cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2083-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-dACC/2083-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 12496 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 21b1add825)
cellbender:remove-background: 2024-06-06 14:54:01
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/2083-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: 31351 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 607
cellbender:remove-background: Prior on counts for empty droplets is 89
cellbender:remove-background: Excluding 5088 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 26263 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 44
cellbender:remove-background: Using 12496 probable cell barcodes, plus an additional 7504 barcodes, and 30865 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 87 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpxls7s5pl
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: 2513.8792
cellbender:remove-background: [epoch 002]  average training loss: 2213.1144  (7.7 seconds per epoch)
cellbender:remove-background: Will checkpoint every 55 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2034.8679
cellbender:remove-background: [epoch 004]  average training loss: 1932.7407
cellbender:remove-background: [epoch 005]  average training loss: 1886.4525
cellbender:remove-background: [epoch 005] average test loss: 1922.2659
cellbender:remove-background: [epoch 006]  average training loss: 1861.3383
cellbender:remove-background: [epoch 007]  average training loss: 1846.1417
cellbender:remove-background: [epoch 008]  average training loss: 1827.3826
cellbender:remove-background: [epoch 009]  average training loss: 1827.2746
cellbender:remove-background: [epoch 010]  average training loss: 1809.7406
cellbender:remove-background: [epoch 010] average test loss: 1846.0915
cellbender:remove-background: [epoch 011]  average training loss: 1821.2649
cellbender:remove-background: [epoch 012]  average training loss: 1817.8718
cellbender:remove-background: [epoch 013]  average training loss: 1806.8846
cellbender:remove-background: [epoch 014]  average training loss: 1815.3342
cellbender:remove-background: [epoch 015]  average training loss: 1794.8477
cellbender:remove-background: [epoch 015] average test loss: 1836.1916
cellbender:remove-background: [epoch 016]  average training loss: 1784.0444
cellbender:remove-background: [epoch 017]  average training loss: 1732.9144
cellbender:remove-background: [epoch 018]  average training loss: 1700.4215
cellbender:remove-background: [epoch 019]  average training loss: 1689.3751
cellbender:remove-background: [epoch 020]  average training loss: 1681.1228
cellbender:remove-background: [epoch 020] average test loss: 1728.2969
cellbender:remove-background: [epoch 021]  average training loss: 1679.4079
cellbender:remove-background: [epoch 022]  average training loss: 1677.2111
cellbender:remove-background: [epoch 023]  average training loss: 1672.6878
cellbender:remove-background: [epoch 024]  average training loss: 1668.0777
cellbender:remove-background: [epoch 025]  average training loss: 1665.6272
cellbender:remove-background: [epoch 025] average test loss: 1687.5180
cellbender:remove-background: [epoch 026]  average training loss: 1660.6628
cellbender:remove-background: [epoch 027]  average training loss: 1658.9340
cellbender:remove-background: [epoch 028]  average training loss: 1659.5296
cellbender:remove-background: [epoch 029]  average training loss: 1656.0958
cellbender:remove-background: [epoch 030]  average training loss: 1654.3458
cellbender:remove-background: [epoch 030] average test loss: 1697.3777
cellbender:remove-background: [epoch 031]  average training loss: 1654.4984
cellbender:remove-background: [epoch 032]  average training loss: 1652.5294
cellbender:remove-background: [epoch 033]  average training loss: 1652.4082
cellbender:remove-background: [epoch 034]  average training loss: 1650.1448
cellbender:remove-background: [epoch 035]  average training loss: 1648.1329
cellbender:remove-background: [epoch 035] average test loss: 1675.2424
cellbender:remove-background: [epoch 036]  average training loss: 1648.2272
cellbender:remove-background: [epoch 037]  average training loss: 1646.6587
cellbender:remove-background: [epoch 038]  average training loss: 1645.5421
cellbender:remove-background: [epoch 039]  average training loss: 1644.7837
cellbender:remove-background: [epoch 040]  average training loss: 1643.4119
cellbender:remove-background: [epoch 040] average test loss: 1665.5979
cellbender:remove-background: [epoch 041]  average training loss: 1643.6434
cellbender:remove-background: [epoch 042]  average training loss: 1641.3788
cellbender:remove-background: [epoch 043]  average training loss: 1641.6658
cellbender:remove-background: [epoch 044]  average training loss: 1640.4507
cellbender:remove-background: [epoch 045]  average training loss: 1639.7403
cellbender:remove-background: [epoch 045] average test loss: 1664.4256
cellbender:remove-background: [epoch 046]  average training loss: 1639.6189
cellbender:remove-background: [epoch 047]  average training loss: 1639.2662
cellbender:remove-background: [epoch 048]  average training loss: 1639.2443
cellbender:remove-background: [epoch 049]  average training loss: 1638.8623
cellbender:remove-background: [epoch 050]  average training loss: 1638.9191
cellbender:remove-background: [epoch 050] average test loss: 1659.1681
cellbender:remove-background: [epoch 051]  average training loss: 1637.2420
cellbender:remove-background: [epoch 052]  average training loss: 1636.4554
cellbender:remove-background: [epoch 053]  average training loss: 1636.5448
cellbender:remove-background: [epoch 054]  average training loss: 1636.1673
cellbender:remove-background: [epoch 055]  average training loss: 1635.8655
cellbender:remove-background: [epoch 055] average test loss: 1659.1679
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/2083-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 056]  average training loss: 1635.7925
cellbender:remove-background: [epoch 057]  average training loss: 1636.1033
cellbender:remove-background: [epoch 058]  average training loss: 1636.0488
cellbender:remove-background: [epoch 059]  average training loss: 1635.6951
cellbender:remove-background: [epoch 060]  average training loss: 1635.1295
cellbender:remove-background: [epoch 060] average test loss: 1656.4438
cellbender:remove-background: [epoch 061]  average training loss: 1632.8175
cellbender:remove-background: [epoch 062]  average training loss: 1634.6635
cellbender:remove-background: [epoch 063]  average training loss: 1635.4935
cellbender:remove-background: [epoch 064]  average training loss: 1635.4359
cellbender:remove-background: [epoch 065]  average training loss: 1635.4934
cellbender:remove-background: [epoch 065] average test loss: 1656.5213
cellbender:remove-background: [epoch 066]  average training loss: 1633.7137
cellbender:remove-background: [epoch 067]  average training loss: 1634.9438
cellbender:remove-background: [epoch 068]  average training loss: 1634.1546
cellbender:remove-background: [epoch 069]  average training loss: 1633.9258
cellbender:remove-background: [epoch 070]  average training loss: 1634.6471
cellbender:remove-background: [epoch 070] average test loss: 1657.9513
cellbender:remove-background: [epoch 071]  average training loss: 1633.0708
cellbender:remove-background: [epoch 072]  average training loss: 1633.9083
cellbender:remove-background: [epoch 073]  average training loss: 1633.8241
cellbender:remove-background: [epoch 074]  average training loss: 1634.2457
cellbender:remove-background: [epoch 075]  average training loss: 1633.6991
cellbender:remove-background: [epoch 075] average test loss: 1659.0103
cellbender:remove-background: [epoch 076]  average training loss: 1633.2510
cellbender:remove-background: [epoch 077]  average training loss: 1633.4733
cellbender:remove-background: [epoch 078]  average training loss: 1632.5384
cellbender:remove-background: [epoch 079]  average training loss: 1632.3048
cellbender:remove-background: [epoch 080]  average training loss: 1634.1458
cellbender:remove-background: [epoch 080] average test loss: 1668.7770
cellbender:remove-background: [epoch 081]  average training loss: 1633.3899
cellbender:remove-background: [epoch 082]  average training loss: 1632.3175
cellbender:remove-background: [epoch 083]  average training loss: 1631.9063
cellbender:remove-background: [epoch 084]  average training loss: 1632.5369
cellbender:remove-background: [epoch 085]  average training loss: 1632.4119
cellbender:remove-background: [epoch 085] average test loss: 1663.7130
cellbender:remove-background: [epoch 086]  average training loss: 1632.0093
cellbender:remove-background: [epoch 087]  average training loss: 1631.9585
cellbender:remove-background: [epoch 088]  average training loss: 1632.3631
cellbender:remove-background: [epoch 089]  average training loss: 1631.2126
cellbender:remove-background: [epoch 090]  average training loss: 1631.0578
cellbender:remove-background: [epoch 090] average test loss: 1658.6061
cellbender:remove-background: [epoch 091]  average training loss: 1630.2810
cellbender:remove-background: [epoch 092]  average training loss: 1631.1235
cellbender:remove-background: [epoch 093]  average training loss: 1631.0315
cellbender:remove-background: [epoch 094]  average training loss: 1629.5608
cellbender:remove-background: [epoch 095]  average training loss: 1630.4168
cellbender:remove-background: [epoch 095] average test loss: 1656.8487
cellbender:remove-background: [epoch 096]  average training loss: 1629.7963
cellbender:remove-background: [epoch 097]  average training loss: 1628.8525
cellbender:remove-background: [epoch 098]  average training loss: 1628.6559
cellbender:remove-background: [epoch 099]  average training loss: 1628.6613
cellbender:remove-background: [epoch 100]  average training loss: 1628.2905
cellbender:remove-background: [epoch 100] average test loss: 1657.7135
cellbender:remove-background: [epoch 101]  average training loss: 1628.0701
cellbender:remove-background: [epoch 102]  average training loss: 1627.8715
cellbender:remove-background: [epoch 103]  average training loss: 1627.6604
cellbender:remove-background: [epoch 104]  average training loss: 1629.0539
cellbender:remove-background: [epoch 105]  average training loss: 1626.5017
cellbender:remove-background: [epoch 105] average test loss: 1659.3856
cellbender:remove-background: [epoch 106]  average training loss: 1628.2002
cellbender:remove-background: [epoch 107]  average training loss: 1626.8862
cellbender:remove-background: [epoch 108]  average training loss: 1626.0608
cellbender:remove-background: [epoch 109]  average training loss: 1626.2600
cellbender:remove-background: [epoch 110]  average training loss: 1626.7745
cellbender:remove-background: [epoch 110] average test loss: 1656.4682
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/2083-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 111]  average training loss: 1625.5499
cellbender:remove-background: [epoch 112]  average training loss: 1626.5360
cellbender:remove-background: [epoch 113]  average training loss: 1626.2381
cellbender:remove-background: [epoch 114]  average training loss: 1625.2999
cellbender:remove-background: [epoch 115]  average training loss: 1624.9255
cellbender:remove-background: [epoch 115] average test loss: 1660.6656
cellbender:remove-background: [epoch 116]  average training loss: 1625.2491
cellbender:remove-background: [epoch 117]  average training loss: 1625.2680
cellbender:remove-background: [epoch 118]  average training loss: 1623.8967
cellbender:remove-background: [epoch 119]  average training loss: 1625.5251
cellbender:remove-background: [epoch 120]  average training loss: 1624.4377
cellbender:remove-background: [epoch 120] average test loss: 1658.9835
cellbender:remove-background: [epoch 121]  average training loss: 1624.1391
cellbender:remove-background: [epoch 122]  average training loss: 1624.7857
cellbender:remove-background: [epoch 123]  average training loss: 1624.3472
cellbender:remove-background: [epoch 124]  average training loss: 1624.0546
cellbender:remove-background: [epoch 125]  average training loss: 1625.1299
cellbender:remove-background: [epoch 125] average test loss: 1661.0704
cellbender:remove-background: [epoch 126]  average training loss: 1623.9035
cellbender:remove-background: [epoch 127]  average training loss: 1623.9486
cellbender:remove-background: [epoch 128]  average training loss: 1623.5819
cellbender:remove-background: [epoch 129]  average training loss: 1624.5350
cellbender:remove-background: [epoch 130]  average training loss: 1623.7938
cellbender:remove-background: [epoch 130] average test loss: 1661.6480
cellbender:remove-background: [epoch 131]  average training loss: 1623.7561
cellbender:remove-background: [epoch 132]  average training loss: 1621.9743
cellbender:remove-background: [epoch 133]  average training loss: 1623.0854
cellbender:remove-background: [epoch 134]  average training loss: 1623.8216
cellbender:remove-background: [epoch 135]  average training loss: 1622.2833
cellbender:remove-background: [epoch 135] average test loss: 1658.6631
cellbender:remove-background: [epoch 136]  average training loss: 1623.3528
cellbender:remove-background: [epoch 137]  average training loss: 1623.8095
cellbender:remove-background: [epoch 138]  average training loss: 1622.9812
cellbender:remove-background: [epoch 139]  average training loss: 1622.8756
cellbender:remove-background: [epoch 140]  average training loss: 1623.1451
cellbender:remove-background: [epoch 140] average test loss: 1661.6925
cellbender:remove-background: [epoch 141]  average training loss: 1622.2746
cellbender:remove-background: [epoch 142]  average training loss: 1623.3958
cellbender:remove-background: [epoch 143]  average training loss: 1622.6986
cellbender:remove-background: [epoch 144]  average training loss: 1621.7670
cellbender:remove-background: [epoch 145]  average training loss: 1622.1886
cellbender:remove-background: [epoch 145] average test loss: 1660.2762
cellbender:remove-background: [epoch 146]  average training loss: 1622.4649
cellbender:remove-background: [epoch 147]  average training loss: 1622.5272
cellbender:remove-background: [epoch 148]  average training loss: 1622.4517
cellbender:remove-background: [epoch 149]  average training loss: 1622.0741
cellbender:remove-background: [epoch 150]  average training loss: 1622.5934
cellbender:remove-background: [epoch 150] average test loss: 1661.2721
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/2083-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:17:02
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_cxo1p8i
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_cxo1p8i
/tmp/tmp_cxo1p8i/21b1add825_random.pyro
/tmp/tmp_cxo1p8i/21b1add825_random.cuda
/tmp/tmp_cxo1p8i/21b1add825_model.torch
/tmp/tmp_cxo1p8i/21b1add825_optim.torch
/tmp/tmp_cxo1p8i/21b1add825_optim.pyro
/tmp/tmp_cxo1p8i/21b1add825_params.pyro
/tmp/tmp_cxo1p8i/21b1add825_train.loaderstate
/tmp/tmp_cxo1p8i/21b1add825_test.loaderstate
/tmp/tmp_cxo1p8i/21b1add825_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 (1/89)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/89)
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cellbender:remove-background: Working on chunk (89/89)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-dACC/2083-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/2083-Bipolar-dACC/2083-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:22:15

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-dACC/2083-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/2083-Bipolar-dACC/2083-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:     [0.70 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)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:27:23 Total MCKP estimation time = 294.91 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/2083-Bipolar-dACC/2083-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/2083-Bipolar-dACC/2083-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/2083-Bipolar-dACC/2083-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/2083-Bipolar-dACC/2083-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:27:33