cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2673-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-dACC/2673-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 5480 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 8af471e10e)
cellbender:remove-background: 2024-06-06 15:11:39
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/2673-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: 30819 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 1654
cellbender:remove-background: Prior on counts for empty droplets is 50
cellbender:remove-background: Excluding 9424 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21395 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 25
cellbender:remove-background: Using 5480 probable cell barcodes, plus an additional 14520 barcodes, and 54792 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 50 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzlsa6da4
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: 2495.9334
cellbender:remove-background: [epoch 002]  average training loss: 2082.5241  (7.0 seconds per epoch)
cellbender:remove-background: Will checkpoint every 60 epochs
cellbender:remove-background: [epoch 003]  average training loss: 1872.0267
cellbender:remove-background: [epoch 004]  average training loss: 1724.4845
cellbender:remove-background: [epoch 005]  average training loss: 1680.6886
cellbender:remove-background: [epoch 005] average test loss: 1773.6378
cellbender:remove-background: [epoch 006]  average training loss: 1652.8359
cellbender:remove-background: [epoch 007]  average training loss: 1630.6216
cellbender:remove-background: [epoch 008]  average training loss: 1619.5709
cellbender:remove-background: [epoch 009]  average training loss: 1617.0144
cellbender:remove-background: [epoch 010]  average training loss: 1604.0193
cellbender:remove-background: [epoch 010] average test loss: 1655.1844
cellbender:remove-background: [epoch 011]  average training loss: 1601.7350
cellbender:remove-background: [epoch 012]  average training loss: 1603.9377
cellbender:remove-background: [epoch 013]  average training loss: 1588.4734
cellbender:remove-background: [epoch 014]  average training loss: 1593.7487
cellbender:remove-background: [epoch 015]  average training loss: 1519.8608
cellbender:remove-background: [epoch 015] average test loss: 1553.3951
cellbender:remove-background: [epoch 016]  average training loss: 1491.2710
cellbender:remove-background: [epoch 017]  average training loss: 1472.0701
cellbender:remove-background: [epoch 018]  average training loss: 1459.6328
cellbender:remove-background: [epoch 019]  average training loss: 1449.9083
cellbender:remove-background: [epoch 020]  average training loss: 1443.3516
cellbender:remove-background: [epoch 020] average test loss: 1470.4696
cellbender:remove-background: [epoch 021]  average training loss: 1440.3679
cellbender:remove-background: [epoch 022]  average training loss: 1433.6264
cellbender:remove-background: [epoch 023]  average training loss: 1429.8124
cellbender:remove-background: [epoch 024]  average training loss: 1425.2557
cellbender:remove-background: [epoch 025]  average training loss: 1423.7541
cellbender:remove-background: [epoch 025] average test loss: 1442.3445
cellbender:remove-background: [epoch 026]  average training loss: 1417.4330
cellbender:remove-background: [epoch 027]  average training loss: 1414.0187
cellbender:remove-background: [epoch 028]  average training loss: 1412.4670
cellbender:remove-background: [epoch 029]  average training loss: 1409.7344
cellbender:remove-background: [epoch 030]  average training loss: 1406.0481
cellbender:remove-background: [epoch 030] average test loss: 1426.7640
cellbender:remove-background: [epoch 031]  average training loss: 1404.9661
cellbender:remove-background: [epoch 032]  average training loss: 1403.5399
cellbender:remove-background: [epoch 033]  average training loss: 1402.9466
cellbender:remove-background: [epoch 034]  average training loss: 1398.4922
cellbender:remove-background: [epoch 035]  average training loss: 1395.9841
cellbender:remove-background: [epoch 035] average test loss: 1417.8667
cellbender:remove-background: [epoch 036]  average training loss: 1395.4569
cellbender:remove-background: [epoch 037]  average training loss: 1399.4947
cellbender:remove-background: [epoch 038]  average training loss: 1398.6135
cellbender:remove-background: [epoch 039]  average training loss: 1400.2060
cellbender:remove-background: [epoch 040]  average training loss: 1396.5127
cellbender:remove-background: [epoch 040] average test loss: 1418.3433
cellbender:remove-background: [epoch 041]  average training loss: 1398.6029
cellbender:remove-background: [epoch 042]  average training loss: 1396.5946
cellbender:remove-background: [epoch 043]  average training loss: 1396.9218
cellbender:remove-background: [epoch 044]  average training loss: 1398.7406
cellbender:remove-background: [epoch 045]  average training loss: 1396.7479
cellbender:remove-background: [epoch 045] average test loss: 1426.6299
cellbender:remove-background: [epoch 046]  average training loss: 1392.0228
cellbender:remove-background: [epoch 047]  average training loss: 1395.2205
cellbender:remove-background: [epoch 048]  average training loss: 1393.9546
cellbender:remove-background: [epoch 049]  average training loss: 1394.0150
cellbender:remove-background: [epoch 050]  average training loss: 1390.7860
cellbender:remove-background: [epoch 050] average test loss: 1431.8872
cellbender:remove-background: [epoch 051]  average training loss: 1394.6563
cellbender:remove-background: [epoch 052]  average training loss: 1391.7745
cellbender:remove-background: [epoch 053]  average training loss: 1391.4166
cellbender:remove-background: [epoch 054]  average training loss: 1389.1962
cellbender:remove-background: [epoch 055]  average training loss: 1388.7889
cellbender:remove-background: [epoch 055] average test loss: 1424.6742
cellbender:remove-background: [epoch 056]  average training loss: 1391.6059
cellbender:remove-background: [epoch 057]  average training loss: 1389.0082
cellbender:remove-background: [epoch 058]  average training loss: 1394.5782
cellbender:remove-background: [epoch 059]  average training loss: 1389.6479
cellbender:remove-background: [epoch 060]  average training loss: 1387.1939
cellbender:remove-background: [epoch 060] average test loss: 1420.1601
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/2673-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 061]  average training loss: 1386.4124
cellbender:remove-background: [epoch 062]  average training loss: 1386.2231
cellbender:remove-background: [epoch 063]  average training loss: 1389.0411
cellbender:remove-background: [epoch 064]  average training loss: 1388.1770
cellbender:remove-background: [epoch 065]  average training loss: 1388.8913
cellbender:remove-background: [epoch 065] average test loss: 1427.2806
cellbender:remove-background: [epoch 066]  average training loss: 1391.4975
cellbender:remove-background: [epoch 067]  average training loss: 1389.4224
cellbender:remove-background: [epoch 068]  average training loss: 1387.4295
cellbender:remove-background: [epoch 069]  average training loss: 1387.0184
cellbender:remove-background: [epoch 070]  average training loss: 1388.5684
cellbender:remove-background: [epoch 070] average test loss: 1417.8447
cellbender:remove-background: [epoch 071]  average training loss: 1387.9691
cellbender:remove-background: [epoch 072]  average training loss: 1389.9322
cellbender:remove-background: [epoch 073]  average training loss: 1388.6786
cellbender:remove-background: [epoch 074]  average training loss: 1389.6139
cellbender:remove-background: [epoch 075]  average training loss: 1390.3237
cellbender:remove-background: [epoch 075] average test loss: 1424.2697
cellbender:remove-background: [epoch 076]  average training loss: 1390.6404
cellbender:remove-background: [epoch 077]  average training loss: 1394.2771
cellbender:remove-background: [epoch 078]  average training loss: 1392.8665
cellbender:remove-background: [epoch 079]  average training loss: 1393.1435
cellbender:remove-background: [epoch 080]  average training loss: 1391.4064
cellbender:remove-background: [epoch 080] average test loss: 1433.9467
cellbender:remove-background: [epoch 081]  average training loss: 1395.9183
cellbender:remove-background: [epoch 082]  average training loss: 1393.4357
cellbender:remove-background: [epoch 083]  average training loss: 1395.5199
cellbender:remove-background: [epoch 084]  average training loss: 1402.5520
cellbender:remove-background: [epoch 085]  average training loss: 1396.5311
cellbender:remove-background: [epoch 085] average test loss: 1430.3301
cellbender:remove-background: [epoch 086]  average training loss: 1398.8081
cellbender:remove-background: [epoch 087]  average training loss: 1396.1491
cellbender:remove-background: [epoch 088]  average training loss: 1394.7580
cellbender:remove-background: [epoch 089]  average training loss: 1395.6626
cellbender:remove-background: [epoch 090]  average training loss: 1397.1018
cellbender:remove-background: [epoch 090] average test loss: 1434.8451
cellbender:remove-background: [epoch 091]  average training loss: 1393.6668
cellbender:remove-background: [epoch 092]  average training loss: 1393.1868
cellbender:remove-background: [epoch 093]  average training loss: 1395.1148
cellbender:remove-background: [epoch 094]  average training loss: 1396.2535
cellbender:remove-background: [epoch 095]  average training loss: 1394.5505
cellbender:remove-background: [epoch 095] average test loss: 1439.0447
cellbender:remove-background: [epoch 096]  average training loss: 1395.0769
cellbender:remove-background: [epoch 097]  average training loss: 1394.2826
cellbender:remove-background: [epoch 098]  average training loss: 1391.5600
cellbender:remove-background: [epoch 099]  average training loss: 1393.2950
cellbender:remove-background: [epoch 100]  average training loss: 1393.9090
cellbender:remove-background: [epoch 100] average test loss: 1445.7884
cellbender:remove-background: [epoch 101]  average training loss: 1392.1623
cellbender:remove-background: [epoch 102]  average training loss: 1394.1830
cellbender:remove-background: [epoch 103]  average training loss: 1393.8659
cellbender:remove-background: [epoch 104]  average training loss: 1394.6391
cellbender:remove-background: [epoch 105]  average training loss: 1392.3848
cellbender:remove-background: [epoch 105] average test loss: 1440.1962
cellbender:remove-background: [epoch 106]  average training loss: 1392.9397
cellbender:remove-background: [epoch 107]  average training loss: 1392.3709
cellbender:remove-background: [epoch 108]  average training loss: 1389.3650
cellbender:remove-background: [epoch 109]  average training loss: 1392.3568
cellbender:remove-background: [epoch 110]  average training loss: 1389.6338
cellbender:remove-background: [epoch 110] average test loss: 1443.2267
cellbender:remove-background: [epoch 111]  average training loss: 1392.2726
cellbender:remove-background: [epoch 112]  average training loss: 1391.9924
cellbender:remove-background: [epoch 113]  average training loss: 1389.1978
cellbender:remove-background: [epoch 114]  average training loss: 1389.2728
cellbender:remove-background: [epoch 115]  average training loss: 1389.3787
cellbender:remove-background: [epoch 115] average test loss: 1439.2310
cellbender:remove-background: [epoch 116]  average training loss: 1390.3817
cellbender:remove-background: [epoch 117]  average training loss: 1388.9935
cellbender:remove-background: [epoch 118]  average training loss: 1388.8055
cellbender:remove-background: [epoch 119]  average training loss: 1389.1539
cellbender:remove-background: [epoch 120]  average training loss: 1390.3959
cellbender:remove-background: [epoch 120] average test loss: 1440.7353
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/2673-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 121]  average training loss: 1388.6616
cellbender:remove-background: [epoch 122]  average training loss: 1390.5683
cellbender:remove-background: [epoch 123]  average training loss: 1388.3056
cellbender:remove-background: [epoch 124]  average training loss: 1388.0725
cellbender:remove-background: [epoch 125]  average training loss: 1388.8807
cellbender:remove-background: [epoch 125] average test loss: 1436.6145
cellbender:remove-background: [epoch 126]  average training loss: 1390.0727
cellbender:remove-background: [epoch 127]  average training loss: 1389.3955
cellbender:remove-background: [epoch 128]  average training loss: 1388.4816
cellbender:remove-background: [epoch 129]  average training loss: 1387.5220
cellbender:remove-background: [epoch 130]  average training loss: 1389.1997
cellbender:remove-background: [epoch 130] average test loss: 1440.3230
cellbender:remove-background: [epoch 131]  average training loss: 1389.1966
cellbender:remove-background: [epoch 132]  average training loss: 1387.6996
cellbender:remove-background: [epoch 133]  average training loss: 1388.5684
cellbender:remove-background: [epoch 134]  average training loss: 1388.2803
cellbender:remove-background: [epoch 135]  average training loss: 1387.6456
cellbender:remove-background: [epoch 135] average test loss: 1436.6105
cellbender:remove-background: [epoch 136]  average training loss: 1388.8277
cellbender:remove-background: [epoch 137]  average training loss: 1387.7231
cellbender:remove-background: [epoch 138]  average training loss: 1388.2806
cellbender:remove-background: [epoch 139]  average training loss: 1388.2446
cellbender:remove-background: [epoch 140]  average training loss: 1388.5492
cellbender:remove-background: [epoch 140] average test loss: 1440.7400
cellbender:remove-background: [epoch 141]  average training loss: 1389.7172
cellbender:remove-background: [epoch 142]  average training loss: 1388.1529
cellbender:remove-background: [epoch 143]  average training loss: 1387.4236
cellbender:remove-background: [epoch 144]  average training loss: 1387.8843
cellbender:remove-background: [epoch 145]  average training loss: 1388.2382
cellbender:remove-background: [epoch 145] average test loss: 1440.5040
cellbender:remove-background: [epoch 146]  average training loss: 1387.9366
cellbender:remove-background: [epoch 147]  average training loss: 1388.2351
cellbender:remove-background: [epoch 148]  average training loss: 1388.6311
cellbender:remove-background: [epoch 149]  average training loss: 1387.9419
cellbender:remove-background: [epoch 150]  average training loss: 1388.0132
cellbender:remove-background: [epoch 150] average test loss: 1442.3914
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/2673-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:33:25
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpyqok3cxu
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpyqok3cxu
/tmp/tmpyqok3cxu/8af471e10e_random.pyro
/tmp/tmpyqok3cxu/8af471e10e_random.cuda
/tmp/tmpyqok3cxu/8af471e10e_model.torch
/tmp/tmpyqok3cxu/8af471e10e_optim.torch
/tmp/tmpyqok3cxu/8af471e10e_optim.pyro
/tmp/tmpyqok3cxu/8af471e10e_params.pyro
/tmp/tmpyqok3cxu/8af471e10e_train.loaderstate
/tmp/tmpyqok3cxu/8af471e10e_test.loaderstate
/tmp/tmpyqok3cxu/8af471e10e_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 (1/47)
cellbender:remove-background:     [0.07 mins per chunk]
cellbender:remove-background: Working on chunk (2/47)
cellbender:remove-background: Working on chunk (3/47)
cellbender:remove-background: Working on chunk (4/47)
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cellbender:remove-background: Working on chunk (17/47)
cellbender:remove-background: Working on chunk (18/47)
cellbender:remove-background: Working on chunk (19/47)
cellbender:remove-background: Working on chunk (20/47)
cellbender:remove-background: Working on chunk (21/47)
cellbender:remove-background: Working on chunk (22/47)
cellbender:remove-background: Working on chunk (23/47)
cellbender:remove-background: Working on chunk (24/47)
cellbender:remove-background: Working on chunk (25/47)
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cellbender:remove-background: Working on chunk (27/47)
cellbender:remove-background: Working on chunk (28/47)
cellbender:remove-background: Working on chunk (29/47)
cellbender:remove-background: Working on chunk (30/47)
cellbender:remove-background: Working on chunk (31/47)
cellbender:remove-background: Working on chunk (32/47)
cellbender:remove-background: Working on chunk (33/47)
cellbender:remove-background: Working on chunk (34/47)
cellbender:remove-background: Working on chunk (35/47)
cellbender:remove-background: Working on chunk (36/47)
cellbender:remove-background: Working on chunk (37/47)
cellbender:remove-background: Working on chunk (38/47)
cellbender:remove-background: Working on chunk (39/47)
cellbender:remove-background: Working on chunk (40/47)
cellbender:remove-background: Working on chunk (41/47)
cellbender:remove-background: Working on chunk (42/47)
cellbender:remove-background: Working on chunk (43/47)
cellbender:remove-background: Working on chunk (44/47)
cellbender:remove-background: Working on chunk (45/47)
cellbender:remove-background: Working on chunk (46/47)
cellbender:remove-background: Working on chunk (47/47)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-dACC/2673-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/2673-Bipolar-dACC/2673-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:38:19

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-dACC/2673-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/2673-Bipolar-dACC/2673-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:     [0.78 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 15:44:01 Total MCKP estimation time = 327.60 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/2673-Bipolar-dACC/2673-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/2673-Bipolar-dACC/2673-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/2673-Bipolar-dACC/2673-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/2673-Bipolar-dACC/2673-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:44:12