cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2686-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-DLPFC/2686-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 6485 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 73ab09615e)
cellbender:remove-background: 2024-06-06 15:04:07
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/2686-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: 32287 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4074
cellbender:remove-background: Prior on counts for empty droplets is 114
cellbender:remove-background: Excluding 9148 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 23139 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 57
cellbender:remove-background: Using 6485 probable cell barcodes, plus an additional 13515 barcodes, and 53428 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 113 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp48ccmyp6
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: 5628.1283
cellbender:remove-background: [epoch 002]  average training loss: 4392.0531  (5.2 seconds per epoch)
cellbender:remove-background: Will checkpoint every 82 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3781.7265
cellbender:remove-background: [epoch 004]  average training loss: 3415.5533
cellbender:remove-background: [epoch 005]  average training loss: 3312.1674
cellbender:remove-background: [epoch 005] average test loss: 3411.6786
cellbender:remove-background: [epoch 006]  average training loss: 3271.8733
cellbender:remove-background: [epoch 007]  average training loss: 3226.8991
cellbender:remove-background: [epoch 008]  average training loss: 3188.1535
cellbender:remove-background: [epoch 009]  average training loss: 3176.1341
cellbender:remove-background: [epoch 010]  average training loss: 3107.8171
cellbender:remove-background: [epoch 010] average test loss: 3131.9508
cellbender:remove-background: [epoch 011]  average training loss: 2979.9238
cellbender:remove-background: [epoch 012]  average training loss: 2939.8518
cellbender:remove-background: [epoch 013]  average training loss: 2915.7482
cellbender:remove-background: [epoch 014]  average training loss: 2917.5419
cellbender:remove-background: [epoch 015]  average training loss: 2889.4104
cellbender:remove-background: [epoch 015] average test loss: 2920.1888
cellbender:remove-background: [epoch 016]  average training loss: 2874.6222
cellbender:remove-background: [epoch 017]  average training loss: 2878.9963
cellbender:remove-background: [epoch 018]  average training loss: 2869.4085
cellbender:remove-background: [epoch 019]  average training loss: 2858.2461
cellbender:remove-background: [epoch 020]  average training loss: 2844.5252
cellbender:remove-background: [epoch 020] average test loss: 2878.9273
cellbender:remove-background: [epoch 021]  average training loss: 2842.6537
cellbender:remove-background: [epoch 022]  average training loss: 2845.1286
cellbender:remove-background: [epoch 023]  average training loss: 2841.1606
cellbender:remove-background: [epoch 024]  average training loss: 2835.0079
cellbender:remove-background: [epoch 025]  average training loss: 2834.6225
cellbender:remove-background: [epoch 025] average test loss: 2842.4676
cellbender:remove-background: [epoch 026]  average training loss: 2823.4462
cellbender:remove-background: [epoch 027]  average training loss: 2823.1775
cellbender:remove-background: [epoch 028]  average training loss: 2820.0336
cellbender:remove-background: [epoch 029]  average training loss: 2814.7447
cellbender:remove-background: [epoch 030]  average training loss: 2809.6675
cellbender:remove-background: [epoch 030] average test loss: 2803.3457
cellbender:remove-background: [epoch 031]  average training loss: 2804.5442
cellbender:remove-background: [epoch 032]  average training loss: 2799.1959
cellbender:remove-background: [epoch 033]  average training loss: 2791.5559
cellbender:remove-background: [epoch 034]  average training loss: 2778.9587
cellbender:remove-background: [epoch 035]  average training loss: 2769.2562
cellbender:remove-background: [epoch 035] average test loss: 2759.8711
cellbender:remove-background: [epoch 036]  average training loss: 2759.6688
cellbender:remove-background: [epoch 037]  average training loss: 2752.5596
cellbender:remove-background: [epoch 038]  average training loss: 2749.3218
cellbender:remove-background: [epoch 039]  average training loss: 2744.6871
cellbender:remove-background: [epoch 040]  average training loss: 2740.3343
cellbender:remove-background: [epoch 040] average test loss: 2739.3573
cellbender:remove-background: [epoch 041]  average training loss: 2737.2810
cellbender:remove-background: [epoch 042]  average training loss: 2737.3690
cellbender:remove-background: [epoch 043]  average training loss: 2734.2956
cellbender:remove-background: [epoch 044]  average training loss: 2732.8203
cellbender:remove-background: [epoch 045]  average training loss: 2736.8482
cellbender:remove-background: [epoch 045] average test loss: 2733.9487
cellbender:remove-background: [epoch 046]  average training loss: 2740.6097
cellbender:remove-background: [epoch 047]  average training loss: 2742.9133
cellbender:remove-background: [epoch 048]  average training loss: 2743.1211
cellbender:remove-background: [epoch 049]  average training loss: 2741.9833
cellbender:remove-background: [epoch 050]  average training loss: 2744.2929
cellbender:remove-background: [epoch 050] average test loss: 2758.1781
cellbender:remove-background: [epoch 051]  average training loss: 2742.8511
cellbender:remove-background: [epoch 052]  average training loss: 2745.3205
cellbender:remove-background: [epoch 053]  average training loss: 2753.7820
cellbender:remove-background: [epoch 054]  average training loss: 2753.4202
cellbender:remove-background: [epoch 055]  average training loss: 2753.6205
cellbender:remove-background: [epoch 055] average test loss: 2761.4082
cellbender:remove-background: [epoch 056]  average training loss: 2755.1888
cellbender:remove-background: [epoch 057]  average training loss: 2751.1689
cellbender:remove-background: [epoch 058]  average training loss: 2757.4351
cellbender:remove-background: [epoch 059]  average training loss: 2758.9036
cellbender:remove-background: [epoch 060]  average training loss: 2758.1200
cellbender:remove-background: [epoch 060] average test loss: 2793.6302
cellbender:remove-background: [epoch 061]  average training loss: 2764.6573
cellbender:remove-background: [epoch 062]  average training loss: 2763.0647
cellbender:remove-background: [epoch 063]  average training loss: 2762.4349
cellbender:remove-background: [epoch 064]  average training loss: 2760.9315
cellbender:remove-background: [epoch 065]  average training loss: 2761.1345
cellbender:remove-background: [epoch 065] average test loss: 2771.1398
cellbender:remove-background: [epoch 066]  average training loss: 2763.3152
cellbender:remove-background: [epoch 067]  average training loss: 2755.8489
cellbender:remove-background: [epoch 068]  average training loss: 2759.7608
cellbender:remove-background: [epoch 069]  average training loss: 2755.6365
cellbender:remove-background: [epoch 070]  average training loss: 2752.0456
cellbender:remove-background: [epoch 070] average test loss: 2772.4858
cellbender:remove-background: [epoch 071]  average training loss: 2756.4087
cellbender:remove-background: [epoch 072]  average training loss: 2759.9274
cellbender:remove-background: [epoch 073]  average training loss: 2755.5559
cellbender:remove-background: [epoch 074]  average training loss: 2756.9172
cellbender:remove-background: [epoch 075]  average training loss: 2756.0540
cellbender:remove-background: [epoch 075] average test loss: 2780.5536
cellbender:remove-background: [epoch 076]  average training loss: 2753.8255
cellbender:remove-background: [epoch 077]  average training loss: 2749.6825
cellbender:remove-background: [epoch 078]  average training loss: 2754.1037
cellbender:remove-background: [epoch 079]  average training loss: 2748.5473
cellbender:remove-background: [epoch 080]  average training loss: 2749.5710
cellbender:remove-background: [epoch 080] average test loss: 2794.6503
cellbender:remove-background: [epoch 081]  average training loss: 2750.5745
cellbender:remove-background: [epoch 082]  average training loss: 2753.7532
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/2686-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 083]  average training loss: 2750.6444
cellbender:remove-background: [epoch 084]  average training loss: 2749.3772
cellbender:remove-background: [epoch 085]  average training loss: 2748.9714
cellbender:remove-background: [epoch 085] average test loss: 2791.6344
cellbender:remove-background: [epoch 086]  average training loss: 2749.1196
cellbender:remove-background: [epoch 087]  average training loss: 2752.9828
cellbender:remove-background: [epoch 088]  average training loss: 2749.9722
cellbender:remove-background: [epoch 089]  average training loss: 2750.4967
cellbender:remove-background: [epoch 090]  average training loss: 2748.8848
cellbender:remove-background: [epoch 090] average test loss: 2782.7392
cellbender:remove-background: [epoch 091]  average training loss: 2746.9519
cellbender:remove-background: [epoch 092]  average training loss: 2745.4521
cellbender:remove-background: [epoch 093]  average training loss: 2750.4487
cellbender:remove-background: [epoch 094]  average training loss: 2750.8842
cellbender:remove-background: [epoch 095]  average training loss: 2751.8910
cellbender:remove-background: [epoch 095] average test loss: 2781.2346
cellbender:remove-background: [epoch 096]  average training loss: 2743.7842
cellbender:remove-background: [epoch 097]  average training loss: 2744.4484
cellbender:remove-background: [epoch 098]  average training loss: 2745.3323
cellbender:remove-background: [epoch 099]  average training loss: 2749.5733
cellbender:remove-background: [epoch 100]  average training loss: 2746.1588
cellbender:remove-background: [epoch 100] average test loss: 2787.7183
cellbender:remove-background: [epoch 101]  average training loss: 2745.8213
cellbender:remove-background: [epoch 102]  average training loss: 2745.4989
cellbender:remove-background: [epoch 103]  average training loss: 2747.5136
cellbender:remove-background: [epoch 104]  average training loss: 2744.8320
cellbender:remove-background: [epoch 105]  average training loss: 2743.5982
cellbender:remove-background: [epoch 105] average test loss: 2791.8604
cellbender:remove-background: [epoch 106]  average training loss: 2748.5378
cellbender:remove-background: [epoch 107]  average training loss: 2741.5580
cellbender:remove-background: [epoch 108]  average training loss: 2743.4418
cellbender:remove-background: [epoch 109]  average training loss: 2745.2405
cellbender:remove-background: [epoch 110]  average training loss: 2740.3988
cellbender:remove-background: [epoch 110] average test loss: 2777.2213
cellbender:remove-background: [epoch 111]  average training loss: 2744.2653
cellbender:remove-background: [epoch 112]  average training loss: 2741.7956
cellbender:remove-background: [epoch 113]  average training loss: 2743.5108
cellbender:remove-background: [epoch 114]  average training loss: 2740.3595
cellbender:remove-background: [epoch 115]  average training loss: 2738.8830
cellbender:remove-background: [epoch 115] average test loss: 2780.6013
cellbender:remove-background: [epoch 116]  average training loss: 2742.1207
cellbender:remove-background: [epoch 117]  average training loss: 2739.3853
cellbender:remove-background: [epoch 118]  average training loss: 2739.1961
cellbender:remove-background: [epoch 119]  average training loss: 2742.5744
cellbender:remove-background: [epoch 120]  average training loss: 2741.2514
cellbender:remove-background: [epoch 120] average test loss: 2788.5934
cellbender:remove-background: [epoch 121]  average training loss: 2742.6830
cellbender:remove-background: [epoch 122]  average training loss: 2736.9293
cellbender:remove-background: [epoch 123]  average training loss: 2740.9792
cellbender:remove-background: [epoch 124]  average training loss: 2738.5264
cellbender:remove-background: [epoch 125]  average training loss: 2740.0731
cellbender:remove-background: [epoch 125] average test loss: 2775.2342
cellbender:remove-background: [epoch 126]  average training loss: 2737.8925
cellbender:remove-background: [epoch 127]  average training loss: 2742.1069
cellbender:remove-background: [epoch 128]  average training loss: 2739.7615
cellbender:remove-background: [epoch 129]  average training loss: 2738.8584
cellbender:remove-background: [epoch 130]  average training loss: 2738.6609
cellbender:remove-background: [epoch 130] average test loss: 2777.1586
cellbender:remove-background: [epoch 131]  average training loss: 2739.2497
cellbender:remove-background: [epoch 132]  average training loss: 2738.5623
cellbender:remove-background: [epoch 133]  average training loss: 2738.4404
cellbender:remove-background: [epoch 134]  average training loss: 2740.1021
cellbender:remove-background: [epoch 135]  average training loss: 2739.5029
cellbender:remove-background: [epoch 135] average test loss: 2777.0554
cellbender:remove-background: [epoch 136]  average training loss: 2736.3374
cellbender:remove-background: [epoch 137]  average training loss: 2737.9526
cellbender:remove-background: [epoch 138]  average training loss: 2739.0755
cellbender:remove-background: [epoch 139]  average training loss: 2737.8873
cellbender:remove-background: [epoch 140]  average training loss: 2737.0587
cellbender:remove-background: [epoch 140] average test loss: 2779.0933
cellbender:remove-background: [epoch 141]  average training loss: 2738.4822
cellbender:remove-background: [epoch 142]  average training loss: 2737.1142
cellbender:remove-background: [epoch 143]  average training loss: 2735.9396
cellbender:remove-background: [epoch 144]  average training loss: 2735.7594
cellbender:remove-background: [epoch 145]  average training loss: 2736.7880
cellbender:remove-background: [epoch 145] average test loss: 2779.8274
cellbender:remove-background: [epoch 146]  average training loss: 2737.5210
cellbender:remove-background: [epoch 147]  average training loss: 2738.4406
cellbender:remove-background: [epoch 148]  average training loss: 2738.6275
cellbender:remove-background: [epoch 149]  average training loss: 2736.8790
cellbender:remove-background: [epoch 150]  average training loss: 2738.6306
cellbender:remove-background: [epoch 150] average test loss: 2782.3232
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/2686-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:19:26
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpj6dqstqq
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpj6dqstqq
/tmp/tmpj6dqstqq/73ab09615e_random.pyro
/tmp/tmpj6dqstqq/73ab09615e_random.cuda
/tmp/tmpj6dqstqq/73ab09615e_model.torch
/tmp/tmpj6dqstqq/73ab09615e_optim.torch
/tmp/tmpj6dqstqq/73ab09615e_optim.pyro
/tmp/tmpj6dqstqq/73ab09615e_params.pyro
/tmp/tmpj6dqstqq/73ab09615e_train.loaderstate
/tmp/tmpj6dqstqq/73ab09615e_test.loaderstate
/tmp/tmpj6dqstqq/73ab09615e_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 (1/67)
cellbender:remove-background:     [0.03 mins per chunk]
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cellbender:remove-background: Working on chunk (66/67)
cellbender:remove-background: Working on chunk (67/67)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-DLPFC/2686-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/2686-Bipolar-DLPFC/2686-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:22:45

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-DLPFC/2686-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/2686-Bipolar-DLPFC/2686-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:     [1.23 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 15:31:46 Total MCKP estimation time = 519.70 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/2686-Bipolar-DLPFC/2686-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/2686-Bipolar-DLPFC/2686-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/2686-Bipolar-DLPFC/2686-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/2686-Bipolar-DLPFC/2686-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:32:45