/2780-Control-dACC/2780-Control-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:26:06