cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1461-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-DLPFC/1461-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 7260 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 288231ff59)
cellbender:remove-background: 2024-06-06 14:48:44
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/1461-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: 31971 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3220
cellbender:remove-background: Prior on counts for empty droplets is 101
cellbender:remove-background: Excluding 7143 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 24828 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 50
cellbender:remove-background: Using 7260 probable cell barcodes, plus an additional 12740 barcodes, and 34584 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 100 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmph105zacp
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: 5688.7919
cellbender:remove-background: [epoch 002]  average training loss: 4466.7585  (5.4 seconds per epoch)
cellbender:remove-background: Will checkpoint every 78 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3810.0657
cellbender:remove-background: [epoch 004]  average training loss: 3409.5320
cellbender:remove-background: [epoch 005]  average training loss: 3281.6662
cellbender:remove-background: [epoch 005] average test loss: 3366.2167
cellbender:remove-background: [epoch 006]  average training loss: 3226.2987
cellbender:remove-background: [epoch 007]  average training loss: 3177.8544
cellbender:remove-background: [epoch 008]  average training loss: 3149.0712
cellbender:remove-background: [epoch 009]  average training loss: 3120.3282
cellbender:remove-background: [epoch 010]  average training loss: 3024.2797
cellbender:remove-background: [epoch 010] average test loss: 2996.4422
cellbender:remove-background: [epoch 011]  average training loss: 2985.6875
cellbender:remove-background: [epoch 012]  average training loss: 2957.1897
cellbender:remove-background: [epoch 013]  average training loss: 2933.8234
cellbender:remove-background: [epoch 014]  average training loss: 2947.0049
cellbender:remove-background: [epoch 015]  average training loss: 2920.1893
cellbender:remove-background: [epoch 015] average test loss: 2947.2935
cellbender:remove-background: [epoch 016]  average training loss: 2905.6069
cellbender:remove-background: [epoch 017]  average training loss: 2908.5567
cellbender:remove-background: [epoch 018]  average training loss: 2893.7449
cellbender:remove-background: [epoch 019]  average training loss: 2882.7214
cellbender:remove-background: [epoch 020]  average training loss: 2868.2698
cellbender:remove-background: [epoch 020] average test loss: 2877.3750
cellbender:remove-background: [epoch 021]  average training loss: 2864.0447
cellbender:remove-background: [epoch 022]  average training loss: 2866.4595
cellbender:remove-background: [epoch 023]  average training loss: 2861.0363
cellbender:remove-background: [epoch 024]  average training loss: 2843.9427
cellbender:remove-background: [epoch 025]  average training loss: 2823.0908
cellbender:remove-background: [epoch 025] average test loss: 2807.9671
cellbender:remove-background: [epoch 026]  average training loss: 2800.5345
cellbender:remove-background: [epoch 027]  average training loss: 2788.5672
cellbender:remove-background: [epoch 028]  average training loss: 2779.5831
cellbender:remove-background: [epoch 029]  average training loss: 2771.4820
cellbender:remove-background: [epoch 030]  average training loss: 2769.0799
cellbender:remove-background: [epoch 030] average test loss: 2765.6263
cellbender:remove-background: [epoch 031]  average training loss: 2761.9931
cellbender:remove-background: [epoch 032]  average training loss: 2758.6031
cellbender:remove-background: [epoch 033]  average training loss: 2755.0937
cellbender:remove-background: [epoch 034]  average training loss: 2752.4977
cellbender:remove-background: [epoch 035]  average training loss: 2751.4745
cellbender:remove-background: [epoch 035] average test loss: 2753.4773
cellbender:remove-background: [epoch 036]  average training loss: 2751.7208
cellbender:remove-background: [epoch 037]  average training loss: 2752.9469
cellbender:remove-background: [epoch 038]  average training loss: 2753.3950
cellbender:remove-background: [epoch 039]  average training loss: 2751.0214
cellbender:remove-background: [epoch 040]  average training loss: 2752.5937
cellbender:remove-background: [epoch 040] average test loss: 2744.0080
cellbender:remove-background: [epoch 041]  average training loss: 2753.7094
cellbender:remove-background: [epoch 042]  average training loss: 2754.1932
cellbender:remove-background: [epoch 043]  average training loss: 2755.5597
cellbender:remove-background: [epoch 044]  average training loss: 2756.4720
cellbender:remove-background: [epoch 045]  average training loss: 2758.2553
cellbender:remove-background: [epoch 045] average test loss: 2742.1141
cellbender:remove-background: [epoch 046]  average training loss: 2760.8016
cellbender:remove-background: [epoch 047]  average training loss: 2758.4913
cellbender:remove-background: [epoch 048]  average training loss: 2760.2890
cellbender:remove-background: [epoch 049]  average training loss: 2767.1112
cellbender:remove-background: [epoch 050]  average training loss: 2769.8159
cellbender:remove-background: [epoch 050] average test loss: 2778.0909
cellbender:remove-background: [epoch 051]  average training loss: 2765.7985
cellbender:remove-background: [epoch 052]  average training loss: 2767.9739
cellbender:remove-background: [epoch 053]  average training loss: 2772.4043
cellbender:remove-background: [epoch 054]  average training loss: 2769.2993
cellbender:remove-background: [epoch 055]  average training loss: 2777.1275
cellbender:remove-background: [epoch 055] average test loss: 2756.3149
cellbender:remove-background: [epoch 056]  average training loss: 2772.2123
cellbender:remove-background: [epoch 057]  average training loss: 2772.8330
cellbender:remove-background: [epoch 058]  average training loss: 2782.5828
cellbender:remove-background: [epoch 059]  average training loss: 2786.1379
cellbender:remove-background: [epoch 060]  average training loss: 2777.7991
cellbender:remove-background: [epoch 060] average test loss: 2803.5938
cellbender:remove-background: [epoch 061]  average training loss: 2797.3508
cellbender:remove-background: [epoch 062]  average training loss: 2794.6235
cellbender:remove-background: [epoch 063]  average training loss: 2793.3169
cellbender:remove-background: [epoch 064]  average training loss: 2790.1421
cellbender:remove-background: [epoch 065]  average training loss: 2795.2262
cellbender:remove-background: [epoch 065] average test loss: 2846.5412
cellbender:remove-background: [epoch 066]  average training loss: 2804.4326
cellbender:remove-background: [epoch 067]  average training loss: 2797.3773
cellbender:remove-background: [epoch 068]  average training loss: 2800.9844
cellbender:remove-background: [epoch 069]  average training loss: 2797.3889
cellbender:remove-background: [epoch 070]  average training loss: 2791.9747
cellbender:remove-background: [epoch 070] average test loss: 2812.5142
cellbender:remove-background: [epoch 071]  average training loss: 2804.5907
cellbender:remove-background: [epoch 072]  average training loss: 2803.5806
cellbender:remove-background: [epoch 073]  average training loss: 2800.2281
cellbender:remove-background: [epoch 074]  average training loss: 2797.6042
cellbender:remove-background: [epoch 075]  average training loss: 2804.1453
cellbender:remove-background: [epoch 075] average test loss: 2827.7759
cellbender:remove-background: [epoch 076]  average training loss: 2811.4179
cellbender:remove-background: [epoch 077]  average training loss: 2818.8870
cellbender:remove-background: [epoch 078]  average training loss: 2819.9086
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/1461-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 079]  average training loss: 2805.9029
cellbender:remove-background: [epoch 080]  average training loss: 2797.4331
cellbender:remove-background: [epoch 080] average test loss: 2820.3559
cellbender:remove-background: [epoch 081]  average training loss: 2795.0733
cellbender:remove-background: [epoch 082]  average training loss: 2795.0132
cellbender:remove-background: [epoch 083]  average training loss: 2793.1237
cellbender:remove-background: [epoch 084]  average training loss: 2797.7966
cellbender:remove-background: [epoch 085]  average training loss: 2790.9155
cellbender:remove-background: [epoch 085] average test loss: 2830.7275
cellbender:remove-background: [epoch 086]  average training loss: 2791.7853
cellbender:remove-background: [epoch 087]  average training loss: 2795.8154
cellbender:remove-background: [epoch 088]  average training loss: 2799.1157
cellbender:remove-background: [epoch 089]  average training loss: 2796.9152
cellbender:remove-background: [epoch 090]  average training loss: 2799.1492
cellbender:remove-background: [epoch 090] average test loss: 2837.8805
cellbender:remove-background: [epoch 091]  average training loss: 2798.0366
cellbender:remove-background: [epoch 092]  average training loss: 2784.3773
cellbender:remove-background: [epoch 093]  average training loss: 2787.5799
cellbender:remove-background: [epoch 094]  average training loss: 2784.4061
cellbender:remove-background: [epoch 095]  average training loss: 2795.2688
cellbender:remove-background: [epoch 095] average test loss: 2825.8502
cellbender:remove-background: [epoch 096]  average training loss: 2799.8668
cellbender:remove-background: [epoch 097]  average training loss: 2800.6214
cellbender:remove-background: [epoch 098]  average training loss: 2797.5910
cellbender:remove-background: [epoch 099]  average training loss: 2796.1411
cellbender:remove-background: [epoch 100]  average training loss: 2797.9219
cellbender:remove-background: [epoch 100] average test loss: 2822.8137
cellbender:remove-background: [epoch 101]  average training loss: 2795.2033
cellbender:remove-background: [epoch 102]  average training loss: 2793.3216
cellbender:remove-background: [epoch 103]  average training loss: 2800.1484
cellbender:remove-background: [epoch 104]  average training loss: 2788.9959
cellbender:remove-background: [epoch 105]  average training loss: 2810.2821
cellbender:remove-background: [epoch 105] average test loss: 2836.3982
cellbender:remove-background: [epoch 106]  average training loss: 2795.6471
cellbender:remove-background: [epoch 107]  average training loss: 2794.8637
cellbender:remove-background: [epoch 108]  average training loss: 2788.0410
cellbender:remove-background: [epoch 109]  average training loss: 2792.6866
cellbender:remove-background: [epoch 110]  average training loss: 2789.3819
cellbender:remove-background: [epoch 110] average test loss: 2842.5539
cellbender:remove-background: [epoch 111]  average training loss: 2798.3644
cellbender:remove-background: [epoch 112]  average training loss: 2786.8221
cellbender:remove-background: [epoch 113]  average training loss: 2786.9875
cellbender:remove-background: [epoch 114]  average training loss: 2786.8411
cellbender:remove-background: [epoch 115]  average training loss: 2792.7582
cellbender:remove-background: [epoch 115] average test loss: 2867.1593
cellbender:remove-background: [epoch 116]  average training loss: 2791.2008
cellbender:remove-background: [epoch 117]  average training loss: 2783.8176
cellbender:remove-background: [epoch 118]  average training loss: 2785.7527
cellbender:remove-background: [epoch 119]  average training loss: 2787.7313
cellbender:remove-background: [epoch 120]  average training loss: 2786.1615
cellbender:remove-background: [epoch 120] average test loss: 2823.0888
cellbender:remove-background: [epoch 121]  average training loss: 2781.1573
cellbender:remove-background: [epoch 122]  average training loss: 2782.1736
cellbender:remove-background: [epoch 123]  average training loss: 2776.5164
cellbender:remove-background: [epoch 124]  average training loss: 2784.7935
cellbender:remove-background: [epoch 125]  average training loss: 2779.5036
cellbender:remove-background: [epoch 125] average test loss: 2833.7714
cellbender:remove-background: [epoch 126]  average training loss: 2781.4589
cellbender:remove-background: [epoch 127]  average training loss: 2779.8214
cellbender:remove-background: [epoch 128]  average training loss: 2788.7816
cellbender:remove-background: [epoch 129]  average training loss: 2772.7871
cellbender:remove-background: [epoch 130]  average training loss: 2791.2241
cellbender:remove-background: [epoch 130] average test loss: 2838.8643
cellbender:remove-background: [epoch 131]  average training loss: 2786.1877
cellbender:remove-background: [epoch 132]  average training loss: 2775.3622
cellbender:remove-background: [epoch 133]  average training loss: 2778.7712
cellbender:remove-background: [epoch 134]  average training loss: 2778.9965
cellbender:remove-background: [epoch 135]  average training loss: 2785.0446
cellbender:remove-background: [epoch 135] average test loss: 2819.3571
cellbender:remove-background: [epoch 136]  average training loss: 2775.6503
cellbender:remove-background: [epoch 137]  average training loss: 2780.5173
cellbender:remove-background: [epoch 138]  average training loss: 2780.4811
cellbender:remove-background: [epoch 139]  average training loss: 2774.9543
cellbender:remove-background: [epoch 140]  average training loss: 2783.5492
cellbender:remove-background: [epoch 140] average test loss: 2834.5707
cellbender:remove-background: [epoch 141]  average training loss: 2783.0475
cellbender:remove-background: [epoch 142]  average training loss: 2772.6640
cellbender:remove-background: [epoch 143]  average training loss: 2776.5797
cellbender:remove-background: [epoch 144]  average training loss: 2784.4329
cellbender:remove-background: [epoch 145]  average training loss: 2774.3081
cellbender:remove-background: [epoch 145] average test loss: 2858.6350
cellbender:remove-background: [epoch 146]  average training loss: 2782.5457
cellbender:remove-background: [epoch 147]  average training loss: 2783.0678
cellbender:remove-background: [epoch 148]  average training loss: 2777.2296
cellbender:remove-background: [epoch 149]  average training loss: 2774.4617
cellbender:remove-background: [epoch 150]  average training loss: 2786.7227
cellbender:remove-background: [epoch 150] average test loss: 2818.4509
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/1461-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:05:00
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp2taod7vp
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp2taod7vp
/tmp/tmp2taod7vp/288231ff59_random.pyro
/tmp/tmp2taod7vp/288231ff59_random.cuda
/tmp/tmp2taod7vp/288231ff59_model.torch
/tmp/tmp2taod7vp/288231ff59_optim.torch
/tmp/tmp2taod7vp/288231ff59_optim.pyro
/tmp/tmp2taod7vp/288231ff59_params.pyro
/tmp/tmp2taod7vp/288231ff59_train.loaderstate
/tmp/tmp2taod7vp/288231ff59_test.loaderstate
/tmp/tmp2taod7vp/288231ff59_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 (1/100)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/100)
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cellbender:remove-background: Working on chunk (48/100)
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cellbender:remove-background: Working on chunk (50/100)
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cellbender:remove-background: Working on chunk (97/100)
cellbender:remove-background: Working on chunk (98/100)
cellbender:remove-background: Working on chunk (99/100)
cellbender:remove-background: Working on chunk (100/100)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-DLPFC/1461-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/1461-Bipolar-DLPFC/1461-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:09:50

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1461-Bipolar-DLPFC/1461-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/1461-Bipolar-DLPFC/1461-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:     [1.41 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 15:19:58 Total MCKP estimation time = 583.69 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/1461-Bipolar-DLPFC/1461-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/1461-Bipolar-DLPFC/1461-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/1461-Bipolar-DLPFC/1461-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/1461-Bipolar-DLPFC/1461-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:20:14