cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1604-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-dACC/1604-Control-dACC.cellbender.output.h5 --cuda --expected-cells 5914 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 42ef1dfaf5)
cellbender:remove-background: 2024-06-06 15:32:23
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/1604-Control-dACC.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: 32184 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3748
cellbender:remove-background: Prior on counts for empty droplets is 85
cellbender:remove-background: Excluding 10953 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21231 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 42
cellbender:remove-background: Using 5914 probable cell barcodes, plus an additional 14086 barcodes, and 48611 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/tmp5kh0l1_9
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: 5694.0822
cellbender:remove-background: [epoch 002]  average training loss: 4275.0390  (6.8 seconds per epoch)
cellbender:remove-background: Will checkpoint every 62 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3602.2310
cellbender:remove-background: [epoch 004]  average training loss: 3159.5603
cellbender:remove-background: [epoch 005]  average training loss: 3052.6041
cellbender:remove-background: [epoch 005] average test loss: 3308.6308
cellbender:remove-background: [epoch 006]  average training loss: 3016.9571
cellbender:remove-background: [epoch 007]  average training loss: 2981.8913
cellbender:remove-background: [epoch 008]  average training loss: 2942.7609
cellbender:remove-background: [epoch 009]  average training loss: 2907.8122
cellbender:remove-background: [epoch 010]  average training loss: 2809.9936
cellbender:remove-background: [epoch 010] average test loss: 2815.9551
cellbender:remove-background: [epoch 011]  average training loss: 2760.9954
cellbender:remove-background: [epoch 012]  average training loss: 2740.9411
cellbender:remove-background: [epoch 013]  average training loss: 2717.6512
cellbender:remove-background: [epoch 014]  average training loss: 2724.3281
cellbender:remove-background: [epoch 015]  average training loss: 2694.1152
cellbender:remove-background: [epoch 015] average test loss: 2795.0586
cellbender:remove-background: [epoch 016]  average training loss: 2682.3113
cellbender:remove-background: [epoch 017]  average training loss: 2691.5001
cellbender:remove-background: [epoch 018]  average training loss: 2676.8513
cellbender:remove-background: [epoch 019]  average training loss: 2661.4924
cellbender:remove-background: [epoch 020]  average training loss: 2636.8944
cellbender:remove-background: [epoch 020] average test loss: 2687.3883
cellbender:remove-background: [epoch 021]  average training loss: 2630.0809
cellbender:remove-background: [epoch 022]  average training loss: 2626.6227
cellbender:remove-background: [epoch 023]  average training loss: 2608.9075
cellbender:remove-background: [epoch 024]  average training loss: 2586.4581
cellbender:remove-background: [epoch 025]  average training loss: 2577.9802
cellbender:remove-background: [epoch 025] average test loss: 2597.2419
cellbender:remove-background: [epoch 026]  average training loss: 2559.8166
cellbender:remove-background: [epoch 027]  average training loss: 2557.9450
cellbender:remove-background: [epoch 028]  average training loss: 2553.6075
cellbender:remove-background: [epoch 029]  average training loss: 2547.7182
cellbender:remove-background: [epoch 030]  average training loss: 2542.7850
cellbender:remove-background: [epoch 030] average test loss: 2570.3473
cellbender:remove-background: [epoch 031]  average training loss: 2539.6715
cellbender:remove-background: [epoch 032]  average training loss: 2538.0808
cellbender:remove-background: [epoch 033]  average training loss: 2534.4832
cellbender:remove-background: [epoch 034]  average training loss: 2528.3803
cellbender:remove-background: [epoch 035]  average training loss: 2532.2927
cellbender:remove-background: [epoch 035] average test loss: 2559.2147
cellbender:remove-background: [epoch 036]  average training loss: 2529.6791
cellbender:remove-background: [epoch 037]  average training loss: 2532.0303
cellbender:remove-background: [epoch 038]  average training loss: 2531.7177
cellbender:remove-background: [epoch 039]  average training loss: 2530.1815
cellbender:remove-background: [epoch 040]  average training loss: 2529.6180
cellbender:remove-background: [epoch 040] average test loss: 2568.4698
cellbender:remove-background: [epoch 041]  average training loss: 2535.7041
cellbender:remove-background: [epoch 042]  average training loss: 2535.5629
cellbender:remove-background: [epoch 043]  average training loss: 2532.9287
cellbender:remove-background: [epoch 044]  average training loss: 2525.1000
cellbender:remove-background: [epoch 045]  average training loss: 2527.8958
cellbender:remove-background: [epoch 045] average test loss: 2550.8243
cellbender:remove-background: [epoch 046]  average training loss: 2531.3721
cellbender:remove-background: [epoch 047]  average training loss: 2526.8389
cellbender:remove-background: [epoch 048]  average training loss: 2528.2746
cellbender:remove-background: [epoch 049]  average training loss: 2528.8574
cellbender:remove-background: [epoch 050]  average training loss: 2528.4011
cellbender:remove-background: [epoch 050] average test loss: 2550.7654
cellbender:remove-background: [epoch 051]  average training loss: 2527.0556
cellbender:remove-background: [epoch 052]  average training loss: 2535.7428
cellbender:remove-background: [epoch 053]  average training loss: 2529.1221
cellbender:remove-background: [epoch 054]  average training loss: 2524.6223
cellbender:remove-background: [epoch 055]  average training loss: 2527.3579
cellbender:remove-background: [epoch 055] average test loss: 2558.9033
cellbender:remove-background: [epoch 056]  average training loss: 2525.7333
cellbender:remove-background: [epoch 057]  average training loss: 2529.4084
cellbender:remove-background: [epoch 058]  average training loss: 2533.1705
cellbender:remove-background: [epoch 059]  average training loss: 2531.0021
cellbender:remove-background: [epoch 060]  average training loss: 2531.2505
cellbender:remove-background: [epoch 060] average test loss: 2582.2434
cellbender:remove-background: [epoch 061]  average training loss: 2527.9999
cellbender:remove-background: [epoch 062]  average training loss: 2528.3349
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/1604-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 063]  average training loss: 2531.1500
cellbender:remove-background: [epoch 064]  average training loss: 2531.2862
cellbender:remove-background: [epoch 065]  average training loss: 2530.8118
cellbender:remove-background: [epoch 065] average test loss: 2577.0357
cellbender:remove-background: [epoch 066]  average training loss: 2536.3208
cellbender:remove-background: [epoch 067]  average training loss: 2538.9517
cellbender:remove-background: [epoch 068]  average training loss: 2543.2481
cellbender:remove-background: [epoch 069]  average training loss: 2542.0424
cellbender:remove-background: [epoch 070]  average training loss: 2551.3452
cellbender:remove-background: [epoch 070] average test loss: 2585.9151
cellbender:remove-background: [epoch 071]  average training loss: 2541.0591
cellbender:remove-background: [epoch 072]  average training loss: 2545.9737
cellbender:remove-background: [epoch 073]  average training loss: 2534.1806
cellbender:remove-background: [epoch 074]  average training loss: 2549.4840
cellbender:remove-background: [epoch 075]  average training loss: 2553.5384
cellbender:remove-background: [epoch 075] average test loss: 2561.9299
cellbender:remove-background: [epoch 076]  average training loss: 2554.0882
cellbender:remove-background: [epoch 077]  average training loss: 2541.9815
cellbender:remove-background: [epoch 078]  average training loss: 2546.3394
cellbender:remove-background: [epoch 079]  average training loss: 2543.6607
cellbender:remove-background: [epoch 080]  average training loss: 2543.4165
cellbender:remove-background: [epoch 080] average test loss: 2600.4906
cellbender:remove-background: [epoch 081]  average training loss: 2549.1895
cellbender:remove-background: [epoch 082]  average training loss: 2554.4908
cellbender:remove-background: [epoch 083]  average training loss: 2556.6268
cellbender:remove-background: [epoch 084]  average training loss: 2546.0738
cellbender:remove-background: [epoch 085]  average training loss: 2553.0009
cellbender:remove-background: [epoch 085] average test loss: 2599.0838
cellbender:remove-background: [epoch 086]  average training loss: 2545.5874
cellbender:remove-background: [epoch 087]  average training loss: 2540.8000
cellbender:remove-background: [epoch 088]  average training loss: 2548.9831
cellbender:remove-background: [epoch 089]  average training loss: 2547.2728
cellbender:remove-background: [epoch 090]  average training loss: 2555.9255
cellbender:remove-background: [epoch 090] average test loss: 2602.9922
cellbender:remove-background: [epoch 091]  average training loss: 2545.1219
cellbender:remove-background: [epoch 092]  average training loss: 2546.2318
cellbender:remove-background: [epoch 093]  average training loss: 2550.7989
cellbender:remove-background: [epoch 094]  average training loss: 2546.3743
cellbender:remove-background: [epoch 095]  average training loss: 2547.4229
cellbender:remove-background: [epoch 095] average test loss: 2613.5839
cellbender:remove-background: [epoch 096]  average training loss: 2549.0500
cellbender:remove-background: [epoch 097]  average training loss: 2544.8783
cellbender:remove-background: [epoch 098]  average training loss: 2539.5490
cellbender:remove-background: [epoch 099]  average training loss: 2546.1706
cellbender:remove-background: [epoch 100]  average training loss: 2544.1158
cellbender:remove-background: [epoch 100] average test loss: 2622.6608
cellbender:remove-background: [epoch 101]  average training loss: 2546.4267
cellbender:remove-background: [epoch 102]  average training loss: 2544.3352
cellbender:remove-background: [epoch 103]  average training loss: 2544.1441
cellbender:remove-background: [epoch 104]  average training loss: 2541.2500
cellbender:remove-background: [epoch 105]  average training loss: 2544.7859
cellbender:remove-background: [epoch 105] average test loss: 2612.6281
cellbender:remove-background: [epoch 106]  average training loss: 2548.1644
cellbender:remove-background: [epoch 107]  average training loss: 2539.0160
cellbender:remove-background: [epoch 108]  average training loss: 2542.7017
cellbender:remove-background: [epoch 109]  average training loss: 2542.9538
cellbender:remove-background: [epoch 110]  average training loss: 2542.6584
cellbender:remove-background: [epoch 110] average test loss: 2617.0524
cellbender:remove-background: [epoch 111]  average training loss: 2540.9231
cellbender:remove-background: [epoch 112]  average training loss: 2545.6560
cellbender:remove-background: [epoch 113]  average training loss: 2543.3662
cellbender:remove-background: [epoch 114]  average training loss: 2541.8202
cellbender:remove-background: [epoch 115]  average training loss: 2542.1438
cellbender:remove-background: [epoch 115] average test loss: 2614.1458
cellbender:remove-background: [epoch 116]  average training loss: 2543.7842
cellbender:remove-background: [epoch 117]  average training loss: 2543.2441
cellbender:remove-background: [epoch 118]  average training loss: 2542.6676
cellbender:remove-background: [epoch 119]  average training loss: 2541.5082
cellbender:remove-background: [epoch 120]  average training loss: 2543.9217
cellbender:remove-background: [epoch 120] average test loss: 2597.0324
cellbender:remove-background: [epoch 121]  average training loss: 2540.5589
cellbender:remove-background: [epoch 122]  average training loss: 2541.0269
cellbender:remove-background: [epoch 123]  average training loss: 2540.8748
cellbender:remove-background: [epoch 124]  average training loss: 2545.0628
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/1604-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 125]  average training loss: 2537.7445
cellbender:remove-background: [epoch 125] average test loss: 2599.3364
cellbender:remove-background: [epoch 126]  average training loss: 2536.4113
cellbender:remove-background: [epoch 127]  average training loss: 2540.8457
cellbender:remove-background: [epoch 128]  average training loss: 2541.4897
cellbender:remove-background: [epoch 129]  average training loss: 2537.9605
cellbender:remove-background: [epoch 130]  average training loss: 2534.7038
cellbender:remove-background: [epoch 130] average test loss: 2610.0230
cellbender:remove-background: [epoch 131]  average training loss: 2537.9060
cellbender:remove-background: [epoch 132]  average training loss: 2535.6297
cellbender:remove-background: [epoch 133]  average training loss: 2535.3700
cellbender:remove-background: [epoch 134]  average training loss: 2535.5162
cellbender:remove-background: [epoch 135]  average training loss: 2537.4007
cellbender:remove-background: [epoch 135] average test loss: 2601.8477
cellbender:remove-background: [epoch 136]  average training loss: 2533.6833
cellbender:remove-background: [epoch 137]  average training loss: 2538.4889
cellbender:remove-background: [epoch 138]  average training loss: 2536.0906
cellbender:remove-background: [epoch 139]  average training loss: 2538.1382
cellbender:remove-background: [epoch 140]  average training loss: 2535.7965
cellbender:remove-background: [epoch 140] average test loss: 2600.8234
cellbender:remove-background: [epoch 141]  average training loss: 2534.7609
cellbender:remove-background: [epoch 142]  average training loss: 2534.4773
cellbender:remove-background: [epoch 143]  average training loss: 2535.7729
cellbender:remove-background: [epoch 144]  average training loss: 2535.0330
cellbender:remove-background: [epoch 145]  average training loss: 2534.6568
cellbender:remove-background: [epoch 145] average test loss: 2599.6830
cellbender:remove-background: [epoch 146]  average training loss: 2538.3138
cellbender:remove-background: [epoch 147]  average training loss: 2536.1491
cellbender:remove-background: [epoch 148]  average training loss: 2534.9310
cellbender:remove-background: [epoch 149]  average training loss: 2535.7393
cellbender:remove-background: [epoch 150]  average training loss: 2536.2745
cellbender:remove-background: [epoch 150] average test loss: 2606.5495
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/1604-Control-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:52:08
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpl179nt_a
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpl179nt_a
/tmp/tmpl179nt_a/42ef1dfaf5_random.pyro
/tmp/tmpl179nt_a/42ef1dfaf5_random.cuda
/tmp/tmpl179nt_a/42ef1dfaf5_model.torch
/tmp/tmpl179nt_a/42ef1dfaf5_optim.torch
/tmp/tmpl179nt_a/42ef1dfaf5_optim.pyro
/tmp/tmpl179nt_a/42ef1dfaf5_params.pyro
/tmp/tmpl179nt_a/42ef1dfaf5_train.loaderstate
/tmp/tmpl179nt_a/42ef1dfaf5_test.loaderstate
/tmp/tmpl179nt_a/42ef1dfaf5_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 (1/74)
cellbender:remove-background:     [0.04 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/1604-Control-dACC/1604-Control-dACC.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/1604-Control-dACC/1604-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:56:27

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-dACC/1604-Control-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-dACC/1604-Control-dACC.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:     [1.19 mins per chunk]
cellbender:remove-background: Working on chunk (2/7)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 16:04:59 Total MCKP estimation time = 489.77 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/1604-Control-dACC/1604-Control-dACC.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/1604-Control-dACC/1604-Control-dACC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1604-Control-dACC/1604-Control-dACC.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/1604-Control-dACC/1604-Control-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:05:15