cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1604-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-DLPFC/1604-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 6938 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 52c5d80e3d)
cellbender:remove-background: 2024-06-06 15:32:44
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/1604-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: 32233 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 7715
cellbender:remove-background: Prior on counts for empty droplets is 106
cellbender:remove-background: Excluding 12289 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 19944 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 53
cellbender:remove-background: Using 6938 probable cell barcodes, plus an additional 13062 barcodes, and 13359 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 104 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpqqvnt4q2
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: 7676.6885
cellbender:remove-background: [epoch 002]  average training loss: 5842.8127  (6.1 seconds per epoch)
cellbender:remove-background: Will checkpoint every 70 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4953.4302
cellbender:remove-background: [epoch 004]  average training loss: 4464.6088
cellbender:remove-background: [epoch 005]  average training loss: 4353.7273
cellbender:remove-background: [epoch 005] average test loss: 4401.0393
cellbender:remove-background: [epoch 006]  average training loss: 4322.8884
cellbender:remove-background: [epoch 007]  average training loss: 4260.1339
cellbender:remove-background: [epoch 008]  average training loss: 4213.4741
cellbender:remove-background: [epoch 009]  average training loss: 4151.6901
cellbender:remove-background: [epoch 010]  average training loss: 3986.1214
cellbender:remove-background: [epoch 010] average test loss: 3995.0143
cellbender:remove-background: [epoch 011]  average training loss: 3953.4313
cellbender:remove-background: [epoch 012]  average training loss: 3934.3225
cellbender:remove-background: [epoch 013]  average training loss: 3898.1458
cellbender:remove-background: [epoch 014]  average training loss: 3902.0381
cellbender:remove-background: [epoch 015]  average training loss: 3860.6639
cellbender:remove-background: [epoch 015] average test loss: 3942.1048
cellbender:remove-background: [epoch 016]  average training loss: 3842.5611
cellbender:remove-background: [epoch 017]  average training loss: 3852.3071
cellbender:remove-background: [epoch 018]  average training loss: 3837.9347
cellbender:remove-background: [epoch 019]  average training loss: 3822.9269
cellbender:remove-background: [epoch 020]  average training loss: 3800.8242
cellbender:remove-background: [epoch 020] average test loss: 3804.7680
cellbender:remove-background: [epoch 021]  average training loss: 3792.2066
cellbender:remove-background: [epoch 022]  average training loss: 3770.8199
cellbender:remove-background: [epoch 023]  average training loss: 3735.9969
cellbender:remove-background: [epoch 024]  average training loss: 3698.5321
cellbender:remove-background: [epoch 025]  average training loss: 3687.6196
cellbender:remove-background: [epoch 025] average test loss: 3668.5676
cellbender:remove-background: [epoch 026]  average training loss: 3670.5723
cellbender:remove-background: [epoch 027]  average training loss: 3663.3870
cellbender:remove-background: [epoch 028]  average training loss: 3659.2783
cellbender:remove-background: [epoch 029]  average training loss: 3652.5828
cellbender:remove-background: [epoch 030]  average training loss: 3649.7539
cellbender:remove-background: [epoch 030] average test loss: 3609.2172
cellbender:remove-background: [epoch 031]  average training loss: 3646.0885
cellbender:remove-background: [epoch 032]  average training loss: 3637.7900
cellbender:remove-background: [epoch 033]  average training loss: 3637.7235
cellbender:remove-background: [epoch 034]  average training loss: 3630.6224
cellbender:remove-background: [epoch 035]  average training loss: 3626.7311
cellbender:remove-background: [epoch 035] average test loss: 3589.2784
cellbender:remove-background: [epoch 036]  average training loss: 3627.2470
cellbender:remove-background: [epoch 037]  average training loss: 3628.2955
cellbender:remove-background: [epoch 038]  average training loss: 3623.6816
cellbender:remove-background: [epoch 039]  average training loss: 3624.1746
cellbender:remove-background: [epoch 040]  average training loss: 3623.5889
cellbender:remove-background: [epoch 040] average test loss: 3583.7308
cellbender:remove-background: [epoch 041]  average training loss: 3619.1308
cellbender:remove-background: [epoch 042]  average training loss: 3625.4560
cellbender:remove-background: [epoch 043]  average training loss: 3628.4949
cellbender:remove-background: [epoch 044]  average training loss: 3626.6163
cellbender:remove-background: [epoch 045]  average training loss: 3633.8074
cellbender:remove-background: [epoch 045] average test loss: 3578.4926
cellbender:remove-background: [epoch 046]  average training loss: 3630.0128
cellbender:remove-background: [epoch 047]  average training loss: 3629.7343
cellbender:remove-background: [epoch 048]  average training loss: 3635.5686
cellbender:remove-background: [epoch 049]  average training loss: 3644.2662
cellbender:remove-background: [epoch 050]  average training loss: 3642.3361
cellbender:remove-background: [epoch 050] average test loss: 3609.5594
cellbender:remove-background: [epoch 051]  average training loss: 3648.7152
cellbender:remove-background: [epoch 052]  average training loss: 3647.2579
cellbender:remove-background: [epoch 053]  average training loss: 3670.5927
cellbender:remove-background: [epoch 054]  average training loss: 3648.4681
cellbender:remove-background: [epoch 055]  average training loss: 3684.8025
cellbender:remove-background: [epoch 055] average test loss: 3641.0636
cellbender:remove-background: [epoch 056]  average training loss: 3707.0527
cellbender:remove-background: [epoch 057]  average training loss: 3676.3547
cellbender:remove-background: [epoch 058]  average training loss: 3650.7122
cellbender:remove-background: [epoch 059]  average training loss: 3651.5419
cellbender:remove-background: [epoch 060]  average training loss: 3658.2161
cellbender:remove-background: [epoch 060] average test loss: 3732.9023
cellbender:remove-background: [epoch 061]  average training loss: 3649.9239
cellbender:remove-background: [epoch 062]  average training loss: 3651.2674
cellbender:remove-background: [epoch 063]  average training loss: 3639.5968
cellbender:remove-background: [epoch 064]  average training loss: 3658.2488
cellbender:remove-background: [epoch 065]  average training loss: 3668.0744
cellbender:remove-background: [epoch 065] average test loss: 3666.0965
cellbender:remove-background: [epoch 066]  average training loss: 3641.5287
cellbender:remove-background: [epoch 067]  average training loss: 3662.0124
cellbender:remove-background: [epoch 068]  average training loss: 3648.0268
cellbender:remove-background: [epoch 069]  average training loss: 3660.6970
cellbender:remove-background: [epoch 070]  average training loss: 3649.5688
cellbender:remove-background: [epoch 070] average test loss: 3789.9062
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/1604-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 071]  average training loss: 3682.0052
cellbender:remove-background: [epoch 072]  average training loss: 3643.4316
cellbender:remove-background: [epoch 073]  average training loss: 3672.1227
cellbender:remove-background: [epoch 074]  average training loss: 3659.8139
cellbender:remove-background: [epoch 075]  average training loss: 3659.8720
cellbender:remove-background: [epoch 075] average test loss: 3645.3449
cellbender:remove-background: [epoch 076]  average training loss: 3698.5060
cellbender:remove-background: [epoch 077]  average training loss: 3658.8027
cellbender:remove-background: [epoch 078]  average training loss: 3649.8696
cellbender:remove-background: [epoch 079]  average training loss: 3642.1377
cellbender:remove-background: [epoch 080]  average training loss: 3663.1885
cellbender:remove-background: [epoch 080] average test loss: 3680.8299
cellbender:remove-background: [epoch 081]  average training loss: 3663.7844
cellbender:remove-background: [epoch 082]  average training loss: 3645.7789
cellbender:remove-background: [epoch 083]  average training loss: 3660.4162
cellbender:remove-background: [epoch 084]  average training loss: 3688.5778
cellbender:remove-background: [epoch 085]  average training loss: 3663.3079
cellbender:remove-background: [epoch 085] average test loss: 3698.0515
cellbender:remove-background: [epoch 086]  average training loss: 3681.0426
cellbender:remove-background: [epoch 087]  average training loss: 3655.6441
cellbender:remove-background: [epoch 088]  average training loss: 3714.1214
cellbender:remove-background: [epoch 089]  average training loss: 3672.5762
cellbender:remove-background: [epoch 090]  average training loss: 3649.5777
cellbender:remove-background: [epoch 090] average test loss: 3685.4941
cellbender:remove-background: [epoch 091]  average training loss: 3673.4750
cellbender:remove-background: [epoch 092]  average training loss: 3650.7400
cellbender:remove-background: [epoch 093]  average training loss: 3649.5854
cellbender:remove-background: [epoch 094]  average training loss: 3668.5454
cellbender:remove-background: [epoch 095]  average training loss: 3639.8038
cellbender:remove-background: [epoch 095] average test loss: 3646.6708
cellbender:remove-background: [epoch 096]  average training loss: 3656.3440
cellbender:remove-background: [epoch 097]  average training loss: 3661.0121
cellbender:remove-background: [epoch 098]  average training loss: 3687.9196
cellbender:remove-background: [epoch 099]  average training loss: 3668.4585
cellbender:remove-background: [epoch 100]  average training loss: 3645.5100
cellbender:remove-background: [epoch 100] average test loss: 3786.2861
cellbender:remove-background: [epoch 101]  average training loss: 3676.6472
cellbender:remove-background: [epoch 102]  average training loss: 3643.9806
cellbender:remove-background: [epoch 103]  average training loss: 3644.0490
cellbender:remove-background: [epoch 104]  average training loss: 3671.4679
cellbender:remove-background: [epoch 105]  average training loss: 3639.4704
cellbender:remove-background: [epoch 105] average test loss: 3675.6092
cellbender:remove-background: [epoch 106]  average training loss: 3636.9649
cellbender:remove-background: [epoch 107]  average training loss: 3647.2852
cellbender:remove-background: [epoch 108]  average training loss: 3653.9491
cellbender:remove-background: [epoch 109]  average training loss: 3657.3507
cellbender:remove-background: [epoch 110]  average training loss: 3653.2561
cellbender:remove-background: [epoch 110] average test loss: 3792.6954
cellbender:remove-background: [epoch 111]  average training loss: 3633.0401
cellbender:remove-background: [epoch 112]  average training loss: 3639.4134
cellbender:remove-background: [epoch 113]  average training loss: 3634.8028
cellbender:remove-background: [epoch 114]  average training loss: 3626.9568
cellbender:remove-background: [epoch 115]  average training loss: 3678.0752
cellbender:remove-background: [epoch 115] average test loss: 3656.5078
cellbender:remove-background: [epoch 116]  average training loss: 3654.9507
cellbender:remove-background: [epoch 117]  average training loss: 3618.6317
cellbender:remove-background: [epoch 118]  average training loss: 3667.0171
cellbender:remove-background: [epoch 119]  average training loss: 3648.3857
cellbender:remove-background: [epoch 120]  average training loss: 3637.1211
cellbender:remove-background: [epoch 120] average test loss: 3663.7123
cellbender:remove-background: [epoch 121]  average training loss: 3642.4832
cellbender:remove-background: [epoch 122]  average training loss: 3631.7734
cellbender:remove-background: [epoch 123]  average training loss: 3619.4262
cellbender:remove-background: [epoch 124]  average training loss: 3643.5369
cellbender:remove-background: [epoch 125]  average training loss: 3644.5055
cellbender:remove-background: [epoch 125] average test loss: 3654.7237
cellbender:remove-background: [epoch 126]  average training loss: 3654.3228
cellbender:remove-background: [epoch 127]  average training loss: 3640.7639
cellbender:remove-background: [epoch 128]  average training loss: 3624.8371
cellbender:remove-background: [epoch 129]  average training loss: 3636.5120
cellbender:remove-background: [epoch 130]  average training loss: 3642.4286
cellbender:remove-background: [epoch 130] average test loss: 3659.9533
cellbender:remove-background: [epoch 131]  average training loss: 3637.0071
cellbender:remove-background: [epoch 132]  average training loss: 3653.4029
cellbender:remove-background: [epoch 133]  average training loss: 3655.4752
cellbender:remove-background: [epoch 134]  average training loss: 3656.8479
cellbender:remove-background: [epoch 135]  average training loss: 3629.3466
cellbender:remove-background: [epoch 135] average test loss: 3714.6639
cellbender:remove-background: [epoch 136]  average training loss: 3626.4814
cellbender:remove-background: [epoch 137]  average training loss: 3648.7691
cellbender:remove-background: [epoch 138]  average training loss: 3638.8921
cellbender:remove-background: [epoch 139]  average training loss: 3653.5512
cellbender:remove-background: [epoch 140]  average training loss: 3635.0744
cellbender:remove-background: [epoch 140] average test loss: 3684.9530
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/1604-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 141]  average training loss: 3646.4123
cellbender:remove-background: [epoch 142]  average training loss: 3667.0190
cellbender:remove-background: [epoch 143]  average training loss: 3628.0933
cellbender:remove-background: [epoch 144]  average training loss: 3654.1132
cellbender:remove-background: [epoch 145]  average training loss: 3635.5167
cellbender:remove-background: [epoch 145] average test loss: 3664.5427
cellbender:remove-background: [epoch 146]  average training loss: 3657.9295
cellbender:remove-background: [epoch 147]  average training loss: 3648.4061
cellbender:remove-background: [epoch 148]  average training loss: 3672.9944
cellbender:remove-background: [epoch 149]  average training loss: 3655.2182
cellbender:remove-background: [epoch 150]  average training loss: 3627.2421
cellbender:remove-background: [epoch 150] average test loss: 3670.9621
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/1604-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:51:46
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpljx97va7
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpljx97va7
/tmp/tmpljx97va7/52c5d80e3d_random.pyro
/tmp/tmpljx97va7/52c5d80e3d_random.cuda
/tmp/tmpljx97va7/52c5d80e3d_model.torch
/tmp/tmpljx97va7/52c5d80e3d_optim.torch
/tmp/tmpljx97va7/52c5d80e3d_optim.pyro
/tmp/tmpljx97va7/52c5d80e3d_params.pyro
/tmp/tmpljx97va7/52c5d80e3d_train.loaderstate
/tmp/tmpljx97va7/52c5d80e3d_test.loaderstate
/tmp/tmpljx97va7/52c5d80e3d_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 (1/106)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/106)
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cellbender:remove-background: Working on chunk (99/106)
cellbender:remove-background: Working on chunk (100/106)
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cellbender:remove-background: Working on chunk (102/106)
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cellbender:remove-background: Working on chunk (104/106)
cellbender:remove-background: Working on chunk (105/106)
cellbender:remove-background: Working on chunk (106/106)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-DLPFC/1604-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/1604-Control-DLPFC/1604-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:57:35

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-DLPFC/1604-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/1604-Control-DLPFC/1604-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:     [2.68 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 16:17:06 Total MCKP estimation time = 1125.70 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/1604-Control-DLPFC/1604-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/1604-Control-DLPFC/1604-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/1604-Control-DLPFC/1604-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/1604-Control-DLPFC/1604-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:17:31