cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1601-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-DLPFC/1601-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 8425 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 329010e55e)
cellbender:remove-background: 2024-06-06 15:04:11
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-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: 31998 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4310
cellbender:remove-background: Prior on counts for empty droplets is 135
cellbender:remove-background: Excluding 5239 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 26759 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 67
cellbender:remove-background: Using 8425 probable cell barcodes, plus an additional 11575 barcodes, and 52787 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 134 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpgz0pikkv
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: 6193.6153
cellbender:remove-background: [epoch 002]  average training loss: 5014.0012  (5.8 seconds per epoch)
cellbender:remove-background: Will checkpoint every 73 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4373.6999
cellbender:remove-background: [epoch 004]  average training loss: 3938.5413
cellbender:remove-background: [epoch 005]  average training loss: 3794.7781
cellbender:remove-background: [epoch 005] average test loss: 3829.2563
cellbender:remove-background: [epoch 006]  average training loss: 3721.3637
cellbender:remove-background: [epoch 007]  average training loss: 3652.8284
cellbender:remove-background: [epoch 008]  average training loss: 3610.8326
cellbender:remove-background: [epoch 009]  average training loss: 3604.7712
cellbender:remove-background: [epoch 010]  average training loss: 3569.7873
cellbender:remove-background: [epoch 010] average test loss: 3574.4173
cellbender:remove-background: [epoch 011]  average training loss: 3537.1146
cellbender:remove-background: [epoch 012]  average training loss: 3350.6739
cellbender:remove-background: [epoch 013]  average training loss: 3285.8341
cellbender:remove-background: [epoch 014]  average training loss: 3285.5956
cellbender:remove-background: [epoch 015]  average training loss: 3254.4352
cellbender:remove-background: [epoch 015] average test loss: 3275.6018
cellbender:remove-background: [epoch 016]  average training loss: 3235.9871
cellbender:remove-background: [epoch 017]  average training loss: 3236.6140
cellbender:remove-background: [epoch 018]  average training loss: 3221.7300
cellbender:remove-background: [epoch 019]  average training loss: 3206.5914
cellbender:remove-background: [epoch 020]  average training loss: 3195.6924
cellbender:remove-background: [epoch 020] average test loss: 3222.4423
cellbender:remove-background: [epoch 021]  average training loss: 3192.0271
cellbender:remove-background: [epoch 022]  average training loss: 3190.1219
cellbender:remove-background: [epoch 023]  average training loss: 3189.1969
cellbender:remove-background: [epoch 024]  average training loss: 3178.0324
cellbender:remove-background: [epoch 025]  average training loss: 3169.5111
cellbender:remove-background: [epoch 025] average test loss: 3172.3938
cellbender:remove-background: [epoch 026]  average training loss: 3153.7028
cellbender:remove-background: [epoch 027]  average training loss: 3149.6033
cellbender:remove-background: [epoch 028]  average training loss: 3144.8831
cellbender:remove-background: [epoch 029]  average training loss: 3137.9120
cellbender:remove-background: [epoch 030]  average training loss: 3133.2559
cellbender:remove-background: [epoch 030] average test loss: 3132.7828
cellbender:remove-background: [epoch 031]  average training loss: 3127.7264
cellbender:remove-background: [epoch 032]  average training loss: 3125.6213
cellbender:remove-background: [epoch 033]  average training loss: 3122.1241
cellbender:remove-background: [epoch 034]  average training loss: 3120.6046
cellbender:remove-background: [epoch 035]  average training loss: 3116.2956
cellbender:remove-background: [epoch 035] average test loss: 3135.1557
cellbender:remove-background: [epoch 036]  average training loss: 3115.9708
cellbender:remove-background: [epoch 037]  average training loss: 3116.7292
cellbender:remove-background: [epoch 038]  average training loss: 3113.6917
cellbender:remove-background: [epoch 039]  average training loss: 3113.1639
cellbender:remove-background: [epoch 040]  average training loss: 3117.0616
cellbender:remove-background: [epoch 040] average test loss: 3135.0374
cellbender:remove-background: [epoch 041]  average training loss: 3111.1502
cellbender:remove-background: [epoch 042]  average training loss: 3109.1156
cellbender:remove-background: [epoch 043]  average training loss: 3106.8431
cellbender:remove-background: [epoch 044]  average training loss: 3107.5850
cellbender:remove-background: [epoch 045]  average training loss: 3108.6752
cellbender:remove-background: [epoch 045] average test loss: 3134.7333
cellbender:remove-background: [epoch 046]  average training loss: 3105.5572
cellbender:remove-background: [epoch 047]  average training loss: 3105.4439
cellbender:remove-background: [epoch 048]  average training loss: 3104.9869
cellbender:remove-background: [epoch 049]  average training loss: 3104.1554
cellbender:remove-background: [epoch 050]  average training loss: 3103.7255
cellbender:remove-background: [epoch 050] average test loss: 3115.0643
cellbender:remove-background: [epoch 051]  average training loss: 3100.9289
cellbender:remove-background: [epoch 052]  average training loss: 3101.1640
cellbender:remove-background: [epoch 053]  average training loss: 3100.3608
cellbender:remove-background: [epoch 054]  average training loss: 3102.6704
cellbender:remove-background: [epoch 055]  average training loss: 3104.2765
cellbender:remove-background: [epoch 055] average test loss: 3132.8470
cellbender:remove-background: [epoch 056]  average training loss: 3102.9678
cellbender:remove-background: [epoch 057]  average training loss: 3101.4111
cellbender:remove-background: [epoch 058]  average training loss: 3105.9830
cellbender:remove-background: [epoch 059]  average training loss: 3102.1635
cellbender:remove-background: [epoch 060]  average training loss: 3102.7581
cellbender:remove-background: [epoch 060] average test loss: 3110.7870
cellbender:remove-background: [epoch 061]  average training loss: 3099.3019
cellbender:remove-background: [epoch 062]  average training loss: 3099.4498
cellbender:remove-background: [epoch 063]  average training loss: 3097.6344
cellbender:remove-background: [epoch 064]  average training loss: 3099.2302
cellbender:remove-background: [epoch 065]  average training loss: 3095.2229
cellbender:remove-background: [epoch 065] average test loss: 3115.7647
cellbender:remove-background: [epoch 066]  average training loss: 3095.5532
cellbender:remove-background: [epoch 067]  average training loss: 3095.7402
cellbender:remove-background: [epoch 068]  average training loss: 3094.2322
cellbender:remove-background: [epoch 069]  average training loss: 3092.5167
cellbender:remove-background: [epoch 070]  average training loss: 3091.2090
cellbender:remove-background: [epoch 070] average test loss: 3095.6901
cellbender:remove-background: [epoch 071]  average training loss: 3089.6732
cellbender:remove-background: [epoch 072]  average training loss: 3089.9851
cellbender:remove-background: [epoch 073]  average training loss: 3089.7775
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 074]  average training loss: 3088.7527
cellbender:remove-background: [epoch 075]  average training loss: 3090.4277
cellbender:remove-background: [epoch 075] average test loss: 3109.9015
cellbender:remove-background: [epoch 076]  average training loss: 3089.3638
cellbender:remove-background: [epoch 077]  average training loss: 3088.1592
cellbender:remove-background: [epoch 078]  average training loss: 3088.2931
cellbender:remove-background: [epoch 079]  average training loss: 3086.1117
cellbender:remove-background: [epoch 080]  average training loss: 3083.3298
cellbender:remove-background: [epoch 080] average test loss: 3112.7331
cellbender:remove-background: [epoch 081]  average training loss: 3086.2591
cellbender:remove-background: [epoch 082]  average training loss: 3085.0648
cellbender:remove-background: [epoch 083]  average training loss: 3084.3522
cellbender:remove-background: [epoch 084]  average training loss: 3082.8859
cellbender:remove-background: [epoch 085]  average training loss: 3080.1420
cellbender:remove-background: [epoch 085] average test loss: 3100.2301
cellbender:remove-background: [epoch 086]  average training loss: 3081.6542
cellbender:remove-background: [epoch 087]  average training loss: 3080.0020
cellbender:remove-background: [epoch 088]  average training loss: 3080.8923
cellbender:remove-background: [epoch 089]  average training loss: 3081.0539
cellbender:remove-background: [epoch 090]  average training loss: 3079.1253
cellbender:remove-background: [epoch 090] average test loss: 3111.6548
cellbender:remove-background: [epoch 091]  average training loss: 3079.5304
cellbender:remove-background: [epoch 092]  average training loss: 3080.5865
cellbender:remove-background: [epoch 093]  average training loss: 3080.8960
cellbender:remove-background: [epoch 094]  average training loss: 3079.0670
cellbender:remove-background: [epoch 095]  average training loss: 3079.3277
cellbender:remove-background: [epoch 095] average test loss: 3096.1458
cellbender:remove-background: [epoch 096]  average training loss: 3078.5395
cellbender:remove-background: [epoch 097]  average training loss: 3077.0367
cellbender:remove-background: [epoch 098]  average training loss: 3078.6058
cellbender:remove-background: [epoch 099]  average training loss: 3079.0509
cellbender:remove-background: [epoch 100]  average training loss: 3076.9221
cellbender:remove-background: [epoch 100] average test loss: 3108.6486
cellbender:remove-background: [epoch 101]  average training loss: 3077.9878
cellbender:remove-background: [epoch 102]  average training loss: 3076.4750
cellbender:remove-background: [epoch 103]  average training loss: 3076.1357
cellbender:remove-background: [epoch 104]  average training loss: 3075.6611
cellbender:remove-background: [epoch 105]  average training loss: 3075.7058
cellbender:remove-background: [epoch 105] average test loss: 3094.0151
cellbender:remove-background: [epoch 106]  average training loss: 3074.3039
cellbender:remove-background: [epoch 107]  average training loss: 3076.5363
cellbender:remove-background: [epoch 108]  average training loss: 3076.4507
cellbender:remove-background: [epoch 109]  average training loss: 3076.5373
cellbender:remove-background: [epoch 110]  average training loss: 3075.0337
cellbender:remove-background: [epoch 110] average test loss: 3093.6417
cellbender:remove-background: [epoch 111]  average training loss: 3075.3748
cellbender:remove-background: [epoch 112]  average training loss: 3075.2275
cellbender:remove-background: [epoch 113]  average training loss: 3075.3164
cellbender:remove-background: [epoch 114]  average training loss: 3073.2033
cellbender:remove-background: [epoch 115]  average training loss: 3074.4282
cellbender:remove-background: [epoch 115] average test loss: 3094.4033
cellbender:remove-background: [epoch 116]  average training loss: 3073.1348
cellbender:remove-background: [epoch 117]  average training loss: 3074.2097
cellbender:remove-background: [epoch 118]  average training loss: 3073.8345
cellbender:remove-background: [epoch 119]  average training loss: 3074.2445
cellbender:remove-background: [epoch 120]  average training loss: 3072.3974
cellbender:remove-background: [epoch 120] average test loss: 3096.3455
cellbender:remove-background: [epoch 121]  average training loss: 3074.4060
cellbender:remove-background: [epoch 122]  average training loss: 3073.2930
cellbender:remove-background: [epoch 123]  average training loss: 3072.1129
cellbender:remove-background: [epoch 124]  average training loss: 3073.3467
cellbender:remove-background: [epoch 125]  average training loss: 3074.4029
cellbender:remove-background: [epoch 125] average test loss: 3093.2601
cellbender:remove-background: [epoch 126]  average training loss: 3072.4355
cellbender:remove-background: [epoch 127]  average training loss: 3071.8440
cellbender:remove-background: [epoch 128]  average training loss: 3071.9193
cellbender:remove-background: [epoch 129]  average training loss: 3072.2743
cellbender:remove-background: [epoch 130]  average training loss: 3074.5260
cellbender:remove-background: [epoch 130] average test loss: 3094.9377
cellbender:remove-background: [epoch 131]  average training loss: 3073.1739
cellbender:remove-background: [epoch 132]  average training loss: 3069.6824
cellbender:remove-background: [epoch 133]  average training loss: 3071.4770
cellbender:remove-background: [epoch 134]  average training loss: 3069.4600
cellbender:remove-background: [epoch 135]  average training loss: 3071.0734
cellbender:remove-background: [epoch 135] average test loss: 3092.5185
cellbender:remove-background: [epoch 136]  average training loss: 3071.3086
cellbender:remove-background: [epoch 137]  average training loss: 3070.1636
cellbender:remove-background: [epoch 138]  average training loss: 3070.9130
cellbender:remove-background: [epoch 139]  average training loss: 3070.1990
cellbender:remove-background: [epoch 140]  average training loss: 3069.9887
cellbender:remove-background: [epoch 140] average test loss: 3093.7337
cellbender:remove-background: [epoch 141]  average training loss: 3069.6875
cellbender:remove-background: [epoch 142]  average training loss: 3071.0301
cellbender:remove-background: [epoch 143]  average training loss: 3070.5058
cellbender:remove-background: [epoch 144]  average training loss: 3070.2325
cellbender:remove-background: [epoch 145]  average training loss: 3069.7957
cellbender:remove-background: [epoch 145] average test loss: 3091.3815
cellbender:remove-background: [epoch 146]  average training loss: 3070.0187
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 147]  average training loss: 3071.0695
cellbender:remove-background: [epoch 148]  average training loss: 3071.2117
cellbender:remove-background: [epoch 149]  average training loss: 3071.1901
cellbender:remove-background: [epoch 150]  average training loss: 3070.3466
cellbender:remove-background: [epoch 150] average test loss: 3095.1414
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:22:09
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpav0vfh61
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpav0vfh61
/tmp/tmpav0vfh61/329010e55e_random.pyro
/tmp/tmpav0vfh61/329010e55e_random.cuda
/tmp/tmpav0vfh61/329010e55e_model.torch
/tmp/tmpav0vfh61/329010e55e_optim.torch
/tmp/tmpav0vfh61/329010e55e_optim.pyro
/tmp/tmpav0vfh61/329010e55e_params.pyro
/tmp/tmpav0vfh61/329010e55e_train.loaderstate
/tmp/tmpav0vfh61/329010e55e_test.loaderstate
/tmp/tmpav0vfh61/329010e55e_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 (1/71)
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/1601-Bipolar-DLPFC/1601-Bipolar-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/1601-Bipolar-DLPFC/1601-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:26:24

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-DLPFC/1601-Bipolar-DLPFC.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-DLPFC/1601-Bipolar-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:     [1.53 mins per chunk]
cellbender:remove-background: Working on chunk (2/7)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:37:31 Total MCKP estimation time = 640.15 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-DLPFC/1601-Bipolar-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/1601-Bipolar-DLPFC/1601-Bipolar-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/1601-Bipolar-DLPFC/1601-Bipolar-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/1601-Bipolar-DLPFC/1601-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:38:05