cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2791-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output.h5 --cuda --expected-cells 9260 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 86a64cd4da)
cellbender:remove-background: 2024-06-06 15:04:06
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/2791-Control-dACC.raw_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Features in dataset: 36601 Gene Expression
cellbender:remove-background: Trimming features for inference.
cellbender:remove-background: 32317 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4272
cellbender:remove-background: Prior on counts for empty droplets is 125
cellbender:remove-background: Excluding 6168 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 26149 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 62
cellbender:remove-background: Using 9260 probable cell barcodes, plus an additional 10740 barcodes, and 51833 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 124 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzw930vsu
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: 7472.2739
cellbender:remove-background: [epoch 002]  average training loss: 5809.8745  (8.2 seconds per epoch)
cellbender:remove-background: Will checkpoint every 52 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4919.5463
cellbender:remove-background: [epoch 004]  average training loss: 4375.5726
cellbender:remove-background: [epoch 005]  average training loss: 4192.5103
cellbender:remove-background: [epoch 005] average test loss: 4285.7218
cellbender:remove-background: [epoch 006]  average training loss: 4106.8513
cellbender:remove-background: [epoch 007]  average training loss: 4043.5807
cellbender:remove-background: [epoch 008]  average training loss: 4004.2129
cellbender:remove-background: [epoch 009]  average training loss: 3997.5695
cellbender:remove-background: [epoch 010]  average training loss: 3931.3158
cellbender:remove-background: [epoch 010] average test loss: 3964.6333
cellbender:remove-background: [epoch 011]  average training loss: 3961.9792
cellbender:remove-background: [epoch 012]  average training loss: 3933.7890
cellbender:remove-background: [epoch 013]  average training loss: 3901.8992
cellbender:remove-background: [epoch 014]  average training loss: 3747.8491
cellbender:remove-background: [epoch 015]  average training loss: 3603.2286
cellbender:remove-background: [epoch 015] average test loss: 3638.1664
cellbender:remove-background: [epoch 016]  average training loss: 3557.5678
cellbender:remove-background: [epoch 017]  average training loss: 3540.8400
cellbender:remove-background: [epoch 018]  average training loss: 3517.0231
cellbender:remove-background: [epoch 019]  average training loss: 3499.5413
cellbender:remove-background: [epoch 020]  average training loss: 3470.4102
cellbender:remove-background: [epoch 020] average test loss: 3520.2253
cellbender:remove-background: [epoch 021]  average training loss: 3459.0771
cellbender:remove-background: [epoch 022]  average training loss: 3452.2907
cellbender:remove-background: [epoch 023]  average training loss: 3440.5816
cellbender:remove-background: [epoch 024]  average training loss: 3428.6323
cellbender:remove-background: [epoch 025]  average training loss: 3424.1660
cellbender:remove-background: [epoch 025] average test loss: 3447.1035
cellbender:remove-background: [epoch 026]  average training loss: 3405.3235
cellbender:remove-background: [epoch 027]  average training loss: 3404.7903
cellbender:remove-background: [epoch 028]  average training loss: 3400.8232
cellbender:remove-background: [epoch 029]  average training loss: 3393.3028
cellbender:remove-background: [epoch 030]  average training loss: 3389.3250
cellbender:remove-background: [epoch 030] average test loss: 3402.4241
cellbender:remove-background: [epoch 031]  average training loss: 3384.9183
cellbender:remove-background: [epoch 032]  average training loss: 3378.3032
cellbender:remove-background: [epoch 033]  average training loss: 3375.5826
cellbender:remove-background: [epoch 034]  average training loss: 3375.4480
cellbender:remove-background: [epoch 035]  average training loss: 3371.3912
cellbender:remove-background: [epoch 035] average test loss: 3382.9571
cellbender:remove-background: [epoch 036]  average training loss: 3368.0458
cellbender:remove-background: [epoch 037]  average training loss: 3364.5269
cellbender:remove-background: [epoch 038]  average training loss: 3362.4741
cellbender:remove-background: [epoch 039]  average training loss: 3359.4187
cellbender:remove-background: [epoch 040]  average training loss: 3356.7281
cellbender:remove-background: [epoch 040] average test loss: 3367.8789
cellbender:remove-background: [epoch 041]  average training loss: 3354.6962
cellbender:remove-background: [epoch 042]  average training loss: 3352.6902
cellbender:remove-background: [epoch 043]  average training loss: 3350.2765
cellbender:remove-background: [epoch 044]  average training loss: 3349.4193
cellbender:remove-background: [epoch 045]  average training loss: 3349.4481
cellbender:remove-background: [epoch 045] average test loss: 3354.1908
cellbender:remove-background: [epoch 046]  average training loss: 3350.4042
cellbender:remove-background: [epoch 047]  average training loss: 3347.4914
cellbender:remove-background: [epoch 048]  average training loss: 3349.0908
cellbender:remove-background: [epoch 049]  average training loss: 3349.1307
cellbender:remove-background: [epoch 050]  average training loss: 3350.9302
cellbender:remove-background: [epoch 050] average test loss: 3366.4009
cellbender:remove-background: [epoch 051]  average training loss: 3348.2210
cellbender:remove-background: [epoch 052]  average training loss: 3351.2382
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/2791-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 053]  average training loss: 3352.4448
cellbender:remove-background: [epoch 054]  average training loss: 3351.6140
cellbender:remove-background: [epoch 055]  average training loss: 3354.8992
cellbender:remove-background: [epoch 055] average test loss: 3364.3276
cellbender:remove-background: [epoch 056]  average training loss: 3361.0162
cellbender:remove-background: [epoch 057]  average training loss: 3362.4002
cellbender:remove-background: [epoch 058]  average training loss: 3361.2572
cellbender:remove-background: [epoch 059]  average training loss: 3360.7842
cellbender:remove-background: [epoch 060]  average training loss: 3360.7592
cellbender:remove-background: [epoch 060] average test loss: 3413.5759
cellbender:remove-background: [epoch 061]  average training loss: 3367.1049
cellbender:remove-background: [epoch 062]  average training loss: 3360.5886
cellbender:remove-background: [epoch 063]  average training loss: 3364.8411
cellbender:remove-background: [epoch 064]  average training loss: 3370.1597
cellbender:remove-background: [epoch 065]  average training loss: 3363.1281
cellbender:remove-background: [epoch 065] average test loss: 3377.6475
cellbender:remove-background: [epoch 066]  average training loss: 3373.7567
cellbender:remove-background: [epoch 067]  average training loss: 3386.1959
cellbender:remove-background: [epoch 068]  average training loss: 3388.1954
cellbender:remove-background: [epoch 069]  average training loss: 3369.3825
cellbender:remove-background: [epoch 070]  average training loss: 3376.3329
cellbender:remove-background: [epoch 070] average test loss: 3399.1687
cellbender:remove-background: [epoch 071]  average training loss: 3377.0645
cellbender:remove-background: [epoch 072]  average training loss: 3384.6968
cellbender:remove-background: [epoch 073]  average training loss: 3373.6363
cellbender:remove-background: [epoch 074]  average training loss: 3378.1625
cellbender:remove-background: [epoch 075]  average training loss: 3372.1002
cellbender:remove-background: [epoch 075] average test loss: 3403.8846
cellbender:remove-background: [epoch 076]  average training loss: 3376.5409
cellbender:remove-background: [epoch 077]  average training loss: 3384.0023
cellbender:remove-background: [epoch 078]  average training loss: 3377.1688
cellbender:remove-background: [epoch 079]  average training loss: 3375.1501
cellbender:remove-background: [epoch 080]  average training loss: 3371.8852
cellbender:remove-background: [epoch 080] average test loss: 3401.4228
cellbender:remove-background: [epoch 081]  average training loss: 3376.8115
cellbender:remove-background: [epoch 082]  average training loss: 3370.0764
cellbender:remove-background: [epoch 083]  average training loss: 3373.6641
cellbender:remove-background: [epoch 084]  average training loss: 3370.5803
cellbender:remove-background: [epoch 085]  average training loss: 3365.5140
cellbender:remove-background: [epoch 085] average test loss: 3393.9931
cellbender:remove-background: [epoch 086]  average training loss: 3370.9816
cellbender:remove-background: [epoch 087]  average training loss: 3370.3095
cellbender:remove-background: [epoch 088]  average training loss: 3368.2632
cellbender:remove-background: [epoch 089]  average training loss: 3382.6455
cellbender:remove-background: [epoch 090]  average training loss: 3366.3054
cellbender:remove-background: [epoch 090] average test loss: 3396.4964
cellbender:remove-background: [epoch 091]  average training loss: 3367.1152
cellbender:remove-background: [epoch 092]  average training loss: 3359.0117
cellbender:remove-background: [epoch 093]  average training loss: 3367.7170
cellbender:remove-background: [epoch 094]  average training loss: 3361.4575
cellbender:remove-background: [epoch 095]  average training loss: 3362.4118
cellbender:remove-background: [epoch 095] average test loss: 3398.2909
cellbender:remove-background: [epoch 096]  average training loss: 3360.7539
cellbender:remove-background: [epoch 097]  average training loss: 3364.1247
cellbender:remove-background: [epoch 098]  average training loss: 3358.7366
cellbender:remove-background: [epoch 099]  average training loss: 3360.1154
cellbender:remove-background: [epoch 100]  average training loss: 3357.0032
cellbender:remove-background: [epoch 100] average test loss: 3405.8649
cellbender:remove-background: [epoch 101]  average training loss: 3361.7234
cellbender:remove-background: [epoch 102]  average training loss: 3359.0130
cellbender:remove-background: [epoch 103]  average training loss: 3360.8461
cellbender:remove-background: [epoch 104]  average training loss: 3361.1016
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/2791-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 105]  average training loss: 3357.2481
cellbender:remove-background: [epoch 105] average test loss: 3401.5012
cellbender:remove-background: [epoch 106]  average training loss: 3359.8666
cellbender:remove-background: [epoch 107]  average training loss: 3356.6410
cellbender:remove-background: [epoch 108]  average training loss: 3358.5823
cellbender:remove-background: [epoch 109]  average training loss: 3352.5812
cellbender:remove-background: [epoch 110]  average training loss: 3360.9739
cellbender:remove-background: [epoch 110] average test loss: 3399.1890
cellbender:remove-background: [epoch 111]  average training loss: 3352.9887
cellbender:remove-background: [epoch 112]  average training loss: 3359.4136
cellbender:remove-background: [epoch 113]  average training loss: 3358.2127
cellbender:remove-background: [epoch 114]  average training loss: 3357.3342
cellbender:remove-background: [epoch 115]  average training loss: 3358.6057
cellbender:remove-background: [epoch 115] average test loss: 3393.9676
cellbender:remove-background: [epoch 116]  average training loss: 3352.7612
cellbender:remove-background: [epoch 117]  average training loss: 3355.9969
cellbender:remove-background: [epoch 118]  average training loss: 3355.5896
cellbender:remove-background: [epoch 119]  average training loss: 3356.5857
cellbender:remove-background: [epoch 120]  average training loss: 3352.6328
cellbender:remove-background: [epoch 120] average test loss: 3394.9665
cellbender:remove-background: [epoch 121]  average training loss: 3354.2913
cellbender:remove-background: [epoch 122]  average training loss: 3354.2530
cellbender:remove-background: [epoch 123]  average training loss: 3355.7657
cellbender:remove-background: [epoch 124]  average training loss: 3357.6616
cellbender:remove-background: [epoch 125]  average training loss: 3352.1441
cellbender:remove-background: [epoch 125] average test loss: 3409.4516
cellbender:remove-background: [epoch 126]  average training loss: 3349.7271
cellbender:remove-background: [epoch 127]  average training loss: 3349.8995
cellbender:remove-background: [epoch 128]  average training loss: 3352.0899
cellbender:remove-background: [epoch 129]  average training loss: 3352.4032
cellbender:remove-background: [epoch 130]  average training loss: 3348.3297
cellbender:remove-background: [epoch 130] average test loss: 3395.1767
cellbender:remove-background: [epoch 131]  average training loss: 3352.5693
cellbender:remove-background: [epoch 132]  average training loss: 3351.8213
cellbender:remove-background: [epoch 133]  average training loss: 3348.3887
cellbender:remove-background: [epoch 134]  average training loss: 3345.7850
cellbender:remove-background: [epoch 135]  average training loss: 3346.5492
cellbender:remove-background: [epoch 135] average test loss: 3405.4521
cellbender:remove-background: [epoch 136]  average training loss: 3352.2732
cellbender:remove-background: [epoch 137]  average training loss: 3347.5272
cellbender:remove-background: [epoch 138]  average training loss: 3345.7797
cellbender:remove-background: [epoch 139]  average training loss: 3347.1428
cellbender:remove-background: [epoch 140]  average training loss: 3343.9043
cellbender:remove-background: [epoch 140] average test loss: 3396.3233
cellbender:remove-background: [epoch 141]  average training loss: 3349.8428
cellbender:remove-background: [epoch 142]  average training loss: 3344.5235
cellbender:remove-background: [epoch 143]  average training loss: 3345.0351
cellbender:remove-background: [epoch 144]  average training loss: 3344.3585
cellbender:remove-background: [epoch 145]  average training loss: 3346.1234
cellbender:remove-background: [epoch 145] average test loss: 3393.6465
cellbender:remove-background: [epoch 146]  average training loss: 3349.1493
cellbender:remove-background: [epoch 147]  average training loss: 3346.1349
cellbender:remove-background: [epoch 148]  average training loss: 3341.4384
cellbender:remove-background: [epoch 149]  average training loss: 3340.9742
cellbender:remove-background: [epoch 150]  average training loss: 3344.5255
cellbender:remove-background: [epoch 150] average test loss: 3393.9907
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/2791-Control-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:28:47
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpou1w2jwp
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpou1w2jwp
/tmp/tmpou1w2jwp/86a64cd4da_random.pyro
/tmp/tmpou1w2jwp/86a64cd4da_random.cuda
/tmp/tmpou1w2jwp/86a64cd4da_model.torch
/tmp/tmpou1w2jwp/86a64cd4da_optim.torch
/tmp/tmpou1w2jwp/86a64cd4da_optim.pyro
/tmp/tmpou1w2jwp/86a64cd4da_params.pyro
/tmp/tmpou1w2jwp/86a64cd4da_train.loaderstate
/tmp/tmpou1w2jwp/86a64cd4da_test.loaderstate
/tmp/tmpou1w2jwp/86a64cd4da_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 (1/88)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/88)
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cellbender:remove-background: Working on chunk (86/88)
cellbender:remove-background: Working on chunk (87/88)
cellbender:remove-background: Working on chunk (88/88)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:35:03

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_cell_barcodes.csv
cellbender:remove-background: Computing target noise counts per gene for MCKP estimator
cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01
cellbender:remove-background: Computing denoised counts using mckp estimator
cellbender:remove-background: Working on chunk (1/7)
cellbender:remove-background:     [2.44 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 15:52:50 Total MCKP estimation time = 1031.76 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/2791-Control-dACC/2791-Control-dACC.cellbender.output.h5
cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_metrics.csv
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory
rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics
    output=html_report_file,
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html
    title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')),
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html
    with open(file, mode='r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-dACC/2791-Control-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:53:14