cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1601-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-dACC/1601-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 7606 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash a3e3eb470f)
cellbender:remove-background: 2024-06-06 15:05:06
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/1601-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: 32387 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3879
cellbender:remove-background: Prior on counts for empty droplets is 149
cellbender:remove-background: Excluding 5515 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 26872 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 74
cellbender:remove-background: Using 7606 probable cell barcodes, plus an additional 12394 barcodes, and 49651 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 147 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpavl7l_4_
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: 6477.9057
cellbender:remove-background: [epoch 002]  average training loss: 5121.3118  (8.8 seconds per epoch)
cellbender:remove-background: Will checkpoint every 48 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4363.0213
cellbender:remove-background: [epoch 004]  average training loss: 3866.0711
cellbender:remove-background: [epoch 005]  average training loss: 3689.8121
cellbender:remove-background: [epoch 005] average test loss: 3727.9158
cellbender:remove-background: [epoch 006]  average training loss: 3601.6792
cellbender:remove-background: [epoch 007]  average training loss: 3551.8834
cellbender:remove-background: [epoch 008]  average training loss: 3519.1950
cellbender:remove-background: [epoch 009]  average training loss: 3502.3319
cellbender:remove-background: [epoch 010]  average training loss: 3439.9683
cellbender:remove-background: [epoch 010] average test loss: 3465.0943
cellbender:remove-background: [epoch 011]  average training loss: 3347.5792
cellbender:remove-background: [epoch 012]  average training loss: 3314.8749
cellbender:remove-background: [epoch 013]  average training loss: 3287.8281
cellbender:remove-background: [epoch 014]  average training loss: 3295.8027
cellbender:remove-background: [epoch 015]  average training loss: 3268.9861
cellbender:remove-background: [epoch 015] average test loss: 3242.6238
cellbender:remove-background: [epoch 016]  average training loss: 3259.1174
cellbender:remove-background: [epoch 017]  average training loss: 3266.8336
cellbender:remove-background: [epoch 018]  average training loss: 3254.4914
cellbender:remove-background: [epoch 019]  average training loss: 3237.5382
cellbender:remove-background: [epoch 020]  average training loss: 3218.5194
cellbender:remove-background: [epoch 020] average test loss: 3215.6760
cellbender:remove-background: [epoch 021]  average training loss: 3215.9219
cellbender:remove-background: [epoch 022]  average training loss: 3210.9056
cellbender:remove-background: [epoch 023]  average training loss: 3196.2870
cellbender:remove-background: [epoch 024]  average training loss: 3172.8015
cellbender:remove-background: [epoch 025]  average training loss: 3154.8442
cellbender:remove-background: [epoch 025] average test loss: 3134.7056
cellbender:remove-background: [epoch 026]  average training loss: 3133.3669
cellbender:remove-background: [epoch 027]  average training loss: 3126.4213
cellbender:remove-background: [epoch 028]  average training loss: 3121.9396
cellbender:remove-background: [epoch 029]  average training loss: 3118.1437
cellbender:remove-background: [epoch 030]  average training loss: 3115.6056
cellbender:remove-background: [epoch 030] average test loss: 3090.8978
cellbender:remove-background: [epoch 031]  average training loss: 3113.8331
cellbender:remove-background: [epoch 032]  average training loss: 3111.9427
cellbender:remove-background: [epoch 033]  average training loss: 3108.0422
cellbender:remove-background: [epoch 034]  average training loss: 3109.8592
cellbender:remove-background: [epoch 035]  average training loss: 3109.9322
cellbender:remove-background: [epoch 035] average test loss: 3068.1310
cellbender:remove-background: [epoch 036]  average training loss: 3109.4997
cellbender:remove-background: [epoch 037]  average training loss: 3106.1597
cellbender:remove-background: [epoch 038]  average training loss: 3104.1287
cellbender:remove-background: [epoch 039]  average training loss: 3106.7934
cellbender:remove-background: [epoch 040]  average training loss: 3104.3453
cellbender:remove-background: [epoch 040] average test loss: 3067.5622
cellbender:remove-background: [epoch 041]  average training loss: 3104.6580
cellbender:remove-background: [epoch 042]  average training loss: 3106.4019
cellbender:remove-background: [epoch 043]  average training loss: 3105.1586
cellbender:remove-background: [epoch 044]  average training loss: 3104.7240
cellbender:remove-background: [epoch 045]  average training loss: 3111.5018
cellbender:remove-background: [epoch 045] average test loss: 3092.6857
cellbender:remove-background: [epoch 046]  average training loss: 3118.4135
cellbender:remove-background: [epoch 047]  average training loss: 3115.7935
cellbender:remove-background: [epoch 048]  average training loss: 3110.8118
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/1601-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 049]  average training loss: 3119.2742
cellbender:remove-background: [epoch 050]  average training loss: 3130.2664
cellbender:remove-background: [epoch 050] average test loss: 3121.8123
cellbender:remove-background: [epoch 051]  average training loss: 3132.3436
cellbender:remove-background: [epoch 052]  average training loss: 3130.3170
cellbender:remove-background: [epoch 053]  average training loss: 3109.6125
cellbender:remove-background: [epoch 054]  average training loss: 3119.6209
cellbender:remove-background: [epoch 055]  average training loss: 3109.2972
cellbender:remove-background: [epoch 055] average test loss: 3099.0856
cellbender:remove-background: [epoch 056]  average training loss: 3119.9686
cellbender:remove-background: [epoch 057]  average training loss: 3119.0639
cellbender:remove-background: [epoch 058]  average training loss: 3132.1334
cellbender:remove-background: [epoch 059]  average training loss: 3138.4831
cellbender:remove-background: [epoch 060]  average training loss: 3122.3328
cellbender:remove-background: [epoch 060] average test loss: 3118.7166
cellbender:remove-background: [epoch 061]  average training loss: 3123.7407
cellbender:remove-background: [epoch 062]  average training loss: 3127.8473
cellbender:remove-background: [epoch 063]  average training loss: 3118.3360
cellbender:remove-background: [epoch 064]  average training loss: 3123.7441
cellbender:remove-background: [epoch 065]  average training loss: 3141.3460
cellbender:remove-background: [epoch 065] average test loss: 3120.5083
cellbender:remove-background: [epoch 066]  average training loss: 3124.0442
cellbender:remove-background: [epoch 067]  average training loss: 3126.9050
cellbender:remove-background: [epoch 068]  average training loss: 3125.2127
cellbender:remove-background: [epoch 069]  average training loss: 3118.5465
cellbender:remove-background: [epoch 070]  average training loss: 3131.3514
cellbender:remove-background: [epoch 070] average test loss: 3143.3934
cellbender:remove-background: [epoch 071]  average training loss: 3138.5912
cellbender:remove-background: [epoch 072]  average training loss: 3120.8609
cellbender:remove-background: [epoch 073]  average training loss: 3133.0856
cellbender:remove-background: [epoch 074]  average training loss: 3118.0405
cellbender:remove-background: [epoch 075]  average training loss: 3136.4543
cellbender:remove-background: [epoch 075] average test loss: 3149.6764
cellbender:remove-background: [epoch 076]  average training loss: 3126.9641
cellbender:remove-background: [epoch 077]  average training loss: 3111.4210
cellbender:remove-background: [epoch 078]  average training loss: 3123.3263
cellbender:remove-background: [epoch 079]  average training loss: 3114.1436
cellbender:remove-background: [epoch 080]  average training loss: 3123.4252
cellbender:remove-background: [epoch 080] average test loss: 3127.4281
cellbender:remove-background: [epoch 081]  average training loss: 3116.5030
cellbender:remove-background: [epoch 082]  average training loss: 3115.5642
cellbender:remove-background: [epoch 083]  average training loss: 3120.4872
cellbender:remove-background: [epoch 084]  average training loss: 3119.5868
cellbender:remove-background: [epoch 085]  average training loss: 3123.0339
cellbender:remove-background: [epoch 085] average test loss: 3134.5881
cellbender:remove-background: [epoch 086]  average training loss: 3125.4424
cellbender:remove-background: [epoch 087]  average training loss: 3131.8219
cellbender:remove-background: [epoch 088]  average training loss: 3132.4059
cellbender:remove-background: [epoch 089]  average training loss: 3120.7890
cellbender:remove-background: [epoch 090]  average training loss: 3127.7371
cellbender:remove-background: [epoch 090] average test loss: 3161.8008
cellbender:remove-background: [epoch 091]  average training loss: 3112.7264
cellbender:remove-background: [epoch 092]  average training loss: 3113.3377
cellbender:remove-background: [epoch 093]  average training loss: 3108.2110
cellbender:remove-background: [epoch 094]  average training loss: 3115.0823
cellbender:remove-background: [epoch 095]  average training loss: 3114.9421
cellbender:remove-background: [epoch 095] average test loss: 3132.3053
cellbender:remove-background: [epoch 096]  average training loss: 3108.2543
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/1601-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 097]  average training loss: 3113.2678
cellbender:remove-background: [epoch 098]  average training loss: 3116.4197
cellbender:remove-background: [epoch 099]  average training loss: 3107.8611
cellbender:remove-background: [epoch 100]  average training loss: 3112.8872
cellbender:remove-background: [epoch 100] average test loss: 3139.8352
cellbender:remove-background: [epoch 101]  average training loss: 3116.3496
cellbender:remove-background: [epoch 102]  average training loss: 3106.8827
cellbender:remove-background: [epoch 103]  average training loss: 3109.0443
cellbender:remove-background: [epoch 104]  average training loss: 3109.8923
cellbender:remove-background: [epoch 105]  average training loss: 3101.3965
cellbender:remove-background: [epoch 105] average test loss: 3133.9576
cellbender:remove-background: [epoch 106]  average training loss: 3098.9154
cellbender:remove-background: [epoch 107]  average training loss: 3099.1934
cellbender:remove-background: [epoch 108]  average training loss: 3111.1445
cellbender:remove-background: [epoch 109]  average training loss: 3088.9105
cellbender:remove-background: [epoch 110]  average training loss: 3110.0990
cellbender:remove-background: [epoch 110] average test loss: 3118.7002
cellbender:remove-background: [epoch 111]  average training loss: 3099.5632
cellbender:remove-background: [epoch 112]  average training loss: 3098.5352
cellbender:remove-background: [epoch 113]  average training loss: 3107.9840
cellbender:remove-background: [epoch 114]  average training loss: 3102.4236
cellbender:remove-background: [epoch 115]  average training loss: 3108.5814
cellbender:remove-background: [epoch 115] average test loss: 3139.3002
cellbender:remove-background: [epoch 116]  average training loss: 3103.8723
cellbender:remove-background: [epoch 117]  average training loss: 3105.2713
cellbender:remove-background: [epoch 118]  average training loss: 3101.0203
cellbender:remove-background: [epoch 119]  average training loss: 3094.1358
cellbender:remove-background: [epoch 120]  average training loss: 3094.9385
cellbender:remove-background: [epoch 120] average test loss: 3120.8769
cellbender:remove-background: [epoch 121]  average training loss: 3097.4221
cellbender:remove-background: [epoch 122]  average training loss: 3094.7841
cellbender:remove-background: [epoch 123]  average training loss: 3102.7521
cellbender:remove-background: [epoch 124]  average training loss: 3090.7679
cellbender:remove-background: [epoch 125]  average training loss: 3094.1928
cellbender:remove-background: [epoch 125] average test loss: 3120.6114
cellbender:remove-background: [epoch 126]  average training loss: 3094.7929
cellbender:remove-background: [epoch 127]  average training loss: 3094.9493
cellbender:remove-background: [epoch 128]  average training loss: 3092.2257
cellbender:remove-background: [epoch 129]  average training loss: 3097.5295
cellbender:remove-background: [epoch 130]  average training loss: 3093.3054
cellbender:remove-background: [epoch 130] average test loss: 3138.1187
cellbender:remove-background: [epoch 131]  average training loss: 3098.1429
cellbender:remove-background: [epoch 132]  average training loss: 3088.5631
cellbender:remove-background: [epoch 133]  average training loss: 3101.1787
cellbender:remove-background: [epoch 134]  average training loss: 3082.4736
cellbender:remove-background: [epoch 135]  average training loss: 3090.3844
cellbender:remove-background: [epoch 135] average test loss: 3112.1040
cellbender:remove-background: [epoch 136]  average training loss: 3093.6608
cellbender:remove-background: [epoch 137]  average training loss: 3090.9176
cellbender:remove-background: [epoch 138]  average training loss: 3094.2289
cellbender:remove-background: [epoch 139]  average training loss: 3097.4971
cellbender:remove-background: [epoch 140]  average training loss: 3091.8663
cellbender:remove-background: [epoch 140] average test loss: 3118.8601
cellbender:remove-background: [epoch 141]  average training loss: 3082.2519
cellbender:remove-background: [epoch 142]  average training loss: 3094.4071
cellbender:remove-background: [epoch 143]  average training loss: 3090.0392
cellbender:remove-background: [epoch 144]  average training loss: 3097.6785
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/1601-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 145]  average training loss: 3091.5529
cellbender:remove-background: [epoch 145] average test loss: 3122.3953
cellbender:remove-background: [epoch 146]  average training loss: 3095.1784
cellbender:remove-background: [epoch 147]  average training loss: 3086.2562
cellbender:remove-background: [epoch 148]  average training loss: 3088.4719
cellbender:remove-background: [epoch 149]  average training loss: 3091.7594
cellbender:remove-background: [epoch 150]  average training loss: 3090.7139
cellbender:remove-background: [epoch 150] average test loss: 3130.0780
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/1601-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:32:14
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpf4oegzzi
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpf4oegzzi
/tmp/tmpf4oegzzi/a3e3eb470f_random.pyro
/tmp/tmpf4oegzzi/a3e3eb470f_random.cuda
/tmp/tmpf4oegzzi/a3e3eb470f_model.torch
/tmp/tmpf4oegzzi/a3e3eb470f_optim.torch
/tmp/tmpf4oegzzi/a3e3eb470f_optim.pyro
/tmp/tmpf4oegzzi/a3e3eb470f_params.pyro
/tmp/tmpf4oegzzi/a3e3eb470f_train.loaderstate
/tmp/tmpf4oegzzi/a3e3eb470f_test.loaderstate
/tmp/tmpf4oegzzi/a3e3eb470f_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 (1/73)
cellbender:remove-background:     [0.05 mins per chunk]
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cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-dACC/1601-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/1601-Bipolar-dACC/1601-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:38:04

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-dACC/1601-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/1601-Bipolar-dACC/1601-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:     [2.14 mins per chunk]
cellbender:remove-background: Working on chunk (2/7)
cellbender:remove-background: Working on chunk (3/7)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:53:36 Total MCKP estimation time = 901.83 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/1601-Bipolar-dACC/1601-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/1601-Bipolar-dACC/1601-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/1601-Bipolar-dACC/1601-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/1601-Bipolar-dACC/1601-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:53:56