cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1156-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1156-Control-DLPFC/1156-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 5852 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 905a509990)
cellbender:remove-background: 2024-06-06 15:15:03
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/1156-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: 32460 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 8266
cellbender:remove-background: Prior on counts for empty droplets is 85
cellbender:remove-background: Excluding 12789 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 19671 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 42
cellbender:remove-background: Using 5852 probable cell barcodes, plus an additional 14148 barcodes, and 30196 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 84 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpue761uca
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: 6381.3449
cellbender:remove-background: [epoch 002]  average training loss: 4946.5790  (4.5 seconds per epoch)
cellbender:remove-background: Will checkpoint every 94 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4285.9445
cellbender:remove-background: [epoch 004]  average training loss: 3921.3897
cellbender:remove-background: [epoch 005]  average training loss: 3834.4112
cellbender:remove-background: [epoch 005] average test loss: 3843.6453
cellbender:remove-background: [epoch 006]  average training loss: 3819.8600
cellbender:remove-background: [epoch 007]  average training loss: 3769.4540
cellbender:remove-background: [epoch 008]  average training loss: 3741.4380
cellbender:remove-background: [epoch 009]  average training loss: 3725.8939
cellbender:remove-background: [epoch 010]  average training loss: 3632.3055
cellbender:remove-background: [epoch 010] average test loss: 3731.0563
cellbender:remove-background: [epoch 011]  average training loss: 3524.7541
cellbender:remove-background: [epoch 012]  average training loss: 3492.0281
cellbender:remove-background: [epoch 013]  average training loss: 3465.9149
cellbender:remove-background: [epoch 014]  average training loss: 3469.0885
cellbender:remove-background: [epoch 015]  average training loss: 3434.1695
cellbender:remove-background: [epoch 015] average test loss: 3425.6699
cellbender:remove-background: [epoch 016]  average training loss: 3417.5873
cellbender:remove-background: [epoch 017]  average training loss: 3421.0225
cellbender:remove-background: [epoch 018]  average training loss: 3411.5945
cellbender:remove-background: [epoch 019]  average training loss: 3397.6789
cellbender:remove-background: [epoch 020]  average training loss: 3377.8089
cellbender:remove-background: [epoch 020] average test loss: 3382.8969
cellbender:remove-background: [epoch 021]  average training loss: 3376.9062
cellbender:remove-background: [epoch 022]  average training loss: 3375.9311
cellbender:remove-background: [epoch 023]  average training loss: 3370.4696
cellbender:remove-background: [epoch 024]  average training loss: 3359.5116
cellbender:remove-background: [epoch 025]  average training loss: 3351.7452
cellbender:remove-background: [epoch 025] average test loss: 3298.3650
cellbender:remove-background: [epoch 026]  average training loss: 3316.5385
cellbender:remove-background: [epoch 027]  average training loss: 3281.9642
cellbender:remove-background: [epoch 028]  average training loss: 3269.1867
cellbender:remove-background: [epoch 029]  average training loss: 3257.3771
cellbender:remove-background: [epoch 030]  average training loss: 3253.2927
cellbender:remove-background: [epoch 030] average test loss: 3191.1782
cellbender:remove-background: [epoch 031]  average training loss: 3247.2054
cellbender:remove-background: [epoch 032]  average training loss: 3244.1307
cellbender:remove-background: [epoch 033]  average training loss: 3238.4264
cellbender:remove-background: [epoch 034]  average training loss: 3239.8257
cellbender:remove-background: [epoch 035]  average training loss: 3235.4771
cellbender:remove-background: [epoch 035] average test loss: 3186.2283
cellbender:remove-background: [epoch 036]  average training loss: 3233.8277
cellbender:remove-background: [epoch 037]  average training loss: 3231.2577
cellbender:remove-background: [epoch 038]  average training loss: 3227.2484
cellbender:remove-background: [epoch 039]  average training loss: 3225.1222
cellbender:remove-background: [epoch 040]  average training loss: 3220.9407
cellbender:remove-background: [epoch 040] average test loss: 3169.1670
cellbender:remove-background: [epoch 041]  average training loss: 3218.1395
cellbender:remove-background: [epoch 042]  average training loss: 3221.9385
cellbender:remove-background: [epoch 043]  average training loss: 3217.9875
cellbender:remove-background: [epoch 044]  average training loss: 3217.0369
cellbender:remove-background: [epoch 045]  average training loss: 3218.9899
cellbender:remove-background: [epoch 045] average test loss: 3171.9127
cellbender:remove-background: [epoch 046]  average training loss: 3222.9041
cellbender:remove-background: [epoch 047]  average training loss: 3220.4570
cellbender:remove-background: [epoch 048]  average training loss: 3216.0079
cellbender:remove-background: [epoch 049]  average training loss: 3218.7678
cellbender:remove-background: [epoch 050]  average training loss: 3220.0739
cellbender:remove-background: [epoch 050] average test loss: 3178.0601
cellbender:remove-background: [epoch 051]  average training loss: 3225.7096
cellbender:remove-background: [epoch 052]  average training loss: 3224.3345
cellbender:remove-background: [epoch 053]  average training loss: 3225.5680
cellbender:remove-background: [epoch 054]  average training loss: 3221.1328
cellbender:remove-background: [epoch 055]  average training loss: 3223.5503
cellbender:remove-background: [epoch 055] average test loss: 3213.5809
cellbender:remove-background: [epoch 056]  average training loss: 3222.5751
cellbender:remove-background: [epoch 057]  average training loss: 3231.6390
cellbender:remove-background: [epoch 058]  average training loss: 3245.2209
cellbender:remove-background: [epoch 059]  average training loss: 3239.2503
cellbender:remove-background: [epoch 060]  average training loss: 3259.1103
cellbender:remove-background: [epoch 060] average test loss: 3232.6870
cellbender:remove-background: [epoch 061]  average training loss: 3289.5238
cellbender:remove-background: [epoch 062]  average training loss: 3291.7410
cellbender:remove-background: [epoch 063]  average training loss: 3257.0067
cellbender:remove-background: [epoch 064]  average training loss: 3281.2753
cellbender:remove-background: [epoch 065]  average training loss: 3276.8571
cellbender:remove-background: [epoch 065] average test loss: 3253.6456
cellbender:remove-background: [epoch 066]  average training loss: 3242.8110
cellbender:remove-background: [epoch 067]  average training loss: 3250.4374
cellbender:remove-background: [epoch 068]  average training loss: 3248.1091
cellbender:remove-background: [epoch 069]  average training loss: 3281.6346
cellbender:remove-background: [epoch 070]  average training loss: 3244.6316
cellbender:remove-background: [epoch 070] average test loss: 3195.5399
cellbender:remove-background: [epoch 071]  average training loss: 3257.3587
cellbender:remove-background: [epoch 072]  average training loss: 3244.0516
cellbender:remove-background: [epoch 073]  average training loss: 3254.9333
cellbender:remove-background: [epoch 074]  average training loss: 3250.4265
cellbender:remove-background: [epoch 075]  average training loss: 3251.5444
cellbender:remove-background: [epoch 075] average test loss: 3230.4075
cellbender:remove-background: [epoch 076]  average training loss: 3273.0064
cellbender:remove-background: [epoch 077]  average training loss: 3248.1466
cellbender:remove-background: [epoch 078]  average training loss: 3243.8385
cellbender:remove-background: [epoch 079]  average training loss: 3248.1366
cellbender:remove-background: [epoch 080]  average training loss: 3234.1714
cellbender:remove-background: [epoch 080] average test loss: 3203.8585
cellbender:remove-background: [epoch 081]  average training loss: 3244.3932
cellbender:remove-background: [epoch 082]  average training loss: 3252.0932
cellbender:remove-background: [epoch 083]  average training loss: 3231.6056
cellbender:remove-background: [epoch 084]  average training loss: 3235.3472
cellbender:remove-background: [epoch 085]  average training loss: 3261.3465
cellbender:remove-background: [epoch 085] average test loss: 3299.8581
cellbender:remove-background: [epoch 086]  average training loss: 3242.3330
cellbender:remove-background: [epoch 087]  average training loss: 3229.4018
cellbender:remove-background: [epoch 088]  average training loss: 3230.6112
cellbender:remove-background: [epoch 089]  average training loss: 3224.3007
cellbender:remove-background: [epoch 090]  average training loss: 3229.7854
cellbender:remove-background: [epoch 090] average test loss: 3225.5753
cellbender:remove-background: [epoch 091]  average training loss: 3225.6884
cellbender:remove-background: [epoch 092]  average training loss: 3225.6807
cellbender:remove-background: [epoch 093]  average training loss: 3223.5875
cellbender:remove-background: [epoch 094]  average training loss: 3218.3905
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/1156-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 095]  average training loss: 3230.6926
cellbender:remove-background: [epoch 095] average test loss: 3208.5666
cellbender:remove-background: [epoch 096]  average training loss: 3228.9504
cellbender:remove-background: [epoch 097]  average training loss: 3237.0809
cellbender:remove-background: [epoch 098]  average training loss: 3240.1719
cellbender:remove-background: [epoch 099]  average training loss: 3225.1862
cellbender:remove-background: [epoch 100]  average training loss: 3219.5617
cellbender:remove-background: [epoch 100] average test loss: 3245.6305
cellbender:remove-background: [epoch 101]  average training loss: 3215.0533
cellbender:remove-background: [epoch 102]  average training loss: 3212.8355
cellbender:remove-background: [epoch 103]  average training loss: 3234.4232
cellbender:remove-background: [epoch 104]  average training loss: 3266.8814
cellbender:remove-background: [epoch 105]  average training loss: 3234.8405
cellbender:remove-background: [epoch 105] average test loss: 3245.9426
cellbender:remove-background: [epoch 106]  average training loss: 3226.0249
cellbender:remove-background: [epoch 107]  average training loss: 3222.5598
cellbender:remove-background: [epoch 108]  average training loss: 3219.3560
cellbender:remove-background: [epoch 109]  average training loss: 3242.0596
cellbender:remove-background: [epoch 110]  average training loss: 3229.2800
cellbender:remove-background: [epoch 110] average test loss: 3234.5819
cellbender:remove-background: [epoch 111]  average training loss: 3222.1123
cellbender:remove-background: [epoch 112]  average training loss: 3231.1098
cellbender:remove-background: [epoch 113]  average training loss: 3221.6719
cellbender:remove-background: [epoch 114]  average training loss: 3241.3980
cellbender:remove-background: [epoch 115]  average training loss: 3225.6850
cellbender:remove-background: [epoch 115] average test loss: 3234.4540
cellbender:remove-background: [epoch 116]  average training loss: 3238.8686
cellbender:remove-background: [epoch 117]  average training loss: 3219.1148
cellbender:remove-background: [epoch 118]  average training loss: 3217.1694
cellbender:remove-background: [epoch 119]  average training loss: 3227.1801
cellbender:remove-background: [epoch 120]  average training loss: 3218.2352
cellbender:remove-background: [epoch 120] average test loss: 3234.4854
cellbender:remove-background: [epoch 121]  average training loss: 3244.0294
cellbender:remove-background: [epoch 122]  average training loss: 3220.1278
cellbender:remove-background: [epoch 123]  average training loss: 3212.8009
cellbender:remove-background: [epoch 124]  average training loss: 3204.7609
cellbender:remove-background: [epoch 125]  average training loss: 3227.5599
cellbender:remove-background: [epoch 125] average test loss: 3210.6445
cellbender:remove-background: [epoch 126]  average training loss: 3217.6325
cellbender:remove-background: [epoch 127]  average training loss: 3220.1092
cellbender:remove-background: [epoch 128]  average training loss: 3232.1329
cellbender:remove-background: [epoch 129]  average training loss: 3217.3276
cellbender:remove-background: [epoch 130]  average training loss: 3218.3555
cellbender:remove-background: [epoch 130] average test loss: 3237.9014
cellbender:remove-background: [epoch 131]  average training loss: 3211.0440
cellbender:remove-background: [epoch 132]  average training loss: 3212.6808
cellbender:remove-background: [epoch 133]  average training loss: 3206.8376
cellbender:remove-background: [epoch 134]  average training loss: 3235.7651
cellbender:remove-background: [epoch 135]  average training loss: 3219.8711
cellbender:remove-background: [epoch 135] average test loss: 3235.6614
cellbender:remove-background: [epoch 136]  average training loss: 3213.8782
cellbender:remove-background: [epoch 137]  average training loss: 3211.6360
cellbender:remove-background: [epoch 138]  average training loss: 3214.3100
cellbender:remove-background: [epoch 139]  average training loss: 3215.9684
cellbender:remove-background: [epoch 140]  average training loss: 3216.0364
cellbender:remove-background: [epoch 140] average test loss: 3247.1032
cellbender:remove-background: [epoch 141]  average training loss: 3214.3475
cellbender:remove-background: [epoch 142]  average training loss: 3224.7648
cellbender:remove-background: [epoch 143]  average training loss: 3230.1027
cellbender:remove-background: [epoch 144]  average training loss: 3215.9324
cellbender:remove-background: [epoch 145]  average training loss: 3216.6641
cellbender:remove-background: [epoch 145] average test loss: 3213.2771
cellbender:remove-background: [epoch 146]  average training loss: 3214.9189
cellbender:remove-background: [epoch 147]  average training loss: 3223.3895
cellbender:remove-background: [epoch 148]  average training loss: 3222.7457
cellbender:remove-background: [epoch 149]  average training loss: 3210.4016
cellbender:remove-background: [epoch 150]  average training loss: 3216.4471
cellbender:remove-background: [epoch 150] average test loss: 3225.0331
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/1156-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:29:01
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpxre9xa35
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpxre9xa35
/tmp/tmpxre9xa35/905a509990_random.pyro
/tmp/tmpxre9xa35/905a509990_random.cuda
/tmp/tmpxre9xa35/905a509990_model.torch
/tmp/tmpxre9xa35/905a509990_optim.torch
/tmp/tmpxre9xa35/905a509990_optim.pyro
/tmp/tmpxre9xa35/905a509990_params.pyro
/tmp/tmpxre9xa35/905a509990_train.loaderstate
/tmp/tmpxre9xa35/905a509990_test.loaderstate
/tmp/tmpxre9xa35/905a509990_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 (1/77)
cellbender:remove-background:     [0.02 mins per chunk]
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cellbender:remove-background: Working on chunk (77/77)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1156-Control-DLPFC/1156-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/1156-Control-DLPFC/1156-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:32:21

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1156-Control-DLPFC/1156-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/1156-Control-DLPFC/1156-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:     [1.64 mins per chunk]
cellbender:remove-background: Working on chunk (2/7)
cellbender:remove-background: Working on chunk (3/7)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:44:27 Total MCKP estimation time = 699.71 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/1156-Control-DLPFC/1156-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/1156-Control-DLPFC/1156-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/1156-Control-DLPFC/1156-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/1156-Control-DLPFC/1156-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:44:47