cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2791-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-DLPFC/2791-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 5509 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash d7483e7780)
cellbender:remove-background: 2024-06-06 15:04:11
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2791-Control-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: 32578 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 9321
cellbender:remove-background: Prior on counts for empty droplets is 100
cellbender:remove-background: Excluding 9989 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 22589 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 50
cellbender:remove-background: Using 5509 probable cell barcodes, plus an additional 14491 barcodes, and 50637 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 99 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmptpskgkz1
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: 8086.1962
cellbender:remove-background: [epoch 002]  average training loss: 5621.5063  (5.4 seconds per epoch)
cellbender:remove-background: Will checkpoint every 79 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4601.1213
cellbender:remove-background: [epoch 004]  average training loss: 4029.6834
cellbender:remove-background: [epoch 005]  average training loss: 3893.0300
cellbender:remove-background: [epoch 005] average test loss: 3998.1077
cellbender:remove-background: [epoch 006]  average training loss: 3841.6554
cellbender:remove-background: [epoch 007]  average training loss: 3786.4606
cellbender:remove-background: [epoch 008]  average training loss: 3745.9321
cellbender:remove-background: [epoch 009]  average training loss: 3721.8440
cellbender:remove-background: [epoch 010]  average training loss: 3618.0481
cellbender:remove-background: [epoch 010] average test loss: 3691.4916
cellbender:remove-background: [epoch 011]  average training loss: 3516.1764
cellbender:remove-background: [epoch 012]  average training loss: 3472.4769
cellbender:remove-background: [epoch 013]  average training loss: 3443.3598
cellbender:remove-background: [epoch 014]  average training loss: 3453.5802
cellbender:remove-background: [epoch 015]  average training loss: 3414.5618
cellbender:remove-background: [epoch 015] average test loss: 3421.4274
cellbender:remove-background: [epoch 016]  average training loss: 3398.0781
cellbender:remove-background: [epoch 017]  average training loss: 3407.2430
cellbender:remove-background: [epoch 018]  average training loss: 3389.4213
cellbender:remove-background: [epoch 019]  average training loss: 3365.1922
cellbender:remove-background: [epoch 020]  average training loss: 3338.2641
cellbender:remove-background: [epoch 020] average test loss: 3343.3440
cellbender:remove-background: [epoch 021]  average training loss: 3325.9983
cellbender:remove-background: [epoch 022]  average training loss: 3304.5902
cellbender:remove-background: [epoch 023]  average training loss: 3273.7000
cellbender:remove-background: [epoch 024]  average training loss: 3252.5182
cellbender:remove-background: [epoch 025]  average training loss: 3241.0308
cellbender:remove-background: [epoch 025] average test loss: 3229.9282
cellbender:remove-background: [epoch 026]  average training loss: 3227.9499
cellbender:remove-background: [epoch 027]  average training loss: 3222.4822
cellbender:remove-background: [epoch 028]  average training loss: 3217.6630
cellbender:remove-background: [epoch 029]  average training loss: 3210.7083
cellbender:remove-background: [epoch 030]  average training loss: 3203.8925
cellbender:remove-background: [epoch 030] average test loss: 3178.9184
cellbender:remove-background: [epoch 031]  average training loss: 3197.6102
cellbender:remove-background: [epoch 032]  average training loss: 3191.8619
cellbender:remove-background: [epoch 033]  average training loss: 3186.4534
cellbender:remove-background: [epoch 034]  average training loss: 3181.2115
cellbender:remove-background: [epoch 035]  average training loss: 3176.3991
cellbender:remove-background: [epoch 035] average test loss: 3135.3572
cellbender:remove-background: [epoch 036]  average training loss: 3175.0417
cellbender:remove-background: [epoch 037]  average training loss: 3172.6332
cellbender:remove-background: [epoch 038]  average training loss: 3169.0306
cellbender:remove-background: [epoch 039]  average training loss: 3165.5978
cellbender:remove-background: [epoch 040]  average training loss: 3165.0828
cellbender:remove-background: [epoch 040] average test loss: 3120.7632
cellbender:remove-background: [epoch 041]  average training loss: 3161.5524
cellbender:remove-background: [epoch 042]  average training loss: 3160.8321
cellbender:remove-background: [epoch 043]  average training loss: 3159.3703
cellbender:remove-background: [epoch 044]  average training loss: 3159.3468
cellbender:remove-background: [epoch 045]  average training loss: 3159.6116
cellbender:remove-background: [epoch 045] average test loss: 3136.6858
cellbender:remove-background: [epoch 046]  average training loss: 3158.2840
cellbender:remove-background: [epoch 047]  average training loss: 3156.9367
cellbender:remove-background: [epoch 048]  average training loss: 3155.9844
cellbender:remove-background: [epoch 049]  average training loss: 3154.5828
cellbender:remove-background: [epoch 050]  average training loss: 3154.4147
cellbender:remove-background: [epoch 050] average test loss: 3105.9521
cellbender:remove-background: [epoch 051]  average training loss: 3150.1949
cellbender:remove-background: [epoch 052]  average training loss: 3153.2788
cellbender:remove-background: [epoch 053]  average training loss: 3152.0343
cellbender:remove-background: [epoch 054]  average training loss: 3151.9737
cellbender:remove-background: [epoch 055]  average training loss: 3151.9226
cellbender:remove-background: [epoch 055] average test loss: 3135.6783
cellbender:remove-background: [epoch 056]  average training loss: 3150.8112
cellbender:remove-background: [epoch 057]  average training loss: 3145.2548
cellbender:remove-background: [epoch 058]  average training loss: 3144.5661
cellbender:remove-background: [epoch 059]  average training loss: 3142.7686
cellbender:remove-background: [epoch 060]  average training loss: 3147.9774
cellbender:remove-background: [epoch 060] average test loss: 3121.4033
cellbender:remove-background: [epoch 061]  average training loss: 3142.7492
cellbender:remove-background: [epoch 062]  average training loss: 3142.3969
cellbender:remove-background: [epoch 063]  average training loss: 3144.4946
cellbender:remove-background: [epoch 064]  average training loss: 3141.6813
cellbender:remove-background: [epoch 065]  average training loss: 3143.7670
cellbender:remove-background: [epoch 065] average test loss: 3136.9864
cellbender:remove-background: [epoch 066]  average training loss: 3140.3144
cellbender:remove-background: [epoch 067]  average training loss: 3142.1273
cellbender:remove-background: [epoch 068]  average training loss: 3139.9460
cellbender:remove-background: [epoch 069]  average training loss: 3143.1035
cellbender:remove-background: [epoch 070]  average training loss: 3144.1316
cellbender:remove-background: [epoch 070] average test loss: 3134.4605
cellbender:remove-background: [epoch 071]  average training loss: 3145.1676
cellbender:remove-background: [epoch 072]  average training loss: 3141.8958
cellbender:remove-background: [epoch 073]  average training loss: 3147.3431
cellbender:remove-background: [epoch 074]  average training loss: 3148.0622
cellbender:remove-background: [epoch 075]  average training loss: 3148.8837
cellbender:remove-background: [epoch 075] average test loss: 3140.8658
cellbender:remove-background: [epoch 076]  average training loss: 3147.7968
cellbender:remove-background: [epoch 077]  average training loss: 3145.0256
cellbender:remove-background: [epoch 078]  average training loss: 3150.6959
cellbender:remove-background: [epoch 079]  average training loss: 3150.7888
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/2791-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 080]  average training loss: 3151.9455
cellbender:remove-background: [epoch 080] average test loss: 3154.0232
cellbender:remove-background: [epoch 081]  average training loss: 3150.2509
cellbender:remove-background: [epoch 082]  average training loss: 3154.8012
cellbender:remove-background: [epoch 083]  average training loss: 3161.5454
cellbender:remove-background: [epoch 084]  average training loss: 3163.4571
cellbender:remove-background: [epoch 085]  average training loss: 3161.3876
cellbender:remove-background: [epoch 085] average test loss: 3153.6066
cellbender:remove-background: [epoch 086]  average training loss: 3153.5718
cellbender:remove-background: [epoch 087]  average training loss: 3156.9588
cellbender:remove-background: [epoch 088]  average training loss: 3160.6653
cellbender:remove-background: [epoch 089]  average training loss: 3158.0742
cellbender:remove-background: [epoch 090]  average training loss: 3155.8665
cellbender:remove-background: [epoch 090] average test loss: 3160.5779
cellbender:remove-background: [epoch 091]  average training loss: 3150.2410
cellbender:remove-background: [epoch 092]  average training loss: 3148.6511
cellbender:remove-background: [epoch 093]  average training loss: 3151.3655
cellbender:remove-background: [epoch 094]  average training loss: 3147.6835
cellbender:remove-background: [epoch 095]  average training loss: 3146.7007
cellbender:remove-background: [epoch 095] average test loss: 3171.6405
cellbender:remove-background: [epoch 096]  average training loss: 3150.0710
cellbender:remove-background: [epoch 097]  average training loss: 3149.6957
cellbender:remove-background: [epoch 098]  average training loss: 3148.4544
cellbender:remove-background: [epoch 099]  average training loss: 3155.8777
cellbender:remove-background: [epoch 100]  average training loss: 3145.1225
cellbender:remove-background: [epoch 100] average test loss: 3168.6845
cellbender:remove-background: [epoch 101]  average training loss: 3147.6891
cellbender:remove-background: [epoch 102]  average training loss: 3146.2488
cellbender:remove-background: [epoch 103]  average training loss: 3144.9848
cellbender:remove-background: [epoch 104]  average training loss: 3145.3073
cellbender:remove-background: [epoch 105]  average training loss: 3147.3631
cellbender:remove-background: [epoch 105] average test loss: 3167.4198
cellbender:remove-background: [epoch 106]  average training loss: 3142.9370
cellbender:remove-background: [epoch 107]  average training loss: 3142.9822
cellbender:remove-background: [epoch 108]  average training loss: 3147.4353
cellbender:remove-background: [epoch 109]  average training loss: 3149.6861
cellbender:remove-background: [epoch 110]  average training loss: 3145.3089
cellbender:remove-background: [epoch 110] average test loss: 3208.5174
cellbender:remove-background: [epoch 111]  average training loss: 3149.5885
cellbender:remove-background: [epoch 112]  average training loss: 3143.8375
cellbender:remove-background: [epoch 113]  average training loss: 3145.8544
cellbender:remove-background: [epoch 114]  average training loss: 3146.4972
cellbender:remove-background: [epoch 115]  average training loss: 3150.9710
cellbender:remove-background: [epoch 115] average test loss: 3178.3338
cellbender:remove-background: [epoch 116]  average training loss: 3147.2992
cellbender:remove-background: [epoch 117]  average training loss: 3145.3969
cellbender:remove-background: [epoch 118]  average training loss: 3140.7455
cellbender:remove-background: [epoch 119]  average training loss: 3145.2284
cellbender:remove-background: [epoch 120]  average training loss: 3144.9031
cellbender:remove-background: [epoch 120] average test loss: 3175.8209
cellbender:remove-background: [epoch 121]  average training loss: 3140.4137
cellbender:remove-background: [epoch 122]  average training loss: 3142.4976
cellbender:remove-background: [epoch 123]  average training loss: 3147.2247
cellbender:remove-background: [epoch 124]  average training loss: 3146.7608
cellbender:remove-background: [epoch 125]  average training loss: 3142.0857
cellbender:remove-background: [epoch 125] average test loss: 3173.3618
cellbender:remove-background: [epoch 126]  average training loss: 3145.0008
cellbender:remove-background: [epoch 127]  average training loss: 3146.1322
cellbender:remove-background: [epoch 128]  average training loss: 3143.7237
cellbender:remove-background: [epoch 129]  average training loss: 3140.0149
cellbender:remove-background: [epoch 130]  average training loss: 3149.1595
cellbender:remove-background: [epoch 130] average test loss: 3236.5720
cellbender:remove-background: [epoch 131]  average training loss: 3146.1125
cellbender:remove-background: [epoch 132]  average training loss: 3142.6155
cellbender:remove-background: [epoch 133]  average training loss: 3146.2175
cellbender:remove-background: [epoch 134]  average training loss: 3142.2652
cellbender:remove-background: [epoch 135]  average training loss: 3142.0794
cellbender:remove-background: [epoch 135] average test loss: 3179.9370
cellbender:remove-background: [epoch 136]  average training loss: 3149.0571
cellbender:remove-background: [epoch 137]  average training loss: 3139.8727
cellbender:remove-background: [epoch 138]  average training loss: 3143.7365
cellbender:remove-background: [epoch 139]  average training loss: 3143.3872
cellbender:remove-background: [epoch 140]  average training loss: 3142.4585
cellbender:remove-background: [epoch 140] average test loss: 3175.0551
cellbender:remove-background: [epoch 141]  average training loss: 3146.5253
cellbender:remove-background: [epoch 142]  average training loss: 3142.8077
cellbender:remove-background: [epoch 143]  average training loss: 3142.2610
cellbender:remove-background: [epoch 144]  average training loss: 3142.0000
cellbender:remove-background: [epoch 145]  average training loss: 3142.5434
cellbender:remove-background: [epoch 145] average test loss: 3194.4412
cellbender:remove-background: [epoch 146]  average training loss: 3143.0509
cellbender:remove-background: [epoch 147]  average training loss: 3142.9824
cellbender:remove-background: [epoch 148]  average training loss: 3143.5332
cellbender:remove-background: [epoch 149]  average training loss: 3139.8901
cellbender:remove-background: [epoch 150]  average training loss: 3146.6599
cellbender:remove-background: [epoch 150] average test loss: 3185.0145
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/2791-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:19:52
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_jxkv90e
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_jxkv90e
/tmp/tmp_jxkv90e/d7483e7780_random.pyro
/tmp/tmp_jxkv90e/d7483e7780_random.cuda
/tmp/tmp_jxkv90e/d7483e7780_model.torch
/tmp/tmp_jxkv90e/d7483e7780_optim.torch
/tmp/tmp_jxkv90e/d7483e7780_optim.pyro
/tmp/tmp_jxkv90e/d7483e7780_params.pyro
/tmp/tmp_jxkv90e/d7483e7780_train.loaderstate
/tmp/tmp_jxkv90e/d7483e7780_test.loaderstate
/tmp/tmp_jxkv90e/d7483e7780_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 (1/56)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/56)
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cellbender:remove-background: Working on chunk (52/56)
cellbender:remove-background: Working on chunk (53/56)
cellbender:remove-background: Working on chunk (54/56)
cellbender:remove-background: Working on chunk (55/56)
cellbender:remove-background: Working on chunk (56/56)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-DLPFC/2791-Control-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/2791-Control-DLPFC/2791-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:23:29

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-DLPFC/2791-Control-DLPFC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2791-Control-DLPFC/2791-Control-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:     [1.56 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 15:34:58 Total MCKP estimation time = 660.94 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/2791-Control-DLPFC/2791-Control-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/2791-Control-DLPFC/2791-Control-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/2791-Control-DLPFC/2791-Control-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/2791-Control-DLPFC/2791-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:35:18