cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1838-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 7397 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 4c009282bb)
cellbender:remove-background: 2024-06-06 15:32:50
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/1838-Bipolar-Hippocampus.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: 32130 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4872
cellbender:remove-background: Prior on counts for empty droplets is 82
cellbender:remove-background: Excluding 11867 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 20263 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 41
cellbender:remove-background: Using 7397 probable cell barcodes, plus an additional 12603 barcodes, and 27083 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 81 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpbnp3u8j6
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: 7961.5212
cellbender:remove-background: [epoch 002]  average training loss: 5876.3328  (12.5 seconds per epoch)
cellbender:remove-background: Will checkpoint every 34 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4783.5445
cellbender:remove-background: [epoch 004]  average training loss: 4096.9128
cellbender:remove-background: [epoch 005]  average training loss: 3826.9294
cellbender:remove-background: [epoch 005] average test loss: 3751.2680
cellbender:remove-background: [epoch 006]  average training loss: 3712.4737
cellbender:remove-background: [epoch 007]  average training loss: 3648.4537
cellbender:remove-background: [epoch 008]  average training loss: 3604.3782
cellbender:remove-background: [epoch 009]  average training loss: 3590.7977
cellbender:remove-background: [epoch 010]  average training loss: 3551.1070
cellbender:remove-background: [epoch 010] average test loss: 3472.1260
cellbender:remove-background: [epoch 011]  average training loss: 3548.5191
cellbender:remove-background: [epoch 012]  average training loss: 3515.1928
cellbender:remove-background: [epoch 013]  average training loss: 3403.1072
cellbender:remove-background: [epoch 014]  average training loss: 3382.2827
cellbender:remove-background: [epoch 015]  average training loss: 3353.4067
cellbender:remove-background: [epoch 015] average test loss: 3338.6031
cellbender:remove-background: [epoch 016]  average training loss: 3339.1292
cellbender:remove-background: [epoch 017]  average training loss: 3344.8009
cellbender:remove-background: [epoch 018]  average training loss: 3336.8999
cellbender:remove-background: [epoch 019]  average training loss: 3326.6714
cellbender:remove-background: [epoch 020]  average training loss: 3300.7609
cellbender:remove-background: [epoch 020] average test loss: 3290.0785
cellbender:remove-background: [epoch 021]  average training loss: 3295.3981
cellbender:remove-background: [epoch 022]  average training loss: 3283.9269
cellbender:remove-background: [epoch 023]  average training loss: 3252.1652
cellbender:remove-background: [epoch 024]  average training loss: 3228.9417
cellbender:remove-background: [epoch 025]  average training loss: 3219.9585
cellbender:remove-background: [epoch 025] average test loss: 3163.4726
cellbender:remove-background: [epoch 026]  average training loss: 3201.5692
cellbender:remove-background: [epoch 027]  average training loss: 3195.8045
cellbender:remove-background: [epoch 028]  average training loss: 3192.8370
cellbender:remove-background: [epoch 029]  average training loss: 3187.3508
cellbender:remove-background: [epoch 030]  average training loss: 3182.3741
cellbender:remove-background: [epoch 030] average test loss: 3129.9092
cellbender:remove-background: [epoch 031]  average training loss: 3181.0187
cellbender:remove-background: [epoch 032]  average training loss: 3176.5881
cellbender:remove-background: [epoch 033]  average training loss: 3174.4015
cellbender:remove-background: [epoch 034]  average training loss: 3172.3978
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/1838-Bipolar-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 035]  average training loss: 3170.8983
cellbender:remove-background: [epoch 035] average test loss: 3142.7146
cellbender:remove-background: [epoch 036]  average training loss: 3170.5485
cellbender:remove-background: [epoch 037]  average training loss: 3169.3147
cellbender:remove-background: [epoch 038]  average training loss: 3165.7555
cellbender:remove-background: [epoch 039]  average training loss: 3166.7792
cellbender:remove-background: [epoch 040]  average training loss: 3171.9168
cellbender:remove-background: [epoch 040] average test loss: 3116.1532
cellbender:remove-background: [epoch 041]  average training loss: 3171.8131
cellbender:remove-background: [epoch 042]  average training loss: 3173.4387
cellbender:remove-background: [epoch 043]  average training loss: 3170.3444
cellbender:remove-background: [epoch 044]  average training loss: 3174.2925
cellbender:remove-background: [epoch 045]  average training loss: 3175.6118
cellbender:remove-background: [epoch 045] average test loss: 3129.3594
cellbender:remove-background: [epoch 046]  average training loss: 3175.2724
cellbender:remove-background: [epoch 047]  average training loss: 3171.1253
cellbender:remove-background: [epoch 048]  average training loss: 3169.2923
cellbender:remove-background: [epoch 049]  average training loss: 3175.9414
cellbender:remove-background: [epoch 050]  average training loss: 3168.0481
cellbender:remove-background: [epoch 050] average test loss: 3112.2629
cellbender:remove-background: [epoch 051]  average training loss: 3168.8383
cellbender:remove-background: [epoch 052]  average training loss: 3166.3274
cellbender:remove-background: [epoch 053]  average training loss: 3173.9104
cellbender:remove-background: [epoch 054]  average training loss: 3163.4882
cellbender:remove-background: [epoch 055]  average training loss: 3174.2163
cellbender:remove-background: [epoch 055] average test loss: 3111.2728
cellbender:remove-background: [epoch 056]  average training loss: 3165.7326
cellbender:remove-background: [epoch 057]  average training loss: 3161.1469
cellbender:remove-background: [epoch 058]  average training loss: 3165.6256
cellbender:remove-background: [epoch 059]  average training loss: 3163.3147
cellbender:remove-background: [epoch 060]  average training loss: 3162.6786
cellbender:remove-background: [epoch 060] average test loss: 3133.2564
cellbender:remove-background: [epoch 061]  average training loss: 3159.9736
cellbender:remove-background: [epoch 062]  average training loss: 3159.9058
cellbender:remove-background: [epoch 063]  average training loss: 3157.2818
cellbender:remove-background: [epoch 064]  average training loss: 3155.8384
cellbender:remove-background: [epoch 065]  average training loss: 3160.2288
cellbender:remove-background: [epoch 065] average test loss: 3115.3613
cellbender:remove-background: [epoch 066]  average training loss: 3155.0626
cellbender:remove-background: [epoch 067]  average training loss: 3160.9980
cellbender:remove-background: [epoch 068]  average training loss: 3161.0381
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/1838-Bipolar-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 069]  average training loss: 3171.2269
cellbender:remove-background: [epoch 070]  average training loss: 3163.4764
cellbender:remove-background: [epoch 070] average test loss: 3136.7968
cellbender:remove-background: [epoch 071]  average training loss: 3167.8627
cellbender:remove-background: [epoch 072]  average training loss: 3168.1746
cellbender:remove-background: [epoch 073]  average training loss: 3171.5084
cellbender:remove-background: [epoch 074]  average training loss: 3175.0138
cellbender:remove-background: [epoch 075]  average training loss: 3174.9859
cellbender:remove-background: [epoch 075] average test loss: 3181.9614
cellbender:remove-background: [epoch 076]  average training loss: 3176.3712
cellbender:remove-background: [epoch 077]  average training loss: 3176.1128
cellbender:remove-background: [epoch 078]  average training loss: 3179.7255
cellbender:remove-background: [epoch 079]  average training loss: 3186.6797
cellbender:remove-background: [epoch 080]  average training loss: 3186.6477
cellbender:remove-background: [epoch 080] average test loss: 3152.8353
cellbender:remove-background: [epoch 081]  average training loss: 3186.2383
cellbender:remove-background: [epoch 082]  average training loss: 3196.3808
cellbender:remove-background: [epoch 083]  average training loss: 3192.7033
cellbender:remove-background: [epoch 084]  average training loss: 3186.8067
cellbender:remove-background: [epoch 085]  average training loss: 3190.5756
cellbender:remove-background: [epoch 085] average test loss: 3180.8239
cellbender:remove-background: [epoch 086]  average training loss: 3197.0889
cellbender:remove-background: [epoch 087]  average training loss: 3194.0163
cellbender:remove-background: [epoch 088]  average training loss: 3196.6008
cellbender:remove-background: [epoch 089]  average training loss: 3192.2976
cellbender:remove-background: [epoch 090]  average training loss: 3195.9512
cellbender:remove-background: [epoch 090] average test loss: 3212.1682
cellbender:remove-background: [epoch 091]  average training loss: 3201.8797
cellbender:remove-background: [epoch 092]  average training loss: 3206.7709
cellbender:remove-background: [epoch 093]  average training loss: 3195.3993
cellbender:remove-background: [epoch 094]  average training loss: 3197.2652
cellbender:remove-background: [epoch 095]  average training loss: 3192.4390
cellbender:remove-background: [epoch 095] average test loss: 3182.4080
cellbender:remove-background: [epoch 096]  average training loss: 3206.7763
cellbender:remove-background: [epoch 097]  average training loss: 3196.4849
cellbender:remove-background: [epoch 098]  average training loss: 3192.2189
cellbender:remove-background: [epoch 099]  average training loss: 3188.7232
cellbender:remove-background: [epoch 100]  average training loss: 3196.0499
cellbender:remove-background: [epoch 100] average test loss: 3205.0797
cellbender:remove-background: [epoch 101]  average training loss: 3190.2520
cellbender:remove-background: [epoch 102]  average training loss: 3189.4763
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/1838-Bipolar-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 103]  average training loss: 3196.0777
cellbender:remove-background: [epoch 104]  average training loss: 3185.6189
cellbender:remove-background: [epoch 105]  average training loss: 3190.1900
cellbender:remove-background: [epoch 105] average test loss: 3155.8358
cellbender:remove-background: [epoch 106]  average training loss: 3190.6179
cellbender:remove-background: [epoch 107]  average training loss: 3185.2282
cellbender:remove-background: [epoch 108]  average training loss: 3189.1510
cellbender:remove-background: [epoch 109]  average training loss: 3191.7263
cellbender:remove-background: [epoch 110]  average training loss: 3192.2939
cellbender:remove-background: [epoch 110] average test loss: 3185.4242
cellbender:remove-background: [epoch 111]  average training loss: 3184.2623
cellbender:remove-background: [epoch 112]  average training loss: 3184.4824
cellbender:remove-background: [epoch 113]  average training loss: 3186.9539
cellbender:remove-background: [epoch 114]  average training loss: 3185.2053
cellbender:remove-background: [epoch 115]  average training loss: 3178.7638
cellbender:remove-background: [epoch 115] average test loss: 3204.6837
cellbender:remove-background: [epoch 116]  average training loss: 3186.1811
cellbender:remove-background: [epoch 117]  average training loss: 3188.4800
cellbender:remove-background: [epoch 118]  average training loss: 3176.7577
cellbender:remove-background: [epoch 119]  average training loss: 3188.4274
cellbender:remove-background: [epoch 120]  average training loss: 3183.0297
cellbender:remove-background: [epoch 120] average test loss: 3209.8978
cellbender:remove-background: [epoch 121]  average training loss: 3186.5682
cellbender:remove-background: [epoch 122]  average training loss: 3183.9816
cellbender:remove-background: [epoch 123]  average training loss: 3189.5001
cellbender:remove-background: [epoch 124]  average training loss: 3187.2904
cellbender:remove-background: [epoch 125]  average training loss: 3183.0100
cellbender:remove-background: [epoch 125] average test loss: 3163.3718
cellbender:remove-background: [epoch 126]  average training loss: 3174.4369
cellbender:remove-background: [epoch 127]  average training loss: 3185.7287
cellbender:remove-background: [epoch 128]  average training loss: 3182.0332
cellbender:remove-background: [epoch 129]  average training loss: 3182.8124
cellbender:remove-background: [epoch 130]  average training loss: 3193.3325
cellbender:remove-background: [epoch 130] average test loss: 3185.4589
cellbender:remove-background: [epoch 131]  average training loss: 3171.0749
cellbender:remove-background: [epoch 132]  average training loss: 3183.1452
cellbender:remove-background: [epoch 133]  average training loss: 3182.3410
cellbender:remove-background: [epoch 134]  average training loss: 3184.9819
cellbender:remove-background: [epoch 135]  average training loss: 3182.0912
cellbender:remove-background: [epoch 135] average test loss: 3189.0418
cellbender:remove-background: [epoch 136]  average training loss: 3172.8942
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/1838-Bipolar-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 137]  average training loss: 3180.2597
cellbender:remove-background: [epoch 138]  average training loss: 3177.3447
cellbender:remove-background: [epoch 139]  average training loss: 3183.7205
cellbender:remove-background: [epoch 140]  average training loss: 3186.2062
cellbender:remove-background: [epoch 140] average test loss: 3185.4549
cellbender:remove-background: [epoch 141]  average training loss: 3185.7228
cellbender:remove-background: [epoch 142]  average training loss: 3183.2802
cellbender:remove-background: [epoch 143]  average training loss: 3175.5002
cellbender:remove-background: [epoch 144]  average training loss: 3175.9180
cellbender:remove-background: [epoch 145]  average training loss: 3185.0621
cellbender:remove-background: [epoch 145] average test loss: 3187.3038
cellbender:remove-background: [epoch 146]  average training loss: 3177.7176
cellbender:remove-background: [epoch 147]  average training loss: 3181.0949
cellbender:remove-background: [epoch 148]  average training loss: 3178.5433
cellbender:remove-background: [epoch 149]  average training loss: 3181.5274
cellbender:remove-background: [epoch 150]  average training loss: 3181.1325
cellbender:remove-background: [epoch 150] average test loss: 3188.1648
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/1838-Bipolar-Hippocampus/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 16:09:41
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpj6p_eiqt
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpj6p_eiqt
/tmp/tmpj6p_eiqt/4c009282bb_random.pyro
/tmp/tmpj6p_eiqt/4c009282bb_random.cuda
/tmp/tmpj6p_eiqt/4c009282bb_model.torch
/tmp/tmpj6p_eiqt/4c009282bb_optim.torch
/tmp/tmpj6p_eiqt/4c009282bb_optim.pyro
/tmp/tmpj6p_eiqt/4c009282bb_params.pyro
/tmp/tmpj6p_eiqt/4c009282bb_train.loaderstate
/tmp/tmpj6p_eiqt/4c009282bb_test.loaderstate
/tmp/tmpj6p_eiqt/4c009282bb_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 (1/84)
cellbender:remove-background:     [0.06 mins per chunk]
cellbender:remove-background: Working on chunk (2/84)
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cellbender:remove-background: Working on chunk (84/84)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.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/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 16:16:29

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.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:     [1.91 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 16:30:36 Total MCKP estimation time = 803.86 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/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.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/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.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/1838-Bipolar-Hippocampus/1838-Bipolar-Hippocampus.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:31:04