cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2477-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-DLPFC/2477-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 6292 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash e21a086d8b)
cellbender:remove-background: 2024-06-06 15:15:02
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/2477-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: 31754 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3243
cellbender:remove-background: Prior on counts for empty droplets is 209
cellbender:remove-background: Excluding 8851 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 22903 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 104
cellbender:remove-background: Using 6292 probable cell barcodes, plus an additional 13708 barcodes, and 14084 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 206 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpm5okujez
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: 5038.8484
cellbender:remove-background: [epoch 002]  average training loss: 4165.1380  (6.2 seconds per epoch)
cellbender:remove-background: Will checkpoint every 69 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3635.5996
cellbender:remove-background: [epoch 004]  average training loss: 3313.8403
cellbender:remove-background: [epoch 005]  average training loss: 3208.6658
cellbender:remove-background: [epoch 005] average test loss: 3371.7152
cellbender:remove-background: [epoch 006]  average training loss: 3175.0606
cellbender:remove-background: [epoch 007]  average training loss: 3134.3376
cellbender:remove-background: [epoch 008]  average training loss: 3113.8670
cellbender:remove-background: [epoch 009]  average training loss: 3104.5532
cellbender:remove-background: [epoch 010]  average training loss: 3054.1530
cellbender:remove-background: [epoch 010] average test loss: 3074.1225
cellbender:remove-background: [epoch 011]  average training loss: 3010.9184
cellbender:remove-background: [epoch 012]  average training loss: 2988.1825
cellbender:remove-background: [epoch 013]  average training loss: 2970.0439
cellbender:remove-background: [epoch 014]  average training loss: 2981.7238
cellbender:remove-background: [epoch 015]  average training loss: 2961.6964
cellbender:remove-background: [epoch 015] average test loss: 3013.7738
cellbender:remove-background: [epoch 016]  average training loss: 2954.2075
cellbender:remove-background: [epoch 017]  average training loss: 2957.8707
cellbender:remove-background: [epoch 018]  average training loss: 2949.3763
cellbender:remove-background: [epoch 019]  average training loss: 2938.6428
cellbender:remove-background: [epoch 020]  average training loss: 2924.4301
cellbender:remove-background: [epoch 020] average test loss: 2979.2500
cellbender:remove-background: [epoch 021]  average training loss: 2921.0135
cellbender:remove-background: [epoch 022]  average training loss: 2926.1479
cellbender:remove-background: [epoch 023]  average training loss: 2922.7098
cellbender:remove-background: [epoch 024]  average training loss: 2914.6872
cellbender:remove-background: [epoch 025]  average training loss: 2913.8312
cellbender:remove-background: [epoch 025] average test loss: 2953.7088
cellbender:remove-background: [epoch 026]  average training loss: 2902.3749
cellbender:remove-background: [epoch 027]  average training loss: 2900.2895
cellbender:remove-background: [epoch 028]  average training loss: 2894.5303
cellbender:remove-background: [epoch 029]  average training loss: 2894.4814
cellbender:remove-background: [epoch 030]  average training loss: 2889.8802
cellbender:remove-background: [epoch 030] average test loss: 2931.3392
cellbender:remove-background: [epoch 031]  average training loss: 2885.5163
cellbender:remove-background: [epoch 032]  average training loss: 2880.3215
cellbender:remove-background: [epoch 033]  average training loss: 2878.7229
cellbender:remove-background: [epoch 034]  average training loss: 2876.6487
cellbender:remove-background: [epoch 035]  average training loss: 2882.8366
cellbender:remove-background: [epoch 035] average test loss: 2901.4935
cellbender:remove-background: [epoch 036]  average training loss: 2882.4525
cellbender:remove-background: [epoch 037]  average training loss: 2881.6506
cellbender:remove-background: [epoch 038]  average training loss: 2885.0172
cellbender:remove-background: [epoch 039]  average training loss: 2879.9161
cellbender:remove-background: [epoch 040]  average training loss: 2878.4309
cellbender:remove-background: [epoch 040] average test loss: 2909.5961
cellbender:remove-background: [epoch 041]  average training loss: 2891.5573
cellbender:remove-background: [epoch 042]  average training loss: 2888.7243
cellbender:remove-background: [epoch 043]  average training loss: 2887.7377
cellbender:remove-background: [epoch 044]  average training loss: 2890.5482
cellbender:remove-background: [epoch 045]  average training loss: 2886.1937
cellbender:remove-background: [epoch 045] average test loss: 2892.6041
cellbender:remove-background: [epoch 046]  average training loss: 2884.9793
cellbender:remove-background: [epoch 047]  average training loss: 2895.3075
cellbender:remove-background: [epoch 048]  average training loss: 2888.0842
cellbender:remove-background: [epoch 049]  average training loss: 2889.9935
cellbender:remove-background: [epoch 050]  average training loss: 2887.2013
cellbender:remove-background: [epoch 050] average test loss: 2941.1447
cellbender:remove-background: [epoch 051]  average training loss: 2891.1318
cellbender:remove-background: [epoch 052]  average training loss: 2894.1568
cellbender:remove-background: [epoch 053]  average training loss: 2888.2841
cellbender:remove-background: [epoch 054]  average training loss: 2891.0404
cellbender:remove-background: [epoch 055]  average training loss: 2891.8488
cellbender:remove-background: [epoch 055] average test loss: 2957.0864
cellbender:remove-background: [epoch 056]  average training loss: 2898.6825
cellbender:remove-background: [epoch 057]  average training loss: 2889.7373
cellbender:remove-background: [epoch 058]  average training loss: 2896.2556
cellbender:remove-background: [epoch 059]  average training loss: 2896.5165
cellbender:remove-background: [epoch 060]  average training loss: 2912.4902
cellbender:remove-background: [epoch 060] average test loss: 2980.0324
cellbender:remove-background: [epoch 061]  average training loss: 2908.5167
cellbender:remove-background: [epoch 062]  average training loss: 2915.2454
cellbender:remove-background: [epoch 063]  average training loss: 2919.3965
cellbender:remove-background: [epoch 064]  average training loss: 2926.3512
cellbender:remove-background: [epoch 065]  average training loss: 2934.6592
cellbender:remove-background: [epoch 065] average test loss: 3006.1519
cellbender:remove-background: [epoch 066]  average training loss: 2927.2460
cellbender:remove-background: [epoch 067]  average training loss: 2948.3605
cellbender:remove-background: [epoch 068]  average training loss: 2949.2887
cellbender:remove-background: [epoch 069]  average training loss: 2944.5948
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/2477-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 070]  average training loss: 2943.2022
cellbender:remove-background: [epoch 070] average test loss: 3066.9853
cellbender:remove-background: [epoch 071]  average training loss: 2953.4283
cellbender:remove-background: [epoch 072]  average training loss: 2958.6755
cellbender:remove-background: [epoch 073]  average training loss: 2974.7153
cellbender:remove-background: [epoch 074]  average training loss: 2969.8417
cellbender:remove-background: [epoch 075]  average training loss: 2974.8912
cellbender:remove-background: [epoch 075] average test loss: 3051.8458
cellbender:remove-background: [epoch 076]  average training loss: 2974.9745
cellbender:remove-background: [epoch 077]  average training loss: 2968.9168
cellbender:remove-background: [epoch 078]  average training loss: 2983.5137
cellbender:remove-background: [epoch 079]  average training loss: 2980.8712
cellbender:remove-background: [epoch 080]  average training loss: 2971.0177
cellbender:remove-background: [epoch 080] average test loss: 3026.9094
cellbender:remove-background: [epoch 081]  average training loss: 2979.3501
cellbender:remove-background: [epoch 082]  average training loss: 2972.5621
cellbender:remove-background: [epoch 083]  average training loss: 2971.9333
cellbender:remove-background: [epoch 084]  average training loss: 2985.4081
cellbender:remove-background: [epoch 085]  average training loss: 2974.2935
cellbender:remove-background: [epoch 085] average test loss: 3043.6132
cellbender:remove-background: [epoch 086]  average training loss: 2988.2866
cellbender:remove-background: [epoch 087]  average training loss: 2981.2708
cellbender:remove-background: [epoch 088]  average training loss: 2988.9486
cellbender:remove-background: [epoch 089]  average training loss: 2980.8988
cellbender:remove-background: [epoch 090]  average training loss: 2975.8918
cellbender:remove-background: [epoch 090] average test loss: 3038.9392
cellbender:remove-background: [epoch 091]  average training loss: 2960.0514
cellbender:remove-background: [epoch 092]  average training loss: 2975.5769
cellbender:remove-background: [epoch 093]  average training loss: 2972.2559
cellbender:remove-background: [epoch 094]  average training loss: 2977.7385
cellbender:remove-background: [epoch 095]  average training loss: 2972.2888
cellbender:remove-background: [epoch 095] average test loss: 3050.5086
cellbender:remove-background: [epoch 096]  average training loss: 2959.8958
cellbender:remove-background: [epoch 097]  average training loss: 2964.1941
cellbender:remove-background: [epoch 098]  average training loss: 2972.5322
cellbender:remove-background: [epoch 099]  average training loss: 2973.1455
cellbender:remove-background: [epoch 100]  average training loss: 2960.1230
cellbender:remove-background: [epoch 100] average test loss: 3037.8985
cellbender:remove-background: [epoch 101]  average training loss: 2961.7473
cellbender:remove-background: [epoch 102]  average training loss: 2960.2312
cellbender:remove-background: [epoch 103]  average training loss: 2962.3751
cellbender:remove-background: [epoch 104]  average training loss: 2958.6195
cellbender:remove-background: [epoch 105]  average training loss: 2965.9399
cellbender:remove-background: [epoch 105] average test loss: 3043.8917
cellbender:remove-background: [epoch 106]  average training loss: 2958.2011
cellbender:remove-background: [epoch 107]  average training loss: 2946.9303
cellbender:remove-background: [epoch 108]  average training loss: 2965.2255
cellbender:remove-background: [epoch 109]  average training loss: 2957.4657
cellbender:remove-background: [epoch 110]  average training loss: 2957.5711
cellbender:remove-background: [epoch 110] average test loss: 3044.3650
cellbender:remove-background: [epoch 111]  average training loss: 2951.4804
cellbender:remove-background: [epoch 112]  average training loss: 2968.6722
cellbender:remove-background: [epoch 113]  average training loss: 2952.2815
cellbender:remove-background: [epoch 114]  average training loss: 2952.5618
cellbender:remove-background: [epoch 115]  average training loss: 2945.3047
cellbender:remove-background: [epoch 115] average test loss: 3065.0225
cellbender:remove-background: [epoch 116]  average training loss: 2939.5515
cellbender:remove-background: [epoch 117]  average training loss: 2953.4606
cellbender:remove-background: [epoch 118]  average training loss: 2948.9305
cellbender:remove-background: [epoch 119]  average training loss: 2940.2669
cellbender:remove-background: [epoch 120]  average training loss: 2952.5278
cellbender:remove-background: [epoch 120] average test loss: 3036.6247
cellbender:remove-background: [epoch 121]  average training loss: 2950.2570
cellbender:remove-background: [epoch 122]  average training loss: 2946.8061
cellbender:remove-background: [epoch 123]  average training loss: 2938.5687
cellbender:remove-background: [epoch 124]  average training loss: 2938.8230
cellbender:remove-background: [epoch 125]  average training loss: 2939.8734
cellbender:remove-background: [epoch 125] average test loss: 3050.7094
cellbender:remove-background: [epoch 126]  average training loss: 2934.4966
cellbender:remove-background: [epoch 127]  average training loss: 2931.9912
cellbender:remove-background: [epoch 128]  average training loss: 2942.3911
cellbender:remove-background: [epoch 129]  average training loss: 2926.7103
cellbender:remove-background: [epoch 130]  average training loss: 2939.1427
cellbender:remove-background: [epoch 130] average test loss: 3035.7196
cellbender:remove-background: [epoch 131]  average training loss: 2945.3178
cellbender:remove-background: [epoch 132]  average training loss: 2938.3769
cellbender:remove-background: [epoch 133]  average training loss: 2937.7480
cellbender:remove-background: [epoch 134]  average training loss: 2939.3967
cellbender:remove-background: [epoch 135]  average training loss: 2944.8494
cellbender:remove-background: [epoch 135] average test loss: 3059.5946
cellbender:remove-background: [epoch 136]  average training loss: 2942.6522
cellbender:remove-background: [epoch 137]  average training loss: 2934.6409
cellbender:remove-background: [epoch 138]  average training loss: 2943.0261
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/2477-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 139]  average training loss: 2940.6385
cellbender:remove-background: [epoch 140]  average training loss: 2935.0505
cellbender:remove-background: [epoch 140] average test loss: 3038.4927
cellbender:remove-background: [epoch 141]  average training loss: 2940.9788
cellbender:remove-background: [epoch 142]  average training loss: 2954.8312
cellbender:remove-background: [epoch 143]  average training loss: 2944.8399
cellbender:remove-background: [epoch 144]  average training loss: 2934.1558
cellbender:remove-background: [epoch 145]  average training loss: 2933.0882
cellbender:remove-background: [epoch 145] average test loss: 3052.3234
cellbender:remove-background: [epoch 146]  average training loss: 2939.1694
cellbender:remove-background: [epoch 147]  average training loss: 2937.6834
cellbender:remove-background: [epoch 148]  average training loss: 2940.3142
cellbender:remove-background: [epoch 149]  average training loss: 2937.2544
cellbender:remove-background: [epoch 150]  average training loss: 2936.1777
cellbender:remove-background: [epoch 150] average test loss: 3026.0739
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/2477-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:34:30
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpe85tsver
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpe85tsver
/tmp/tmpe85tsver/e21a086d8b_random.pyro
/tmp/tmpe85tsver/e21a086d8b_random.cuda
/tmp/tmpe85tsver/e21a086d8b_model.torch
/tmp/tmpe85tsver/e21a086d8b_optim.torch
/tmp/tmpe85tsver/e21a086d8b_optim.pyro
/tmp/tmpe85tsver/e21a086d8b_params.pyro
/tmp/tmpe85tsver/e21a086d8b_train.loaderstate
/tmp/tmpe85tsver/e21a086d8b_test.loaderstate
/tmp/tmpe85tsver/e21a086d8b_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 (1/110)
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/2477-Bipolar-DLPFC/2477-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/2477-Bipolar-DLPFC/2477-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:39:51

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2477-Bipolar-DLPFC/2477-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/2477-Bipolar-DLPFC/2477-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:     [1.83 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 15:53:09 Total MCKP estimation time = 770.69 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/2477-Bipolar-DLPFC/2477-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/2477-Bipolar-DLPFC/2477-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/2477-Bipolar-DLPFC/2477-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/2477-Bipolar-DLPFC/2477-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:53:27