cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2052-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2052-Control-DLPFC/2052-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 9268 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 5593fca46c)
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/2052-Control-DLPFC.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: 32033 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4819
cellbender:remove-background: Prior on counts for empty droplets is 33
cellbender:remove-background: Excluding 10764 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21269 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 16
cellbender:remove-background: Using 9268 probable cell barcodes, plus an additional 10732 barcodes, and 35621 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 33 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpetlh2c70
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: 7361.8107
cellbender:remove-background: [epoch 002]  average training loss: 5745.6652  (6.7 seconds per epoch)
cellbender:remove-background: Will checkpoint every 63 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4851.9727
cellbender:remove-background: [epoch 004]  average training loss: 4316.4011
cellbender:remove-background: [epoch 005]  average training loss: 4068.3361
cellbender:remove-background: [epoch 005] average test loss: 3956.2831
cellbender:remove-background: [epoch 006]  average training loss: 3928.2280
cellbender:remove-background: [epoch 007]  average training loss: 3832.9862
cellbender:remove-background: [epoch 008]  average training loss: 3791.3628
cellbender:remove-background: [epoch 009]  average training loss: 3774.3939
cellbender:remove-background: [epoch 010]  average training loss: 3727.2797
cellbender:remove-background: [epoch 010] average test loss: 3733.8516
cellbender:remove-background: [epoch 011]  average training loss: 3653.9042
cellbender:remove-background: [epoch 012]  average training loss: 3590.0166
cellbender:remove-background: [epoch 013]  average training loss: 3564.7592
cellbender:remove-background: [epoch 014]  average training loss: 3571.0914
cellbender:remove-background: [epoch 015]  average training loss: 3546.3140
cellbender:remove-background: [epoch 015] average test loss: 3513.3914
cellbender:remove-background: [epoch 016]  average training loss: 3531.2700
cellbender:remove-background: [epoch 017]  average training loss: 3534.6225
cellbender:remove-background: [epoch 018]  average training loss: 3515.3517
cellbender:remove-background: [epoch 019]  average training loss: 3499.4110
cellbender:remove-background: [epoch 020]  average training loss: 3468.5094
cellbender:remove-background: [epoch 020] average test loss: 3424.5361
cellbender:remove-background: [epoch 021]  average training loss: 3443.3444
cellbender:remove-background: [epoch 022]  average training loss: 3419.6236
cellbender:remove-background: [epoch 023]  average training loss: 3405.3589
cellbender:remove-background: [epoch 024]  average training loss: 3392.8288
cellbender:remove-background: [epoch 025]  average training loss: 3390.4764
cellbender:remove-background: [epoch 025] average test loss: 3337.5574
cellbender:remove-background: [epoch 026]  average training loss: 3378.3891
cellbender:remove-background: [epoch 027]  average training loss: 3376.7760
cellbender:remove-background: [epoch 028]  average training loss: 3371.7500
cellbender:remove-background: [epoch 029]  average training loss: 3365.1806
cellbender:remove-background: [epoch 030]  average training loss: 3360.2270
cellbender:remove-background: [epoch 030] average test loss: 3298.5062
cellbender:remove-background: [epoch 031]  average training loss: 3355.8809
cellbender:remove-background: [epoch 032]  average training loss: 3350.0276
cellbender:remove-background: [epoch 033]  average training loss: 3349.6680
cellbender:remove-background: [epoch 034]  average training loss: 3345.9370
cellbender:remove-background: [epoch 035]  average training loss: 3342.5708
cellbender:remove-background: [epoch 035] average test loss: 3284.9920
cellbender:remove-background: [epoch 036]  average training loss: 3341.1830
cellbender:remove-background: [epoch 037]  average training loss: 3337.6906
cellbender:remove-background: [epoch 038]  average training loss: 3335.0133
cellbender:remove-background: [epoch 039]  average training loss: 3334.4342
cellbender:remove-background: [epoch 040]  average training loss: 3334.7286
cellbender:remove-background: [epoch 040] average test loss: 3273.2645
cellbender:remove-background: [epoch 041]  average training loss: 3328.3472
cellbender:remove-background: [epoch 042]  average training loss: 3326.6020
cellbender:remove-background: [epoch 043]  average training loss: 3320.9118
cellbender:remove-background: [epoch 044]  average training loss: 3319.4483
cellbender:remove-background: [epoch 045]  average training loss: 3324.8301
cellbender:remove-background: [epoch 045] average test loss: 3263.5886
cellbender:remove-background: [epoch 046]  average training loss: 3320.4464
cellbender:remove-background: [epoch 047]  average training loss: 3313.9837
cellbender:remove-background: [epoch 048]  average training loss: 3310.7184
cellbender:remove-background: [epoch 049]  average training loss: 3323.7855
cellbender:remove-background: [epoch 050]  average training loss: 3329.2437
cellbender:remove-background: [epoch 050] average test loss: 3258.2426
cellbender:remove-background: [epoch 051]  average training loss: 3308.6593
cellbender:remove-background: [epoch 052]  average training loss: 3301.4018
cellbender:remove-background: [epoch 053]  average training loss: 3307.8510
cellbender:remove-background: [epoch 054]  average training loss: 3335.0303
cellbender:remove-background: [epoch 055]  average training loss: 3306.3689
cellbender:remove-background: [epoch 055] average test loss: 3245.8282
cellbender:remove-background: [epoch 056]  average training loss: 3309.6529
cellbender:remove-background: [epoch 057]  average training loss: 3298.1282
cellbender:remove-background: [epoch 058]  average training loss: 3306.0293
cellbender:remove-background: [epoch 059]  average training loss: 3319.2167
cellbender:remove-background: [epoch 060]  average training loss: 3308.4890
cellbender:remove-background: [epoch 060] average test loss: 3248.2243
cellbender:remove-background: [epoch 061]  average training loss: 3301.2907
cellbender:remove-background: [epoch 062]  average training loss: 3302.1844
cellbender:remove-background: [epoch 063]  average training loss: 3309.1327
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/2052-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 064]  average training loss: 3288.7468
cellbender:remove-background: [epoch 065]  average training loss: 3288.6746
cellbender:remove-background: [epoch 065] average test loss: 3243.3829
cellbender:remove-background: [epoch 066]  average training loss: 3290.2998
cellbender:remove-background: [epoch 067]  average training loss: 3290.4541
cellbender:remove-background: [epoch 068]  average training loss: 3296.6863
cellbender:remove-background: [epoch 069]  average training loss: 3286.7824
cellbender:remove-background: [epoch 070]  average training loss: 3331.6033
cellbender:remove-background: [epoch 070] average test loss: 3253.1164
cellbender:remove-background: [epoch 071]  average training loss: 3283.5507
cellbender:remove-background: [epoch 072]  average training loss: 3313.8525
cellbender:remove-background: [epoch 073]  average training loss: 3286.9222
cellbender:remove-background: [epoch 074]  average training loss: 3297.1265
cellbender:remove-background: [epoch 075]  average training loss: 3281.7085
cellbender:remove-background: [epoch 075] average test loss: 3238.6552
cellbender:remove-background: [epoch 076]  average training loss: 3273.8697
cellbender:remove-background: [epoch 077]  average training loss: 3285.5412
cellbender:remove-background: [epoch 078]  average training loss: 3289.4532
cellbender:remove-background: [epoch 079]  average training loss: 3288.5434
cellbender:remove-background: [epoch 080]  average training loss: 3282.3330
cellbender:remove-background: [epoch 080] average test loss: 3246.0183
cellbender:remove-background: [epoch 081]  average training loss: 3310.6439
cellbender:remove-background: [epoch 082]  average training loss: 3283.6893
cellbender:remove-background: [epoch 083]  average training loss: 3321.3668
cellbender:remove-background: [epoch 084]  average training loss: 3287.8151
cellbender:remove-background: [epoch 085]  average training loss: 3298.0569
cellbender:remove-background: [epoch 085] average test loss: 3256.5767
cellbender:remove-background: [epoch 086]  average training loss: 3309.8588
cellbender:remove-background: [epoch 087]  average training loss: 3283.5024
cellbender:remove-background: [epoch 088]  average training loss: 3280.1398
cellbender:remove-background: [epoch 089]  average training loss: 3281.6683
cellbender:remove-background: [epoch 090]  average training loss: 3277.4279
cellbender:remove-background: [epoch 090] average test loss: 3248.3143
cellbender:remove-background: [epoch 091]  average training loss: 3279.1450
cellbender:remove-background: [epoch 092]  average training loss: 3286.1903
cellbender:remove-background: [epoch 093]  average training loss: 3272.6138
cellbender:remove-background: [epoch 094]  average training loss: 3281.0962
cellbender:remove-background: [epoch 095]  average training loss: 3279.6475
cellbender:remove-background: [epoch 095] average test loss: 3249.4036
cellbender:remove-background: [epoch 096]  average training loss: 3273.9475
cellbender:remove-background: [epoch 097]  average training loss: 3287.1667
cellbender:remove-background: [epoch 098]  average training loss: 3275.5505
cellbender:remove-background: [epoch 099]  average training loss: 3278.5165
cellbender:remove-background: [epoch 100]  average training loss: 3282.8802
cellbender:remove-background: [epoch 100] average test loss: 3229.8503
cellbender:remove-background: [epoch 101]  average training loss: 3278.3190
cellbender:remove-background: [epoch 102]  average training loss: 3278.2559
cellbender:remove-background: [epoch 103]  average training loss: 3292.1636
cellbender:remove-background: [epoch 104]  average training loss: 3275.2544
cellbender:remove-background: [epoch 105]  average training loss: 3282.1887
cellbender:remove-background: [epoch 105] average test loss: 3250.5391
cellbender:remove-background: [epoch 106]  average training loss: 3271.5892
cellbender:remove-background: [epoch 107]  average training loss: 3282.2656
cellbender:remove-background: [epoch 108]  average training loss: 3271.1716
cellbender:remove-background: [epoch 109]  average training loss: 3261.2355
cellbender:remove-background: [epoch 110]  average training loss: 3270.9473
cellbender:remove-background: [epoch 110] average test loss: 3241.4389
cellbender:remove-background: [epoch 111]  average training loss: 3269.4330
cellbender:remove-background: [epoch 112]  average training loss: 3256.4715
cellbender:remove-background: [epoch 113]  average training loss: 3271.5710
cellbender:remove-background: [epoch 114]  average training loss: 3258.1369
cellbender:remove-background: [epoch 115]  average training loss: 3254.3445
cellbender:remove-background: [epoch 115] average test loss: 3254.6984
cellbender:remove-background: [epoch 116]  average training loss: 3260.9067
cellbender:remove-background: [epoch 117]  average training loss: 3259.7605
cellbender:remove-background: [epoch 118]  average training loss: 3260.9933
cellbender:remove-background: [epoch 119]  average training loss: 3256.3995
cellbender:remove-background: [epoch 120]  average training loss: 3258.7902
cellbender:remove-background: [epoch 120] average test loss: 3211.9322
cellbender:remove-background: [epoch 121]  average training loss: 3252.8360
cellbender:remove-background: [epoch 122]  average training loss: 3253.3015
cellbender:remove-background: [epoch 123]  average training loss: 3261.4681
cellbender:remove-background: [epoch 124]  average training loss: 3250.7754
cellbender:remove-background: [epoch 125]  average training loss: 3254.2258
cellbender:remove-background: [epoch 125] average test loss: 3219.6681
cellbender:remove-background: [epoch 126]  average training loss: 3252.1667
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/2052-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 127]  average training loss: 3252.7039
cellbender:remove-background: [epoch 128]  average training loss: 3253.2125
cellbender:remove-background: [epoch 129]  average training loss: 3249.9169
cellbender:remove-background: [epoch 130]  average training loss: 3250.2793
cellbender:remove-background: [epoch 130] average test loss: 3222.5689
cellbender:remove-background: [epoch 131]  average training loss: 3249.0721
cellbender:remove-background: [epoch 132]  average training loss: 3251.3593
cellbender:remove-background: [epoch 133]  average training loss: 3248.7934
cellbender:remove-background: [epoch 134]  average training loss: 3248.3135
cellbender:remove-background: [epoch 135]  average training loss: 3249.0265
cellbender:remove-background: [epoch 135] average test loss: 3225.0573
cellbender:remove-background: [epoch 136]  average training loss: 3247.2576
cellbender:remove-background: [epoch 137]  average training loss: 3253.5014
cellbender:remove-background: [epoch 138]  average training loss: 3247.9038
cellbender:remove-background: [epoch 139]  average training loss: 3247.7313
cellbender:remove-background: [epoch 140]  average training loss: 3249.9534
cellbender:remove-background: [epoch 140] average test loss: 3225.0889
cellbender:remove-background: [epoch 141]  average training loss: 3248.9730
cellbender:remove-background: [epoch 142]  average training loss: 3247.6236
cellbender:remove-background: [epoch 143]  average training loss: 3248.7133
cellbender:remove-background: [epoch 144]  average training loss: 3248.3367
cellbender:remove-background: [epoch 145]  average training loss: 3245.8816
cellbender:remove-background: [epoch 145] average test loss: 3228.1861
cellbender:remove-background: [epoch 146]  average training loss: 3249.2049
cellbender:remove-background: [epoch 147]  average training loss: 3255.2467
cellbender:remove-background: [epoch 148]  average training loss: 3247.4968
cellbender:remove-background: [epoch 149]  average training loss: 3248.3907
cellbender:remove-background: [epoch 150]  average training loss: 3248.3057
cellbender:remove-background: [epoch 150] average test loss: 3234.2147
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/2052-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:14:02
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpqx7_a6e9
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpqx7_a6e9
/tmp/tmpqx7_a6e9/5593fca46c_random.pyro
/tmp/tmpqx7_a6e9/5593fca46c_random.cuda
/tmp/tmpqx7_a6e9/5593fca46c_model.torch
/tmp/tmpqx7_a6e9/5593fca46c_optim.torch
/tmp/tmpqx7_a6e9/5593fca46c_optim.pyro
/tmp/tmpqx7_a6e9/5593fca46c_params.pyro
/tmp/tmpqx7_a6e9/5593fca46c_train.loaderstate
/tmp/tmpqx7_a6e9/5593fca46c_test.loaderstate
/tmp/tmpqx7_a6e9/5593fca46c_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 (1/83)
cellbender:remove-background:     [0.03 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/2052-Control-DLPFC/2052-Control-DLPFC.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/2052-Control-DLPFC/2052-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:19:08

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2052-Control-DLPFC/2052-Control-DLPFC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2052-Control-DLPFC/2052-Control-DLPFC.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:     [1.93 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 15:33:12 Total MCKP estimation time = 806.20 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/2052-Control-DLPFC/2052-Control-DLPFC.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/2052-Control-DLPFC/2052-Control-DLPFC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2052-Control-DLPFC/2052-Control-DLPFC.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/2052-Control-DLPFC/2052-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:33:34